WorldWideScience

Sample records for paraffin-embedded skin biopsies

  1. Digital dewaxing of Raman signals: discrimination between nevi and melanoma spectra obtained from paraffin-embedded skin biopsies.

    Science.gov (United States)

    Tfayli, Ali; Gobinet, Cyril; Vrabie, Valeriu; Huez, Regis; Manfait, Michel; Piot, Olivier

    2009-05-01

    Malignant melanoma (MM) is the most severe tumor affecting the skin and accounts for three quarters of all skin cancer deaths. Raman spectroscopy is a promising nondestructive tool that has been increasingly used for characterization of the molecular features of cancerous tissues. Different multivariate statistical analysis techniques are used in order to extract relevant information that can be considered as functional spectroscopic descriptors of a particular pathology. Paraffin embedding (waxing) is a highly efficient process used to conserve biopsies in tumor banks for several years. However, the use of non-dewaxed formalin-fixed paraffin-embedded tissues for Raman spectroscopic investigations remains very restricted, limiting the development of the technique as a routine analytical tool for biomedical purposes. This is due to the highly intense signal of paraffin, which masks important vibrations of the biological tissues. In addition to being time consuming and chemical intensive, chemical dewaxing methods are not efficient and they leave traces of the paraffin in tissues, which affects the Raman signal. In the present study, we use independent component analysis (ICA) on Raman spectral images collected on melanoma and nevus samples. The sources obtained from these images are then used to eliminate, using non-negativity constrained least squares (NCLS), the paraffin contribution from each individual spectrum of the spectral images of nevi and melanomas. Corrected spectra of both types of lesion are then compared and classified into dendrograms using hierarchical cluster analysis (HCA).

  2. Unmasking of complements using proteinase-K in formalin fixed paraffin embedded renal biopsies

    Directory of Open Access Journals (Sweden)

    R Nada

    2016-01-01

    Full Text Available Renal biopsy interpretation requires histopathology, direct immunofluorescence (DIF and electron microscopy. Formalin-fixed, paraffin-embedded tissue (FFPE sent for light microscopy can be used for DIF after antigen retrieval. However, complement staining has not been satisfactory. We standardized DIF using proteinase-K for antigen retrieval in FFPE renal biopsies. A pilot study was conducted on known cases of membranous glomerulonephritis (MGN, membranoproliferative type-1 (MPGN-1, immunoglobulin A nephropathy (IgAN, and anti-glomerular basement disease (anti-GBM. Immunofluorescence panel included fluorescein isothiocyanate (FITC conjugated IgG, IgA, IgM, complements (C3 and C1q, light chains (kappa, lambda and fibrinogen antibodies. After standardization of the technique, 75 renal biopsies and 43 autopsies cases were stained. Out of 43 autopsy cases, immune-complex mediated glomerulonephritis (GN was confirmed in 18 cases (Lupus nephritis-11, IgAN-6, MGN-1, complement-mediated dense deposit disease (DDD-1 and monoclonal diseases in 4 cases (amyloidosis-3, cast nephropathy-1. Immune-mediated injury was excluded in 17 cases (focal segmental glomerulosclerosis -3, crescentic GN-6 [pauci-immune-3, anti-GBM-3], thrombotic microangiopathy-5, atherosclerosis-3. Renal biopsies (n-75 where inadequate or no frozen sample was available; this technique classified 52 mesangiocapillary pattern as MPGN type-1-46, DDD-2 and (C3GN-4. Others were diagnosed as IgAN-3, lupus nephritis-2, MGN-4, diffuse proliferative glomerulonephritis (DPGN-1, Non-IC crescentic GN-1, monoclonal diseases-3. In nine cases, DIF on FFPE tissue could not help in making diagnosis. Proteinase-K enzymatic digestion of FFPE renal biopsies can unmask complements (both C3 and C1q in immune-complexes mediated and complement-mediated diseases. This method showed good results on autopsy tissues archived for as long as 15 years.

  3. Predicting response to primary chemotherapy: gene expression profiling of paraffin-embedded core biopsy tissue.

    Science.gov (United States)

    Mina, Lida; Soule, Sharon E; Badve, Sunil; Baehner, Fredrick L; Baker, Joffre; Cronin, Maureen; Watson, Drew; Liu, Mei-Lan; Sledge, George W; Shak, Steve; Miller, Kathy D

    2007-06-01

    Primary chemotherapy provides an ideal opportunity to correlate gene expression with response to treatment. We used paraffin-embedded core biopsies from a completed phase II trial to identify genes that correlate with response to primary chemotherapy. Patients with newly diagnosed stage II or III breast cancer were treated with sequential doxorubicin 75 mg/M2 q2 wks x 3 and docetaxel 40 mg/M2 weekly x 6; treatment order was randomly assigned. Pretreatment core biopsy samples were interrogated for genes that might correlate with pathologic complete response (pCR). In addition to the individual genes, the correlation of the Oncotype DX Recurrence Score with pCR was examined. Of 70 patients enrolled in the parent trial, core biopsies samples with sufficient RNA for gene analyses were available from 45 patients; 9 (20%) had inflammatory breast cancer (IBC). Six (14%) patients achieved a pCR. Twenty-two of the 274 candidate genes assessed correlated with pCR (p < 0.05). Genes correlating with pCR could be grouped into three large clusters: angiogenesis-related genes, proliferation related genes, and invasion-related genes. Expression of estrogen receptor (ER)-related genes and Recurrence Score did not correlate with pCR. In an exploratory analysis we compared gene expression in IBC to non-inflammatory breast cancer; twenty-four (9%) of the genes were differentially expressed (p < 0.05), 5 were upregulated and 19 were downregulated in IBC. Gene expression analysis on core biopsy samples is feasible and identifies candidate genes that correlate with pCR to primary chemotherapy. Gene expression in IBC differs significantly from noninflammatory breast cancer.

  4. Proteome stability analysis of snap frozen, RNAlater preserved, and formalin-fixed paraffin-embedded human colon mucosal biopsies

    Directory of Open Access Journals (Sweden)

    Tue Bjerg Bennike

    2016-03-01

    Full Text Available Large repositories of well characterized RNAlater preserved samples and formalin-fixed, paraffin-embedded samples have been generated worldwide. However, the impact on the proteome of the preservation methods remain poorly described. Therefore, we analyzed the impact on the proteome of preserving samples in RNAlater, and by formalin-fixation, paraffin-embedding on human soft tissue, using directly frozen samples as a control (“Comparing the proteome of snap frozen, RNAlater preserved, and formalin-fixed paraffin-embedded human tissue samples” [1]. We here report the data from the analysis. The comparative analysis was performed on 24 colon mucosa biopsies, extracted from the sigmoideum of two gastroenterologically healthy participants for the purpose of this study. A set of biopsies were additionally stored for 30 min at room temperature prior to formalin-fixation. The samples were analyzed by high throughput gel free quantitative proteomics. The MS proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PRIDE: http://www.ebi.ac.uk/pride/archive/projects/PXD002029. Keywords: Human, Colon, Mucosa, RNAlater, FFPE, Snap-frozen, Stability, LC–MS, Proteomics

  5. Detection of hepatitis C viral RNA sequences in fresh and paraffin-embedded liver biopsy specimens of non-A, non-B hepatitis patients

    NARCIS (Netherlands)

    Bresters, D.; Cuypers, H. T.; Reesink, H. W.; Chamuleau, R. A.; Schipper, M. E.; Boeser-Nunnink, B. D.; Lelie, P. N.; Jansen, P. L.

    1992-01-01

    In this study methods of HCV-RNA detection in fresh frozen and formalin-fixed, paraffin-embedded liver biopsies are described. Of 22 untreated chronic non-A, non-B hepatitis patients and 6 control patients, a plasma sample and part of a liver biopsy were freshly frozen for hepatitis C virus (HCV)

  6. Proteome stability analysis of snap frozen, RNAlater preserved, and formalin-fixed paraffin-embedded human colon mucosal biopsies

    DEFF Research Database (Denmark)

    Bjerg Bennike, Tue; Kastaniegaard, Kenneth; Padurariu, Simona

    2016-01-01

    Large repositories of well characterized RNAlater preserved samples and formalin-fixed, paraffin-embedded samples have been generated worldwide. However, the impact on the proteome of the preservation methods remain poorly described. Therefore, we analyzed the impact on the proteome of preserving...... samples in RNAlater, and by formalin-fixation, paraffin-embedding on human soft tissue, using directly frozen samples as a control ("Comparing the proteome of snap frozen, RNAlater preserved, and formalin-fixed paraffin-embedded human tissue samples" [1]). We here report the data from the analysis...

  7. Molecular diagnosis of skin infections using paraffin-embedded tissue - review and interdisciplinary consensus.

    Science.gov (United States)

    Sunderkötter, Cord; Becker, Karsten; Kutzner, Heinz; Meyer, Thomas; Blödorn-Schlicht, Norbert; Reischl, Udo; Nenoff, Pietro; Geißdörfer, Walter; Gräser, Yvonne; Herrmann, Mathias; Kühn, Joachim; Bogdan, Christian

    2018-02-01

    Nucleic acid amplification techniques (NATs), such as PCR, are highly sensitive and specific methods that have become valuable supplements to culture and serology in the diagnosis of infectious disorders. However, especially when using formalin-fixed and paraffin-embedded tissue, these techniques are associated with both false-negative and false-positive results, a pitfall that is frequently misjudged. Representatives of the German Society of Hygiene and Microbiology (DGHM) and the German Society of Dermatology (DDG) therefore set out to develop a consensus - in the form of a review article - on the appropriate indications for NATs using paraffin-embedded tissue, its contraindications, and the key points to be considered in the pre- and post-analytical phase. Given that fresh, naive tissue is preferably to be used in the workup of a suspected infection, PCR analysis on paraffin sections represents an exception. The latter may be considered if an infection is suspected at a later point in time and fresh tissue has not been preserved or can no longer be obtained. Potential indications include confirmation of histologically suspected infections with Leishmania spp., Bartonella spp., Rickettsia spp., or in case of ecthyma contagiosum. Infections with, for example, mycobacteria or RNA viruses, on the other hand, are not considered useful indications for NATs using paraffin sections. In order to avoid misinterpretation of test results, it is essential that laboratory reports on NATs using paraffin-embedded tissue contain information on the indication/diagnostic circumstances, the required and chosen pre-analytical steps, the limitations of the method, and on diagnostic alternatives. © 2018 Deutsche Dermatologische Gesellschaft (DDG). Published by John Wiley & Sons Ltd.

  8. Proteome stability analysis of snap frozen, RNAlater preserved, and formalin-fixed paraffin-embedded human colon mucosal biopsies

    DEFF Research Database (Denmark)

    Bennike, Tue Bjerg; Kastaniegaard, Kenneth; Padurariu, Simona

    2016-01-01

    Large repositories of well characterized RNAlater preserved samples and formalin-fixed, paraffin-embedded samples have been generated worldwide. However, the impact on the proteome of the preservation methods remain poorly described. Therefore, we analyzed the impact on the proteome of preserving...... throughput gel free quantitative proteomics. The MS proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PRIDE: PXD002029....

  9. Improved method for extraction and detection of Helicobacter pylori DNA in formalin-fixed paraffin embedded gastric biopsies using laser micro-dissection.

    Science.gov (United States)

    Loayza, María Fernanda; Villavicencio, Fernando Xavier; Santander, Stephanie Carolina; Baldeón, Manuel; Ponce, Lourdes Karina; Salvador, Iván; Vivar Díaz, Nicolás

    2015-01-01

    To assess the molecular events exerted by Helicobacter pylori interacting directly with gastric epithelial cells, an improved procedure for microbial DNA isolation from stained hematoxilin-eosin gastric biopsies was developed based on laser micro-dissection (LM) [1]. Few articles have described the use of LM to select and detect H. pylori genome from formalin-fixed paraffin embedded gastric tissue [2]. To improve the yield and quality of DNA isolated from H. pylori contacting intestinal epithelial cells, the following conditions were established after modification of the QIAamp DNA Micro kit. •Use of at least 25 cut sections of 10-20 μm of diameter and 3 μm thick with more than 10 bacteria in each cut.•Lysis with 30 μL of tissue lysis buffer and 20 μL of proteinase K (PK) with the tube in an upside-down position.•The use of thin purification columns with 35 μL of elution buffer. The mean of DNA concentration obtained from 25 LM cut sections was 1.94± 0 .16 ng/μL, and it was efficiently amplified with qPCR in a Bio Rad iCycler instrument. The LM can improve the sample selection and DNA extraction for molecular analysis of H. pylori associated with human gastric epithelium.

  10. Gene expression patterns in formalin-fixed, paraffin-embedded core biopsies predict docetaxel chemosensitivity in breast cancer patients.

    Science.gov (United States)

    Chang, Jenny C; Makris, Andreas; Gutierrez, M Carolina; Hilsenbeck, Susan G; Hackett, James R; Jeong, Jennie; Liu, Mei-Lan; Baker, Joffre; Clark-Langone, Kim; Baehner, Frederick L; Sexton, Krsytal; Mohsin, Syed; Gray, Tara; Alvarez, Laura; Chamness, Gary C; Osborne, C Kent; Shak, Steven

    2008-03-01

    Previously, we had identified gene expression patterns that predicted response to neoadjuvant docetaxel. Other studies have validated that a high Recurrence Score (RS) by the 21-gene RT-PCR assay is predictive of worse prognosis but better response to chemotherapy. We investigated whether tumor expression of these 21 genes and other candidate genes can predict response to docetaxel. Core biopsies from 97 patients were obtained before treatment with neoadjuvant docetaxel (4 cycles, 100 mg/m2 q3 weeks). Three 10-microm FFPE sections were submitted for quantitative RT-PCR assays of 192 genes that were selected from our previous work and the literature. Of the 97 patients, 81 (84%) had sufficient invasive cancer, 80 (82%) had sufficient RNA for QRTPCR assay, and 72 (74%) had clinical response data. Mean age was 48.5 years, and the median tumor size was 6 cm. Clinical complete responses (CR) were observed in 12 (17%), partial responses in 41 (57%), stable disease in 17 (24%), and progressive disease in 2 patients (3%). A significant relationship (P<0.05) between gene expression and CR was observed for 14 genes, including CYBA. CR was associated with lower expression of the ER gene group and higher expression of the proliferation gene group from the 21 gene assay. Of note, CR was more likely with a high RS (P=0.008). We have established molecular profiles of sensitivity to docetaxel. RT-PCR technology provides a potential platform for a predictive test of docetaxel chemosensitivity using small amounts of routinely processed material.

  11. Gene expression profiles in paraffin-embedded core biopsy tissue predict response to chemotherapy in women with locally advanced breast cancer.

    Science.gov (United States)

    Gianni, Luca; Zambetti, Milvia; Clark, Kim; Baker, Joffre; Cronin, Maureen; Wu, Jenny; Mariani, Gabriella; Rodriguez, Jaime; Carcangiu, Marialuisa; Watson, Drew; Valagussa, Pinuccia; Rouzier, Roman; Symmans, W Fraser; Ross, Jeffrey S; Hortobagyi, Gabriel N; Pusztai, Lajos; Shak, Steven

    2005-10-10

    We sought to identify gene expression markers that predict the likelihood of chemotherapy response. We also tested whether chemotherapy response is correlated with the 21-gene Recurrence Score assay that quantifies recurrence risk. Patients with locally advanced breast cancer received neoadjuvant paclitaxel and doxorubicin. RNA was extracted from the pretreatment formalin-fixed paraffin-embedded core biopsies. The expression of 384 genes was quantified using reverse transcriptase polymerase chain reaction and correlated with pathologic complete response (pCR). The performance of genes predicting for pCR was tested in patients from an independent neoadjuvant study where gene expression was obtained using DNA microarrays. Of 89 assessable patients (mean age, 49.9 years; mean tumor size, 6.4 cm), 11 (12%) had a pCR. Eighty-six genes correlated with pCR (unadjusted P < .05); pCR was more likely with higher expression of proliferation-related genes and immune-related genes, and with lower expression of estrogen receptor (ER) -related genes. In 82 independent patients treated with neoadjuvant paclitaxel and doxorubicin, DNA microarray data were available for 79 of the 86 genes. In univariate analysis, 24 genes correlated with pCR with P < .05 (false discovery, four genes) and 32 genes showed correlation with P < .1 (false discovery, eight genes). The Recurrence Score was positively associated with the likelihood of pCR (P = .005), suggesting that the patients who are at greatest recurrence risk are more likely to have chemotherapy benefit. Quantitative expression of ER-related genes, proliferation genes, and immune-related genes are strong predictors of pCR in women with locally advanced breast cancer receiving neoadjuvant anthracyclines and paclitaxel.

  12. Integrative analysis of copy number and gene expression in breast cancer using formalin-fixed paraffin-embedded core biopsy tissue: a feasibility study.

    Science.gov (United States)

    Iddawela, Mahesh; Rueda, Oscar; Eremin, Jenny; Eremin, Oleg; Cowley, Jed; Earl, Helena M; Caldas, Carlos

    2017-07-11

    An absence of reliable molecular markers has hampered individualised breast cancer treatments, and a major limitation for translational research is the lack of fresh tissue. There are, however, abundant banks of formalin-fixed paraffin-embedded (FFPE) tissue. This study evaluated two platforms available for the analysis of DNA copy number and gene expression using FFPE samples. The cDNA-mediated annealing, selection, extension, and ligation assay (DASL™) has been developed for gene expression analysis and the Molecular Inversion Probes assay (Oncoscan™), were used for copy number analysis using FFPE tissues. Gene expression and copy number were evaluated in core-biopsy samples from patients with breast cancer undergoing neoadjuvant chemotherapy (NAC). Forty-three core-biopsies were evaluated and characteristic copy number changes in breast cancers, gains in 1q, 8q, 11q, 17q and 20q and losses in 6q, 8p, 13q and 16q, were confirmed. Regions that frequently exhibited gains in tumours showing a pathological complete response (pCR) to NAC were 1q (55%), 8q (40%) and 17q (40%), whereas 11q11 (37%) gain was the most frequent change in non-pCR tumours. Gains associated with poor survival were 11q13 (62%), 8q24 (54%) and 20q (47%). Gene expression assessed by DASL correlated with immunohistochemistry (IHC) analysis for oestrogen receptor (ER) [area under the curve (AUC) = 0.95], progesterone receptor (PR)(AUC = 0.90) and human epidermal growth factor type-2 receptor (HER-2) (AUC = 0.96). Differential expression analysis between ER+ and ER- cancers identified over-expression of TTF1, LAF-4 and C-MYB (p ≤ 0.05), and between pCR vs non-pCRs, over-expression of CXCL9, AREG, B-MYB and under-expression of ABCG2. This study was an integrative analysis of copy number and gene expression using FFPE core biopsies and showed that molecular marker data from FFPE tissues were consistent with those in previous studies using fresh-frozen samples. FFPE tissue can provide

  13. Droplet digital PCR (ddPCR) vs quantitative real-time PCR (qPCR) approach for detection and quantification of Merkel cell polyomavirus (MCPyV) DNA in formalin fixed paraffin embedded (FFPE) cutaneous biopsies.

    Science.gov (United States)

    Arvia, Rosaria; Sollai, Mauro; Pierucci, Federica; Urso, Carmelo; Massi, Daniela; Zakrzewska, Krystyna

    2017-08-01

    Merkel cell polyomavirus (MCPyV) is associated with Merkel cell carcinoma and high viral load in the skin was proposed as a risk factor for the occurrence of this tumour. MCPyV DNA was detected, with lower frequency, in different skin cancers but since the viral load was usually low, the real prevalence of viral DNA could be underestimated. To evaluate the performance of two assays (qPCR and ddPCR) for MCPyV detection and quantification in formalin fixed paraffin embedded (FFPE) tissue samples. Both assays were designed to simultaneous detection and quantification of both MCPyV as well as house-keeping DNA in clinical samples. The performance of MCPyV quantification was investigated using serial dilutions of cloned target DNA. We also evaluated the applicability of both tests for the analysis of 76 FFPE cutaneous biopsies. The two approaches resulted equivalent with regard to the reproducibility and repeatability and showed a high degree of linearity in the dynamic range tested in the present study. Moreover, qPCR was able to quantify ≥10 5 copies per reaction, while the upper limit of ddPCR was 10 4 copies. There was not significant difference between viral load measured by the two methods The detection limit of both tests was 0,15 copies per reaction, however, the number of positive samples obtained by ddPCR was higher than that obtained by qPCR (45% and 37% respectively). The ddPCR represents a better method for detection of MCPyV in FFPE biopsies, mostly these containing low copies number of viral genome. Copyright © 2017 Elsevier B.V. All rights reserved.

  14. Skin Biopsy

    Science.gov (United States)

    ... Development Infections Diseases & Conditions Pregnancy & Baby Nutrition & Fitness Emotions & Behavior School & Family Life First Aid & Safety Doctors & ... like these: skin rashes or conditions, such as eczema or psoriasis skin infections, such as staph diseases, ...

  15. Highly sensitive KRAS mutation detection from formalin-fixed paraffin-embedded biopsies and circulating tumour cells using wild-type blocking polymerase chain reaction and Sanger sequencing.

    Science.gov (United States)

    Huang, Meggie Mo Chao; Leong, Sai Mun; Chua, Hui Wen; Tucker, Steven; Cheong, Wai Chye; Chiu, Lily; Li, Mo-Huang; Koay, Evelyn Siew-Chuan

    2014-08-01

    Among patients with colorectal cancer (CRC), KRAS mutations were reported to occur in 30-51 % of all cases. CRC patients with KRAS mutations were reported to be non-responsive to anti-epidermal growth factor receptor (EGFR) monoclonal antibody (MoAb) treatment in many clinical trials. Hence, accurate detection of KRAS mutations would be critical in guiding the use of anti-EGFR MoAb therapies in CRC. In this study, we carried out a detailed investigation of the efficacy of a wild-type (WT) blocking real-time polymerase chain reaction (PCR), employing WT KRAS locked nucleic acid blockers, and Sanger sequencing, for KRAS mutation detection in rare cells. Analyses were first conducted on cell lines to optimize the assay protocol which was subsequently applied to peripheral blood and tissue samples from patients with CRC. The optimized assay provided a superior sensitivity enabling detection of as little as two cells with mutated KRAS in the background of 10(4) WT cells (0.02 %). The feasibility of this assay was further investigated to assess the KRAS status of 45 colorectal tissue samples, which had been tested previously, using a conventional PCR sequencing approach. The analysis showed a mutational discordance between these two methods in 4 of 18 WT cases. Our results present a simple, effective, and robust method for KRAS mutation detection in both paraffin embedded tissues and circulating tumour cells, at single-cell level. The method greatly enhances the detection sensitivity and alleviates the need of exhaustively removing co-enriched contaminating lymphocytes.

  16. Improving the Prediction of Prostate Cancer Overall Survival by Supplementing Readily Available Clinical Data with Gene Expression Levels of IGFBP3 and F3 in Formalin-Fixed Paraffin Embedded Core Needle Biopsy Material.

    Directory of Open Access Journals (Sweden)

    Zhuochun Peng

    Full Text Available A previously reported expression signature of three genes (IGFBP3, F3 and VGLL3 was shown to have potential prognostic value in estimating overall and cancer-specific survivals at diagnosis of prostate cancer in a pilot cohort study using freshly frozen Fine Needle Aspiration (FNA samples.We carried out a new cohort study with 241 prostate cancer patients diagnosed from 2004-2007 with a follow-up exceeding 6 years in order to verify the prognostic value of gene expression signature in formalin fixed paraffin embedded (FFPE prostate core needle biopsy tissue samples. The cohort consisted of four patient groups with different survival times and death causes. A four multiplex one-step RT-qPCR test kit, designed and optimized for measuring the expression signature in FFPE core needle biopsy samples, was used. In archive FFPE biopsy samples the expression differences of two genes (IGFBP3 and F3 were measured. The survival time predictions using the current clinical parameters only, such as age at diagnosis, Gleason score, PSA value and tumor stage, and clinical parameters supplemented with the expression levels of IGFBP3 and F3, were compared.When combined with currently used clinical parameters, the gene expression levels of IGFBP3 and F3 are improving the prediction of survival time as compared to using clinical parameters alone.The assessment of IGFBP3 and F3 gene expression levels in FFPE prostate cancer tissue would provide an improved survival prediction for prostate cancer patients at the time of diagnosis.

  17. Multi-elemental imaging of paraffin-embedded human samples by laser-induced breakdown spectroscopy

    Science.gov (United States)

    Moncayo, S.; Trichard, F.; Busser, B.; Sabatier-Vincent, M.; Pelascini, F.; Pinel, N.; Templier, I.; Charles, J.; Sancey, L.; Motto-Ros, V.

    2017-07-01

    Chemical elements play central roles for physiological homeostasis in human cells, and their dysregulation might lead to a certain number of pathologies. Novel imaging techniques that improve the work of pathologists for tissue analysis and diagnostics are continuously sought. We report the use of Laser-Induced Breakdown Spectroscopy (LIBS) to perform multi-elemental images of human paraffin-embedded skin samples on the entire biopsy scale in a complementary and compatible way with microscope histopathological examination. A specific instrumental configuration is proposed in order to detect most of the elements of medical interest (i.e. P, Al, Mg, Na, Zn, Si, Fe, and Cu). As an example of medical application, we selected and analysed skin biopsies, including healthy skin tissue, cutaneous metastasis of melanoma, Merkel-cell carcinoma and squamous cell carcinoma. Clear distinctions in the distribution of chemical elements are observed from the different samples investigated. This study demonstrates the high complementarity of LIBS elemental imaging with conventional histopathology, opening new opportunities for any medical application involving metals.

  18. Comparing the proteome of snap frozen, RNAlater preserved, and formalin-fixed paraffin-embedded human tissue samples

    DEFF Research Database (Denmark)

    Bennike, Tue Bjerg; Kastaniegaard, Kenneth; Padurariu, Simona

    2016-01-01

    Large biobanks exist worldwide containing formalin-fixed, paraffin-embedded samples and samples stored in RNAlater. However, the impact of tissue preservation on the result of a quantative proteome analysis remains poorly described.Human colon mucosal biopsies were extracted from the sigmoideum...

  19. Semi-Nested Real-Time Reverse Transcription Polymerase Chain Reaction Methods for the Successful Quantitation of Cytokeratin mRNA Expression Levels for the Subtyping of Non-Small-Cell Lung Carcinoma Using Paraffin-Embedded and Microdissected Lung Biopsy Specimens

    International Nuclear Information System (INIS)

    Nakanishi, Yoko; Shimizu, Tetsuo; Tsujino, Ichiro; Obana, Yukari; Seki, Toshimi; Fuchinoue, Fumi; Ohni, Sumie; Oinuma, Toshinori; Kusumi, Yoshiaki; Yamada, Tsutomu; Takahashi, Noriaki; Hashimoto, Shu; Nemoto, Norimichi

    2013-01-01

    In patients with inoperable advanced non-small cell lung carcinomas (NSCLCs), histological subtyping using small-mount biopsy specimens was often required to decide the indications for drug treatment. The aim of this study was to assess the utility of highly sensitive mRNA quantitation for the subtyping of advanced NSCLC using small formalin fixing and paraffin embedding (FFPE) biopsy samples. Cytokeratin (CK) 6, CK7, CK14, CK18, and thyroid transcription factor (TTF)-1 mRNA expression levels were measured using semi-nested real-time quantitative (snq) reverse-transcribed polymerase chain reaction (RT-PCR) in microdissected tumor cells collected from 52 lung biopsies. Our results using the present snqRT-PCR method showed an improvement in mRNA quantitation from small FFPE samples, and the mRNA expression level using snqRT-PCR was correlated with the immunohistochemical protein expression level. CK7, CK18, and TTF-1 mRNA were expressed at significantly higher levels (P<0.05) in adenocarcinoma (AD) than in squamous cell carcinoma (SQ), while CK6 and CK14 mRNA expression was significantly higher (P<0.05) in SQ than in AD. Each histology-specific CK, particularly CK18 in AD and CK6 in SQ, were shown to be correlated with a poor prognosis (P=0.02, 0.02, respectively). Our results demonstrated that a quantitative CK subtype mRNA analysis from lung biopsy samples can be useful for predicting the histology subtype and prognosis of advanced NSCLC

  20. Fluorescence in situ hybridization on formalin-fixed and paraffin-embedded tissue

    DEFF Research Database (Denmark)

    Laub Petersen, Bodil; Zeuthen, Mette Christa; Pedersen, Sanni

    2004-01-01

    , such as quantitation of signals as in triploidy, it is possible to isolate nuclei from paraffin-embedded tissue. However, using formalin-fixed paraffin-embedded tissue, either in thin sections or as isolated nuclei, one encounters a range of technical problems, paralleling those met in immunohistochemistry. Variations...... nuclei and tissue sections from formalin-fixed, paraffin-embedded tissue....

  1. Establishment of a Pcr Technique for Determination of Htlv-1 Infection in Paraffin-Embedded Tissues

    Directory of Open Access Journals (Sweden)

    M Rastin

    2007-04-01

    Full Text Available Introduction: HTLV-1 , the first known human retrovirus belongs to oncovirus subfamily of retroviruses. The major characteristic of HTLV-1 is its highly restricted geographic prevalence. Northern part of Khorasan is an endemic region of HTLV-1 infection. Epidemiological studies can help in designing preventive programs for HTLV-1 infection. The aim of this study was the establishment of a PCR technique for determination of HTLV-1 infection in paraffin-embedded tissues. Methods: In this experimental laboratory study for establishment of a technique, PCR was initially optimized using Beta-actin primers on various formalin fixed paraffin-embedded tissues from liver, spleen, skin and lymph nodes. The optimized concentration of Mgcl2 was 2mm, primer was 8 pmol. Optimized concentration of DNA was different according to the kind of tissue. HTLV-1 infection was determined by applying tax, pol, env and LTR primers on 50 paraffin-embedded lymph node tissues . The reporoducibility of this technique was shown for skin and lymph node tissues infected with HTLV-1. Resuls: In 50 lymph node tissues, one case with pathologic diagnosis of NHL was positive with all 5 sets of primers (tax, Pol, env and LTR primers and the other case was positive with only two sets of tax primers but was negative with pol, env and LTR primers. The prevalence of infection was 2% among lymph node specimens. (1 of 50 specimens and if the second case is considered, the prevalence would be 4%. Conclusion: Comparison of the results of this study with another study on blood specimens (seroprevalence2.3% was not statistically significant thus confirming the results of one another. (P=0.883

  2. Replacing xylene with n-heptane for paraffin embedding.

    Science.gov (United States)

    Stockert, J C; López-Arias, B; Del Castillo, P; Romero, A; Blázquez-Castro, A

    2012-10-01

    In standard histological technique, aromatic solvents such as xylene and toluene are used as clearing agents between ethanol dehydration and paraffin embedding. In addition, these solvents are used for de-waxing paraffin sections. Unfortunately, these solvents are harmful and therefore adequate substitutes would be useful. We suggest the use of n-heptane as a convenient substitute for xylene. Paraffin sections of rat tissues processed with n-heptane and stained with hematoxylin-eosin or Masson's trichrome showed proper embedment, well preserved morphology and excellent staining.

  3. Evaluation of two methods DNA extraction from formalin-fixed, paraffin-embedded tissues on non-optimal conditions

    International Nuclear Information System (INIS)

    Bustamante, Javier Andres; Astudillo, Miryam; Pazos, Alvaro Jairo; Bravo, Luis Eduardo

    2011-01-01

    Paraffin wax embedded tissues are an invaluable material for retrospective studies requiring the application of molecular analysis. Multiple methods are available to extract DNA from these kinds of samples. However, the most common methods are slow and the reagents often contribute to the fragmentation of genetic material. In order to optimize the procedure, two methods for DNA extraction from paraffin embedded tissue non-optimal conditions were used. 47 blocks containing paraffin-embedded biopsies of pleura, lung and pericardium from 24 patients (66.6% males) older than 18 years, with biopsy proven chronic granulomatous inflammation referred to the department of pathology at University Hospital of Valle between 2002 and 2007 were selected. Each sample was subjected to 10 cuts and was to two methods of DNA extraction: 1. conventional and 2. QIAamp - DNA mini kit. The efficiency of the extracted DNA was assessed by spectrophotometry and PCR amplification of a fragment of the housekeeping gene GAPDH. The concentration of DNA samples extracted by the conventional method was of 65.52 ng/Mu l ± 11.47 (mean ± SE) and the 260/280 absorbance ratio ranged between 0.52 and 2.30 the average concentration of DNA of the samples extracted by the commercial method was 60.89 ng/Mu l ± 6.02 (mean ± SE), with an absorbance that fluctuated between 0 and 2.64. The DNA obtained was amplified by PCR, of 47 samples extracted by methods, 25 and 23 respectively the GAPDH gene amplified successfully. The methods used to obtain DNA showed similar performance, highlighting the potential utility of both extraction methods for the retrospective studies from paraffin embedded tissues in unsuitable conditions.

  4. Biopsy

    Science.gov (United States)

    ... Oropharynx lesion biopsy Pleural needle biopsy Polyp biopsy Rectal biopsy Renal biopsy Salivary gland biopsy Skin lesion ... Copyright 1997-2018, A.D.A.M., Inc. Duplication for commercial use must be authorized in writing ...

  5. Measurement of Gene Expression in Archival Paraffin-Embedded Tissues

    Science.gov (United States)

    Cronin, Maureen; Pho, Mylan; Dutta, Debjani; Stephans, James C.; Shak, Steven; Kiefer, Michael C.; Esteban, Jose M.; Baker, Joffre B.

    2004-01-01

    Throughout the last decade many laboratories have shown that mRNA levels in formalin-fixed and paraffin-embedded (FPE) tissue specimens can be quantified by reverse transcriptase-polymerase chain reaction (RT-PCR) techniques despite the extensive RNA fragmentation that occurs in tissues so preserved. We have developed RT-PCR methods that are sensitive, precise, and that have multianalyte capability for potential wide use in clinical research and diagnostic assays. Here it is shown that the extent of fragmentation of extracted FPE tissue RNA significantly increases with archive storage time. Probe and primer sets for RT-PCR assays based on amplicons that are both short and homogeneous in length enable effective reference gene-based data normalization for cross comparison of specimens that differ substantially in age. A 48-gene assay used to compare gene expression profiles from the same breast cancer tissue that had been either frozen or FPE showed very similar profiles after reference gene-based normalization. A 92-gene assay, using RNA extracted from three 10-μm FPE sections of archival breast cancer specimens (dating from 1985 to 2001) yielded analyzable data for these genes in all 62 tested specimens. The results were substantially concordant when estrogen receptor, progesterone receptor, and HER2 receptor status determined by RT-PCR was compared with immunohistochemistry assays for these receptors. Furthermore, the results highlight the advantages of RT-PCR over immunohistochemistry with respect to quantitation and dynamic range. These findings support the development of RT-PCR analysis of FPE tissue RNA as a platform for multianalyte clinical diagnostic tests. PMID:14695316

  6. Immunohistochemical detection of PGL-1, LAM, 30 kD and 65 kD antigens in leprosy infected paraffin preserved skin and nerve sections

    NARCIS (Netherlands)

    van den Bos, I. C.; Khanolkar-Young, S.; Das, P. K.; Lockwood, D. N.

    1999-01-01

    A panel of lipid, carbohydrate and protein antibodies were optimized for use in detecting M. leprae antigens in paraffin embedded material. Skin and nerve biopsies from 13 patients across the leprosy spectrum were studied. All antibodies detected antigen in tissues with a BI > 1. Phenolic-glycolipid

  7. Molecular Markers for Prostate Cancer in Formalin-Fixed Paraffin-Embedded Tissues

    Directory of Open Access Journals (Sweden)

    Tamara Sequeiros

    2013-01-01

    Full Text Available Prostate cancer (PCa is the most frequently diagnosed type of cancer in developed countries. The decisive method of diagnosis is based on the results of biopsies, morphologically evaluated to determine the presence or absence of cancer. Although this approach leads to a confident diagnosis in most cases, it can be improved by using the molecular markers present in the tissue. Both miRNAs and proteins are considered excellent candidates for biomarkers in formalin-fixed paraffin-embedded (FFPE tissues, due to their stability over long periods of time. In the last few years, a concerted effort has been made to develop the necessary tools for their reliable measurement in these types of samples. Furthermore, the use of these kinds of markers may also help in establishing tumor grade and aggressiveness, as well as predicting the possible outcomes in each particular case for the different treatments available. This would aid clinicians in the decision-making process. In this review, we attempt to summarize and discuss the potential use of microRNA and protein profiles in FFPE tissue samples as markers to better predict PCa diagnosis, progression, and response to therapy.

  8. Amplification of chromosomal translocation junctions from paraffin-embedded tissues of follicular lymphoma patients

    International Nuclear Information System (INIS)

    Nambiar, Mridula; Raghavan, Sathees C; Choudhary, Bibha; Rao, Clementina R

    2008-01-01

    Follicular lymphoma is associated with the t(14;18) translocation, which is one of the most common chromosomal translocations in cancer. Generally, tissues from such patients are preserved as formalin-fixed and paraffin-embedded samples. Most of the time, retrieving the molecular information from such samples is hampered due to quality of preservation, extraction procedures and reaction conditions. In the present study, we isolate the chromosomal DNA from the paraffin-embedded nodal tissues of lymphoma patients and use a highly sensitive nested PCR approach to detect t(14;18) translocation. Our studies show that despite the sheared DNA obtained, appropriate modification of PCR reaction conditions can help in obtaining the desired amplifications. The DNA extraction protocol from paraffin-embedded nodal tissues and modifications in the PCR conditions are discussed. This study would contribute to the successful use of archival tissue samples in obtaining valuable information for cancer research

  9. Amplification of chromosomal translocation junctions from paraffin-embedded tissues of follicular lymphoma patients

    Energy Technology Data Exchange (ETDEWEB)

    Nambiar, Mridula; Raghavan, Sathees C [Department of Biochemistry, Indian Institute of Science, Bangalore-560 012 (India); Choudhary, Bibha [Manipal Institute of Regenerative Medicine, Manipal University, Bangalore-560 071 (India); Rao, Clementina R [Department of Pathology, Kidwai Memorial Institute of Oncology, Bangalore-560 029 (India)], E-mail: sathees@biochem.iisc.ernet.in

    2008-09-01

    Follicular lymphoma is associated with the t(14;18) translocation, which is one of the most common chromosomal translocations in cancer. Generally, tissues from such patients are preserved as formalin-fixed and paraffin-embedded samples. Most of the time, retrieving the molecular information from such samples is hampered due to quality of preservation, extraction procedures and reaction conditions. In the present study, we isolate the chromosomal DNA from the paraffin-embedded nodal tissues of lymphoma patients and use a highly sensitive nested PCR approach to detect t(14;18) translocation. Our studies show that despite the sheared DNA obtained, appropriate modification of PCR reaction conditions can help in obtaining the desired amplifications. The DNA extraction protocol from paraffin-embedded nodal tissues and modifications in the PCR conditions are discussed. This study would contribute to the successful use of archival tissue samples in obtaining valuable information for cancer research.

  10. DNA degrades during storage in formalin-fixed and paraffin-embedded tissue blocks.

    Science.gov (United States)

    Guyard, Alice; Boyez, Alice; Pujals, Anaïs; Robe, Cyrielle; Tran Van Nhieu, Jeanne; Allory, Yves; Moroch, Julien; Georges, Odette; Fournet, Jean-Christophe; Zafrani, Elie-Serge; Leroy, Karen

    2017-10-01

    Formalin-fixed paraffin-embedded (FFPE) tissue blocks are widely used to identify clinically actionable molecular alterations or perform retrospective molecular studies. Our goal was to quantify degradation of DNA occurring during mid to long-term storage of samples in usual conditions. We selected 46 FFPE samples of surgically resected carcinomas of lung, colon, and urothelial tract, of which DNA had been previously extracted. We performed a second DNA extraction on the same blocks under identical conditions after a median period of storage of 5.5 years. Quantitation of DNA by fluorimetry showed a 53% decrease in DNA quantity after storage. Quantitative PCR (qPCR) targeting KRAS exon 2 showed delayed amplification of DNA extracted after storage in all samples but one. The qPCR/fluorimetry quantification ratio decreased from 56 to 15% after storage (p DNA analyzable by qPCR represented only 11% of the amount obtained at first extraction. Maximal length of amplifiable DNA fragments assessed with a multiplex PCR was reduced in DNA extracted from stored tissue, indicating that DNA fragmentation had increased in the paraffin blocks during storage. Next-generation sequencing was performed on 12 samples and showed a mean 3.3-fold decrease in library yield and a mean 4.5-fold increase in the number of single-nucleotide variants detected after storage. In conclusion, we observed significant degradation of DNA extracted from the same FFPE block after 4 to 6 years of storage. Better preservation strategies should be considered for storage of FFPE biopsy specimens.

  11. Multiplex polymerase chain reaction for the detection of high-risk-human papillomavirus types in formalin-fixed paraffin-embedded cervical tissues

    Directory of Open Access Journals (Sweden)

    Mini P Singh

    2017-01-01

    Full Text Available Detecting high-risk-human papillomavirus (HPV types has become an integral part of the cervical cancer screening programmes. This study aimed to develop a multiplex polymerase chain reaction (PCR for identification of HPV types 16 and 18 along with the beta globin gene in formalin-fixed and paraffin-embedded cervical biopsy specimens. A total of 59 samples from patients with cervical abnormalities were tested. HPV 16 positivity was 50% in cervical cancers and 52.9% in cervical intraepithelial neoplasia. Our multiplex PCR protocol can be used as a simple and cost-effective tool for high-risk-HPV detection in cervical cancer screening programmes.

  12. Real-time quantitative PCR of microdissected paraffin-embedded breast carcinoma

    DEFF Research Database (Denmark)

    Gjerdrum, Lise Mette; Sorensen, Boe Sandahl; Kjeldsen, Eigil

    2004-01-01

    We studied the feasibility of using real-time quantitative PCR to determine HER-2 DNA amplification and mRNA expression in microdissected formalin-fixed, paraffin-embedded breast tumors and compared this with standard immunohistochemistry (IHC) and fluorescent in situ hybridization (FISH) methods...

  13. Detection of apoptosis in paraffin embedded tissues: the influence of tissue type and fixation

    Czech Academy of Sciences Publication Activity Database

    Matalová, Eva; Dubská, L.; Míšek, Ivan

    2002-01-01

    Roč. 71, č. 4 (2002), s. 529-533 ISSN 0001-7213 R&D Projects: GA ČR GP204/02/P112; GA AV ČR KSK6005114 Keywords : apoptosis * TUNEL test * paraffin embedded tissues Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 0.370, year: 2002

  14. Virus characterization and discovery in formalin-fixed paraffin-embedded tissues

    NARCIS (Netherlands)

    Bodewes, Rogier; van Run, Peter R W A; Schürch, Anita C; Koopmans, Marion P G; Osterhaus, Albert D M E; Baumgärtner, Wolfgang; Kuiken, Thijs; Smits, Saskia L

    2015-01-01

    Detection and characterization of novel viruses is hampered frequently by the lack of properly stored materials. Especially for the retrospective identification of viruses responsible for past disease outbreaks, often only formalin-fixed paraffin-embedded (FFPE) tissue samples are available.

  15. Evaluating Quality of Aged Archival Formalin-Fixed Paraffin-Embedded Samples for RNA-Sequencing

    Science.gov (United States)

    Archival formalin-fixed paraffin-embedded (FFPE) samples offer a vast, untapped source of genomic data for biomarker discovery. However, the quality of FFPE samples is often highly variable, and conventional methods to assess RNA quality for RNA-sequencing (RNA-seq) are not infor...

  16. Human papillomavirus detection in paraffin-embedded colorectal cancer tissues.

    Science.gov (United States)

    Tanzi, Elisabetta; Bianchi, Silvia; Frati, Elena R; Amicizia, Daniela; Martinelli, Marianna; Bragazzi, Nicola L; Brisigotti, Maria Pia; Colzani, Daniela; Fasoli, Ester; Zehender, Gianguglielmo; Panatto, Donatella; Gasparini, Roberto

    2015-01-01

    Human papillomavirus (HPV) has a well-recognized aetiological role in the development of cervical cancer and other anogenital tumours. Recently, an association between colorectal cancer and HPV infection has been suggested, although this is still controversial. This study aimed at detecting and characterizing HPV infection in 57 paired biopsies from colorectal cancers and adjacent intact tissues using a degenerate PCR approach. All amplified fragments were genotyped by means of sequencing. Overall, HPV prevalence was 12.3 %. In particular, 15.8 % of tumour tissues and 8.8 % of non-cancerous tissue samples were HPV DNA-positive. Of these samples, 85.7 % were genotyped successfully, with 41.7 % of sequences identifying four genotypes of the HR (high oncogenic risk) clade Group 1; the remaining 58.3 % of HPV-genotyped specimens had an unclassified β-HPV. Examining additional cases and analysing whole genomes will help to outline the significance of these findings.

  17. Whole-genome gene expression profiling of formalin-fixed, paraffin-embedded tissue samples.

    Directory of Open Access Journals (Sweden)

    Craig April

    2009-12-01

    Full Text Available We have developed a gene expression assay (Whole-Genome DASL, capable of generating whole-genome gene expression profiles from degraded samples such as formalin-fixed, paraffin-embedded (FFPE specimens.We demonstrated a similar level of sensitivity in gene detection between matched fresh-frozen (FF and FFPE samples, with the number and overlap of probes detected in the FFPE samples being approximately 88% and 95% of that in the corresponding FF samples, respectively; 74% of the differentially expressed probes overlapped between the FF and FFPE pairs. The WG-DASL assay is also able to detect 1.3-1.5 and 1.5-2 -fold changes in intact and FFPE samples, respectively. The dynamic range for the assay is approximately 3 logs. Comparing the WG-DASL assay with an in vitro transcription-based labeling method yielded fold-change correlations of R(2 approximately 0.83, while fold-change comparisons with quantitative RT-PCR assays yielded R(2 approximately 0.86 and R(2 approximately 0.55 for intact and FFPE samples, respectively. Additionally, the WG-DASL assay yielded high self-correlations (R(2>0.98 with low intact RNA inputs ranging from 1 ng to 100 ng; reproducible expression profiles were also obtained with 250 pg total RNA (R(2 approximately 0.92, with approximately 71% of the probes detected in 100 ng total RNA also detected at the 250 pg level. When FFPE samples were assayed, 1 ng total RNA yielded self-correlations of R(2 approximately 0.80, while still maintaining a correlation of R(2 approximately 0.75 with standard FFPE inputs (200 ng.Taken together, these results show that WG-DASL assay provides a reliable platform for genome-wide expression profiling in archived materials. It also possesses utility within clinical settings where only limited quantities of samples may be available (e.g. microdissected material or when minimally invasive procedures are performed (e.g. biopsied specimens.

  18. Influence of parasite density and sample storage time on the reliability of Entamoeba histolytica-specific PCR from formalin-fixed and paraffin-embedded tissues.

    Science.gov (United States)

    Frickmann, Hagen; Tenner-Racz, Klara; Eggert, Petra; Schwarz, Norbert G; Poppert, Sven; Tannich, Egbert; Hagen, Ralf M

    2013-12-01

    We report on the reliability of polymerase chain reaction (PCR) for the detection of Entamoeba histolytica from formalin-fixed, paraffin-embedded tissue in comparison with microscopy and have determined predictors that may influence PCR results. E. histolytica-specific and Entamoeba dispar-specific real-time PCR and microscopy from adjacent histologic sections were performed using a collection of formalin-fixed, paraffin-embedded tissue specimens obtained from patients with invasive amebiasis. Specimens had been collected during the previous 4 decades. Association of sample age, parasite density, and reliability of PCR was analyzed. E. histolytica PCR was positive in 20 of 34 biopsies (58.8%); 2 of these 20 were microscopically negative for amebae in neighboring tissue sections. PCR was negative in 9 samples with visible amebae in neighboring sections and in 5 samples without visible parasites in neighboring sections. PCR was negative in all specimens that were older than 3 decades. Low parasite counts and sample ages older than 20 years were predictors for false-negative PCR results. All samples were negative for E. dispar DNA. PCR is suitable for the detection of E. histolytica in formalin-fixed, paraffin-embedded tissue samples that are younger than 2 decades and that contain intermediate to high parasite numbers. Negative results in older samples were due to progressive degradation of DNA over time as indicated by control PCRs targeting the human 18S rRNA gene. Moreover, our findings support previous suggestions that only E. histolytica but not E. dispar is responsible for invasive amebiasis.

  19. Advantages of infrared transflection micro spectroscopy and paraffin-embedded sample preparation for biological studies

    Science.gov (United States)

    Yao, Jie; Li, Qian; Zhou, Bo; Wang, Dan; Wu, Rie

    2018-04-01

    Fourier-Transform Infrared micro-spectroscopy is an excellent method for biological analyses. In this paper, series metal coating films on ITO glass were prepared by the electrochemical method and the different thicknesses of paraffin embedding rat's brain tissue on the substrates were studied by IR micro-spetroscopy in attenuated total reflection (ATR) mode and transflection mode respectively. The Co-Ni-Cu alloy coating film with low cost is good reflection substrates for the IR analysis. The infrared microscopic transflection mode needs not to touch the sample at all and can get the IR spectra with higher signal to noise ratios. The Paraffin-embedding method allows tissues to be stored for a long time for re-analysis to ensure the traceability of the sample. Also it isolates the sample from the metal and avoids the interaction of biological tissue with the metals. The best thickness of the tissues is 4 μm.

  20. Protein extraction from methanol fixed paraffin embedded tissue blocks: A new possibility using cell blocks

    Science.gov (United States)

    Kokkat, Theresa J.; McGarvey, Diane; Patel, Miral S.; Tieniber, Andrew D.; LiVolsi, Virginia A.; Baloch, Zubair W.

    2013-01-01

    Background: Methanol fixed and paraffin embedded (MFPE) cellblocks are an essential cytology preparation. However, MFPE cellblocks often contain limited material and their relatively small size has caused them to be overlooked in biomarker discovery. Advances in the field of molecular biotechnology have made it possible to extract proteins from formalin fixed and paraffin embedded (FFPE) tissue blocks. In contrast, there are no established methods for extracting proteins from MFPE cellblocks. We investigated commonly available CHAPS (3-[(3-cholamidopropyl) dimethylammonio]-1-propanesulfonate) buffer, as well as two commercially available Qiagen® kits and compared their effectiveness on MFPE tissue for protein yields. Materials and Methods: MFPE blocks were made by Cellient™ automated system using human tissue specimens from normal and malignant specimens collected in ThinPrep™ Vials. Protein was extracted from Cellient-methanol fixed and paraffin embedded blocks with CHAPS buffer method as well as FFPE and Mammalian Qiagen® kits. Results: Comparison of protein yields demonstrated the effectiveness of various protein extraction methods on MFPE cellblocks. Conclusion: In the current era of minimally invasive techniques to obtain minimal amount of tissue for diagnostic and prognostic purposes, the use of commercial and lab made buffer on low weight MFPE scrapings obtained by Cellient® processor opens new possibilities for protein biomarker research. PMID:24403950

  1. Optimization of Glial Fibrillary Acidic Protein Immunoreactivity in Formalin-fixed, Paraffin-Embedded Guinea Pig Brain Sections

    Science.gov (United States)

    2003-09-01

    fixed, paraffin-embedded guinea pig brain sections using a variety of commercially available GFAP antibody clones. Of the 7 clones tested for cross...determining neuropathological consequences in the guinea pig following exposure to chemical warfare nerve agent.

  2. Detection of Mycobacterium tuberculosis Complex in Paraffin-Embedded Tissues by the New Automated Abbott RealTime MTB Assay.

    Science.gov (United States)

    Fu, Yung-Chieh; Liao, I-Chuang; Chen, Hung-Mo; Yan, Jing-Jou

    2016-07-01

    The Abbott RealTime MTB assay, launched in June 2014, has been shown to have a competitive performance in the detection of the Mycobacterium tuberculosis (MTB) complex in respiratory specimens. The present study was conducted to investigate the usefulness of the Abbott MTB Realtime assay in the detection of MTB in formalin-fixed paraffin-embedded (FFPE) tissues. A total of 96 FFPE specimens obtained from microbiologically proven MTB cases (N=60) and nontuberculous Mycobacterium cases (N=36) were analyzed. The performance of the Abbott MTB Realtime assay was compared with that of the Roche Cobas TaqMan MTB assay. The overall sensitivity and specificity of the Abbott assay were 63.3% and 97.2%, respectively, compared with 11.7% and 100% for the Cobas assay. The detection rate of the Abbott assay was much higher among 37 acid-fast-positive specimens than among 23 acid-fast-negative specimens (89.3% versus 21.7%, respectively). The detection rate of the assay was higher among 29 resection specimens than among 31 small biopsy specimens (86.2% versus 41.9%, respectively). Our results suggest that the Abbott RealTime MTB assay can be used to differentiate MTB from nontuberculous mycobacterial infections in acid-fast-positive FFPE tissues. © 2016 by the Association of Clinical Scientists, Inc.

  3. Real-time quantitative PCR of microdissected paraffin-embedded breast carcinoma

    DEFF Research Database (Denmark)

    Gjerdrum, Lise Mette; Sorensen, Boe Sandahl; Kjeldsen, Eigil

    2004-01-01

    We studied the feasibility of using real-time quantitative PCR to determine HER-2 DNA amplification and mRNA expression in microdissected formalin-fixed, paraffin-embedded breast tumors and compared this with standard immunohistochemistry (IHC) and fluorescent in situ hybridization (FISH) methods...... tumors as being amplified. Interestingly, all these scored 2+ with the HercepTest, but were negative using FISH. We believe that real-time quantitative PCR analysis of HER-2 DNA amplification following microdissection represents a useful supplementary or perhaps even an alternative technique...

  4. Diagnosis of Nocardia paucivorans central nervous system infection by DNA sequencing from paraffin-embedded tissue.

    Science.gov (United States)

    Schiaroli, Elisabetta; Pasticci, Maria Bruna; De Carolis, Elena; Mello, Enrica; Pallotto, Carlo; Leli, Christian; De Socio, Giuseppe Vittorio; Baldelli, Franco; Sanguinetti, Maurizio; Mencacci, Antonella

    2016-06-01

    Infections by Nocardia spp. are generally regarded as opportunistic diseases in immunocompromised patients, but can also affect immunocompetent subjects. Such infections represent an important diagnostic challenge for clinicians and microbiologists, and diagnosis is frequently delayed or even conducted post mortem. A 54-year-old man was admitted to our hospital because of ventriculitis and relapsing brain abscess. Five months prior, this patient had undergone external ventricular drain and surgery for a cerebellar abscess. Histopathology demonstrated pyogenic inflammatory reaction, microbiologic investigations proved negative and empiric antimicrobial therapy was administered for a total of eight weeks. Six weeks later, the patient developed relapsing neurologic manifestations. On reviewing the patient's clinical history it emerged that the patient had suffered pneumonia two months prior to neurosurgery, treated with amoxicillin/clavulanate 3g a day and levofloxacin 500mg a day for three weeks. On the CNS relapsing manifestations, nocardiosis was suspected and DNA sequencing from the formalin-fixed paraffin-embedded cerebellar tissue collected during neurosurgery allowed diagnosis of Nocardia paucivorans infection. The patient received medical therapy for 11 months. At follow-up, eight months after treatment was discontinued, the patient was aymptomatic. Nocardia spp. infections need to be suspected not only in immunocompromised, but also in immunocompetent patients. Proper samples need to be collected for proper microbiologic investigations. Paraffin-embedded tissue genomic sequencing can be a useful tool for diagnosis of nocardiosis.

  5. PrPSc detection in formalin-fixed paraffin-embedded tissue by ELISA

    Directory of Open Access Journals (Sweden)

    Nicholson Eric M

    2011-10-01

    Full Text Available Abstract Background Formalin-fixed paraffin-embedded tissue is regularly employed in the diagnosis of transmissible spongiform encephalopathies (TSE by immunohistochemistry (IHC, the standard by which all other TSE diagnostic protocols are judged. While IHC affords advantages over diagnostic approaches that typically utilize fresh or frozen tissue, such as Western blot and ELISA, the process of fixing, staining, and analyzing individual sections by hand does not allow for rapid or high throughput screening. However, preservation of tissues in formalin is not dependent upon the availability of refrigeration. Findings Formalin-fixed paraffin-embedded tissues from TSE transmission studies of scrapie in sheep, chronic wasting disease in white-tailed deer or transmissible mink encephalopathy in cattle were cut at 5 μm thickness. Samples containing the tissue equivalent of as little as one 5 μm section can be used to readily discriminate positive from negative samples. Conclusions This approach cannot replace IHC but may be used along with IHC as both a more rapid and readily high throughput screen where fresh or frozen tissues are not available or impractical.

  6. STR typing of formalin-fixed paraffin embedded (FFPE) aborted foetal tissue in criminal paternity cases.

    Science.gov (United States)

    Reshef, Ayeleth; Barash, Mark; Voskoboinik, Lev; Brauner, Paul; Gafny, Roni

    2011-03-01

    Sexual assault or rape cases occasionally result in unwanted pregnancies. In almost all such cases the foetus is aborted. A forensic laboratory may receive the foetus, the placenta, or paraffin embedded abortion material for paternity testing. Obtaining a foetal profile DNA from a foetus or placenta may not be successful due to the age or condition of the tissue. Moreover, maternal contamination of placental material will invariably result in a mixed DNA profile. However, the use of properly screened abortion material from paraffin blocks will almost always result in obtaining a foetal DNA profile. Furthermore, foetal tissue fixed in paraffin blocks does not require special conditions for submission and storage as required to preserve fresh foetal or placental tissue. As hospitals routinely prepare foetal tissue in paraffin blocks, which should be readily obtainable by forensic laboratories, these samples would appear to be the preferred choice for paternity testing. 2010 Forensic Science Society. Published by Elsevier Ireland Ltd. All rights reserved.

  7. Terahertz spectroscopy for the study of paraffin-embedded gastric cancer samples

    Science.gov (United States)

    Wahaia, Faustino; Kasalynas, Irmantas; Seliuta, Dalius; Molis, Gediminas; Urbanowicz, Andrzej; Carvalho Silva, Catia D.; Carneiro, Fatima; Valusis, Gintaras; Granja, Pedro L.

    2015-01-01

    Terahertz (THz) spectroscopy constitute promising technique for biomedical applications as a complementary and powerful tool for diseases screening specially for early cancer diagnostic. The THz radiation is not harmful to biological tissues. As increased blood supply in cancer-affected tissues and consequent local increase in tissue water content makes THz technology a potentially attractive. In the present work, samples of healthy and adenocarcinoma-affected gastric tissue were analyzed using transmission time-domain THz spectroscopy (THz-TDS). The work shows the capability of the technique to distinguish between normal and cancerous regions in dried and paraffin-embedded samples. Plots of absorption coefficient α and refractive index n of normal and cancer affected tissues, are presented and the conditions for discrimination between normal and affected tissues are discussed.

  8. Russell bodies in a skin biopsy: a case report

    Directory of Open Access Journals (Sweden)

    Verheij Joanne

    2009-11-01

    Full Text Available Abstract Introduction The presence of eosinophilic bodies in a skin biopsy can be found in a variety of situations and this may present a challenge to the pathologist. The differential diagnosis of these eosinophilic structures include microorganisms such as histoplasmosis or cryptococcosis, fungi, Michaelis-Gutmann bodies, deposits of amyloid or immunoglobulins, colloid bodies or elastic bodies. Case presentation During a routine examination of a skin biopsy with actinic keratosis taken from the cheek of a 61-year-old man, clusters of eosinophilic bodies were seen within an inflammatory infiltrate in the dermis, both intracytoplasmic and extracellular. Using additional immunohistochemical staining, these structures were identified as polyclonal Russell bodies. Conclusion The differential diagnosis of intracytoplasmic eosinophilic structures in a skin biopsy includes Russell bodies, an uncommon finding that may be associated with chronic inflammatory conditions.

  9. Light microscopic identification and semiquantification of polyethylene particles in methylmethacrylate and paraffin-embedded experimental bone implant specimens

    DEFF Research Database (Denmark)

    Rahbek, O; Kold, S; Overgaard, S

    2005-01-01

    The aim of this study was to evaluate the identification of polyethylene (PE) particles in relatively thick methylmethacrylate (MMA) sections widely used in bone implant research. The sensitivity and specificity were compared between decalcified paraffin-embedded oil red O (ORO) stained and MMA-e...

  10. Combined in situ zymography, immunofluorescence, and staining of iron oxide particles in paraffin-embedded, zinc-fixed tissue sections.

    Science.gov (United States)

    Haeckel, Akvile; Schoenzart, Lena; Appler, Franziska; Schnorr, Joerg; Taupitz, Matthias; Hamm, Bernd; Schellenberger, Eyk

    2012-01-01

    Superparamagnetic iron oxide particles are used as potent contrast agents in magnetic resonance imaging. In histology, these particles are frequently visualized by Prussian blue iron staining of aldehyde-fixed, paraffin-embedded tissues. Recently, zinc salt-based fixative was shown to preserve enzyme activity in paraffin-embedded tissues. In this study, we demonstrate that zinc fixation allows combining in situ zymography with fluorescence immunohistochemistry (IHC) and iron staining for advanced biologic investigation of iron oxide particle accumulation. Very small iron oxide particles, developed for magnetic resonance angiography, were applied intravenously to BALB/c nude mice. After 3 hours, spleens were explanted and subjected to zinc fixation and paraffin embedding. Cut tissue sections were further processed to in situ zymography, IHC, and Prussian blue staining procedures. The combination of in situ zymography as well as IHC with subsequent Prussian blue iron staining on zinc-fixed paraffin-embedded tissues resulted in excellent histologic images of enzyme activity, protease distribution, and iron oxide particle accumulation. The combination of all three stains on a single section allowed direct comparison with only moderate degradation of fluorescein isothiocyanate-labeled substrate. This protocol is useful for investigating the biologic environment of accumulating iron oxide particles, with excellent preservation of morphology.

  11. Limited numbers of apoptotic cells in fresh paraffin embedded bone marrow samples of patients with myelodysplastic syndrome

    NARCIS (Netherlands)

    Brada, SJL; van de Loosdrecht, AA; Koudstaal, J; de Wolf, JTM; Vellenga, E

    In myelodysplasia (MDS) the precise mechanism of ineffective erythropoiesis is not fully elucidated, but it is suggested that apoptosis may contribute to this process. We performed TdT-mediated dUTP-nick end labelling (TUNEL) staining of paraffin embedded bone marrow specimens to assess the amount

  12. New comprehensive denaturing-gradient-gel-electrophoresis assay for KRAS mutation detection applied to paraffin-embedded tumours

    NARCIS (Netherlands)

    Hayes, VM; Westra, JL; Verlind, E; Bleeker, W; Plukker, JT; Hofstra, RMW; Buys, CHCM

    2000-01-01

    A comprehensive mutation detection assay is presented for the entire coding region and all splice site junctions of the KRAS oncogene. The assay is based on denaturing gradient gel electrophoresis and applicable to archival paraffin-embedded tumour material. All KRAS amplicons are analysed within

  13. Investigation of archived formalin-fixed paraffin-embedded pancreatic tissue with whole-genome gene expression microarray

    DEFF Research Database (Denmark)

    Michelsen, Nete Vinstrup; Brusgaard, Klaus; Tan, Qihua

    2011-01-01

    The use of formalin-fixed, paraffin-embedded (FFPE) tissue overcomes the most prominent issues related to research on relatively rare diseases: limited sample size, availability of control tissue, and time frame. The use of FFPE pancreatic tissue in GEM may be especially challenging due to its very...

  14. Dose-Response Analysis of RNA-Seq Profiles in Archival Formalin-Fixed Paraffin-Embedded (FFPE) Samples.

    Science.gov (United States)

    Use of archival resources has been limited to date by inconsistent methods for genomic profiling of degraded RNA from formalin-fixed paraffin-embedded (FFPE) samples. RNA-sequencing offers a promising way to address this problem. Here we evaluated transcriptomic dose responses us...

  15. Psoriasis skin biopsy image segmentation using Deep Convolutional Neural Network.

    Science.gov (United States)

    Pal, Anabik; Garain, Utpal; Chandra, Aditi; Chatterjee, Raghunath; Senapati, Swapan

    2018-06-01

    Development of machine assisted tools for automatic analysis of psoriasis skin biopsy image plays an important role in clinical assistance. Development of automatic approach for accurate segmentation of psoriasis skin biopsy image is the initial prerequisite for developing such system. However, the complex cellular structure, presence of imaging artifacts, uneven staining variation make the task challenging. This paper presents a pioneering attempt for automatic segmentation of psoriasis skin biopsy images. Several deep neural architectures are tried for segmenting psoriasis skin biopsy images. Deep models are used for classifying the super-pixels generated by Simple Linear Iterative Clustering (SLIC) and the segmentation performance of these architectures is compared with the traditional hand-crafted feature based classifiers built on popularly used classifiers like K-Nearest Neighbor (KNN), Support Vector Machine (SVM) and Random Forest (RF). A U-shaped Fully Convolutional Neural Network (FCN) is also used in an end to end learning fashion where input is the original color image and the output is the segmentation class map for the skin layers. An annotated real psoriasis skin biopsy image data set of ninety (90) images is developed and used for this research. The segmentation performance is evaluated with two metrics namely, Jaccard's Coefficient (JC) and the Ratio of Correct Pixel Classification (RCPC) accuracy. The experimental results show that the CNN based approaches outperform the traditional hand-crafted feature based classification approaches. The present research shows that practical system can be developed for machine assisted analysis of psoriasis disease. Copyright © 2018 Elsevier B.V. All rights reserved.

  16. Tubuloreticular inclusions in skin biopsies from patients with HIV infection

    DEFF Research Database (Denmark)

    Pedersen, C; Horn, T; Junge, Jette

    1989-01-01

    Skin biopsies obtained from apparently normal skin from 15 HIV infected patients and 6 anti-HIV negative patients were examined by electron microscopy. Tubuloreticular inclusions (TRI) were detected within the cytoplasm of capillary endothelial cells in 5/5 AIDS patients and in 2/5 patients...... of the patients without TRI, interferon activity was below detection level. The occurrence of TRI was not dependent on the presence of free p24 antigen in serum. It is concluded that the occurrence of TRI in entothelial cells of skin capillaries is associated with late stages of HIV infection and this may...

  17. Histopathological Features Of Granulomatous Skin Diseases : An Analysis Of 22 Skin Biopsies

    Directory of Open Access Journals (Sweden)

    Dhar Subhra

    2002-01-01

    Full Text Available In the present study, skin biopsies were analysed for histopathological (HP changes in 22 patients with various granulomatous dermatoses. In 6 specimens, HP features were diagnostic of BT leprosy, in 1 each of BB, BL and historid LL. The HP features were was lupus valugaris (LV in 6 biopsies, tuberculosis verrucosa cutis (TBVC in 2, sarcoidosis in 3 and sporotrichosis in remaining 2. The study reiterated the usefulness of HP examination of all suspected cases of granulomatous skin diseases.

  18. Histopathological Features Of Granulomatous Skin Diseases : An Analysis Of 22 Skin Biopsies

    OpenAIRE

    Dhar Subhra; Dhar Sandipan

    2002-01-01

    In the present study, skin biopsies were analysed for histopathological (HP) changes in 22 patients with various granulomatous dermatoses. In 6 specimens, HP features were diagnostic of BT leprosy, in 1 each of BB, BL and historid LL. The HP features were was lupus valugaris (LV) in 6 biopsies, tuberculosis verrucosa cutis (TBVC) in 2, sarcoidosis in 3 and sporotrichosis in remaining 2. The study reiterated the usefulness of HP examination of all suspected cases of granulomatous skin diseases.

  19. Clinical relevance of DNA microarray analyses using archival formalin-fixed paraffin-embedded breast cancer specimens

    International Nuclear Information System (INIS)

    Sadi, Al Muktafi; Wang, Dong-Yu; Youngson, Bruce J; Miller, Naomi; Boerner, Scott; Done, Susan J; Leong, Wey L

    2011-01-01

    The ability of gene profiling to predict treatment response and prognosis in breast cancers has been demonstrated in many studies using DNA microarray analyses on RNA from fresh frozen tumor specimens. In certain clinical and research situations, performing such analyses on archival formalin fixed paraffin-embedded (FFPE) surgical specimens would be advantageous as large libraries of such specimens with long-term follow-up data are widely available. However, FFPE tissue processing can cause fragmentation and chemical modifications of the RNA. A number of recent technical advances have been reported to overcome these issues. Our current study evaluates whether or not the technology is ready for clinical applications. A modified RNA extraction method and a recent DNA microarray technique, cDNA-mediated annealing, selection, extension and ligation (DASL, Illumina Inc) were evaluated. The gene profiles generated from FFPE specimens were compared to those obtained from paired fresh fine needle aspiration biopsies (FNAB) of 25 breast cancers of different clinical subtypes (based on ER and Her2/neu status). Selected RNA levels were validated using RT-qPCR, and two public databases were used to demonstrate the prognostic significance of the gene profiles generated from FFPE specimens. Compared to FNAB, RNA isolated from FFPE samples was relatively more degraded, nonetheless, over 80% of the RNA samples were deemed suitable for subsequent DASL assay. Despite a higher noise level, a set of genes from FFPE specimens correlated very well with the gene profiles obtained from FNAB, and could differentiate breast cancer subtypes. Expression levels of these genes were validated using RT-qPCR. Finally, for the first time we correlated gene expression profiles from FFPE samples to survival using two independent microarray databases. Specifically, over-expression of ANLN and KIF2C, and under-expression of MAPT strongly correlated with poor outcomes in breast cancer patients. We

  20. A SIMPLE PARAFFIN EMBEDDED PROTOCOL FOR FISH EGG, EMBRYO, AND LARVAE

    Directory of Open Access Journals (Sweden)

    Gratiana Eka Wijayanti

    2017-06-01

    Full Text Available This paper describes a simple protocol of paraffin-embedded histological section for fish eggs, embryo and larvae of the hard-lipped barb and the giant gourami. The specimens were fixed in Bouin solution, washed in 70% ethanol, then were dehydrated in a series of ethanol solution of increasing concentration until absolute ethanol was reached. The specimens were cleared in graded xylene and were infiltrated with liquid paraffin then were embedded in pure paraffin. Upon sectioning, at 4–5 µm thick the specimens were attached to the gelatin-coated glass slide and let to dry at room temperature or 37°C overnight. The specimens were deparaffinized in xylene, rehydrated then were stained with hematoxylin and eosin. After being dehydrated in graded ethanol, the specimens were cleared in xylene and were mounted with an organic mounting agent. Any step in preparing histological section including samples collection, fixation, dehydration, infiltration and embedding might contribute to the quality of histological features. A proper knowledge of the tissues beeing processed, fixative solution and the histological techniques is essential to gain good results. Bouin fixative is preferable to fix fish larvae and produce a good histological feature. Decalcification is necessary to produce a good histological section on the specimens containing bone.

  1. Polymerase chain reaction detection of retinoblastoma gene deletions in paraffin-embedded mouse lung adenocarcinomas

    International Nuclear Information System (INIS)

    Churchill, M.E.; Gemmell, M.A.; Woloschak, G.E.

    1991-01-01

    A Polymerase chain reaction (PCR) technique was used to detect deletions in the mouse retinoblastoma (mRb) gene using microtomed sections from paraffin-embedded radiation-induced and spontaneous tumors as the DNA source. Six mRb gene exon fragments were amplified in a 40-cycle, 3-temperature PCR protocol. Absence of any of these fragments relative to control PCR products on a Southern blot indicated a deletion of that portion of the mRb gene. Tumors chosen for analysis were lung adenocarcinomas that were judged to be the cause of death. Spontaneous tumors as well as those from irradiated mice (569 cGy of 60 Co γ rays or 60 cGy of JANUS neutrons) were analyzed. Tumors in six neutron-irradiated mice also had no mRb deletions. However, one of six tumors from γ-irradiated mice and 6 of 18 spontaneous tumors from unirradiated mice showed a deletion in one or both mRb alleles. All deletions detected were in the 5' region of the mRb gene

  2. Comparison of Different Double Immunostaining Protocols for Paraffin Embedded Liver Tissue

    Directory of Open Access Journals (Sweden)

    Alexander Schütz

    1999-01-01

    Full Text Available Most of the double immunostaining protocols that have been introduced so far have been developed for application on fresh frozen material or based on different species antibodies. In liver tissue, general problems of double immunostaining techniques are further complicated by tissue‐specific difficulties, such as necrosis or high intracellular protein content. To assess a reliable double immunostaining protocol for archived, paraffin embedded liver tissue, different protocols based on the use of same species primary antibodies were evaluated in terms of sensitivity, specificity and non‐specific background staining in pathological liver specimens. We compared peroxidase–anti‐peroxidase, alkaline phosphatase–anti‐alkaline phosphatase (PAP/APAP, labelled‐avidin–biotin (LAB/LAB and digoxigenin–anti‐digoxigenin (dig–a‐dig/PAP techniques using different cytokeratin antibodies and an antibody against PCNA. Comparison of the double immunostaining techniques revealed a high sensitivity and specificity in all procedures. Sections, which were stained employing PAP/APAP‐technique, displayed a higher background staining compared to sections which were treated with the LAB/LAB or dig–a‐dig/PAP protocol. In contrast to the dig–a‐dig/PAP protocol, the LAB/LAB technique provides a better time/cost relationship. Therefore, we would like to recommend a modified LAB/LAB protocol for simultaneous detection of different antigens in archived liver tissue.

  3. In situ hybridization for the detection of rust fungi in paraffin embedded plant tissue sections.

    Science.gov (United States)

    Ellison, Mitchell A; McMahon, Michael B; Bonde, Morris R; Palmer, Cristi L; Luster, Douglas G

    2016-01-01

    Rust fungi are obligate pathogens with multiple life stages often including different spore types and multiple plant hosts. While individual rust pathogens are often associated with specific plants, a wide range of plant species are infected with rust fungi. To study the interactions between these important pathogenic fungi and their host plants, one must be able to differentiate fungal tissue from plant tissue. This can be accomplished using the In situ hybridization (ISH) protocol described here. To validate reproducibility using the ISH protocol, samples of Chrysanthemum × morifolium infected with Puccinia horiana, Gladiolus × hortulanus infected with Uromyces transversalis and Glycine max infected with Phakopsora pachyrhizi were tested alongside uninfected leaf tissue samples. The results of these tests show that this technique clearly distinguishes between rust pathogens and their respective host plant tissues. This ISH protocol is applicable to rust fungi and potentially other plant pathogenic fungi as well. It has been shown here that this protocol can be applied to pathogens from different genera of rust fungi with no background staining of plant tissue. We encourage the use of this protocol for the study of plant pathogenic fungi in paraffin embedded sections of host plant tissue.

  4. Virus characterization and discovery in formalin-fixed paraffin-embedded tissues.

    Science.gov (United States)

    Bodewes, Rogier; van Run, Peter R W A; Schürch, Anita C; Koopmans, Marion P G; Osterhaus, Albert D M E; Baumgärtner, Wolfgang; Kuiken, Thijs; Smits, Saskia L

    2015-03-01

    Detection and characterization of novel viruses is hampered frequently by the lack of properly stored materials. Especially for the retrospective identification of viruses responsible for past disease outbreaks, often only formalin-fixed paraffin-embedded (FFPE) tissue samples are available. Although FFPE tissues can be used to detect known viral sequences, the application of FFPE tissues for detection of novel viruses is currently unclear. In the present study it was shown that sequence-independent amplification in combination with next-generation sequencing can be used to detect sequences of known and unknown viruses, although with relatively low sensitivity. These findings indicate that this technique could be useful for detecting novel viral sequences in FFPE tissues collected from humans and animals with disease of unknown origin, when other samples are not available. In addition, application of this method to FFPE tissues allows to correlate with the presence of histopathological changes in the corresponding tissue sections. Copyright © 2015 Elsevier B.V. All rights reserved.

  5. Improved protein extraction and protein identification from archival formalin-fixed paraffin-embedded human aortas.

    Science.gov (United States)

    Fu, Zongming; Yan, Kun; Rosenberg, Avraham; Jin, Zhicheng; Crain, Barbara; Athas, Grace; Heide, Richard S Vander; Howard, Timothy; Everett, Allen D; Herrington, David; Van Eyk, Jennifer E

    2013-04-01

    Evaluate combination of heat and elevated pressure to enhance protein extraction and quality of formalin-fixed (FF), and FF paraffin-embedded (FFPE) aorta for proteomics. Proteins were extracted from fresh frozen aorta at room temperature (RT). FF and FFPE aortas (3 months and 15 years) were extracted at RT, heat alone, or a combination of heat and high pressure. Protein yields were compared, and digested peptides from the extracts were analyzed with MS. Combined heat and elevated pressure increased protein yield from human FF or FFPE aorta compared to matched tissues with heat alone (1.5-fold) or at RT (8.3-fold), resulting in more proteins identified and with more sequence coverage. The length of storage did adversely affect the quality of proteins from FF tissue. For long-term storage, aorta was preserved better with FFPE than FF alone. Periostin and MGF-E8 were demonstrated suitable for MRM assays from FFPE aorta. Combination of heat and high pressure is an effective method to extract proteins from FFPE aorta for downstream proteomics. This method opens the possibility for use of archival and often rare FFPE aortas and possibly other tissues available to proteomics for biomarker discovery and quantification. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Complete solubilization of formalin-fixed, paraffin-embedded tissue may improve proteomic studies.

    Science.gov (United States)

    Shi, Shan-Rong; Taylor, Clive R; Fowler, Carol B; Mason, Jeffrey T

    2013-04-01

    Tissue-based proteomic approaches (tissue proteomics) are essential for discovering and evaluating biomarkers for personalized medicine. In any proteomics study, the most critical issue is sample extraction and preparation. This problem is especially difficult when recovering proteins from formalin-fixed, paraffin-embedded (FFPE) tissue sections. However, improving and standardizing protein extraction from FFPE tissue is a critical need because of the millions of archival FFPE tissues available in tissue banks worldwide. Recent progress in the application of heat-induced antigen retrieval principles for protein extraction from FFPE tissue has resulted in a number of published FFPE tissue proteomics studies. However, there is currently no consensus on the optimal protocol for protein extraction from FFPE tissue or accepted standards for quantitative evaluation of the extracts. Standardization is critical to ensure the accurate evaluation of FFPE protein extracts by proteomic methods such as reverse phase protein arrays, which is now in clinical use. In our view, complete solubilization of FFPE tissue samples is the best way to achieve the goal of standardizing the recovery of proteins from FFPE tissues. However, further studies are recommended to develop standardized protein extraction methods to ensure quantitative and qualitative reproducibility in the recovery of proteins from FFPE tissues. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. Multiplexed color-coded probe-based gene expression assessment for clinical molecular diagnostics in formalin-fixed paraffin-embedded human renal allograft tissue.

    Science.gov (United States)

    Adam, Benjamin; Afzali, Bahman; Dominy, Katherine M; Chapman, Erin; Gill, Reeda; Hidalgo, Luis G; Roufosse, Candice; Sis, Banu; Mengel, Michael

    2016-03-01

    Histopathologic diagnoses in transplantation can be improved with molecular testing. Preferably, molecular diagnostics should fit into standard-of-care workflows for transplant biopsies, that is, formalin-fixed paraffin-embedded (FFPE) processing. The NanoString(®) gene expression platform has recently been shown to work with FFPE samples. We aimed to evaluate its methodological robustness and feasibility for gene expression studies in human FFPE renal allograft samples. A literature-derived antibody-mediated rejection (ABMR) 34-gene set, comprised of endothelial, NK cell, and inflammation transcripts, was analyzed in different retrospective biopsy cohorts and showed potential to molecularly discriminate ABMR cases, including FFPE samples. NanoString(®) results were reproducible across a range of RNA input quantities (r = 0.998), with different operators (r = 0.998), and between different reagent lots (r = 0.983). There was moderate correlation between NanoString(®) with FFPE tissue and quantitative reverse transcription polymerase chain reaction (qRT-PCR) with corresponding dedicated fresh-stabilized tissue (r = 0.487). Better overall correlation with histology was observed with NanoString(®) (r = 0.354) than with qRT-PCR (r = 0.146). Our results demonstrate the feasibility of multiplexed gene expression quantification from FFPE renal allograft tissue. This represents a method for prospective and retrospective validation of molecular diagnostics and its adoption in clinical transplantation pathology. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  8. Biomedical analysis of formalin-fixed, paraffin-embedded tissue samples: The Holy Grail for molecular diagnostics.

    Science.gov (United States)

    Donczo, Boglarka; Guttman, Andras

    2018-06-05

    More than a century ago in 1893, a revolutionary idea about fixing biological tissue specimens was introduced by Ferdinand Blum, a German physician. Since then, a plethora of fixation methods have been investigated and used. Formalin fixation with paraffin embedment became the most widely used types of fixation and preservation method, due to its proper architectural conservation of tissue structures and cellular shape. The huge collection of formalin-fixed, paraffin-embedded (FFPE) sample archives worldwide holds a large amount of unearthed information about diseases that could be the Holy Grail in contemporary biomarker research utilizing analytical omics based molecular diagnostics. The aim of this review is to critically evaluate the omics options for FFPE tissue sample analysis in the molecular diagnostics field. Copyright © 2018. Published by Elsevier B.V.

  9. Analytical validation of a melanoma diagnostic gene signature using formalin-fixed paraffin-embedded melanocytic lesions.

    Science.gov (United States)

    Warf, M Bryan; Flake, Darl D; Adams, Doug; Gutin, Alexander; Kolquist, Kathryn A; Wenstrup, Richard J; Roa, Benjamin B

    2015-01-01

    These studies were to validate the analytical performance of a gene expression signature that differentiates melanoma and nevi, using RNA expression from 14 signature genes and nine normalization genes that generates a melanoma diagnostic score (MDS). Formalin-fixed paraffin-embedded melanocytic lesions were evaluated in these studies. The overall SD of the assay was determined to be 0.69 MDS units. Individual amplicons within the signature had an average amplification efficiency of 92% and a SD less than 0.5 CT. The MDS was reproducible across a 2000-fold dilution range of input RNA. Melanin, an inhibitor of PCR, does not interfere with the signature. These studies indicate this signature is robust and reproducible and is analytically validated on formalin-fixed paraffin-embedded melanocytic lesions.

  10. Automated Analysis of Protein Expression and Gene Amplification within the Same Cells of Paraffin-Embedded Tumour Tissue

    Directory of Open Access Journals (Sweden)

    Timo Gaiser

    2010-01-01

    Full Text Available Background: The simultaneous detection of protein expression and gene copy number changes in patient samples, like paraffin-embedded tissue sections, is challenging since the procedures of immunohistochemistry (IHC and Fluorescence in situ Hybridization (FISH negatively influence each other which often results in suboptimal staining. Therefore, we developed a novel automated algorithm based on relocation which allows subsequent detection of protein content and gene copy number changes within the same cell.

  11. Validation of putative reference genes for normalization of Q-RT-PCR data from paraffin-embedded lymphoid tissue

    DEFF Research Database (Denmark)

    Green, Tina Marie; de Stricker, Karin; Møller, Michael Boe

    2009-01-01

    Normalization of quantitative reverse transcription-PCR (Q-RT-PCR) data to appropriate tissue-specific reference genes is an essential part of interpreting the results. This study aimed to determine the most appropriate reference genes for normalizing gene expressions in lymphatic tissue...... was 0.93 (Pnormalization with the appropriate reference genes. Thus, we show that formalin-fixed, paraffin-embedded lymphoid samples are suitable for Q-RT-PCR when using thoroughly validated reference genes....

  12. Polymerase chain reaction analysis for viruses in paraffin-embedded myocardium from dogs with dilated cardiomyopathy or myocarditis.

    Science.gov (United States)

    Maxson, T R; Meurs, K M; Lehmkuhl, L B; Magnon, A L; Weisbrode, S E; Atkins, C E

    2001-01-01

    To perform polymerase chain reaction (PCR) analysis on paraffin-embedded myocardium from dogs with dilated cardiomyopathy (DCM) and dogs with myocarditis to screen for canine parvovirus, adenovirus types 1 and 2, and herpesvirus. Myocardial specimens from 18 dogs with an antemortem diagnosis of DCM and 9 dogs with a histopathologic diagnosis of myocarditis were evaluated. Paraffin-embedded myocardial specimens were screened for viral genome by PCR analysis. Positive-control specimens were developed from cell cultures as well as paraffin-embedded tissue specimens from dogs with clinical and histopathologic diagnoses of viral infection with canine parvovirus, adenovirus types 1 and 2, and herpesvirus. The histologic characteristics of all myocardial specimens were classified regarding extent, location, and type of inflammation and fibrosis. Canine adenovirus type 1 was amplified from 1 specimen from a dog with DCM. Canine parvovirus, adenovirus type 2, and herpesvirus were not amplified from any myocardial specimens. Histologic analysis of specimens from dogs with DCM revealed variable amounts of fibrosis; myocardial inflammation was observed in 1 affected dog. Histopathologic analysis of specimens from dogs with myocarditis disclosed variable degrees of inflammation and fibrosis. Viral agents canine parvovirus, adenovirus types 1 and 2, and herpesvirus are not commonly associated with DCM or active myocarditis in dogs. Additional studies evaluating for nucleic acid from viruses that less commonly affect dogs or different types of infectious agents may be warranted to gain insight into the cause of DCM and myocarditis in dogs.

  13. An Optimized Method of Metabolite Extraction from Formalin-Fixed Paraffin-Embedded Tissue for GC/MS Analysis.

    Science.gov (United States)

    Wojakowska, Anna; Marczak, Łukasz; Jelonek, Karol; Polanski, Krzysztof; Widlak, Piotr; Pietrowska, Monika

    2015-01-01

    Formalin-fixed paraffin-embedded (FFPE) tissue specimens constitute a highly valuable source of clinical material for retrospective molecular studies. However, metabolomic assessment of such archival material remains still in its infancy. Hence, there is an urgent need for efficient methods enabling extraction and profiling of metabolites present in FFPE tissue specimens. Here we demonstrate the methodology for isolation of primary metabolites from archival tissues; either fresh-frozen, formalin-fixed or formalin-fixed and paraffin-embedded specimens of mouse kidney were analysed and compared in this work. We used gas chromatography followed by mass spectrometry (GC/MS approach) to identify about 80 metabolites (including amino acids, saccharides, carboxylic acids, fatty acids) present in such archive material. Importantly, about 75% of identified compounds were detected in all three types of specimens. Moreover, we observed that fixation with formalin itself (and their duration) did not affect markedly the presence of particular metabolites in tissue-extracted material, yet fixation for 24h could be recommended as a practical standard. Paraffin embedding influenced efficiency of extraction, which resulted in reduced quantities of several compounds. Nevertheless, we proved applicability of FFPE specimens for non-targeted GS/MS-based profiling of tissue metabolome, which is of great importance for feasibility of metabolomics studies using retrospective clinical material.

  14. The spectrum of skin biopsies and excisions in a pediatric skin center.

    Science.gov (United States)

    Theiler, Martin; Neuhaus, Kathrin; Kerl, Katrin; Weibel, Lisa

    2017-12-01

    Little is known about the spectrum of pediatric skin disorders requiring biopsy/excision, their indication, impact on further management, and the accuracy of clinical diagnosis. We aimed to address these questions in the patient population seen at our Swiss University referral center for Pediatric Dermatology and Plastic Surgery. All skin biopsies/excisions performed in patients aged ≤ 16 years over a period of 2 years were retrospectively analyzed. A total of 506 samples were included. The majority of biopsies/excisions (n = 413, 82%) was performed for tumors, cysts, and hamartomas and 18% for other skin conditions. Malignant tumors were found in 12 samples (2%) from four patients. In 121 (24%) patients, the histopathology had an important impact on patient management. In 80 (16%) cases, the pathology did not match with the clinical diagnosis. In 382 (75%) cases, excision was the treatment of choice. Of these, the indication for surgery was based on patient's request in 181 (47%) cases. Surgical interventions for pediatric skin disorders are performed for diagnostic and therapeutic reasons. In this cohort, histopathology was essential for treatment in one quarter of cases. Skin tumors, cysts, and hamartomas often require excision during childhood, with families' request and esthetic considerations playing an important role. What is Known: • The spectrum of pediatric skin conditions has been studied in outpatient, inpatient, and emergency settings. • In contrast, no data exist on the spectrum of pediatric skin disorders undergoing biopsy/excision specifically. What is New: • We analyze biopsies/excisions in children, focusing on diagnosis, indication, and impact on patient management. • Surgical interventions for skin disorders in children are often performed for tumors and hamartomas with esthetic considerations playing a relevant role. If used for diagnostic purposes, they are often performed to confirm or rule out severe skin disease.

  15. Staining of E-selectin ligands on paraffin-embedded sections of tumor tissue.

    Science.gov (United States)

    Carrascal, Mylène A; Talina, Catarina; Borralho, Paula; Gonçalo Mineiro, A; Henriques, Ana Raquel; Pen, Cláudia; Martins, Manuela; Braga, Sofia; Sackstein, Robert; Videira, Paula A

    2018-05-02

    The E-selectin ligands expressed by cancer cells mediate adhesion of circulating cancer cells to endothelial cells, as well as within tissue microenvironments important for tumor progression and metastasis. The identification of E-selectin ligands within cancer tissue could yield new biomarkers for patient stratification and aid in identifying novel therapeutic targets. The determinants of selectin ligands consist of sialylated tetrasaccharides, the sialyl Lewis X and A (sLe X and sLe A ), displayed on protein or lipid scaffolds. Standardized procedures for immunohistochemistry make use of the antibodies against sLe X and/or sLe A . However, antibody binding does not define E-selectin binding activity. In this study, we developed an immunohistochemical staining technique, using E-selectin-human Ig Fc chimera (E-Ig) to characterize the expression and localization of E-selectin binding sites on paraffin-embedded sections of different cancer tissue. E-Ig successfully stained cancer cells with high specificity. The E-Ig staining show high reactivity scores in colon and lung adenocarcinoma and moderate reactivity in triple negative breast cancer. Compared with reactivity of antibody against sLe X/A , the E-Ig staining presented higher specificity to cancer tissue with better defined borders and less background. The E-Ig staining technique allows the qualitative and semi-quantitative analysis of E-selectin binding activity on cancer cells. The development of accurate techniques for detection of selectin ligands may contribute to better diagnostic and better understanding of the molecular basis of tumor progression and metastasis.

  16. Single-Nucleotide Polymorphism-Microarray Ploidy Analysis of Paraffin-Embedded Products of Conception in Recurrent Pregnancy Loss Evaluations.

    Science.gov (United States)

    Maslow, Bat-Sheva L; Budinetz, Tara; Sueldo, Carolina; Anspach, Erica; Engmann, Lawrence; Benadiva, Claudio; Nulsen, John C

    2015-07-01

    To compare the analysis of chromosome number from paraffin-embedded products of conception using single-nucleotide polymorphism (SNP) microarray with the recommended screening for the evaluation of couples presenting with recurrent pregnancy loss who do not have previous fetal cytogenetic data. We performed a retrospective cohort study including all women who presented for a new evaluation of recurrent pregnancy loss over a 2-year period (January 1, 2012, to December 31, 2013). All participants had at least two documented first-trimester losses and both the recommended screening tests and SNP microarray performed on at least one paraffin-embedded products of conception sample. Single-nucleotide polymorphism microarray identifies all 24 chromosomes (22 autosomes, X, and Y). Forty-two women with a total of 178 losses were included in the study. Paraffin-embedded products of conception from 62 losses were sent for SNP microarray. Single-nucleotide polymorphism microarray successfully diagnosed fetal chromosome number in 71% (44/62) of samples, of which 43% (19/44) were euploid and 57% (25/44) were noneuploid. Seven of 42 (17%) participants had abnormalities on recurrent pregnancy loss screening. The per-person detection rate for a cause of pregnancy loss was significantly higher in the SNP microarray (0.50; 95% confidence interval [CI] 0.36-0.64) compared with recurrent pregnancy loss evaluation (0.17; 95% CI 0.08-0.31) (P=.002). Participants with one or more euploid loss identified on paraffin-embedded products of conception were significantly more likely to have an abnormality on recurrent pregnancy loss screening than those with only noneuploid results (P=.028). The significance remained when controlling for age, number of losses, number of samples, and total pregnancies. These results suggest that SNP microarray testing of paraffin-embedded products of conception is a valuable tool for the evaluation of recurrent pregnancy loss in patients without prior fetal

  17. A single simple procedure for dewaxing, hydration and heat-induced epitope retrieval (HIER) for immunohistochemistry in formalin fixed paraffin-embedded tissue

    DEFF Research Database (Denmark)

    Paulsen, I M S; Dimke, H; Frische, S

    2015-01-01

    Heat-induced epitope retrieval (HIER) is widely used for immunohistochemistry on formalin fixed paraffin-embedded tissue and includes temperatures well above the melting point of paraffin. We therefore tested whether traditional xylene-based removal of paraffin is required on sections from paraff...... of dewaxing in xylene. In conclusion, the HIER procedure described and tested can be used as a single procedure enabling dewaxing, hydration and epitope retrieval for immunohistochemistry in formalin fixed paraffin-embedded tissue....

  18. Melanoma-specific marker expression in skin biopsy tissues as a tool to facilitate melanoma diagnosis.

    Science.gov (United States)

    Alexandrescu, Doru T; Kauffman, C Lisa; Jatkoe, Timothy A; Hartmann, Dan P; Vener, Tatiana; Wang, Haiying; Derecho, Carlo; Rajpurohit, Yashoda; Wang, Yixin; Palma, John F

    2010-07-01

    Diagnosis of cutaneous melanoma requires accurate differentiation of true malignant tumors from highly atypical lesions, which lack the capacity to develop uncontrolled proliferation and to metastasize. We used melanoma markers from previous work to differentiate benign and atypical lesions from melanoma using paraffin-embedded tissue. This critical step in diagnosis generates the most uncertainty and discrepancy between dermatopathologists. A total of 193 biopsy tissues were selected: 47 melanomas, 48 benign nevi, and 98 atypical/suspicious, including 48 atypical nevi and 50 melanomas as later assigned by expert dermatopathologists. Performance for SILV, GDF15, and L1CAM normalized to TYR in unequivocal melanoma versus benign nevi resulted in an area under the curve (AUC) of 0.94, 0.67, and 0.5, respectively. SILV also differentiated atypical cases classified as melanoma from atypical nevi with an AUC=0.74. Furthermore, SILV showed a significant difference between suspicious melanoma and each suspicious atypia group: melanoma versus severe atypia and melanoma versus moderate atypia had P-values of 0.0077 and 0.0009, respectively. SILV showed clear discrimination between melanoma and benign unequivocal cases as well as between different atypia subgroups in the group of suspicious samples. The role and potential utility of this molecular assay as an adjunct to the morphological diagnosis of melanoma are discussed.

  19. Ultrastructural examination of skin biopsies may assist in diagnosing mitochondrial cytopathy when muscle biopsies yield negative results.

    Science.gov (United States)

    McAfee, John L; Warren, Christine B; Prayson, Richard A

    2017-08-01

    Ultrastructural evaluation of skin biopsies has been utilized for diagnosis of mitochondrial disease. This study investigates how frequently skin biopsies reveal mitochondrial abnormalities, correlates skin and muscle biopsy findings, and describes clinical diagnoses rendered following the evaluation. A retrospective review of surgical pathology reports from 1990 to 2015 identified skin biopsies examined by electron microscopy for suspected metabolic disease. A total of 630 biopsies were included from 615 patients. Of these patients, 178 also underwent a muscle biopsy. Of the 630 skin biopsies, 75 (12%) showed ultrastructural abnormalities and 34 (5%) specifically showed mitochondrial abnormalities including increased size (n=27), reduced or abnormal cristae (n=23), dense matrices (n=20), and increased number (n=8). Additional findings included lysosomal abnormalities (n=13), lipid accumulation (n=2) or glycogen accumulation (n=1). Of the 34 patients with mitochondrial abnormalities on skin biopsy, 20 also had muscle biopsies performed and nine showed abnormalities suggestive of a mitochondrial disorder including absent cytochrome oxidase staining (n=2), increased subsarcolemmal NADH, SDH, or cytochrome oxidase staining (n=1), or ultrastructural findings including large mitochondrial size (n=5), abnormal mitochondrial structure (n=5), and increased mitochondrial number (n=4). The most common presenting symptoms were intellectual disability (n=13), seizures (n=12), encephalopathy (n=9), and gastrointestinal disturbances (n=9). At last known follow-up, 12 patients had a definitive diagnosis of a mitochondrial disorder. One patient each had Complex I deficiency, Complex III deficiency, Charcot-Marie-Tooth disease, pyruvate dehydrogenase deficiency, and Phelan-McDermid syndrome. Our results suggest that skin biopsy sometimes yields diagnostic clues suggestive of a mitochondrial cytopathy in cases with a negative muscle biopsy. Copyright © 2017 Elsevier Inc. All rights

  20. Validation of tumor markers in central nervous system germ cell tumors by real-time reverse transcriptase polymerase chain reaction using formalin-fixed paraffin-embedded tissues.

    Science.gov (United States)

    Kim, Dowhan; Lee, Da Hye; Choi, Junjeong; Shim, Kyu Won; Kim, Se Hoon

    2013-01-01

    The therapeutic protocols for treatment of germinomas and non-germinomatous germ cell tumors (NGGCTs) are completely different, so it is important to distinguish pure germinomas from NGGCTs. As it can be difficult to diagnose by morphology alone, immunohisto-chemistry (IHC) has been widely used as an ancillary test to improve diagnostic accuracy. However, IHC has limitations due to the misinterpretation of results or the aberrant loss of immunoreactivity. However, real-time RT-PCR has certain advantages over IHC, including its quantitative nature. The aim of our study was to evaluate the usefulness of real-time RT-PCR on formalin-fixed paraffin-embedded (FFPE) tissue blocks for the diagnosis of germ cell tumors of the central nervous system. We selected eight markers of germ cell tumors using a literature search, and validated them using real-time RT-PCR. Among them, POU5F1, NANOG and TGFB2 were statistically significant (P=0.05) in multiple comparisons (MANOVA) of three groups (pure germinomas, mature teratomas and malignant germ cell tumors). Two-group (pure germinomas and NGGCTs) discriminant analysis achieved a 70.0% success rate in cross-validation. We concluded that real-time RT-PCR using FFPE tissue has adequate validating power comparable to IHC in the diagnosis of central nervous system germ cell tumors; therefore, when IHC is not available, not conclusive or not informative, RT-PCR is a potential alternative to a repeat biopsy.

  1. Scores for standardization of on-tissue digestion of formalin-fixed paraffin-embedded tissue in MALDI-MS imaging.

    Science.gov (United States)

    Erich, Katrin; Sammour, Denis A; Marx, Alexander; Hopf, Carsten

    2017-07-01

    On-slide digestion of formalin-fixed and paraffin-embedded human biopsy tissue followed by mass spectrometry imaging of resulting peptides may have the potential to become an additional analytical modality in future ePathology. Multiple workflows have been described for dewaxing, antigen retrieval, digestion and imaging in the past decade. However, little is known about suitable statistical scores for method comparison and systematic workflow standardization required for development of processes that would be robust enough to be compatible with clinical routine. To define scores for homogeneity of tissue processing and imaging as well as inter-day repeatability for five different processing methods, we used human liver and gastrointestinal stromal tumor tissue, both judged by an expert pathologist to be >98% histologically homogeneous. For mean spectra-based as well as pixel-wise data analysis, we propose the coefficient of determination R 2 , the natural fold-change (natFC) value and the digest efficiency DE% as readily accessible scores. Moreover, we introduce two scores derived from principal component analysis, the variance of the mean absolute deviation, MAD, and the interclass overlap, J overlap , as computational scores that may help to avoid user bias during future workflow development. This article is part of a Special Issue entitled: MALDI Imaging, edited by Dr. Corinna Henkel and Prof. Peter Hoffmann. Copyright © 2016 Elsevier B.V. All rights reserved.

  2. [When to ask for a skin biopsy in a patient with leg ulcer? Retrospective study of 143 consecutive biopsies].

    Science.gov (United States)

    Stansal, A; Khayat, K; Duchatelle, V; Tella, E; Gautier, V; Sfeir, D; Attal, R; Lazareth, I; Priollet, P

    2018-02-01

    A vascular cause is found in around 85% of leg ulcer patients, but non-vascular causes are also observed. Their diagnosis is based on a set of clinical arguments and skin biopsy with histological analysis. The aim of this study was to analyze the results of these biopsies and to find common criteria for ulcers whose skin biopsies had led to the diagnosis of a non-vascular ulcer. A retrospective study was carried out on the analysis of 143 skin biopsies of leg ulcers. The reasons for the biopsy were mainly atypical clinical signs and/or the lack of improvement in care after 6 months, as advocated by the French health authorities. The skin biopsies led to a diagnosis of non-vascular ulcer in 4.9% of cases (7/143), including skin cancer (n=5, 3.5%), cutaneous leishmaniasis (n=1, 0.7%) and Pyoderma gangrenosum (n=1, 0.7%). The univariate statistical analysis revealed that an elevated rim and abnormal excessive granulation tissue were significantly more frequently found in these ulcers. All patients with a positive skin biopsy had associated vascular involvement. This study found a 5% rate of non-vascular causes of ulcers, mainly skin cancer. Elevated rims and abnormal excessive granulation tissue were the unusual features most commonly found in these ulcers. All patients whose skin biopsy revealed a non-vascular cause had associated vascular involvement. This information confirms the need to perform a skin biopsy, even in the presence of a vascular disease. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

  3. Novel uses of skin biopsy punches in dermatosurgery

    Directory of Open Access Journals (Sweden)

    Deepak S Hurkudli

    2015-01-01

    Full Text Available The skin punch or surgical punch is an instrument which is used almost exclusively by dermatologists. It is a circular hollow blade attached to a pencil-like handle ranging in size from 0.5 to 10 mm. It is available as a disposable, reusable, and automated instrument. The punch can be used as a diagnostic, therapeutic, and cosmetic tool in dermatology. We have used punch as a diagnostic, therapeutic, and cosmetic tool in our dermatosurgery practice in our hospital. Various original research articles, text book publications, and review articles were studied and compiled. Techniques used by various authors and our own experiences with punch have been described. This article aims at providing the novel usefulness of skin biopsy punch in dermatology as the basic punch surgery is quick and easy to learn. Complications such as bleeding and infection are minimal.

  4. [Comparison of two different real-time PCR systems in postmortem diagnosis of tuberculosis in paraffin-embedded tissues].

    Science.gov (United States)

    Yağmur, Gülhan; Albayrak, Nurhan; Daş, Taner; Yıldırım, Muzaffer; Ozgün, Ayşe; Büyük, Yalçın

    2014-10-01

    Tuberculosis (TB) is one of those infections with high morbidity and mortality in all around the world. Hundreds of people died from this disease without diagnosed or due to resistant strains in Turkey. Therefore, it is important to identify postmortem cases who have died from tuberculosis. Molecular methods have been widely used as well as conventional methods in the diagnosis of tuberculosis. The aim of this study was to compare the two different real-time polymerase chain reaction (Rt-PCR) system in the postmortem diagnosis of Mycobacterium tuberculosis infections in paraffin-embedded tissues. A total of 40 paraffin-embedded tissue samples [lung (n= 35), brain (n= 2), heart (n= 2), lymph node (n= 1)] in which histopathologic findings consistent with TB (necrotizing granulomatous inflammation, gelatinous caseous pneumonia, necrotic fibrous nodul) obtained from 37 autopsy cases (31 male, 6 female; age range: 25-85 yrs) were included in the study. Paraffin-embedded tissues were deparafinized with xylene and ethyl alcohol and then DNA isolation was done with QIAsymphony DSP Virus/Pathogen Midi kit in the QIAsymphony device. DNA amplification process was performed by Rt-PCR using the kit Artus® M. tuberculosis RG-PCR in the Rotor-Gene® Q device (Qiagen, Germany). Likewise, after deparafinization process, samples placed in the cartridge and isolation and Rt-PCR was performed by Xpert® MTB/RIF (Cepheid, USA) system, simultaneosly. Seventeen and 20 out of the 40 paraffin-embedded tissues yielded positive results with Qiagen and Xpert system, respectively. M.tuberculosis DNA was found positive in 13 (32.5%) and negative in 16 (40%) of the samples by both of the systems, exhibiting 72.5% (29/40) of concordance. On the other hand, seven (17.5%) samples that were positive with Xpert system yielded negative result with the Qiagen, while four (10%) samples that were positive with Qiagen yielded negative result with the Xpert system. Of the 20 positive cases detected with

  5. Stereological quantification of lymphocytes in skin biopsies from atopic dermatitis patients

    DEFF Research Database (Denmark)

    Ellingsen, A R; Sørensen, F B; Larsen, Jytte Overgaard

    2001-01-01

    with active eczema in 8 adults with AD and from clinically normal skin from 4 of the patients. Five persons without allergy or skin disease served as controls. The mean number of lymphocytes in 4-mm skin biopsies was 469,000 and 124,000 in active eczema and in clinically normal skin, respectively. Compared......Atopic dermatitis (AD) is histologically characterized by lymphocytic infiltration of the skin and quantitative assessment is required. This study introduces stereological techniques to quantify the number of lymphocytes in skin biopsies. Four-millimetre punch biopsies were taken from skin...... with controls, the number of lymphocytes in biopsies increased by a factor of 6.8 in active eczema and a factor of 1.8 in clinically normal skin. If 20% of skin is affected by eczema the total number of lymphocytes located in the affected skin can be estimated to 1.27 x 10(10). A patient with clinically...

  6. Optical coherence tomography and polarimetry of superficial skin biopsies

    Directory of Open Access Journals (Sweden)

    S. R. Utz

    2015-01-01

    Full Text Available The goal. Of this study was to develop and assess the efficacy of polarization probing of biotissues in vitro. The method is based on the determination of polarization parameters of scattered radiation. Materials and methods. The well-known superficial epidermis stripping method was applied using the Sulfacrylate self-sterile medical adhesive. Small portions of thin layers of the adhesive were applied to slide plates and then to different skin sites. The corneous layer in the normal condition and in case of skin diseases (psoriasis, lichen acuminatus, discoid lupus erythematosus, alopecia, itching and demodectic mange was examined based on the optical coherence tomography (OCT method using the 0CS1300SS device (Thorlabs Inc, USA. Results. The authors obtained pictures visualizing the structural organization of different layers of the epidermis using the superficial epidermis biopsy method in case of lichen acuminatus, hyperkeratosis, itching and other skin diseases. Conclusion. This method ensures non-invasive high-precision measurement of the structure of different layers of the epidermis, which may be useful both for research purposes and practical dermatology.

  7. A method to evaluate genome-wide methylation in archival formalin-fixed, paraffin-embedded ovarian epithelial cells.

    Directory of Open Access Journals (Sweden)

    Qiling Li

    Full Text Available The use of DNA from archival formalin and paraffin embedded (FFPE tissue for genetic and epigenetic analyses may be problematic, since the DNA is often degraded and only limited amounts may be available. Thus, it is currently not known whether genome-wide methylation can be reliably assessed in DNA from archival FFPE tissue.Ovarian tissues, which were obtained and formalin-fixed and paraffin-embedded in either 1999 or 2011, were sectioned and stained with hematoxylin-eosin (H&E.Epithelial cells were captured by laser micro dissection, and their DNA subjected to whole genomic bisulfite conversion, whole genomic polymerase chain reaction (PCR amplification, and purification. Sequencing and software analyses were performed to identify the extent of genomic methylation. We observed that 31.7% of sequence reads from the DNA in the 1999 archival FFPE tissue, and 70.6% of the reads from the 2011 sample, could be matched with the genome. Methylation rates of CpG on the Watson and Crick strands were 32.2% and 45.5%, respectively, in the 1999 sample, and 65.1% and 42.7% in the 2011 sample.We have developed an efficient method that allows DNA methylation to be assessed in archival FFPE tissue samples.

  8. Multicenter Evaluation of a Novel Automated Rapid Detection System of BRAF Status in Formalin-Fixed, Paraffin-Embedded Tissues.

    Science.gov (United States)

    Schiefer, Ana-Iris; Parlow, Laura; Gabler, Lisa; Mesteri, Ildiko; Koperek, Oskar; von Deimling, Andreas; Streubel, Berthold; Preusser, Matthias; Lehmann, Annika; Kellner, Udo; Pauwels, Patrick; Lambin, Suzan; Dietel, Manfred; Hummel, Michael; Klauschen, Frederick; Birner, Peter; Möbs, Markus

    2016-05-01

    The mutated BRAF oncogene represents a therapeutic target in malignant melanoma. Because BRAF mutations are also involved in the pathogenesis of other human malignancies, the use of specific BRAF inhibitors might also be extended to other diseases in the future. A prerequisite for the clinical application of BRAF inhibitors is the reliable detection of activating BRAF mutations in routine histopathological samples. In a multicenter approach, we evaluated a novel and fully automated PCR-based system (Idylla) capable of detecting BRAF V600 mutations in formalin-fixed, paraffin-embedded tissue within 90 minutes with high sensitivity. We analyzed a total of 436 samples with the Idylla system. Valid results were obtained in 421 cases (96.56%). Its performance was compared with conventional methods (pyrosequencing or Sanger sequencing). Concordant results were obtained in 406 cases (96.90%). Reanalysis of eight discordant samples by next-generation sequencing and/or pyrosequencing with newly extracted DNA and the BRAF RGQ Kit confirmed the Idylla result in seven cases, resulting in an overall agreement of 98.57%. In conclusion, the Idylla system is a highly reliable and sensitive platform for detection of BRAF V600 mutations in formalin-fixed, paraffin-embedded material, providing an efficient alternative to conventional diagnostic methods, particularly for routine diagnostics laboratories with limited experience in molecular pathology. Copyright © 2016 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

  9. Matrix-comparative genomic hybridization from multicenter formalin-fixed paraffin-embedded colorectal cancer tissue blocks

    Directory of Open Access Journals (Sweden)

    Köhne Claus-Henning

    2007-04-01

    Full Text Available Abstract Background The identification of genomic signatures of colorectal cancer for risk stratification requires the study of large series of cancer patients with an extensive clinical follow-up. Multicentric clinical studies represent an ideal source of well documented archived material for this type of analyses. Methods To verify if this material is technically suitable to perform matrix-CGH, we performed a pilot study using macrodissected 29 formalin-fixed, paraffin-embedded tissue samples collected within the framework of the EORTC-GI/PETACC-2 trial for colorectal cancer. The scientific aim was to identify prognostic genomic signatures differentiating locally restricted (UICC stages II-III from systemically advanced (UICC stage IV colorectal tumours. Results The majority of archived tissue samples collected in the different centers was suitable to perform matrix-CGH. 5/7 advanced tumours displayed 13q-gain and 18q-loss. In locally restricted tumours, only 6/12 tumours showed a gain on 13q and 7/12 tumours showed a loss on 18q. Interphase-FISH and high-resolution array-mapping of the gain on 13q confirmed the validity of the array-data and narrowed the chromosomal interval containing potential oncogenes. Conclusion Archival, paraffin-embedded tissue samples collected in multicentric clinical trials are suitable for matrix-CGH analyses and allow the identification of prognostic signatures and aberrations harbouring potential new oncogenes.

  10. An Adhesive Patch-Based Skin Biopsy Device for Molecular Diagnostics and Skin Microbiome Studies.

    Science.gov (United States)

    Yao, Zuxu; Moy, Ronald; Allen, Talisha; Jansen, Burkhard

    2017-10-01

    A number of diagnoses in clinical dermatology are currently histopathologically confirmed and this image recognition-based confirmation generally requires surgical biopsies. The increasing ability of molecular pathology to corroborate or correct a clinical diagnosis based on objective gene expression, mutation analysis, or molecular microbiome data is on the horizon and would be further supported by a tool or procedure to collect samples non-invasively. This study characterizes such a tool in form of a 'bladeless' adhesive patch-based skin biopsy device. The performance of this device was evaluated through a variety of complementary technologies including assessment of sample biomass, electron microscopy demonstrating the harvesting of layers of epidermal tissue, and isolation of RNA and DNA from epidermal skin samples. Samples were obtained by application of adhesive patches to the anatomical area of interest. Biomass assessment demonstrated collection of approximately 0.3mg of skin tissue per adhesive patch and electron microscopy confirmed the nature of the harvested epidermal skin tissue. The obtained tissue samples are stored in a stable fashion on adhesive patches over a wide range of temperatures (-80oC to +60oC) and for extended periods of time (7 days or more). Total human RNA, human genomic DNA and microbiome DNA yields were 23.35 + 15.75ng, 27.72 + 20.71ng and 576.2 + 376.8pg, respectively, in skin samples obtained from combining 4 full patches collected non-invasively from the forehead of healthy volunteers. The adhesive patch skin sampling procedure is well tolerated and provides robust means to obtain skin tissue, RNA, DNA, and microbiome samples without involving surgical biopsies. The non-invasively obtained skin samples can be shipped cost effectively at ambient temperature by mail or standard courier service, and are suitable for a variety of molecular analyses of the skin microbiome as well as of keratinocytes, T cells, dendritic cells

  11. Evaluation of three methods of DNA extraction from paraffin-embedded material for the amplification of genomic DNA by means of the PCR technique

    Directory of Open Access Journals (Sweden)

    MESQUITA Ricardo Alves

    2001-01-01

    Full Text Available There are several protocols reported in the literature for the extraction of genomic DNA from formalin-fixed paraffin-embedded samples. Genomic DNA is utilized in molecular analyses, including PCR. This study compares three different methods for the extraction of genomic DNA from formalin-fixed paraffin-embedded (inflammatory fibrous hyperplasia and non-formalin-fixed (normal oral mucosa samples: phenol with enzymatic digestion, and silica with and without enzymatic digestion. The amplification of DNA by means of the PCR technique was carried out with primers for the exon 7 of human keratin type 14. Amplicons were analyzed by means of electrophoresis in an 8% polyacrylamide gel with 5% glycerol, followed by silver-staining visualization. The phenol/enzymatic digestion and the silica/enzymatic digestion methods provided amplicons from both tissue samples. The method described is a potential aid in the establishment of the histopathologic diagnosis and in retrospective studies with archival paraffin-embedded samples.

  12. Progesterone receptor isoform analysis by quantitative real-time polymerase chain reaction in formalin-fixed, paraffin-embedded canine mammary dysplasias and tumors

    DEFF Research Database (Denmark)

    Guil-Luna, S.; Stenvang, Jan; Brünner, Nils

    2014-01-01

    and its isoforms in formalin-fixed, paraffin-embedded tissue samples from canine mammary lesions (4 dysplasias, 10 benign tumors, and 46 carcinomas) using 1-step SYBR Green quantitative real-time polymerase chain reaction (RT-qPCR). Progesterone receptor was expressed in 75% of dysplasias, all benign...... in the expression of isoform A versus B. Analysis of progesterone receptor mRNA isoforms by RT-qPCR was successful in routinely formalin-fixed, paraffin-embedded tissue samples and enabled the distribution of isoforms A and B to be identified for the first time in dysplasias, benign tumors, and malignant tumors...

  13. Analysis of formalin-fixed, paraffin-embedded (FFPE) tissue via proteomic techniques and misconceptions of antigen retrieval.

    Science.gov (United States)

    O'Rourke, Matthew B; Padula, Matthew P

    2016-01-01

    Since emerging in the late 19(th) century, formaldehyde fixation has become a standard method for preservation of tissues from clinical samples. The advantage of formaldehyde fixation is that fixed tissues can be stored at room temperature for decades without concern for degradation. This has led to the generation of huge tissue banks containing thousands of clinically significant samples. Here we review techniques for proteomic analysis of formalin-fixed, paraffin-embedded (FFPE) tissue samples with a specific focus on the methods used to extract and break formaldehyde crosslinks. We also discuss an error-of-interpretation associated with the technique known as "antigen retrieval." We have discovered that this term has been mistakenly applied to two disparate molecular techniques; therefore, we argue that a terminology change is needed to ensure accurate reporting of experimental results. Finally, we suggest that more investigation is required to fully understand the process of formaldehyde fixation and its subsequent reversal.

  14. Molecular identification of Coccidioides immitis in formalin-fixed, paraffin-embedded (FFPE) tissues from a Colombian patient.

    Science.gov (United States)

    Canteros, Cristina E; Vélez H, Alejandro; Toranzo, Adriana I; Suárez-Alvarez, Roberto; Tobón O, Ángela; Jimenez A, María del Pilar; Restrepo M, Ángela

    2015-06-01

    Coccidioides immitis and C. posadasii are the etiologic agents of coccidioidomycosis, an endemic fungal disease of the Americas. In Colombia, this mycosis is uncommon, and only five cases, two of them imported, have been documented.By means of DNA sequencing, C. immitis was identified in formalin-fixed, paraffin-embedded archival tissues samples from the 5th Colombian patient diagnosed in 1997. The patient was born in Pinto, Department of Magdalena, and had never visited other geographic regions, a reason to consider that the mycosis had been acquired locally.This species is primarily found in California although it has been occasionally reported in other geographic areas such as Mexico and Brazil. This is the first indigenous report of C. immitis-associated coccidioidomycosis in a Colombian patient. © The Author 2015. Published by Oxford University Press on behalf of The International Society for Human and Animal Mycology.

  15. Ewing's Sarcoma: An Analysis of miRNA Expression Profiles and Target Genes in Paraffin-Embedded Primary Tumor Tissue.

    Science.gov (United States)

    Parafioriti, Antonina; Bason, Caterina; Armiraglio, Elisabetta; Calciano, Lucia; Daolio, Primo Andrea; Berardocco, Martina; Di Bernardo, Andrea; Colosimo, Alessia; Luksch, Roberto; Berardi, Anna C

    2016-04-30

    The molecular mechanism responsible for Ewing's Sarcoma (ES) remains largely unknown. MicroRNAs (miRNAs), a class of small non-coding RNAs able to regulate gene expression, are deregulated in tumors and may serve as a tool for diagnosis and prediction. However, the status of miRNAs in ES has not yet been thoroughly investigated. This study compared global miRNAs expression in paraffin-embedded tumor tissue samples from 20 ES patients, affected by primary untreated tumors, with miRNAs expressed in normal human mesenchymal stromal cells (MSCs) by microarray analysis. A miRTarBase database was used to identify the predicted target genes for differentially expressed miRNAs. The miRNAs microarray analysis revealed distinct patterns of miRNAs expression between ES samples and normal MSCs. 58 of the 954 analyzed miRNAs were significantly differentially expressed in ES samples compared to MSCs. Moreover, the qRT-PCR analysis carried out on three selected miRNAs showed that miR-181b, miR-1915 and miR-1275 were significantly aberrantly regulated, confirming the microarray results. Bio-database analysis identified BCL-2 as a bona fide target gene of the miR-21, miR-181a, miR-181b, miR-29a, miR-29b, miR-497, miR-195, miR-let-7a, miR-34a and miR-1915. Using paraffin-embedded tissues from ES patients, this study has identified several potential target miRNAs and one gene that might be considered a novel critical biomarker for ES pathogenesis.

  16. Development and independent validation of a prognostic assay for stage II colon cancer using formalin-fixed paraffin-embedded tissue.

    LENUS (Irish Health Repository)

    Kennedy, Richard D

    2011-12-10

    Current prognostic factors are poor at identifying patients at risk of disease recurrence after surgery for stage II colon cancer. Here we describe a DNA microarray-based prognostic assay using clinically relevant formalin-fixed paraffin-embedded (FFPE) samples.

  17. Mining the archives: a cross-platform analysis of gene expression profiles in archival formalin-fixed paraffin-embedded (FFPE) tissue.

    Science.gov (United States)

    Formalin-fixed paraffin-embedded (FFPE) tissue samples represent a potentially invaluable resource for genomic research into the molecular basis of disease. However, use of FFPE samples in gene expression studies has been limited by technical challenges resulting from degradation...

  18. MicroRNA expression in melanocytic nevi: the usefulness of formalin-fixed, paraffin-embedded material for miRNA microarray profiling

    DEFF Research Database (Denmark)

    Glud, M.; Klausen, M.; Gniadecki, R.

    2009-01-01

    surgical specimens are formalin fixed and paraffin embedded (FFPE). To explore whether FFPE material would be suitable for miRNA profiling in melanocytic lesions, we compared miRNA expression patterns in FFPE versus fresh frozen samples, obtained from 15 human melanocytic nevi. Out of microarray data, we...

  19. Detection of Streptococcus suis by in situ hybridization, indirect immunofluorescence, and peroxidase-antiperoxidase assays in formalin-fixed, paraffin-embedded tissue sections from pigs

    DEFF Research Database (Denmark)

    Boye, Mette; Feenstra, Anne Avlund; Tegtmeier, Conny

    2000-01-01

    and the immunohistochemical methods were used for detection of S. suis in formalin-fixed, paraffin-embedded tissue sections of brain, endocardium, and lung from pigs infected with S. suis. The methods developed were able to detect single cells of S. suis in situ in the respective samples, whereas no signal was observed from...

  20. The effects of age-in-block on RNA-seq analysis of archival formalin-fixed paraffin-embedded (FFPE) samples

    Science.gov (United States)

    Archival samples represent a vast resource for identification of chemical and pharmaceutical targets. Previous use of formalin-fixed paraffin-embedded (FFPE) samples has been limited due to changes in RNA introduced by fixation and embedding procedures. Recent advances in RNA-seq...

  1. Comparison between single PCR and nested PCR in detection of human papilloma viruses in paraffin-embedded OSCC and fresh oral mucosa.

    Science.gov (United States)

    Jalouli, Miranda; Jalouli, Jamshid; Ibrahim, Salah O; Hirsch, Jan-Michaél; Sand, Lars

    2015-01-01

    Infection with human papilloma virus (HPV) has been implicated as one of the risk factors for the development of oropharyngeal cancer. Many different HPV tests exist, and information regarding their specific technical, analytical, and clinical properties is increasing. This study aimed to compare the level of detection of HPV using two reliable polymerase chain reaction (PCR) methods, nested PCR (NPCR) and single PCR (SPCR), in archival paraffin-embedded oral squamous cell carcinoma (OSCC) samples and fresh oral mucosa specimens. The presence of HPV genome in two groups of tissue samples was analyzed: (i) 57 paraffin-embedded OSCC samples from Sudan and (ii) eight healthy fresh oral mucosal samples from Swedish volunteers. The specimens were tested by SPCR with primer pair MY9/MY11 and NPCR using GP5+/GP6+ primer sets. Eighteen (32%) out of the 57 paraffin-embedded OSCC samples, and five (62%) out of the eight fresh clinically healthy samples were found to be HPV-positive with NPCR. With SPCR, four (7%) out of the paraffin-embedded OSCC samples were HPV-positive. A statistically significant difference between HPV-positive and -negative samples was found when comparing NPCR and SPCR in OSCC and fresh oral mucosa (pnested PCR increased the positivity rate, efficiency rate and sensitivity of HPV detection in oral samples significantly and should be considered as the method of choice. Copyright © 2015 International Institute of Anticancer Research (Dr. John G. Delinassios), All rights reserved.

  2. Optical skin biopsies by clinical CARS and multiphoton fluorescence/SHG tomography

    International Nuclear Information System (INIS)

    König, K; Breunig, H G; Bückle, R; Kellner-Höfer, M; Weinigel, M; Büttner, E; Sterry, W; Lademann, J

    2011-01-01

    The ultimate challenge for early diagnostics is label-free high-resolution intratissue imaging without taking physical biopsies. A novel hybrid femtosecond laser tomograph provides in vivo optical biopsies of human skin based on non-linear excitation of autofluorescence and the detection of lipids and water by CARS. Applications include skin cancer detection, biosafety tests of intradermal nanoparticles, and the testing of anti-aging products

  3. Utility of abdominal skin plus subcutaneous fat and rectal mucosal biopsy in the diagnosis of AL amyloidosis with renal involvement.

    Directory of Open Access Journals (Sweden)

    Ting Li

    Full Text Available Skin fat biopsy of the abdominal wall is a simple and safe method for detecting amyloidosis, and rectal mucosal biopsy is also frequently used for screening for the disease; however, the sensitivity of these approaches has not been fully studied. The aim of this study was to evaluate the efficacy of skin fat biopsy combined with rectal mucosal biopsy as a screening procedure for the diagnosis of systemic immunoglobulin light-chain (AL amyloidosis.We retrospectively analyzed 224 AL amyloidosis patients confirmed by renal biopsy, including a test group of 165 patients and validation group of 59 patients. Surgical skin fat biopsy from the abdominal wall and rectal mucosal biopsy under endoscopy was performed to obtain specimens. Congo red staining and immunofluorescence staining with antibodies against light chains were performed to type the disease. Pathology reports were reviewed to assess the diagnostic sensitivity of skin fat biopsy and rectal mucosal biopsy. Diagnostic specificity was not examined in the present study, because no healthy volunteers and only few patients with other diseases had performed immunofluorescence staining on skin fat and rectal specimens.Of the 165 patients in the test group, Congo red staining of skin fat and rectal mucosal specimens was associated with a sensitivity of 89.3% and 94.8%, respectively. The sensitivity increased to 98.9% by combining both biopsy methods. Immunofluorescence stains were positive in 81.1% of patients undergoing skin fat biopsy and 84.7% of patients undergoing rectal mucosal biopsy. Immunofluorescence stains yielded positive results in 86.7% of cases combining skin fat biopsy with rectal mucosal biopsy. The diagnostic results also performed well in the validation group.Surgical skin biopsy including the subcutaneous fat pad can be performed safely at the bedside and is useful for diagnosing AL amyloidosis. Combining skin fat biopsy with rectal mucosal biopsy may identify amyloid deposits in

  4. CLASSIFICATION OF SEVERAL SKIN CANCER TYPES BASED ON AUTOFLUORESCENCE INTENSITY OF VISIBLE LIGHT TO NEAR INFRARED RATIO

    Directory of Open Access Journals (Sweden)

    Aryo Tedjo

    2009-12-01

    Full Text Available Skin cancer is a malignant growth on the skin caused by many factors. The most common skin cancers are Basal Cell Cancer (BCC and Squamous Cell Cancer (SCC. This research uses a discriminant analysis to classify some tissues of skin cancer based on criterion number of independent variables. An independent variable is variation of excitation light sources (LED lamp, filters, and sensors to measure Autofluorescence Intensity (IAF of visible light to near infrared (VIS/NIR ratio of paraffin embedded tissue biopsy from BCC, SCC, and Lipoma. From the result of discriminant analysis, it is known that the discriminant function is determined by 4 (four independent variables i.e., Blue LED-Red Filter, Blue LED-Yellow Filter, UV LED-Blue Filter, and UV LED-Yellow Filter. The accuracy of discriminant in classifying the analysis of three skin cancer tissues is 100 %.

  5. Identification and validation of differentially expressed transcripts by RNA-sequencing of formalin-fixed, paraffin-embedded (FFPE) lung tissue from patients with Idiopathic Pulmonary Fibrosis.

    Science.gov (United States)

    Vukmirovic, Milica; Herazo-Maya, Jose D; Blackmon, John; Skodric-Trifunovic, Vesna; Jovanovic, Dragana; Pavlovic, Sonja; Stojsic, Jelena; Zeljkovic, Vesna; Yan, Xiting; Homer, Robert; Stefanovic, Branko; Kaminski, Naftali

    2017-01-12

    Idiopathic Pulmonary Fibrosis (IPF) is a lethal lung disease of unknown etiology. A major limitation in transcriptomic profiling of lung tissue in IPF has been a dependence on snap-frozen fresh tissues (FF). In this project we sought to determine whether genome scale transcript profiling using RNA Sequencing (RNA-Seq) could be applied to archived Formalin-Fixed Paraffin-Embedded (FFPE) IPF tissues. We isolated total RNA from 7 IPF and 5 control FFPE lung tissues and performed 50 base pair paired-end sequencing on Illumina 2000 HiSeq. TopHat2 was used to map sequencing reads to the human genome. On average ~62 million reads (53.4% of ~116 million reads) were mapped per sample. 4,131 genes were differentially expressed between IPF and controls (1,920 increased and 2,211 decreased (FDR < 0.05). We compared our results to differentially expressed genes calculated from a previously published dataset generated from FF tissues analyzed on Agilent microarrays (GSE47460). The overlap of differentially expressed genes was very high (760 increased and 1,413 decreased, FDR < 0.05). Only 92 differentially expressed genes changed in opposite directions. Pathway enrichment analysis performed using MetaCore confirmed numerous IPF relevant genes and pathways including extracellular remodeling, TGF-beta, and WNT. Gene network analysis of MMP7, a highly differentially expressed gene in both datasets, revealed the same canonical pathways and gene network candidates in RNA-Seq and microarray data. For validation by NanoString nCounter® we selected 35 genes that had a fold change of 2 in at least one dataset (10 discordant, 10 significantly differentially expressed in one dataset only and 15 concordant genes). High concordance of fold change and FDR was observed for each type of the samples (FF vs FFPE) with both microarrays (r = 0.92) and RNA-Seq (r = 0.90) and the number of discordant genes was reduced to four. Our results demonstrate that RNA sequencing of RNA

  6. A Method to Correlate mRNA Expression Datasets Obtained from Fresh Frozen and Formalin-Fixed, Paraffin-Embedded Tissue Samples: A Matter of Thresholds.

    Directory of Open Access Journals (Sweden)

    Dana A M Mustafa

    Full Text Available Gene expression profiling of tumors is a successful tool for the discovery of new cancer biomarkers and potential targets for the development of new therapeutic strategies. Reliable profiling is preferably performed on fresh frozen (FF tissues in which the quality of nucleic acids is better preserved than in formalin-fixed paraffin-embedded (FFPE material. However, since snap-freezing of biopsy materials is often not part of daily routine in pathology laboratories, one may have to rely on archival FFPE material. Procedures to retrieve the RNAs from FFPE materials have been developed and therefore, datasets obtained from FFPE and FF materials need to be made compatible to ensure reliable comparisons are possible.To develop an efficient method to compare gene expression profiles obtained from FFPE and FF samples using the same platform.Twenty-six FFPE-FF sample pairs of the same tumors representing various cancer types, and two FFPE-FF sample pairs of breast cancer cell lines, were included. Total RNA was extracted and gene expression profiling was carried out using Illumina's Whole-Genome cDNA-mediated Annealing, Selection, extension and Ligation (WG-DASL V3 arrays, enabling the simultaneous detection of 24,526 mRNA transcripts. A sample exclusion criterion was created based on the expression of 11 stably expressed reference genes. Pearson correlation at the probe level was calculated for paired FFPE-FF, and three cut-off values were chosen. Spearman correlation coefficients between the matched FFPE and FF samples were calculated for three probe lists with varying levels of significance and compared to the correlation based on all measured probes. Unsupervised hierarchical cluster analysis was performed to verify performance of the included probe lists to compare matched FPPE-FF samples.Twenty-seven FFPE-FF pairs passed the sample exclusion criterion. From the profiles of 27 FFPE and FF matched samples, the best correlating probes were identified

  7. Gelatin in situ zymography on fixed, paraffin-embedded tissue: zinc and ethanol fixation preserve enzyme activity.

    Science.gov (United States)

    Hadler-Olsen, Elin; Kanapathippillai, Premasany; Berg, Eli; Svineng, Gunbjørg; Winberg, Jan-Olof; Uhlin-Hansen, Lars

    2010-01-01

    In situ zymography is a method for the detection and localization of enzymatic activity in tissue sections. This method is used with frozen sections because routine fixation of tissue in neutral-buffered formalin inhibits enzyme activity. However, frozen sections present with poor tissue morphology, making precise localization of enzymatic activity difficult to determine. Ethanol- and zinc-buffered fixative (ZBF) are known to preserve both morphological and functional properties of the tissue well, but it has not previously been shown that these fixatives preserve enzyme activity. In the present study, we show that in situ zymography can be performed on ethanol- and ZBF-fixed paraffin-embedded tissue. Compared with snap-frozen tissue, ethanol- and ZBF-fixed tissue showed stronger signals and superior morphology, allowing for a much more precise detection of gelatinolytic activity. Gelatinolytic enzymes could also be extracted from both ethanol- and ZBF-fixed tissue. The yield, as analyzed by SDS-PAGE gelatin zymography and Western blotting, was influenced by the composition of the extraction buffer, but was generally lower than that obtained from unfixed tissue.

  8. Identification of 5-hydroxytryptamine-producing cells by detection of fluorescence in paraffin-embedded tissue sections

    Directory of Open Access Journals (Sweden)

    Y. Kaneko

    2016-09-01

    Full Text Available 5-Hydroxytryptamine (5-HT produced by enterochromaffin (EC cells is an important enteric mucosal signaling ligand and has been implicated in several gastrointestinal diseases, including inflammatory bowel disease and functional disorders such as irritable bowel syndrome. The present study reports a new, simple and rapid visualization method of 5-HT-producing EC cells utilizing detection of autofluorescence in paraffin-embedded tissue sections after formalin fixation. In human samples, there was a high incidence of autofluorescence+ cells in the 5-HT+ cells in the pyloric, small intestinal and colonic glands, while co-localization was lacking between autofluorescence+ and gastrin+ cells in the pyloric and small intestinal glands. Autofluorescence+ EC cells were detected in the colon of mice and rats. Autofluorescence+ cells were also observed in 5-HT+ β cells in the pancreatic islets of Langerhans in pregnant mice, while non-pregnant mouse pancreatic islet cells showed no 5-HT immunoreactivity or autofluorescence. These results suggest that autofluorescence+ cells are identical to 5-HT+ cells, and the source of autofluorescence may be 5-HT itself or molecules related to its synthesis or degradation. This autofluorescence signal detection method may be applicable for monitoring of inflammatory status of inflammatory bowel diseases in both the experimental and clinical settings.

  9. Molecular genotyping of Echinococcus granulosus using formalin-fixed paraffin-embedded preparations from human isolates in unusual tissue sites.

    Science.gov (United States)

    Hizem, A; M'rad, S; Oudni-M'rad, M; Mestiri, S; Hammedi, F; Mezhoud, H; Zakhama, A; Mokni, M; Babba, H

    2016-07-01

    Cystic echinococcosis (CE) caused by Echinococcus granulosus remains a serious problem worldwide for issues relating to public health and the economy. The most predominantly affected sites are the liver and the lungs, but other organs such as the heart, the spleen and the peritoneum can also be infected. Access to cysts from uncommon sites has limited genomic and molecular investigations. In the present study, genotypes of E. granulosus sensu lato were identified from formalin-fixed paraffin-embedded tissues (FF-PETs) implicated in human CE. Tissue samples were obtained from 57 patients with histologically confirmed CE. DNA samples were analysed using Egss 1 polymerase chain reaction (PCR) specific to the mitochondrial 12S rRNA gene of E. granulosus sensu stricto. All cysts were typed as E. granulosus sensu stricto with up to 35% of the liver and 16.6% of lungs being the most frequently infected, and up to 48.4% of samples being from rare sites. No correlation was found between cyst site and either the gender or the age of patients. This study demonstrates the possibility of exploiting atypical cysts using FF-PET samples and highlights the predominance of E. granulosus sensu stricto species in the Tunisian population, even in unusual infection sites.

  10. KLC1-ALK: a novel fusion in lung cancer identified using a formalin-fixed paraffin-embedded tissue only.

    Directory of Open Access Journals (Sweden)

    Yuki Togashi

    Full Text Available The promising results of anaplastic lymphoma kinase (ALK inhibitors have changed the significance of ALK fusions in several types of cancer. These fusions are no longer mere research targets or diagnostic markers, but they are now directly linked to the therapeutic benefit of patients. However, most available tumor tissues in clinical settings are formalin-fixed and paraffin-embedded (FFPE, and this significantly limits detailed genetic studies in many clinical cases. Although recent technical improvements have allowed the analysis of some known mutations in FFPE tissues, identifying unknown fusion genes by using only FFPE tissues remains difficult. We developed a 5'-rapid amplification of cDNA ends-based system optimized for FFPE tissues and evaluated this system on a lung cancer tissue with ALK rearrangement and without the 2 known ALK fusions EML4-ALK and KIF5B-ALK. With this system, we successfully identified a novel ALK fusion, KLC1-ALK. The result was confirmed by reverse transcription-polymerase chain reaction and fluorescence in situ hybridization. Then, we synthesized the putative full-length cDNA of KLC1-ALK and demonstrated the transforming potential of the fusion kinase with assays using mouse 3T3 cells. To the best of our knowledge, KLC1-ALK is the first novel oncogenic fusion identified using only FFPE tissues. This finding will broaden the potential value of archival FFPE tissues and provide further biological and clinical insights into ALK-positive lung cancer.

  11. Impact of pre-analytical factors on the proteomic analysis of formalin-fixed paraffin-embedded tissue.

    Science.gov (United States)

    Thompson, Seonaid M; Craven, Rachel A; Nirmalan, Niroshini J; Harnden, Patricia; Selby, Peter J; Banks, Rosamonde E

    2013-04-01

    Formalin-fixed paraffin-embedded (FFPE) tissue samples represent a tremendous potential resource for biomarker discovery, with large numbers of samples in hospital pathology departments and links to clinical information. However, the cross-linking of proteins and nucleic acids by formalin fixation has hampered analysis and proteomic studies have been restricted to using frozen tissue, which is more limited in availability as it needs to be collected specifically for research. This means that rare disease subtypes cannot be studied easily. Recently, improved extraction techniques have enabled analysis of FFPE tissue by a number of proteomic techniques. As with all clinical samples, pre-analytical factors are likely to impact on the results obtained, although overlooked in many studies. The aim of this review is to discuss the various pre-analytical factors, which include warm and cold ischaemic time, size of sample, fixation duration and temperature, tissue processing conditions, length of storage of archival tissue and storage conditions, and to review the studies that have considered these factors in more detail. In those areas where investigations are few or non-existent, illustrative examples of the possible importance of specific factors have been drawn from studies using frozen tissue or from immunohistochemical studies of FFPE tissue. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. Optimization of Single- and Dual-Color Immunofluorescence Protocols for Formalin-Fixed, Paraffin-Embedded Archival Tissues.

    Science.gov (United States)

    Kajimura, Junko; Ito, Reiko; Manley, Nancy R; Hale, Laura P

    2016-02-01

    Performance of immunofluorescence staining on archival formalin-fixed paraffin-embedded human tissues is generally not considered to be feasible, primarily due to problems with tissue quality and autofluorescence. We report the development and application of procedures that allowed for the study of a unique archive of thymus tissues derived from autopsies of individuals exposed to atomic bomb radiation in Hiroshima, Japan in 1945. Multiple independent treatments were used to minimize autofluorescence and maximize fluorescent antibody signals. Treatments with NH3/EtOH and Sudan Black B were particularly useful in decreasing autofluorescent moieties present in the tissue. Deconvolution microscopy was used to further enhance the signal-to-noise ratios. Together, these techniques provide high-quality single- and dual-color fluorescent images with low background and high contrast from paraffin blocks of thymus tissue that were prepared up to 60 years ago. The resulting high-quality images allow the application of a variety of image analyses to thymus tissues that previously were not accessible. Whereas the procedures presented remain to be tested for other tissue types and archival conditions, the approach described may facilitate greater utilization of older paraffin block archives for modern immunofluorescence studies. © 2016 The Histochemical Society.

  13. HaloPlex Targeted Resequencing for Mutation Detection in Clinical Formalin-Fixed, Paraffin-Embedded Tumor Samples.

    Science.gov (United States)

    Moens, Lotte N J; Falk-Sörqvist, Elin; Ljungström, Viktor; Mattsson, Johanna; Sundström, Magnus; La Fleur, Linnéa; Mathot, Lucy; Micke, Patrick; Nilsson, Mats; Botling, Johan

    2015-11-01

    In recent years, the advent of massively parallel next-generation sequencing technologies has enabled substantial advances in the study of human diseases. Combined with targeted DNA enrichment methods, high sequence coverage can be obtained for different genes simultaneously at a reduced cost per sample, creating unique opportunities for clinical cancer diagnostics. However, the formalin-fixed, paraffin-embedded (FFPE) process of tissue samples, routinely used in pathology departments, results in DNA fragmentation and nucleotide modifications that introduce a number of technical challenges for downstream biomolecular analyses. We evaluated the HaloPlex target enrichment system for somatic mutation detection in 80 tissue fractions derived from 20 clinical cancer cases with paired tumor and normal tissue available in both FFPE and fresh-frozen format. Several modifications to the standard method were introduced, including a reduced target fragment length and two strand capturing. We found that FFPE material can be used for HaloPlex-based target enrichment and next-generation sequencing, even when starting from small amounts of DNA. By specifically capturing both strands for each target fragment, we were able to reduce the number of false-positive errors caused by FFPE-induced artifacts and lower the detection limit for somatic mutations. We believe that the HaloPlex method presented here will be broadly applicable as a tool for somatic mutation detection in clinical cancer settings. Copyright © 2015 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

  14. A new classification method for MALDI imaging mass spectrometry data acquired on formalin-fixed paraffin-embedded tissue samples.

    Science.gov (United States)

    Boskamp, Tobias; Lachmund, Delf; Oetjen, Janina; Cordero Hernandez, Yovany; Trede, Dennis; Maass, Peter; Casadonte, Rita; Kriegsmann, Jörg; Warth, Arne; Dienemann, Hendrik; Weichert, Wilko; Kriegsmann, Mark

    2017-07-01

    Matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS) shows a high potential for applications in histopathological diagnosis, and in particular for supporting tumor typing and subtyping. The development of such applications requires the extraction of spectral fingerprints that are relevant for the given tissue and the identification of biomarkers associated with these spectral patterns. We propose a novel data analysis method based on the extraction of characteristic spectral patterns (CSPs) that allow automated generation of classification models for spectral data. Formalin-fixed paraffin embedded (FFPE) tissue samples from N=445 patients assembled on 12 tissue microarrays were analyzed. The method was applied to discriminate primary lung and pancreatic cancer, as well as adenocarcinoma and squamous cell carcinoma of the lung. A classification accuracy of 100% and 82.8%, resp., could be achieved on core level, assessed by cross-validation. The method outperformed the more conventional classification method based on the extraction of individual m/z values in the first application, while achieving a comparable accuracy in the second. LC-MS/MS peptide identification demonstrated that the spectral features present in selected CSPs correspond to peptides relevant for the respective classification. This article is part of a Special Issue entitled: MALDI Imaging, edited by Dr. Corinna Henkel and Prof. Peter Hoffmann. Copyright © 2016 Elsevier B.V. All rights reserved.

  15. The use of special stains in liver biopsy interpretation: Implications ...

    African Journals Online (AJOL)

    Materials and Methods: The formalin fixed paraffin embedded blocks of liver biopsies reported in two histopathology laboratories between 2008 and 2013 were retrieved. These were stained with H and E and the following standard special stains for liver tissue histology – Perl's Prussian blue, reticulin, Sirius red, Shikata ...

  16. RNA isolation for transcriptomics of human and mouse small skin biopsies

    Directory of Open Access Journals (Sweden)

    Breit Timo M

    2011-10-01

    Full Text Available Abstract Background Isolation of RNA from skin biopsies presents a challenge, due to the tough nature of skin tissue and a high presence of RNases. As we lacked the dedicated equipment, i.e. homogenizer or bead-beater, needed for the available RNA from skin isolation methods, we adapted and tested our zebrafish single-embryo RNA-isolation protocol for RNA isolation from skin punch biopsies. Findings We tested our new RNA-isolation protocol in two experiments: a large-scale study with 97 human skin samples, and a small study with 16 mouse skin samples. Human skin was sampled with 4.0 mm biopsy punches and for the mouse skin different punch diameter sizes were tested; 1.0, 1.5, 2.0, and 2.5 mm. The average RNA yield in human samples was 1.5 μg with an average RNA quality RIN value of 8.1. For the mouse biopsies, the average RNA yield was 2.4 μg with an average RIN value of 7.5. For 96% of the human biopsies and 100% of the mouse biopsies we obtained enough high-quality RNA. The RNA samples were successfully tested in a transcriptomics analysis using the Affymetrix and Roche NimbleGen platforms. Conclusions Using our new RNA-isolation protocol, we were able to consistently isolate high-quality RNA, which is apt for further transcriptomics analysis. Furthermore, this method is already useable on biopsy material obtained with a punch diameter as small as 1.5 mm.

  17. Immunohistochemical detection of SWC3, CD2, CD3, CD4 and CD8 antigens in paraformaldehyde fixed and paraffin embedded porcine lymphoid tissue

    DEFF Research Database (Denmark)

    Tingstedt, Jens Erik; Tornehave, Ditte; Lind, Peter

    2003-01-01

    Identification of the different cell types of the immune system is important for in situ studies on the pathogenesis of infectious diseases in various animals, including the pig. Unfortunately, many monoclonal anti-leukocyte antibodies are only useful for staining frozen tissue sections with inhe......Identification of the different cell types of the immune system is important for in situ studies on the pathogenesis of infectious diseases in various animals, including the pig. Unfortunately, many monoclonal anti-leukocyte antibodies are only useful for staining frozen tissue sections...... with inherent poor tissue morphology, and are not readily adapted to formaldehyde fixed and paraffin embedded tissue with well preserved morphology. Seven well characterised monoclonal antibodies against porcine leukocyte antigens were tested on neutral buffered paraformaldehyde fixed and paraffin embedded...

  18. Applying a Real-Time PCR Assay for Histoplasma capsulatum to Clinically Relevant Formalin-Fixed Paraffin-Embedded Human Tissue

    Science.gov (United States)

    Koepsell, Scott A.; Hinrichs, Steven H.

    2012-01-01

    A real-time PCR assay to detect Histoplasma capsulatum in formalin-fixed, paraffin-embedded (FFPE) tissue is described. The assay had an analytical sensitivity of 6 pg/μl of fungal DNA, analytical specificity of 100%, and clinical sensitivity of 88.9%. This proof-of-concept study may aid in the diagnosis of histoplasmosis from FFPE tissue. PMID:22855519

  19. Detection of Tropical Fungi in Formalin-Fixed, Paraffin-Embedded Tissue: Still an Indication for Microscopy in Times of Sequence-Based Diagnosis?

    Directory of Open Access Journals (Sweden)

    Hagen Frickmann

    2015-01-01

    Full Text Available Introduction. The aim of the study was the evaluation of panfungal PCR protocols with subsequent sequence analysis for the diagnostic identification of invasive mycoses in formalin-fixed, paraffin-embedded tissue samples with rare tropical mycoses. Materials and Methods. Five different previously described panfungal PCR/sequencing protocols targeting 18S and 28S ribosomal RNA gene fragments as well as internal transcribed spacer 1 and 2 fragments were evaluated with a collection of 17 formalin-fixed, paraffin-embedded tissue samples of patients with rare and/or tropical invasive mycoses, comprising chromoblastomycosis, coccidioidomycosis, cryptococcosis, histoplasmosis, mucormycosis, mycetoma/maduromycosis, and rhinosporidiosis, in a proof-of-principle analysis. Results. The primers of the panfungal PCRs readily and predominantly reacted with contaminating environmental fungi that had deposited on the paraffin blocks. Altogether three sequence results of histoplasmosis and mycetoma samples that matched the histological assessment were associated with sample age <10 years and virtually without PCR inhibition. Conclusions. The high risk of amplifying environmental contaminants severely reduces the usefulness of the assessed panfungal PCR/sequencing protocols for the identification of rare and/or tropical mycoses in stored formalin-fixed, paraffin-embedded tissues. Histological assessment remains valuable for such indications if cultural differentiation is impossible from inactivated sample material.

  20. A single simple procedure for dewaxing, hydration and heat-induced epitope retrieval (HIER for immunohistochemistry in formalin fixed paraffin-embedded tissue

    Directory of Open Access Journals (Sweden)

    I.M.S. Paulsen

    2015-11-01

    Full Text Available Heat-induced epitope retrieval (HIER is widely used for immunohistochemistry on formalin fixed paraffin-embedded tissue and includes temperatures well above the melting point of paraffin. We therefore tested whether traditional xylene-based removal of paraffin is required on sections from paraffin-embedded tissue, when HIER is performed by vigorous boiling in 10 mM Tris/0.5 mM EGTA-buffer (pH=9. Immunohistochemical results using HIER with or without prior dewaxing in xylene were evaluated using 7 primary antibodies targeting proteins located in the cytosol, intracellular vesicles and plasma membrane. No effect of omitting prior dewaxing was observed on staining pattern. Semiquantitative analysis did not show HIER to influence the intensity of labelling consistently. Consequently, quantification of immune labelling intensity using fluorescent secondary antibodies was performed at 5 dilutions of primary antibody with and without prior dewaxing in xylene. No effect of omitting prior dewaxing on signal intensity was detectable indicating similar immunoreactivity in dewaxed and non-dewaxed sections. The intensity of staining the nucleus with the DNA-stain ToPro3 was similarly unaffected by omission of dewaxing in xylene. In conclusion, the HIER procedure described and tested can be used as a single procedure enabling dewaxing, hydration and epitope retrieval for immunohistochemistry in formalin fixed paraffin-embedded tissue.

  1. An ecological study of skin biopsies and skin cancer treatment procedures in the United States Medicare population, 2000 to 2015.

    Science.gov (United States)

    Wang, David M; Morgan, Frederick C; Besaw, Robert J; Schmults, Chrysalyne D

    2018-01-01

    Analyses of skin cancer procedures adjusted for population changes are needed. To describe trends in skin cancer-related biopsies and procedures in Medicare beneficiaries. An ecological study of Medicare claims for skin biopsies and skin cancer procedures in 2000 to 2015. Biopsies increased 142%, and skin cancer procedures increased 56%. Mohs micrographic surgery (MMS) utilization increased on the head/neck, hands/feet, and genitalia (increasing from 11% to 27% of all treatment procedures) but was low on the trunk/extremities (increasing from 1% to 4%). Adjusted for increased Medicare enrollment (+36%) between 2000 and 2015, the number of biopsies and MMS procedures performed per 1000 beneficiaries increased (from 56 to 99 and from 5 to 15, respectively), whereas the number of excisions and destructions changed minimally (from 18 to 16 and from 19 to 18, respectively). Growth in biopsies and MMS procedures slowed between each time period studied: 4.3 additional biopsies per year and 0.9 additional MMS procedures per year per 1000 beneficiaries between 2000 and 2007, 2.2 and 0.5 more between 2008 and 2011, and 0.5 and 0.3 more between 2012 and 2015, respectively. Medicare claims-level data do not provide patient-level or nonsurgical treatment information. The increased number of skin cancer procedures performed was largely the result of Medicare population growth over time. MMS utilization increased primarily on high- and medium-risk and functionally and cosmetically significant locations where tissue sparing and maximizing cure are critical. Copyright © 2017 American Academy of Dermatology, Inc. Published by Elsevier Inc. All rights reserved.

  2. Confirmation of immunoglobulin heavy chain rearrangement by polymerase chain reaction using surgically obtained, paraffin-embedded samples to diagnose primary palate mucosa-associated lymphoid tissue lymphoma: A case study

    Directory of Open Access Journals (Sweden)

    Shigehiro Abe

    2015-01-01

    Conclusion: We suggest that, if histological examination is ambiguous or fresh material is insufficient, PCR can be performed using paraffin-embedded materials to definitively diagnose low-grade lymphomas, such as MALT lymphoma.

  3. MicroRNA expression profiles of multiple system atrophy from formalin-fixed paraffin-embedded samples.

    Science.gov (United States)

    Wakabayashi, Koichi; Mori, Fumiaki; Kakita, Akiyoshi; Takahashi, Hitoshi; Tanaka, Shinya; Utsumi, Jun; Sasaki, Hidenao

    2016-12-02

    MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression. Recently, we have shown that informative miRNA data can be derived from archived formalin-fixed paraffin-embedded (FFPE) samples from postmortem cases of amyotrophic lateral sclerosis and normal controls. miRNA analysis has now been performed on FFPE samples from affected brain regions in patients with multiple system atrophy (MSA) and the same areas in neurologically normal controls. We evaluated 50 samples from patients with MSA (n=13) and controls (n=13). Twenty-six samples were selected for miRNA analysis on the basis of the criteria reported previously: (i) a formalin fixation time of less than 4 weeks, (ii) a total RNA yield per sample of more than 500ng, and (iii) sufficient quality of the RNA electrophoresis pattern. These included 11 cases of MSA and 5 controls. Thus, the success rate for analysis of RNA from FFPE samples was 52% (26 of 50). For MSA, a total of 395 and 383 miRNAs were identified in the pons and cerebellum, respectively; 5 were up-regulated and 33 were down-regulated in the pons and 5 were up-regulated and 18 were down-regulated in the cerebellum. Several miRNAs down-regulated in the pons (miR-129-2-3p and miR-129-5p) and cerebellum (miR-129-2-3p, miR-129-5p and miR-132-3p) had already been identified in frozen cerebellum from MSA patients. These findings suggest that archived FFPE postmortem samples can be a valuable source for miRNA profiling in MSA. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  4. [Histopathological Diagnosis of Invasive Fungal Infections in Formalin-Fixed and Paraffin-Embedded Tissues in Conjunction with Molecular Methods].

    Science.gov (United States)

    Shinozaki, Minoru; Tochigi, Naobumi; Sadamoto, Sota; Yamagata Murayama, Somay; Wakayama, Megumi; Nemoto, Tetsuo

    2018-01-01

    The main objective of this study was to evaluate the relationship between histopathology, polymerase chain reaction (PCR), and in situ hybridization (ISH) for the identification of causative fungi in formalin-fixed and paraffin-embedded (FFPE) tissue specimens. Since pathogenic fungi in tissue specimens can be difficult to identify morphologically, PCR and ISH have been usually employed as auxiliary procedures. However, little comparison has been made on the sensitivity and specificity of PCR and ISH using FFPE specimens. Therefore, to compare and clarify the reproducibility and usefulness of PCR and ISH as auxiliary procedures for histological identification, we performed histopathological review, PCR assays, and ISH to identify pathogenic fungi in 59 FFPE tissue specimens obtained from 49 autopsies. The following are the main findings for this retrospective review: i) even for cases classified as "mold not otherwise specified" (MNOS), two cases could be identified as Aspergillus species by molecular methods; ii) all cases classified as non-zygomycetes mold (NZM) were Aspergillus species and were not identified by molecular methods as other fungi; iii) all 3 cases classified as zygomycetes mold (ZM) could be identified by molecular methods as Mucorales; iv) except for 1 case identified by molecular methods as Trichosporon spp., 5 cases were originally identified as dimorphic yeast (DY). As a measure of nucleic acid integrity, PCR and ISH successfully detected human and fungal nucleic acids in approximately 60% of the specimens. Detection of Aspergillus DNA by nested PCR assay and by ISH against the A. fumigatus ALP gene were similarly sensitive and significant (pmolecular methods such as ISH and PCR on FFPE specimens with pathological diagnosis should improve diagnostic accuracy of fungal infection.

  5. Elevated pressure improves the extraction and identification of proteins recovered from formalin-fixed, paraffin-embedded tissue surrogates.

    Directory of Open Access Journals (Sweden)

    Carol B Fowler

    2010-12-01

    Full Text Available Proteomic studies of formalin-fixed paraffin-embedded (FFPE tissues are frustrated by the inability to extract proteins from archival tissue in a form suitable for analysis by 2-D gel electrophoresis or mass spectrometry. This inability arises from the difficulty of reversing formaldehyde-induced protein adducts and cross-links within FFPE tissues. We previously reported the use of elevated hydrostatic pressure as a method for efficient protein recovery from a hen egg-white lysozyme tissue surrogate, a model system developed to study formalin fixation and histochemical processing.In this study, we demonstrate the utility of elevated hydrostatic pressure as a method for efficient protein recovery from FFPE mouse liver tissue and a complex multi-protein FFPE tissue surrogate comprised of hen egg-white lysozyme, bovine carbonic anhydrase, bovine ribonuclease A, bovine serum albumin, and equine myoglobin (55∶15∶15∶10∶5 wt%. Mass spectrometry of the FFPE tissue surrogates retrieved under elevated pressure showed that both the low and high-abundance proteins were identified with sequence coverage comparable to that of the surrogate mixture prior to formaldehyde treatment. In contrast, non-pressure-extracted tissue surrogate samples yielded few positive and many false peptide identifications. Studies with soluble formalin-treated bovine ribonuclease A demonstrated that pressure modestly inhibited the rate of reversal (hydrolysis of formaldehyde-induced protein cross-links. Dynamic light scattering studies suggest that elevated hydrostatic pressure and heat facilitate the recovery of proteins free of formaldehyde adducts and cross-links by promoting protein unfolding and hydration with a concomitant reduction in the average size of the protein aggregates.These studies demonstrate that elevated hydrostatic pressure treatment is a promising approach for improving the recovery of proteins from FFPE tissues in a form suitable for proteomic analysis.

  6. Elevated Pressure Improves the Extraction and Identification of Proteins Recovered from Formalin-Fixed, Paraffin-Embedded Tissue Surrogates

    Science.gov (United States)

    Fowler, Carol B.; Chesnick, Ingrid E.; Moore, Cedric D.; O'Leary, Timothy J.; Mason, Jeffrey T.

    2010-01-01

    Background Proteomic studies of formalin-fixed paraffin-embedded (FFPE) tissues are frustrated by the inability to extract proteins from archival tissue in a form suitable for analysis by 2-D gel electrophoresis or mass spectrometry. This inability arises from the difficulty of reversing formaldehyde-induced protein adducts and cross-links within FFPE tissues. We previously reported the use of elevated hydrostatic pressure as a method for efficient protein recovery from a hen egg-white lysozyme tissue surrogate, a model system developed to study formalin fixation and histochemical processing. Principal Findings In this study, we demonstrate the utility of elevated hydrostatic pressure as a method for efficient protein recovery from FFPE mouse liver tissue and a complex multi-protein FFPE tissue surrogate comprised of hen egg-white lysozyme, bovine carbonic anhydrase, bovine ribonuclease A, bovine serum albumin, and equine myoglobin (55∶15∶15∶10∶5 wt%). Mass spectrometry of the FFPE tissue surrogates retrieved under elevated pressure showed that both the low and high-abundance proteins were identified with sequence coverage comparable to that of the surrogate mixture prior to formaldehyde treatment. In contrast, non-pressure-extracted tissue surrogate samples yielded few positive and many false peptide identifications. Studies with soluble formalin-treated bovine ribonuclease A demonstrated that pressure modestly inhibited the rate of reversal (hydrolysis) of formaldehyde-induced protein cross-links. Dynamic light scattering studies suggest that elevated hydrostatic pressure and heat facilitate the recovery of proteins free of formaldehyde adducts and cross-links by promoting protein unfolding and hydration with a concomitant reduction in the average size of the protein aggregates. Conclusions These studies demonstrate that elevated hydrostatic pressure treatment is a promising approach for improving the recovery of proteins from FFPE tissues in a form

  7. Bisulfite-Based DNA Methylation Analysis from Recent and Archived Formalin-Fixed, Paraffin Embedded Colorectal Tissue Samples.

    Science.gov (United States)

    Kalmár, Alexandra; Péterfia, Bálint; Hollósi, Péter; Wichmann, Barnabás; Bodor, András; Patai, Árpád V; Schöller, Andrea; Krenács, Tibor; Tulassay, Zsolt; Molnár, Béla

    2015-09-01

    We aimed to test the applicability of formalin-fixed and paraffin-embedded (FFPE) tissue samples for gene specific DNA methylation analysis after using two commercially available DNA isolation kits. Genomic DNA was isolated from 5 colorectal adenocarcinomas and 5 normal adjacent tissues from "recent", collected within 6 months, and "archived", collected more than 5 years ago, FFPE tissues using either High Pure FFPET DNA Isolation kit or QIAamp DNA FFPE Tissue kit. DNA methylation analysis of MAL, SFRP1 and SFRP2 genes, known to be hypermethylated in CRC, was performed using methylation-sensitive high resolution melting (MS-HRM) analysis and sequencing. QIAamp (Q) method resulted in slightly higher recovery in archived (HP: 1.22 ± 3.18 μg DNA; Q: 3.00 ± 4.04 μg DNA) and significantly (p < 0.05) higher recovery in recent samples compared to High Pure method (HP) (HP: 4.10 ± 2.91 μg DNA; Q: 11.51 ± 7.50 μg DNA). Both OD260/280 and OD260/230 ratios were lower, but still high in the High Pure isolated archived and recent samples compared to those isolated with QIAamp. Identical DNA methylation patterns were detected for all 3 genes tested by MS-HRM with both isolation kits in the recent group. However, despite of higher DNA recovery in QIAamp slightly more reproducible methylation results were obtained from High Pure isolated archived samples. Sequencing confirmed DNA hypermethylation in CRCs. In conclusion, reproducible DNA methylation patterns were obtained from recent samples using both isolation kits. However, long term storage may affect the reliability of the results leading to moderate differences between the efficiency of isolation kits.

  8. High-risk Human Papillomavirus Determination in Formalin-fixed, Paraffin-embedded Cervical Tissue Using the Roche Cobas 4800 System: A Comparative Study With Liquid-based Cytology.

    Science.gov (United States)

    Tardío, Juan C; Cambero, Olivia; Sánchez-Estévez, Carolina; Sánchez-García, Ana B; Angulo, Fernando; Moreno, Amalia

    2017-11-14

    Roche cobas 4800 human papillomavirus (HPV) test is an automated real-time polymerase chain reaction-based system that allows the simultaneous detection of 14 human papillomavirus high-risk (HR-HPV) genotypes. This test is Food and Drug Administration approved since 2011 for HPV determination in liquid-based cytologic samples, but a clinically validated technique for formalin-fixed, paraffin-embedded (FFPE) tissue specimens is presently not commercially available. In our laboratory, we have developed an HPV detection procedure in FFPE tissue by cobas 4800 HPV test. In order to validate our method, we retrospectively studied 165 FFPE cervical biopsy and conization specimens with varied diagnoses from our files. In 50 of them, we contrasted the results with those obtained from simultaneous liquid-based cytologies from the same patients. Finally, seeking the possible complementary clinical usefulness of the procedure, we compared the HPV genotypes detected in cervical intraepithelial neoplasia grade 1 (CIN1)-diagnosed biopsies from 20 patients with a subsequent high-grade CIN (CIN2+) diagnosis with those from another group of 20 patients without a posterior CIN2+ diagnosis. Eighty-seven percent of the assays provided informative results. HR-HPV was detected in 28 of 32 (88%) invasive cervical squamous carcinomas. Coincidental HR-HPV genotypes were obtained in 32 of 50 (64%) cases with simultaneous cervical biopsy and liquid-based cytologic samples. A significant higher risk of progression to CIN2+ was found when HPV16 (P=0.022) or any HR-HPV genotype (P=0.037) was detected in CIN1 biopsies. The reported procedure provides an automated, technically time-saving, easy to integrate into laboratory routine, and reliable method of HR-HPV determination in FFPE specimens.

  9. Immunohistochemical expression of interleukin 8 in skin biopsies from patients with inflammatory acne vulgaris

    Directory of Open Access Journals (Sweden)

    El Maged Rabee A

    2007-01-01

    Full Text Available Abstract Background This study was conducted to evaluate the immunohistochemical (IHC expression of interleukin 8 (IL-8 in skin biopsies of inflammatory acne vulgaris (IAV in an attempt to understand the disease pathogenesis. Materials and methods A total of 58 biopsies, 29 from lesional IAV and 29 normal non lesional sites were immunostained for IL-8. The intensity of staining was evaluated in the epidermis and dermis and was scored as mild, moderate and severe. The expression was correlated with the clinical grade, disease course and histological changes. Results IL-8 immunoreactivity was expressed in lesional IAV compared to non lesional skin biopsies (p Conclusion We were able to demonstrate altered immunoreactivity of IL-8 in IAV compared to normal skin. Targeted therapy to block IL-8 production may hold promise in limiting the deleterious effects of IL-8-mediated inflammatory response and angiogenesis.

  10. Immunostaining of skin biopsy adds no diagnostic value in MGUS-associated peripheral neuropathy.

    Science.gov (United States)

    Al-Zuhairy, Ali; Schrøder, Henrik Daa; Plesner, Torben; Abildgaard, Niels; Sindrup, Søren H

    2015-02-15

    For several decades an association between MGUS, IgM-MGUS in particular, and peripheral neuropathy has been suspected. Several histopathology studies have shown binding of IgM to myelin and a secondary widening of myelin lamellae in cutaneous nerves and in the sural nerve of patients with IgM-MGUS, or Waldenström's Macroglobulinaemia (WM), and peripheral neuropathy. In this retrospective study we investigated the value of skin biopsy examination in the diagnosis of MGUS- and WM-associated peripheral neuropathy. A total of 117 patients, who were examined for an M-component in serum with associated nerve symptoms, had a skin biopsy taken and examined for immunoglobulin deposition in cutaneous nerves. Thirty-five patients were diagnosed with MGUS or WM and peripheral neuropathy with no other cause of neuropathy. Nineteen patients had MGUS but no peripheral neuropathy. Of the 35 patients with MGUS or WM and peripheral neuropathy, four had immunoglobulin deposition in the skin biopsy, all of whom had an IgM gammopathy. In the control group of 19 without peripheral neuropathy, three had immunoglobulin deposition in the skin biopsy, all of whom had IgM-MGUS. In both groups, there was a trend towards higher IgM blood levels in patients with immunoglobulin deposition. Half of the patients with IgM gammopathy in the neuropathy group had anti-MAG reactivity, whereas only one in the control group had weak anti-MAG reactivity. Our study indicates that examination of skin biopsies for immunoglobulin deposition does not add significant diagnostic value in the evaluation of neuropathies suspected to be caused by MGUS or WM. IgM immunoglobulin deposition in skin biopsy might merely be an epiphenomenon secondary to high IgM blood levels. Copyright © 2014 Elsevier B.V. All rights reserved.

  11. Genome-wide comparison of paired fresh frozen and formalin-fixed paraffin-embedded gliomas by custom BAC and oligonucleotide array comparative genomic hybridization: facilitating analysis of archival gliomas.

    Science.gov (United States)

    Mohapatra, Gayatry; Engler, David A; Starbuck, Kristen D; Kim, James C; Bernay, Derek C; Scangas, George A; Rousseau, Audrey; Batchelor, Tracy T; Betensky, Rebecca A; Louis, David N

    2011-04-01

    Array comparative genomic hybridization (aCGH) is a powerful tool for detecting DNA copy number alterations (CNA). Because diffuse malignant gliomas are often sampled by small biopsies, formalin-fixed paraffin-embedded (FFPE) blocks are often the only tissue available for genetic analysis; FFPE tissues are also needed to study the intratumoral heterogeneity that characterizes these neoplasms. In this paper, we present a combination of evaluations and technical advances that provide strong support for the ready use of oligonucleotide aCGH on FFPE diffuse gliomas. We first compared aCGH using bacterial artificial chromosome (BAC) arrays in 45 paired frozen and FFPE gliomas, and demonstrate a high concordance rate between FFPE and frozen DNA in an individual clone-level analysis of sensitivity and specificity, assuring that under certain array conditions, frozen and FFPE DNA can perform nearly identically. However, because oligonucleotide arrays offer advantages to BAC arrays in genomic coverage and practical availability, we next developed a method of labeling DNA from FFPE tissue that allows efficient hybridization to oligonucleotide arrays. To demonstrate utility in FFPE tissues, we applied this approach to biphasic anaplastic oligoastrocytomas and demonstrate CNA differences between DNA obtained from the two components. Therefore, BAC and oligonucleotide aCGH can be sensitive and specific tools for detecting CNAs in FFPE DNA, and novel labeling techniques enable the routine use of oligonucleotide arrays for FFPE DNA. In combination, these advances should facilitate genome-wide analysis of rare, small and/or histologically heterogeneous gliomas from FFPE tissues.

  12. MicroRNAs are suitable for assessment as biomarkers from formalin-fixed paraffin-embedded tissue, and miR-24 represents an appropriate reference microRNA for diffuse large B-cell lymphoma studies.

    Science.gov (United States)

    Culpin, Rachel Emily; Sieniawski, Michal; Proctor, Stephen John; Menon, Geetha; Mainou-Fowler, Tryfonia

    2013-03-01

    Tissue biopsy specimens in the form of formalin-fixed paraffin-embedded tissue (FFPET) represent a valuable resource for biomarker identification and validation. However, to date, they remain an underused asset due to uncertainty regarding RNA extraction and the reliability of downstream techniques, including quantitative RT-PCR. Recently, much interest has emerged in the study of microRNAs; small single-stranded RNAs with a role in transcriptional regulation, that are thought to be well preserved in FFPET. In this study, we show that microRNA expression is comparable between FFPET and matched fresh-frozen samples (miR-17-5p: p=0.01, miR-92: p=0.003), and demonstrate that no significant deterioration in expression occurs over prolonged FFPET storage (p=0.06). Furthermore, microRNA expression is equivalent dependant on RNA extraction method (p<0.001) or DNAse treatment of total RNA (p<0.001). Finally, we validate miR-24 as a suitable reference microRNA for diffuse large B-cell lymphoma (DLBCL) FFPET studies.

  13. Diagnosis of Henoch-Schonlein purpura: renal or skin biopsy?

    NARCIS (Netherlands)

    Davin, Jean-Claude; Weening, Jan J.

    2003-01-01

    Henoch-Schonlein purpura (HSP) is a form of systemic vasculitis characterized by vascular wall deposits of predominantly IgA, typically involving small vessels in skin, gut, and glomeruli and associated with purpura, intestinal colic, hematuria, and arthralgia or arthritis. HSP nephritis leads to

  14. Detection of feline coronavirus mutations in paraffin-embedded tissues in cats with feline infectious peritonitis and controls.

    Science.gov (United States)

    Sangl, Laura; Matiasek, Kaspar; Felten, Sandra; Gründl, Stefanie; Bergmann, Michele; Balzer, Hans-Jörg; Pantchev, Nikola; Leutenegger, Christian M; Hartmann, Katrin

    2018-03-01

    Objectives The amino acid substitutions M1058L and S1060A in the spike protein of feline coronavirus (FCoV) have been postulated to be responsible for the development of the pathogenic feline infectious peritonitis virus (FIPV), which causes feline infectious peritonitis (FIP). The aim of the following study was to investigate the presence of mutated virus in tissue samples of cats with and without FIP. Methods The study population consisted of 64 cats, 34 of which were diagnosed with FIP and 30 control cats. All cases underwent autopsy, histopathology and immunohistochemistry (IHC) for FCoV. Furthermore, a genotype-discriminating quantitative reverse transcriptase PCR (RT-qPCR) was performed on shavings of paraffin-embedded tissues to discriminate between cats with FIP and controls, and the sensitivity and specificity of this discriminating RT-qPCR were calculated using 95% confidence intervals (CIs). Results Specificity of genotype-discriminating RT-qPCR was 100.0% (95% CI 88.4-100.0), sensitivity was 70.6% (95% CI 52.5-84.9). In cats with FIP, 24/34 cats tested positive for FIPV. In samples of three control cats and in seven cats with FIP, FCoV was found, but genotyping was not possible owing to low FCoV RNA concentrations. Out of the positive samples, 23 showed the amino acid substitution M1058L in the spike protein and none the substitution S1060A. One sample in a cat with FIP revealed a mixed population of non-mutated FCoV and FIPV (mixed genotype). For one sample genotyping was not possible despite high viral load, and two samples were negative for FCoV. Conclusions and relevance As none of the control animals showed FCoV amino acid substitutions previously demonstrated in cats with FIP, it can be presumed that the substitution M1058L correlates with the presence of FIP. FCoV was detected in low concentration in tissues of control animals, confirming the ability of FCoV to spread systemically. The fact that no negative controls were included in the IHC

  15. Droplet digital polymerase chain reaction detection of HER2 amplification in formalin fixed paraffin embedded breast and gastric carcinoma samples.

    Science.gov (United States)

    Zhu, Yazhen; Lu, Dan; Lira, Maruja E; Xu, Qing; Du, Yunzhi; Xiong, Jianghong; Mao, Mao; Chung, Hyun Cheol; Zheng, Guangjuan

    2016-04-01

    Human epidermal growth factor receptor 2 (HER2) is a key driver of tumorigenesis, and over-expression as a result of HER2 gene amplification has been observed in a number of solid tumors. Recently HER2 has become an important biomarker for the monoclonal antibody treatment of HER2-positive metastatic breast and advanced gastric cancer. The HER2 targeting antibody trastuzumab treatment requires accurate measurement of HER2 levels for proper diagnosis. Droplet digital PCR (ddPCR) with highly direct, precise and absolute nucleic acid quantification could be used to detect HER2 amplification levels. Our objective was to evaluate a robust, accurate and less subjective application of ddPCR for HER2 amplification levels and test the assay performance in clinical formalin-fixed paraffin-embedded (FFPE) breast and gastric carcinoma samples. Genomic DNA from HER2 amplified cell line SK-BR-3 was used to set up the ddPCR assays. The copy number of HER2 was compared to the chromosome 17 centromere reference gene (CEP17), expressed as HER2:CEP17 ratio. Genomic DNAs of FFPE specimens from 145 Asian patients with breast and gastric carcinomas were assayed using both standard methods, immunohistochemistry (IHC) and/or fluorescence in situ hybridization (FISH), and ddPCR. Based on 145 clinical breast and gastric carcinoma cases, our study demonstrated a high concordance of ddPCR results to FISH and IHC. In breast cancer specimens, the ddPCR results had high concordance with FISH and IHC defined HER2 status with a sensitivity of 90.9% (30/33) and a specificity of 100% (77/77). In gastric cancer specimens that were concordant in both FISH and IHC, our assay was 95.5% concordant with FISH and IHC (21/22). ddPCR has the advantage of automation and also allows levels of HER2 amplification to be easily evaluated in large numbers of samples, and presents a potential option to define HER2 status. Copyright © 2015 Elsevier Inc. All rights reserved.

  16. Rapid, sensitive, type specific PCR detection of the E7 region of human papillomavirus type 16 and 18 from paraffin embedded sections of cervical carcinoma

    DEFF Research Database (Denmark)

    Lesnikova, Iana; Lidang, Marianne; Hamilton-Dutoit, Stephen Jacques

    2010-01-01

    ABSTRACT: Human papillomavirus (HPV) infection, and in particularly infection with HPVs 16 and 18 is a central carcinogenic factor in the uterine cervix. We established and optimized a PCR assay for the detection and discrimination of HPV types 16 and 18 in archival formaldehyde fixed and paraffin...... embedded (FFPE) sections of cervical cancer. Tissue blocks from 35 cases of in situ or invasive cervical squamouscell carcinoma and surrogate FFPE sections containing the cell lines HeLa and SiHa were tested for HPV 16 and HPV18 and for the housekeeping gene beta-actin by conventional PCR using type...

  17. Rapid, sensitive, type specific PCR detection of the E7 region of human papillomavirus type 16 and 18 from paraffin embedded sections of cervical carcinoma

    DEFF Research Database (Denmark)

    Lesnikova, Iana; Lidang, Marianne; Hamilton-Dutoit, Steven

    2010-01-01

    ABSTRACT: Human papillomavirus (HPV) infection, and in particularly infection with HPVs 16 and 18, is a central carcinogenic factor in the uterine cervix. We established and optimized a PCR assay for the detection and discrimination of HPV types 16 and 18 in archival formaldehyde fixed and paraffin...... embedded (FFPE) sections of cervical cancer.Tissue blocks from 35 cases of in situ or invasive cervical squamous cell carcinoma and surrogate FFPE sections containing the cell lines HeLa and SiHa were tested for HPV 16 and HPV18 by conventional PCR using type specific primers, and for the housekeeping gene...

  18. Immunoglobulin deposits in peripheral nerve endings detected by skin biopsy in patients with IgM M proteins and neuropathy

    DEFF Research Database (Denmark)

    Jønsson, V; Jensen, T S; Friis, M L

    1987-01-01

    biopsies provide a simple effective method of detecting immunoglobulin binding to peripheral nerves in patients suspected of having an autoimmune neuropathy. In contrast to sural nerve biopsy, skin biopsy does not cause sensory loss or pain in a denervated area and can easily be repeated.......Immunofluorescence studies of sural nerve and skin biopsies from three patients with IgM M proteins and clinical neuropathy showed that IgM M protein was bound to the nerve myelin in two patients and by the peri- and endoneurium in one. It is suggested that immunohistochemical studies of skin...

  19. Adventitious discovery of elastofibroma dorsi on skin biopsy

    Directory of Open Access Journals (Sweden)

    Salsabil Attafi Sehli

    2015-04-01

    Full Text Available Elastofibroma dorsi is a rare soft tissue pseudotumor, slow-growing, sitting in 99% of cases at the subscapular region and occurring in the elderly active people. Its pathogenesis is unclear. It is often asymptomatic. However, the diagnosis can be made on the typical topography of the mass and its characteristic appearance on CT and MRI. Thus, in the literature, most of the reported cases were radiologically discovered. An incidental histological discovery, like in our case is rare. We report the case of a 63 year-old man who had multiple nodular lesions, well circumscribed, firm, sometimes inflammatory, measuring between 3 and 5 cm, and located on the thighs and the paravertebral and scapular regions. The chest x-ray showed a right basal opacity suggesting a malignant processus. These nodules were biopsied in search of cutaneous metastasis of a probable pulmonary neoplasia. At histological examination, the diagnosis of elastofibroma was retained. Despite its rarity, the dorsal elastofibroma deserves to be known, thus avoiding excessive surgery. We propose to study its clinical, radiological and pathological features and its therapeutic modalities.

  20. Simulators of Squamous Cell Carcinoma of the Skin: Diagnostic Challenges on Small Biopsies and Clinicopathological Correlation

    Directory of Open Access Journals (Sweden)

    Kong-Bing Tan

    2013-01-01

    Full Text Available Squamous cell carcinoma (SCC is a common and important primary cutaneous malignancy. On skin biopsies, SCC is characterized by significant squamous cell atypia, abnormal keratinization, and invasive features. Diagnostic challenges may occasionally arise, especially in the setting of small punch biopsies or superficial shave biopsies, where only part of the lesion may be assessable by the pathologist. Benign mimics of SCC include pseudoepitheliomatous hyperplasia, eccrine squamous syringometaplasia, inverted follicular keratosis, and keratoacanthoma, while malignant mimics of SCC include basal cell carcinoma, melanoma, and metastatic carcinoma. The careful application of time-honored diagnostic criteria, close clinicopathological correlation and a selective request for a further, deeper, or wider biopsy remain the most useful strategies to clinch the correct diagnosis. This review aims to present the key differential diagnoses of SCC, to discuss common diagnostic pitfalls, and to recommend ways to deal with diagnostically challenging cases.

  1. Characterization of Melanin Radicals in Paraffin-embedded Malignant Melanoma and Nevus Pigmentosus Using X-band EPR and EPR Imaging.

    Science.gov (United States)

    Nakagawa, Kouichi; Minakawa, Satoko; Sawamura, Daisuke; Hara, Hideyuki

    2017-01-01

    Continuous wave electron paramagnetic resonance (CW EPR) and X-band (9 GHz) EPR imaging (EPRI) were used to nondestructively investigate the possible differentiation between malignant melanoma (MM) and nevus pigmentosus (NP) melanin radicals in paraffin-embedded specimens. The EPR spectra of both samples were analyzed using linewidth, spectral pattern, and X-band EPRI. The CW-EPR spectra of the MM showed an additional signal overlap. Eumelanin- and pheomelanin-related radicals were observed in the MM specimens. The EPR results revealed that the peak-to-peak linewidths (ΔH pp ) of paraffin-embedded MM and NP samples were 0.65 ± 0.01 and 0.69 ± 0.01 mT, respectively. The g-value was 2.005 for both samples. Moreover, the two-dimensional (2D) EPRI of the MM showed different signal intensities at the different tumor stages, unlike the NP, which displayed fewer variations in signal intensity. Thus, the present results suggest that EPR and 2D EPRI can be useful for characterization of the two melanin radicals in the MM and for determination of their size and concentration.

  2. Genetic Characterization of Echinococcus granulosus from a Large Number of Formalin-Fixed, Paraffin-Embedded Tissue Samples of Human Isolates in Iran

    Science.gov (United States)

    Rostami, Sima; Torbaghan, Shams Shariat; Dabiri, Shahriar; Babaei, Zahra; Mohammadi, Mohammad Ali; Sharbatkhori, Mitra; Harandi, Majid Fasihi

    2015-01-01

    Cystic echinococcosis (CE), caused by the larval stage of Echinococcus granulosus, presents an important medical and veterinary problem globally, including that in Iran. Different genotypes of E. granulosus have been reported from human isolates worldwide. This study identifies the genotype of the parasite responsible for human hydatidosis in three provinces of Iran using formalin-fixed paraffin-embedded tissue samples. In this study, 200 formalin-fixed paraffin-embedded tissue samples from human CE cases were collected from Alborz, Tehran, and Kerman provinces. Polymerase chain reaction amplification and sequencing of the partial mitochondrial cytochrome c oxidase subunit 1 gene were performed for genetic characterization of the samples. Phylogenetic analysis of the isolates from this study and reference sequences of different genotypes was done using a maximum likelihood method. In total, 54.4%, 0.8%, 1%, and 40.8% of the samples were identified as the G1, G2, G3, and G6 genotypes, respectively. The findings of the current study confirm the G1 genotype (sheep strain) to be the most prevalent genotype involved in human CE cases in Iran and indicates the high prevalence of the G6 genotype with a high infectivity for humans. Furthermore, this study illustrates the first documented human CE case in Iran infected with the G2 genotype. PMID:25535316

  3. A simple osmium post-fixation paraffin-embedment technique to identify lipid accumulation in fish liver using medaka (Oryziaslatipes) eggs and eleutheroembryos as lipid rich models

    International Nuclear Information System (INIS)

    Mondon, J.A.; Howitt, J.; Tosiano, M.; Kwok, K.W.H.; Hinton, D.E.

    2011-01-01

    Highlights: → Hepatic lipidosis in fish liver is often misdiagnosed or overlooked. → Specific histological fat stains and cryostat sections are not commonly used. → Standard paraffin processing removes lipid leaving vacuoles of unknown origin. → Osmium post-fixed paraffin-embedment is a cost effective alternative. → Medaka trials show suitability for lipid visualization in tissues from egg to adult. - Abstract: Hepatic lipidosis is a non-specific biomarker of effect from pollution exposure in fish. Fatty liver is often misdiagnosed or overlooked in histological assessments due to the decreasing application of specific fat procedures and stains. For example, ethanol dehydration in standard paraffin processing removes lipids, leaving vacuoles of which the precise nature is unknown. Lipids can be identified using osmium post-fixation in semi-thin resin sections or transmission electron microscopy. However, both are expensive and technically demanding procedures, often not available for routine environmental risk assessment and monitoring programs. The current emphasis to reduce and refine animal toxicity testing, requires refinement of the suite of histopathological techniques currently available to maximize information gained from using fish for toxicity testing and as bio-indicators of environmental quality. This investigation has successfully modified an osmium post-fixation technique to conserve lipids in paraffin-embedded tissues using medaka (Oryzias latipes) eleutheroembryos and eggs (embryos) as lipid rich models.

  4. Proteomic workflow for analysis of archival formalin-fixed and paraffin-embedded clinical samples to a depth of 10 000 proteins.

    Science.gov (United States)

    Wiśniewski, Jacek R; Duś, Kamila; Mann, Matthias

    2013-04-01

    Archival formalin-fixed and paraffin-embedded clinical samples represent a very diverse source of material for proteomic investigation of diseases, often with follow-up patient information. Here, we describe an analytical workflow for analysis of laser-capture microdissected formalin-fixed and paraffin-embedded samples that allows studying proteomes to a depth of 10 000 proteins per sample. The workflow involves lysis of tissue in SDS-containing buffer, detergent removal, and consecutive digestion of the proteins with two enzymes by the multienzyme digestion filter-aided sample preparation method. Resulting peptides are fractionated by pipette-tip based strong anion exchange into six fractions and analyzed by LC-MS/MS on a bench top quadrupole Orbitrap mass spectrometer. Analysis of the data using the MaxQuant software resulted in the identification of 9502 ± 28 protein groups per a 110 nL sample of microdissected cells from human colonic adenoma. This depth of proteome analysis enables systemic insights into the organization of the adenoma cells and an estimation of the abundances of known biomarkers. It also allows the identification of proteins expressed from tumor suppressors, oncogenes, and other key players in the development and progression of the colorectal cancer. Our proteomic platform can be used for quantitative comparisons between samples representing different stages of diseases and thus can be applied to the discovery of biomarkers or drug targets. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. Diagnostic value of polymerase chain reaction analysis of skin biopsies in purpura fulminans.

    Science.gov (United States)

    Beau, Caroline; Vlassova, Natalia; Sarlangue, Jean; Brissaud, Olivier; Léauté-Labrèze, Christine; Boralevi, Franck

    2013-01-01

    Even though prompt diagnosis and treatment of purpura fulminans (PF) is essential to reduce mortality, early administration of antibiotics may preclude identification of the causative agent by standard bacterial cultures and thus render definitive diagnosis impossible. Here we present a case of an infant with PF and negative bacterial cultures for whom polymerase chain reaction (PCR) analysis of a cutaneous biopsy specimen obtained 4 days after initiation of antibiotics identified the genomic sequence of Neisseria meningitidis genogroup C. When bacterial cultures fail to provide useful information, PCR of skin biopsy specimens can be a valuable diagnostic tool in PF. © 2013 Wiley Periodicals, Inc.

  6. Skin Microvascular Thrombosis in Fusarium Infection in Two Early Biopsied Cases

    Directory of Open Access Journals (Sweden)

    Yang Fan

    2010-05-01

    Full Text Available Fusarium species cause rare and severe infections. Their incidence is increasing in immunocompromised patients but they are also observed in healthy hosts. Because of the rapid dissemination of infection and the frequent resistance of Fusarium species to antifungal drugs, histopathologic evidence of hyphae is very helpful to obtain the diagnosis rapidly. We report the clinical and pathological features of two patients with initial cutaneous lesions. Cutaneous early biopsies showed microvessel involvement with hyphae and thrombosis. Fusarium infection was confirmed by skin culture. Hyphae within a microvessel thrombus in the skin were highly suggestive of disseminated fungal infection. These pathological features enabled to establish an early diagnosis and to start efficient antifungal treatment. In early cutaneous biopsies of immunocompromised patients, the presence of cutaneous vessel thrombosis can suggest a fungal infection and may help to start specific therapy without delay for these life-threatening infections.

  7. Immunostaining of skin biopsy adds no diagnostic value in MGUS-associated peripheral neuropathy

    DEFF Research Database (Denmark)

    Al-Zuhairy, Ali; Schrøder, Henrik Daa; Plesner, Torben

    2015-01-01

    BACKGROUND AND PURPOSE: For several decades an association between MGUS, IgM-MGUS in particular, and peripheral neuropathy has been suspected. Several histopathology studies have shown binding of IgM to myelin and a secondary widening of myelin lamellae in cutaneous nerves and in the sural nerve...... of patients with IgM-MGUS, or Waldenström's Macroglobulinaemia (WM), and peripheral neuropathy. In this retrospective study we investigated the value of skin biopsy examination in the diagnosis of MGUS- and WM-associated peripheral neuropathy. METHODS: A total of 117 patients, who were examined for an M......-component in serum with associated nerve symptoms, had a skin biopsy taken and examined for immunoglobulin deposition in cutaneous nerves. Thirty-five patients were diagnosed with MGUS or WM and peripheral neuropathy with no other cause of neuropathy. Nineteen patients had MGUS but no peripheral neuropathy. RESULTS...

  8. [Clinicopathological study of purpura: Is a skin biopsy necessary for palpable purpura?].

    Science.gov (United States)

    Jung, A-J; Schaeffer, M; Mitcov, M; Scrivener, Y; Cribier, B; Lipsker, D

    2016-05-01

    For many physicians, palpable purpura is synonymous with vasculitis. However, a skin biopsy is almost always performed in common clinical practice in order to confirm the diagnosis. The aim of our study was to assess whether palpable purpura is always indicative of an inflammatory infiltrate in a vessel wall. Eighty-seven patients were included in this prospective monocentric study, 45 of whom were presenting a palpable purpura. Patients were classified in two categories: "leukocytoclastic vasculitis" or "other diagnosis". The clinical and histopathological features of patients with a palpable purpura were studied. The mean age of patients presenting a palpable purpura was 69 years. There were 26 men and 19 women. Of the 43 patients biopsied, 37 were included in the vasculitis group. The sensitivity, specificity, positive predictive value and negative predictive value for a diagnosis of vasculitis in patients with palpable purpura were respectively 82, 65, 86 and 58 %. The Odds ratio was 8.48 (95 % CI, 2.52-31.80; Ppurpuras examined were indeed related to leukocytoclastic vasculitis. In the remaining cases, biopsy did not contribute to the diagnosis since it only showed purpura without vessel wall inflammation. In our opinion, a skin biopsy is thus not essential where the clinical presentation is typical. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

  9. Genome-wide comparison of paired fresh frozen and formalin-fixed paraffin-embedded gliomas by custom BAC and oligonucleotide array comparative genomic hybridization: facilitating analysis of archival gliomas

    Science.gov (United States)

    Mohapatra, Gayatry; Engler, David A.; Starbuck, Kristen D.; Kim, James C.; Bernay, Derek C.; Scangas, George A.; Rousseau, Audrey; Batchelor, Tracy T.; Betensky, Rebecca A.; Louis, David N.

    2010-01-01

    Molecular genetic analysis of cancer is rapidly evolving as a result of improvement in genomic technologies and the growing applicability of such analyses to clinical oncology. Array based comparative genomic hybridization (aCGH) is a powerful tool for detecting DNA copy number alterations (CNA), particularly in solid tumors, and has been applied to the study of malignant gliomas. In the clinical setting, however, gliomas are often sampled by small biopsies and thus formalin-fixed paraffin-embedded (FFPE) blocks are often the only tissue available for genetic analysis, especially for rare types of gliomas. Moreover, the biological basis for the marked intratumoral heterogeneity in gliomas is most readily addressed in FFPE material. Therefore, for gliomas, the ability to use DNA from FFPE tissue is essential for both clinical and research applications. In this study, we have constructed a custom bacterial artificial chromosome (BAC) array and show excellent sensitivity and specificity for detecting CNAs in a panel of paired frozen and FFPE glioma samples. Our study demonstrates a high concordance rate between CNAs detected in FFPE compared to frozen DNA. We have also developed a method of labeling DNA from FFPE tissue that allows efficient hybridization to oligonucleotide arrays. This labeling technique was applied to a panel of biphasic anaplastic oligoastrocytomas (AOA) to identify genetic changes unique to each component. Together, results from these studies suggest that BAC and oligonucleotide aCGH are sensitive tools for detecting CNAs in FFPE DNA, and can enable genome-wide analysis of rare, small and/or histologically heterogeneous gliomas. PMID:21080181

  10. Implementation of formalin-fixed, paraffin-embedded cell line pellets as high-quality process controls in quality assessment programs for KRAS mutation analysis

    DEFF Research Database (Denmark)

    Dijkstra, Jeroen R; Opdam, Frank J M; Boonyaratanakornkit, Jerry

    2013-01-01

    . We assessed a novel synthetic control for formalin-fixed, paraffin-embedded (FFPE) tumor samples in a blind study conducted within nine laboratories across Europe. We show that FFPE material can, at least in part, mimic clinical samples and we demonstrate this control to be a valuable tool....... For a testing laboratory to become accredited to perform such tests, it is essential that they perform reliability testing, but it has not previously been possible to perform this kind of testing on the complete workflow on a large scale without compromising reproducibility or the mimicry of the control sample...... receptor (EGFR)-targeted therapy with increased progression-free survival only if the tumor does not carry a mutation in KRAS. Many different analytical platforms, both those commercially available and those developed in house, have been used within pathology laboratories to assess KRAS mutational status...

  11. Reliable PCR quantitation of estrogen, progesterone and ERBB2 receptor mRNA from formalin-fixed, paraffin-embedded tissue is independent of prior macro-dissection

    DEFF Research Database (Denmark)

    Tramm, Trine; Hennig, Guido; Kyndi, Marianne

    2013-01-01

    Gene expression analysis on messenger RNA (mRNA) purified from formalin-fixed, paraffin-embedded tissue is increasingly used for research purposes. Tissue heterogeneity may question specificity and interpretation of results from mRNA isolated from a whole slide section, and thresholds for minimal...... tumor content in the paraffin block or macrodissection are used to avoid contamination from non-neoplastic tissue. The aim was to test if mRNA from tissue surrounding breast cancer affected quantification of estrogen receptor α (ESR1), progesterone receptor (PGR) and human epidermal growth factor...... receptor 2 (ERBB2), by comparing gene expression from whole slide and tumor-enriched sections, and correlating gene expression from whole slide sections with corresponding immunohistochemistry. Gene expression, based on mRNA extracted from a training set (36 paraffin blocks) and two validation sets (133...

  12. Antigen retrieval prior to on-tissue digestion of formalin-fixed paraffin-embedded tumour tissue sections yields oxidation of proline residues.

    Science.gov (United States)

    Djidja, Marie-Claude; Claude, Emmanuelle; Scriven, Peter; Allen, David W; Carolan, Vikki A; Clench, Malcolm R

    2017-07-01

    MALDI-mass spectrometry imaging (MALDI-MSI) has been shown to allow the study of protein distribution and identification directly within formalin-fixed paraffin-embedded (FFPE) tissue sections. However, direct protein identification from tissue sections remains challenging due to signal interferences and/or existing post-translational or other chemical modifications. The use of antigen retrieval (AR) has been demonstrated for unlocking proteins prior to in situ enzymatic digestion and MALDI-MSI analysis of FFPE tissue sections. In the work reported here, the identification of proline oxidation, which may occur when performing the AR protocol, is described. This facilitated and considerably increased the number of identified peptides when adding proline oxidation as a variable modification to the MASCOT search criteria. This article is part of a Special Issue entitled: MALDI Imaging, edited by Dr. Corinna Henkel and Prof. Peter Hoffmann. Copyright © 2016 Elsevier B.V. All rights reserved.

  13. Ultrastructural analysis of small blood vessels in skin biopsies in CADASIL

    Directory of Open Access Journals (Sweden)

    Lačković Vesna

    2008-01-01

    Full Text Available Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL is an inherited small- and medium-artery disease of the brain caused by mutation of the Notch3 gene. Very often, this disease is misdiagnosed. We examined skin biopsies in two members of the first discovered Serbian family affected by CADASIL. Electron microscopy showed that skin blood vessels of both patients contain numerous deposits of granular osmiophilic material (GOM around vascular smooth muscle cells (VSMCs. We observed degeneration of VSMCs, reorganization of their cytoskeleton and dense bodies, disruption of myoendothelial contacts, and apoptosis. Our results suggest that the presence of GOM in small skin arteries represents a specific marker in diagnosis of CADASIL.

  14. Differential N-glycan patterns identified in lung adenocarcinoma by N-glycan profiling of formalin-fixed paraffin-embedded (FFPE) tissue sections.

    Science.gov (United States)

    Wang, Xiaoning; Deng, Zaian; Huang, Chuncui; Zhu, Tong; Lou, Jiatao; Wang, Lin; Li, Yan

    2018-02-10

    N-glycan profiling is a powerful approach for analyzing the functional relationship between N-glycosylation and cancer. Current methods rely on either serum or fresh tissue samples; however, N-glycan patterns may differ between serum and tissue, as the proteins of serum originate from a variety of tissues. Furthermore, fresh tissue samples are difficult to ship and store. Here, we used a profiling method based on formalin-fixed paraffin-embedded (FFPE) tissue sections from lung adenocarcinoma patients. We found that our method was highly reproducible. We identified 58 N-glycan compositions from lung adenocarcinoma FFPE samples, 51 of which were further used for MS n -based structure prediction. We show that high mannose type N-glycans are upregulated, while sialylated N-glycans are downregulated in our FFPE lung adenocarcinoma samples, compared to the control samples. Our receiver operating characteristic (ROC) curve analysis shows that high mannose type and sialylated N-glycans are useful discriminators to distinguish between lung adenocarcinoma and control tissue. Together, our results indicate that expression levels of specific N-glycans correlate well with lung adenocarcinoma, and strongly suggest that our FFPE-based method will be useful for N-glycan profiling of cancer tissues. Glycosylation is one of the most important post-translational protein modifications, and is associated with several physiopathological processes, including carcinogenesis. In this study, we tested the feasibility of using formalin-fixed paraffin-embedded (FFPE) tissue sections to identify changes in N-glycan patterns and identified the differentially expressed N-glycans of lung adenocarcinoma. Our study shows that the FFPE-based N-glycan profiling method is useful for clinical diagnosis as well as identification of potential biomarkers, and our data expand current knowledge of differential N-glycan patterns of lung adenocarcinoma. Copyright © 2017 Elsevier B.V. All rights reserved.

  15. Ewing’s Sarcoma: An Analysis of miRNA Expression Profiles and Target Genes in Paraffin-Embedded Primary Tumor Tissue

    Directory of Open Access Journals (Sweden)

    Antonina Parafioriti

    2016-04-01

    Full Text Available The molecular mechanism responsible for Ewing’s Sarcoma (ES remains largely unknown. MicroRNAs (miRNAs, a class of small non-coding RNAs able to regulate gene expression, are deregulated in tumors and may serve as a tool for diagnosis and prediction. However, the status of miRNAs in ES has not yet been thoroughly investigated. This study compared global miRNAs expression in paraffin-embedded tumor tissue samples from 20 ES patients, affected by primary untreated tumors, with miRNAs expressed in normal human mesenchymal stromal cells (MSCs by microarray analysis. A miRTarBase database was used to identify the predicted target genes for differentially expressed miRNAs. The miRNAs microarray analysis revealed distinct patterns of miRNAs expression between ES samples and normal MSCs. 58 of the 954 analyzed miRNAs were significantly differentially expressed in ES samples compared to MSCs. Moreover, the qRT-PCR analysis carried out on three selected miRNAs showed that miR-181b, miR-1915 and miR-1275 were significantly aberrantly regulated, confirming the microarray results. Bio-database analysis identified BCL-2 as a bona fide target gene of the miR-21, miR-181a, miR-181b, miR-29a, miR-29b, miR-497, miR-195, miR-let-7a, miR-34a and miR-1915. Using paraffin-embedded tissues from ES patients, this study has identified several potential target miRNAs and one gene that might be considered a novel critical biomarker for ES pathogenesis.

  16. The effect of aging of formalin-fixed paraffin-embedded tissues on the in situ hybridization and immunohistochemistry signals in cervical lesions.

    Science.gov (United States)

    Nuovo, Allison J; Garofalo, Michela; Mikhail, Alexandria; Nicol, Alcina F; Vianna-Andrade, Cecilia; Nuovo, Gerard J

    2013-09-01

    Formalin-fixed, paraffin-embedded tissues are widely used in biomedical research but little is known about the effect of the age of the block or unstained slides on the in situ hybridization or immunohistochemistry signal. We compared the in situ-based and immunohistochemistry-based signals for cervical intraepithelial neoplasia samples that ranged from 0 to 15 years of age. There was a progressive and statistically significant decrease in the strength of the p16 signal when comparing tissues prepared from recent unstained slides (0 to 1 y old, mean score of 92%) to those of intermediate age (5 to 7 y old, mean score of 49%) to old unstained slides (cut 13 to 15 y ago, mean score of 10%). Equivalent, progressive, and significant decreases in the intensity of the signals for microRNAs, CD45, and human papillomavirus DNA were seen in tissues stored on slides from 5 to 7 years and 13 to 15 years, respectively. However, the diminution of signal was much less, although still statistically significant, if the sections from the 13- to 15-year-old paraffin blocks were prepared in 2012. The data likely does not represent degradation of the targets as extraction of several microRNA from the old blocks showed no detectable degradation, despite the markedly weakened in situ hybridization signal. It is concluded that in situ-based signal for DNA, microRNAs, and proteins in paraffin-embedded tissues are significantly reduced over time, especially when stored long term on glass slides which, in turn, can lead to a significant underestimation of the amount and presence of the nucleic acid or protein target.

  17. Profiling cancer gene mutations in clinical formalin-fixed, paraffin-embedded colorectal tumor specimens using targeted next-generation sequencing.

    Science.gov (United States)

    Zhang, Liangxuan; Chen, Liangjing; Sah, Sachin; Latham, Gary J; Patel, Rajesh; Song, Qinghua; Koeppen, Hartmut; Tam, Rachel; Schleifman, Erica; Mashhedi, Haider; Chalasani, Sreedevi; Fu, Ling; Sumiyoshi, Teiko; Raja, Rajiv; Forrest, William; Hampton, Garret M; Lackner, Mark R; Hegde, Priti; Jia, Shidong

    2014-04-01

    The success of precision oncology relies on accurate and sensitive molecular profiling. The Ion AmpliSeq Cancer Panel, a targeted enrichment method for next-generation sequencing (NGS) using the Ion Torrent platform, provides a fast, easy, and cost-effective sequencing workflow for detecting genomic "hotspot" regions that are frequently mutated in human cancer genes. Most recently, the U.K. has launched the AmpliSeq sequencing test in its National Health Service. This study aimed to evaluate the clinical application of the AmpliSeq methodology. We used 10 ng of genomic DNA from formalin-fixed, paraffin-embedded human colorectal cancer (CRC) tumor specimens to sequence 46 cancer genes using the AmpliSeq platform. In a validation study, we developed an orthogonal NGS-based resequencing approach (SimpliSeq) to assess the AmpliSeq variant calls. Validated mutational analyses revealed that AmpliSeq was effective in profiling gene mutations, and that the method correctly pinpointed "true-positive" gene mutations with variant frequency >5% and demonstrated high-level molecular heterogeneity in CRC. However, AmpliSeq enrichment and NGS also produced several recurrent "false-positive" calls in clinically druggable oncogenes such as PIK3CA. AmpliSeq provided highly sensitive and quantitative mutation detection for most of the genes on its cancer panel using limited DNA quantities from formalin-fixed, paraffin-embedded samples. For those genes with recurrent "false-positive" variant calls, caution should be used in data interpretation, and orthogonal verification of mutations is recommended for clinical decision making.

  18. Multi-Center Evaluation of the Fully Automated PCR-Based Idylla™ KRAS Mutation Assay for Rapid KRAS Mutation Status Determination on Formalin-Fixed Paraffin-Embedded Tissue of Human Colorectal Cancer

    DEFF Research Database (Denmark)

    Solassol, Jérôme; Vendrell, Julie; Märkl, Bruno

    2016-01-01

    , was assessed on archived formalin-fixed paraffin-embedded (FFPE) tissue sections by comparing its results with the results previously obtained by routine reference approaches for KRAS genotyping. In case of discordance, samples were assessed further by additional methods. Among the 374 colorectal cancer FFPE...

  19. 3D imaging of cleared human skin biopsies using light-sheet microscopy: A new way to visualize in-depth skin structure.

    Science.gov (United States)

    Abadie, S; Jardet, C; Colombelli, J; Chaput, B; David, A; Grolleau, J-L; Bedos, P; Lobjois, V; Descargues, P; Rouquette, J

    2018-05-01

    Human skin is composed of the superimposition of tissue layers of various thicknesses and components. Histological staining of skin sections is the benchmark approach to analyse the organization and integrity of human skin biopsies; however, this approach does not allow 3D tissue visualization. Alternatively, confocal or two-photon microscopy is an effective approach to perform fluorescent-based 3D imaging. However, owing to light scattering, these methods display limited light penetration in depth. The objectives of this study were therefore to combine optical clearing and light-sheet fluorescence microscopy (LSFM) to perform in-depth optical sectioning of 5 mm-thick human skin biopsies and generate 3D images of entire human skin biopsies. A benzyl alcohol and benzyl benzoate solution was used to successfully optically clear entire formalin fixed human skin biopsies, making them transparent. In-depth optical sectioning was performed with LSFM on the basis of tissue-autofluorescence observations. 3D image analysis of optical sections generated with LSFM was performed by using the Amira ® software. This new approach allowed us to observe in situ the different layers and compartments of human skin, such as the stratum corneum, the dermis and epidermal appendages. With this approach, we easily performed 3D reconstruction to visualise an entire human skin biopsy. Finally, we demonstrated that this method is useful to visualise and quantify histological anomalies, such as epidermal hyperplasia. The combination of optical clearing and LSFM has new applications in dermatology and dermatological research by allowing 3D visualization and analysis of whole human skin biopsies. © 2018 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  20. Histopathological Features Of Deep Fungal Infections : An Analysis Of Sixteen Skin Biopsies

    Directory of Open Access Journals (Sweden)

    Dhar Subhra

    2003-01-01

    Full Text Available In the present study, skin biopsies in suspected cases of deep fungal infections were subjected to H &E and special stainings. In 2 of the 5 cases of sporotrichosis and in both cases of chromomycosis and of histoplasmosis, PAS positive fungal elements could be demonstrated. In both the cases of histoplasmosis, the fungi were also demonstrated by GMS staining. In 3 cases of sporotrichosis, 2 cases of mycetoma and 3 cases of subcutaneous phycomycosis, fungus could not be demonstrated by PAS staining. However, the histopathological features were corroborative.

  1. Vimentin may reflect areas of pathologic involvement in biopsies from patients with autoimmune skin diseases

    Directory of Open Access Journals (Sweden)

    Ana Maria Abreu Velez

    2014-04-01

    Full Text Available Introduction: Autoimmune bullous skin diseases (ABDs represent a group of disorders of the skin and mucosa commonly associated with deposits of immunoglobulins, complement and fibrinogen, and usually directed against distinct adhesion molecules. After studing these diseases for many years, we noted alterations not only between the cells junctions of the epidermis and/or the dermal/epidermal junction, but also in dermal skin appendageal structures and in mesenchymal tissue around the blisters. Based on our findings, we wanted to determine if the observed patterns of autoimmunity correlated with cutaneous vimentin expression. Materials and Methods: Archival biopsies previously diagnosed with ABDs by clinical, hematoxylin and eosin (H&E and direct and/or immunofluorescence data were stained with antibodies directed against vimentin via immunohistochemistry (IHC. We tested 30 patients affected by endemic pemphigus, 30 controls from the endemic area, and 15 normal controls. We also tested 30 biopsies from patients with bullous pemphigoid (BP, 20 with pemphigus vulgaris (PV, 8 with pemphigus foliaceus, 14 with dermatitis herpetiformis (DH and 3 with Senear-Usher syndrome. Results: The H&E, DIF and vimentin patterns of positivity in the different ABDs confirmed that vimentin was compartmentalized around areas of dermal inflammation, around skin appendages and in epidermal, dermal and mesenchymal cell junction areas. Conclusion: Vimentin may be a useful tool for highlighting patterns of microenvironmental tissue alteration in multiple ABDs. The vimentin staining pattern observed was analogous to that we have previously described for proteases and protease inhibitors in patients affected by ABDs, expanding the concept that the autoimmune process extends beyond cell junctions.

  2. Diagnostic accuracy of morphologic identification of filamentous fungi in paraffin embedded tissue sections: Correlation of histological and culture diagnosis

    Directory of Open Access Journals (Sweden)

    Sundaram Challa

    2014-01-01

    Full Text Available Aims and Objectives: The aim was to investigate the correlation between histological and culture diagnosis of filamentous fungi. Materials and Methods: Tissue sections from biopsy samples stained with Hematoxylin and Eosin and special stains from samples of chronic invasive/noninvasive sinusitis and intracranial space occupying lesions during 2005-2011 diagnosed to have infection due to filamentous fungi were reviewed. The histopathology and culture diagnoses were analyzed for correlation and discrepancy. Results: There were 125 samples positive for filamentous fungi on biopsy. Of these 76 (60.8% were submitted for culture and fungi grew in 30 (39.97% samples. There was a positive correlation between histological and culture diagnosis in 25 (83.33% samples that included Aspergillus species (16/19, Zygomycetes species (8/10 and dematiaceous fungi (1/1. The negative yield of fungi was more in Zygomycetes species (20/30 when compared to Aspergillus species (25/44. There was a discrepancy in diagnosis in 5/30 (16.67% samples which included probable dual infection in two, and dematiaceous fungi being interpreted as Aspergillus species in three samples. Conclusion: Histopathology plays a major role in the diagnosis of infection due to filamentous fungi, especially when cultures are not submitted or negative. The discrepancy between histological and culture diagnosis was either due to dematiaceous fungi being interpreted as Aspergillus species or probable dual infection.

  3. Improved method for extraction and detection of Helicobacter pylori DNA in formalin-fixed paraffin embedded gastric biopsies using laser micro-dissection

    Directory of Open Access Journals (Sweden)

    María Fernanda Loayza

    2015-01-01

    • The use of thin purification columns with 35 μL of elution buffer. The mean of DNA concentration obtained from 25 LM cut sections was 1.94± 0 .16 ng/μL, and it was efficiently amplified with qPCR in a Bio Rad iCycler instrument. The LM can improve the sample selection and DNA extraction for molecular analysis of H. pylori associated with human gastric epithelium.

  4. Comparison of microRNA expression using different preservation methods of matched psoriatic skin samples

    DEFF Research Database (Denmark)

    Løvendorf, Marianne B; Zibert, John R; Hagedorn, Peter H

    2012-01-01

    MicroRNAs are non-coding RNA molecules modulating gene expression post-transcriptionally. Formalin-fixed, paraffin-embedding (FFPE) is a standard preservation method often used in clinical practices, but induces RNA degradation. Extracting high-quality RNA from human skin can be challenging as skin...

  5. Evaluation of a panel of antibodies for the immunohistochemical identification of immune cells in paraffin-embedded lymphoid tissues of new- and old-world camelids.

    Science.gov (United States)

    Uhde, Ann-Kathrin; Lehmbecker, Annika; Baumgärtner, Wolfgang; Spitzbarth, Ingo

    2017-02-01

    Different species of camelids play an important role in the epidemiology of various emerging infectious diseases such as Middle East respiratory syndrome. For precise investigations of the immunopathogenesis in these host species, appropriate immunohistochemical markers are highly needed in order to phenotype distinct immune cells populations in camelids. So far, specific immunohistochemical markers for camelid immune cells are rarely commercially available, and cross-reactivity studies are restricted to the use of frozen dromedary tissues. To bridge this gap, 14 commercially available primary antibodies were tested for their suitability to demonstrate immune cell populations on formalin fixed paraffin-embedded (FFPE) tissue sections of dromedaries, Bactrian camels, llamas, and alpacas in the present study. Out of these, 9 antibodies directed against CD3, CD20, CD79α, HLA-DR, Iba-1, myeloid/histiocyte antigen, CD204, CD208, and CD68 antigen exhibited distinct immunoreaction patterns to certain camelid immune cell subsets. The distribution of these antigens was comparatively evaluated in different anatomical compartments of thymus, spleen, mesenteric, and tracheobronchial lymph nodes. The presented results will provide a basis for further investigations in camelids, especially with respect to the role of the immune response in certain infectious diseases, which harbor a considerable risk to spill over to other species. Copyright © 2017 Elsevier B.V. All rights reserved.

  6. The influence of DNA degradation in formalin-fixed, paraffin-embedded (FFPE) tissue on locus-specific methylation assessment by MS-HRM.

    Science.gov (United States)

    Daugaard, Iben; Kjeldsen, Tina E; Hager, Henrik; Hansen, Lise Lotte; Wojdacz, Tomasz K

    2015-12-01

    Readily accessible formalin-fixed paraffin embedded (FFPE) tissues are a highly valuable source of genetic material for molecular analyses in both research and in vitro diagnostics but frequently genetic material in those samples is highly degraded. With locus-specific methylation changes being widely investigated for use as biomarkers in various aspects of clinical disease management, we aimed to evaluate to what extent standard laboratory procedures can approximate the quality of the DNA extracted from FFPE samples prior to methylation analyses. DNA quality in 107 FFPE non-small cell lung cancer (NSCLC) samples was evaluated using spectrophotometry and gel electrophoresis. Subsequently, the quality assessment results were correlated with the results of locus specific methylation assessment with methylation sensitive high resolution melting (MS-HRM). The correlation of template quality with PCR amplification performance and HRM based methylation detection indicated a significant influence of DNA quality on PCR amplification but not on methylation assessment. In conclusion, standard laboratory procedures fairly well approximate DNA degradation of FFPE samples and DNA degradation does not seem to considerably affect locus-specific methylation assessment by MS-HRM. Copyright © 2015 Elsevier Inc. All rights reserved.

  7. Detection of c-myc amplification in formalin-fixed paraffin-embedded tumor tissue by chromogenic in situ hybridization (CISH).

    Science.gov (United States)

    Todorović-Raković, Nataša

    2013-01-01

    In situ hybridization (ISH) allows evaluation of genetic abnormalities, such as changes in chromosome number, chromosome translocations or gene amplifications, by hybridization of tagged DNA (or RNA) probes with complementary DNA (or RNA) sequences in interphase nuclei of target tissue. However, chromogenic in situ hybridization (CISH) is also applicable to formalin-fixed, paraffin-embedded (FFPE) tissues, besides metaphase chromosome spreads. CISH is similar to fluorescent in situ hybridization (FISH) regarding pretreatments and hybridization protocols but differs in the way of visualization. Indeed, CISH signal detection is similar to that used in immunohistochemistry, making use of a peroxidase-based chromogenic reaction instead of fluorescent dyes. In particular, tagged DNA probes are indirectly detected using an enzyme-conjugated antibody targeting the tags. The enzymatic reaction of the chromogenic substrate leads to the formation of strong permanent brown signals that can be visualized by bright-field microscopy at 40 × magnification. The advantage of CISH is that it allows the simultaneous observation of gene amplification and tissue morphology and the slides can be stored for a long time.

  8. Trypanosoma cruzi Necrotizing Meningoencephalitis in a Venezuelan HIV+-AIDS Patient: Pathological Diagnosis Confirmed by PCR Using Formalin-Fixed- and Paraffin-Embedded-Tissues

    Directory of Open Access Journals (Sweden)

    Marcello Salvatore Rossi Spadafora

    2014-01-01

    Full Text Available Coinfections with human immunodeficiency virus (HIV and infectious agents have been recognized since the early 90s. In the central nervous system (CNS of HIV+ patients, parasitic protozoans like Toxoplasma gondii have been described as responsible for the space occupying lesions (SOL developed. However, the involvement of Trypanosoma cruzi is also described but appears to be less frequent in acquired immunodeficiency syndrome (AIDS and transplant recipients, associated with necrotizing myocarditis and neurological symptoms related to the occurrence of necrotizing pseudotumoral encephalitis (NPE and meningoencephalitis (NME. The present work aims to present a Venezuelan case of NME associated with the coinfection of HIV and a T. cruzi-like trypanosomatid as well as its evolution and diagnosis by histopathological techniques, electron microscopy, and PCR methods using formalin-fixed- (FF- and paraffin-embedded- (PE- tissues. Postmortem cytological studies of leptomeninges imprints reveal the presence of trypomastigotes of Trypanosoma sp. Histopathological and electron microscopy studies allowed us to identify an amastigote stage and to reject the involvement of other opportunistic microorganisms as the etiological agent of the SOL. The definitive confirmation of T. cruzi as the etiological agent was achieved by PCR suggesting that the NME by T. cruzi was due to a reactivation of Chagas’ disease.

  9. A Comparison of Fresh Frozen vs. Formalin-Fixed, Paraffin-Embedded Specimens of Canine Mammary Tumors via Branched-DNA Assay

    Directory of Open Access Journals (Sweden)

    Florenza Lüder Ripoli

    2016-05-01

    Full Text Available Mammary neoplasms are the tumors most affecting female dogs and women. Formalin-fixed, paraffin-embedded (FFPE tissues are an invaluable source of archived biological material. Fresh frozen (FF tissue is considered ideal for gene expression analysis. However, strategies based on FFPE material offer several advantages. Branched-DNA assays permit a reliable and fast workflow when analyzing gene expression. The aim of this study was to assess the comparability of the branched-DNA assay when analyzing certain gene expression patterns between FF and FFPE samples in canine mammary tumors. RNA was isolated from 109 FFPE samples and from 93 FF samples of different canine mammary tissues. Sixteen (16 target genes (Tp53; Myc; HMGA1; Pik3ca; Mcl1; MAPK3; FOXO3; PTEN; GATA4; PFDN5; HMGB1; MAPK1; BRCA2; BRCA1; HMGA2; and Her2 were analyzed via branched-DNA assay (b-DNA. ACTB, GAPDH, and HPRT1 were used as data normalizers. Overall, the relative gene expression of the two different origins of samples showed an agreement of 63%. Still, care should be taken, as FFPE specimens showed lower expression of the analyzed targets when compared to FF samples. The fact that the gene expression in FFPE proved to be lower than in FF specimens is likely to have been caused by the effect of storage time. ACTB had the best performance as a data normalizer.

  10. Development of a monoclonal antibody that specifically detects tissue inhibitor of metalloproteinase-4 (TIMP-4) in formalin-fixed, paraffin-embedded human tissues.

    Science.gov (United States)

    Donover, P Scott; Wojciechowski, Brian S; Thirumaran, Rajesh; Zemba-Palko, Vlasta; Prendergast, George C; Wallon, U Margaretha

    2010-08-01

    Overexpression of the extracellular metalloproteinase inhibitor TIMP-4 in estrogen receptor-negative breast cancers was found recently to be associated with a poor prognosis for survival. To pursue exploration of the theranostic applications of TIMP-4, specific antibodies with favorable properties for immunohistochemical use and other clinical assays are needed. Here we report the characterization of a monoclonal antibody (clone 9:4-7) specific for full-length human TIMP-4 with suitable qualities. The antibody was determined to be an IgG(2b) immunoglobulin. In enzyme-linked immunosorbent assay (ELISA) and immunoblotting assays, it did not exhibit any detectable crossreactivity with recombinant forms of the other human TIMPs 1, 2, and 3. In contrast, the antibody displayed high specificity and sensitivity for TIMP-4 including in formalin-fixed and paraffin-embedded specimens of human breast specimens. An analysis of tissue microarrays of human cancer and corresponding normal tissues revealed specific staining patterns with excellent signal-to-noise ratios. This study documents TIMP-4 monoclonal antibody clone 9:4-7 as an effective tool for preclinical and clinical investigations. Published 2010 Wiley-Liss, Inc.

  11. Trypanosoma cruzi Necrotizing Meningoencephalitis in a Venezuelan HIV+-AIDS Patient: Pathological Diagnosis Confirmed by PCR Using Formalin-Fixed- and Paraffin-Embedded-Tissues

    Science.gov (United States)

    Rossi Spadafora, Marcello Salvatore; Céspedes, Ghislaine; Romero, Sandra; Fuentes, Isabel; Boada-Sucre, Alpidio A.; Cañavate, Carmen; Flores-Chávez, María

    2014-01-01

    Coinfections with human immunodeficiency virus (HIV) and infectious agents have been recognized since the early 90s. In the central nervous system (CNS) of HIV+ patients, parasitic protozoans like Toxoplasma gondii have been described as responsible for the space occupying lesions (SOL) developed. However, the involvement of Trypanosoma cruzi is also described but appears to be less frequent in acquired immunodeficiency syndrome (AIDS) and transplant recipients, associated with necrotizing myocarditis and neurological symptoms related to the occurrence of necrotizing pseudotumoral encephalitis (NPE) and meningoencephalitis (NME). The present work aims to present a Venezuelan case of NME associated with the coinfection of HIV and a T. cruzi-like trypanosomatid as well as its evolution and diagnosis by histopathological techniques, electron microscopy, and PCR methods using formalin-fixed- (FF-) and paraffin-embedded- (PE-) tissues. Postmortem cytological studies of leptomeninges imprints reveal the presence of trypomastigotes of Trypanosoma sp. Histopathological and electron microscopy studies allowed us to identify an amastigote stage and to reject the involvement of other opportunistic microorganisms as the etiological agent of the SOL. The definitive confirmation of T. cruzi as the etiological agent was achieved by PCR suggesting that the NME by T. cruzi was due to a reactivation of Chagas' disease. PMID:25763312

  12. Pre-Analytical Considerations for Successful Next-Generation Sequencing (NGS: Challenges and Opportunities for Formalin-Fixed and Paraffin-Embedded Tumor Tissue (FFPE Samples

    Directory of Open Access Journals (Sweden)

    Gladys Arreaza

    2016-09-01

    Full Text Available In cancer drug discovery, it is important to investigate the genetic determinants of response or resistance to cancer therapy as well as factors that contribute to adverse events in the course of clinical trials. Despite the emergence of new technologies and the ability to measure more diverse analytes (e.g., circulating tumor cell (CTC, circulating tumor DNA (ctDNA, etc., tumor tissue is still the most common and reliable source for biomarker investigation. Because of its worldwide use and ability to preserve samples for many decades at ambient temperature, formalin-fixed, paraffin-embedded tumor tissue (FFPE is likely to be the preferred choice for tissue preservation in clinical practice for the foreseeable future. Multiple analyses are routinely performed on the same FFPE samples (such as Immunohistochemistry (IHC, in situ hybridization, RNAseq, DNAseq, TILseq, Methyl-Seq, etc.. Thus, specimen prioritization and optimization of the isolation of analytes is critical to ensure successful completion of each assay. FFPE is notorious for producing suboptimal DNA quality and low DNA yield. However, commercial vendors tend to request higher DNA sample mass than what is actually required for downstream assays, which restricts the breadth of biomarker work that can be performed. We evaluated multiple genomics service laboratories to assess the current state of NGS pre-analytical processing of FFPE. Significant differences in pre-analytical capabilities were observed. Key aspects are highlighted and recommendations are made to improve the current practice in translational research.

  13. Feasibility of using tissue microarray cores of paraffin-embedded breast cancer tissue for measurement of gene expression: a proof-of-concept study.

    Science.gov (United States)

    Drury, Suzanne; Salter, Janine; Baehner, Frederick L; Shak, Steven; Dowsett, Mitch

    2010-06-01

    To determine whether 0.6 mm cores of formalin-fixed paraffin-embedded (FFPE) tissue, as commonly used to construct immunohistochemical tissue microarrays, may be a valid alternative to tissue sections as source material for quantitative real-time PCR-based transcriptional profiling of breast cancer. Four matched 0.6 mm cores of invasive breast tumour and two 10 microm whole sections were taken from eight FFPE blocks. RNA was extracted and reverse transcribed, and TaqMan assays were performed on the 21 genes of the Oncotype DX Breast Cancer assay. Expression of the 16 recurrence-related genes was normalised to the set of five reference genes, and the recurrence score (RS) was calculated. RNA yield was lower from 0.6 mm cores than from 10 microm whole sections, but was still more than sufficient to perform the assay. RS and single gene data from cores were highly comparable with those from whole sections (RS p=0.005). Greater variability was seen between cores than between sections. FFPE sections are preferable to 0.6 mm cores for RNA profiling in order to maximise RNA yield and to allow for standard histopathological assessment. However, 0.6 mm cores are sufficient and would be appropriate to use for large cohort studies.

  14. A Comparison of RNA-Seq Results from Paired Formalin-Fixed Paraffin-Embedded and Fresh-Frozen Glioblastoma Tissue Samples.

    Directory of Open Access Journals (Sweden)

    Anna Esteve-Codina

    Full Text Available The molecular classification of glioblastoma (GBM based on gene expression might better explain outcome and response to treatment than clinical factors. Whole transcriptome sequencing using next-generation sequencing platforms is rapidly becoming accepted as a tool for measuring gene expression for both research and clinical use. Fresh frozen (FF tissue specimens of GBM are difficult to obtain since tumor tissue obtained at surgery is often scarce and necrotic and diagnosis is prioritized over freezing. After diagnosis, leftover tissue is usually stored as formalin-fixed paraffin-embedded (FFPE tissue. However, RNA from FFPE tissues is usually degraded, which could hamper gene expression analysis. We compared RNA-Seq data obtained from matched pairs of FF and FFPE GBM specimens. Only three FFPE out of eleven FFPE-FF matched samples yielded informative results. Several quality-control measurements showed that RNA from FFPE samples was highly degraded but maintained transcriptomic similarities to RNA from FF samples. Certain issues regarding mutation analysis and subtype prediction were detected. Nevertheless, our results suggest that RNA-Seq of FFPE GBM specimens provides reliable gene expression data that can be used in molecular studies of GBM if the RNA is sufficiently preserved.

  15. Numerical and structural genomic aberrations are reliably detectable in tissue microarrays of formalin-fixed paraffin-embedded tumor samples by fluorescence in-situ hybridization.

    Directory of Open Access Journals (Sweden)

    Heike Horn

    Full Text Available Few data are available regarding the reliability of fluorescence in-situ hybridization (FISH, especially for chromosomal deletions, in high-throughput settings using tissue microarrays (TMAs. We performed a comprehensive FISH study for the detection of chromosomal translocations and deletions in formalin-fixed and paraffin-embedded (FFPE tumor specimens arranged in TMA format. We analyzed 46 B-cell lymphoma (B-NHL specimens with known karyotypes for translocations of IGH-, BCL2-, BCL6- and MYC-genes. Locus-specific DNA probes were used for the detection of deletions in chromosome bands 6q21 and 9p21 in 62 follicular lymphomas (FL and six malignant mesothelioma (MM samples, respectively. To test for aberrant signals generated by truncation of nuclei following sectioning of FFPE tissue samples, cell line dilutions with 9p21-deletions were embedded into paraffin blocks. The overall TMA hybridization efficiency was 94%. FISH results regarding translocations matched karyotyping data in 93%. As for chromosomal deletions, sectioning artefacts occurred in 17% to 25% of cells, suggesting that the proportion of cells showing deletions should exceed 25% to be reliably detectable. In conclusion, FISH represents a robust tool for the detection of structural as well as numerical aberrations in FFPE tissue samples in a TMA-based high-throughput setting, when rigorous cut-off values and appropriate controls are maintained, and, of note, was superior to quantitative PCR approaches.

  16. A rapid technique for analysis of formalin-fixed, paraffin-embedded tissues by fluorescent in situ hybridization with alpha-satellite probes

    Directory of Open Access Journals (Sweden)

    Nilce Barril

    1998-12-01

    Full Text Available We describe a rapid procedure for preparing archival tissues for interphase FISH analysis. The present protocol differs from others previously described because it allows the obtention of nuclei in satisfactory number and quality without using special equipments, adhesive-treated slides or solutions for chromatin decondensation. The method is of low cost and useful for retrospective analyses of formalin-fixed, paraffin-embedded samples.Descrevemos aqui um procedimento rápido para obtenção de núcleos interfásicos a partir de amostras arquivadas que podem ser utilizados para análise citogenética através da técnica de FISH. Este procedimento difere de outros previamente descritos porque permite a obtenção de núcleos em número e qualidade satisfatórios sem a utilização de equipamentos ou lâminas especiais e soluções para descondensação da cromatina. O método é de baixo custo e possibilita estudos retrospectivos de tecidos fixados em formol e emblocados em parafina.

  17. Utility of the Roche Cobas 4800 for detection of high-risk human papillomavirus in formalin-fixed paraffin-embedded oropharyngeal squamous cell carcinoma.

    Science.gov (United States)

    Pettus, Jason R; Wilson, Terri L; Steinmetz, Heather B; Lefferts, Joel A; Tafe, Laura J

    2017-02-01

    Clinical laboratories are expected to reliably identify human papilloma virus (HPV) associated oropharyngeal squamous cell carcinoma (OPSCC) for prognostic and potential therapeutic applications. In addition to surrogate p16 immunohistochemistry (IHC) testing, DNA-based HPV-specific testing strategies are widely utilized. Recognizing the efficiency of the Roche Cobas 4800 platform for testing gynecological cytology specimens for high-risk HPV, we elected to evaluate the potential utility of this platform for testing formalin-fixed paraffin-embedded (FFPE) OPSCC tissue. Using the Roche Linear Array assay for comparison, we tested twenty-eight samples (16 primary OPSCC, 2 lymph node metastases from primary OPSCC, 1 oral tongue carcinoma, 3 benign squamous papillomas, and 3 non-oropharyngeal carcinoma tissues). Excluding two invalid results, the Roche Cobas 4800 testing resulted in excellent inter-assay concordance (25/26, 96.2%) and 100% concordance for HPV-16/HPV-18 positive samples. This data suggests that the Roche Cobas 4800 platform may be a cost-effective method for testing OPSCC FFPE tissues in a clinical molecular pathology laboratory setting. Copyright © 2016 Elsevier Inc. All rights reserved.

  18. PCR-based clonality analysis of B-cell lymphomas in paraffin-embedded tissues: diagnostic value of immunoglobulin kappa and lambda light chain gene rearrangement investigation.

    Science.gov (United States)

    Amara, Khaled; Trimeche, Mounir; Ziadi, Sonia; Sriha, Badreddine; Mokni, Moncef; Korbi, Sadok

    2006-01-01

    Polymerase chain reaction (PCR)-based analysis, employed for detecting immunoglobulin heavy chain (IgH) gene rearrangements, has become a diagnostic tool widely used in the investigation of B-cell lymphomas, but the overall sensitivity of these methods does not exceed 80%, notably in germinal center (GC) and post-GC B-cell origin lymphomas. Many PCR strategies devised for detecting immunoglobulin light chain (IgL) gene rearrangements have been developed to enhance the clonality detection rates. However, the feasibility of these methods in routine clinical diagnosis using paraffin-embedded tissues has not yet been investigated sufficiently. We studied a large series of 108 cases of B-cell lymphomas, as well as 20 reactive lymphoid tissues using degenerate primers to amplify immunoglobulin kappa (Igkappa) and lambda (Iglambda) light chain genes. B-cell clonality was further investigated using semi-nested PCR for IgH gene rearrangements. B-cell clonality was detected in 74%, 56.5%, and 43.5% of cases using IgH, Igkappa, and Iglambda PCR, respectively. By combining these methods, the clonality detection rate increased to 93.5%. Only polyclonal patterns were noted in reactive lymphoid samples. We concluded that in addition to the established methods for IgH analysis, a PCR-based approach for IgL gene rearrangements analysis improves the clonality detection rate in over 90% of B-cell lymphoma cases using routine histological specimens with poor preservation of the genomic DNA.

  19. Determination of the cell tropism of serotype 1 feline infectious peritonitis virus using the spike affinity histochemistry in paraffin-embedded tissues.

    Science.gov (United States)

    Cham, Tat-Chuan; Chang, Yen-Chen; Tsai, Pei-Shiue; Wu, Ching-Ho; Chen, Hui-Wen; Jeng, Chian-Ren; Pang, Victor Fei; Chang, Hui-Wen

    2017-08-01

    Unlike for serotype II feline coronaviruses (FCoV II), the cellular receptor for serotype I FCoV (FCoV I), the most prevalent FCoV serotype, is unknown. To provide a platform for assessing the pattern by which FCoV I attaches to its host receptor(s), HEK293 cell lines that stably express the ectodomains of the spike (S) proteins derived from a FCoV I feline enteric coronavirus strain UU7 (FECV UU7) and a feline infectious peritonitis virus strain UU4 (FIPV UU4) were established. Using the recombinant S proteins as probes to perform S protein affinity histochemistry in paraffin-embedded tissues, although no tissue or enteric binding of FECV UU7 S protein was detected, it was found that by immunohistochemistry that the tissue distribution of FIPV UU4 S protein-bound cells correlated with that of FIPV antigen-positive cells and lesions associated with FIP and that the affinity binding of FIPV UU4 S protein on macrophages was not affected by enzymatic removal of host cell-surface sialic acid with neuraminidase. These findings suggest that a factor(s) other than sialic acid contribute(s) to the macrophage tropism of FIPV strain UU4. This approach allowed obtaining more information about both virus-host cell interactions and the biological characteristics of the unidentified cellular receptor for FCoV I. © 2017 The Societies and John Wiley & Sons Australia, Ltd.

  20. Molecular glycopathology by capillary electrophoresis: Analysis of the N-glycome of formalin-fixed paraffin-embedded mouse tissue samples.

    Science.gov (United States)

    Donczo, Boglarka; Szarka, Mate; Tovari, Jozsef; Ostoros, Gyorgyi; Csanky, Eszter; Guttman, Andras

    2017-06-01

    Capillary electrophoresis with laser-induced fluorescence (CE-LIF) detection was used to analyze endoglycosidase released and fluorophore-labeled N-glycans from formalin-fixed paraffin-embedded (FFPE) mouse tissue samples of lung, brain, heart, spleen, liver, kidney and intestine. The FFPE samples were first deparaffinized followed by solubilization and glycoprotein retrieval. PNGase F mediated release of the N-linked oligosaccharides was followed by labeling with aminopyrene trisulfonate. After CE-LIF glycoprofiling of the FFPE mouse tissues, the N-glycan pool of the lung specimen was subject to further investigation by exoglycosidase array based carbohydrate sequencing. Structural assignment of the oligosaccharides was accomplished by the help of the GUcal software and the associated database, based on the mobility shifts after treatments with the corresponding exoglycosidase reaction mixtures. Sixteen major N-linked carbohydrate structures were sequenced from the mouse lung FFPE tissue glycome and identified, as high mannose (3) neutral biantennary (3) sialylated monoantennary (1) and sialylated bianennary (9) oligosaccharides. Two of these latter ones also possessed alpha(1-3) linked galactose residues. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. Label-free protein profiling of formalin-fixed paraffin-embedded (FFPE) heart tissue reveals immediate mitochondrial impairment after ionising radiation.

    Science.gov (United States)

    Azimzadeh, Omid; Scherthan, Harry; Yentrapalli, Ramesh; Barjaktarovic, Zarko; Ueffing, Marius; Conrad, Marcus; Neff, Frauke; Calzada-Wack, Julia; Aubele, Michaela; Buske, Christian; Atkinson, Michael J; Hauck, Stefanie M; Tapio, Soile

    2012-04-18

    Qualitative proteome profiling of formalin-fixed, paraffin-embedded (FFPE) tissue is advancing the field of clinical proteomics. However, quantitative proteome analysis of FFPE tissue is hampered by the lack of an efficient labelling method. The usage of conventional protein labelling on FFPE tissue has turned out to be inefficient. Classical labelling targets lysine residues that are blocked by the formalin treatment. The aim of this study was to establish a quantitative proteomics analysis of FFPE tissue by combining the label-free approach with optimised protein extraction and separation conditions. As a model system we used FFPE heart tissue of control and exposed C57BL/6 mice after total body irradiation using a gamma ray dose of 3 gray. We identified 32 deregulated proteins (p≤0.05) in irradiated hearts 24h after the exposure. The proteomics data were further evaluated and validated by bioinformatics and immunoblotting investigation. In good agreement with our previous results using fresh-frozen tissue, the analysis indicated radiation-induced alterations in three main biological pathways: respiratory chain, lipid metabolism and pyruvate metabolism. The label-free approach enables the quantitative measurement of radiation-induced alterations in FFPE tissue and facilitates retrospective biomarker identification using clinical archives. Copyright © 2012 Elsevier B.V. All rights reserved.

  2. MicroRNA expression in melanocytic nevi: the usefulness of formalin-fixed, paraffin-embedded material for miRNA microarray profiling.

    Science.gov (United States)

    Glud, Martin; Klausen, Mikkel; Gniadecki, Robert; Rossing, Maria; Hastrup, Nina; Nielsen, Finn C; Drzewiecki, Krzysztof T

    2009-05-01

    MicroRNAs (miRNAs) are small, noncoding RNA molecules that regulate cellular differentiation, proliferation, and apoptosis. MiRNAs are expressed in a developmentally regulated and tissue-specific manner. Aberrant expression may contribute to pathological processes such as cancer, and miRNA may therefore serve as biomarkers that may be useful in a clinical environment for diagnosis of various diseases. Most miRNA profiling studies have used fresh tissue samples. However, in some types of cancer, including malignant melanoma, fresh material is difficult to obtain from primary tumors, and most surgical specimens are formalin fixed and paraffin embedded (FFPE). To explore whether FFPE material would be suitable for miRNA profiling in melanocytic lesions, we compared miRNA expression patterns in FFPE versus fresh frozen samples, obtained from 15 human melanocytic nevi. Out of microarray data, we identified 84 miRNAs that were expressed in both types of samples and represented an miRNA profile of melanocytic nevi. Our results showed a high correlation in miRNA expression (Spearman r-value of 0.80) between paired FFPE and fresh frozen material. The data were further validated by quantitative RT-PCR. In conclusion, FFPE specimens of melanocytic lesions are suitable as a source for miRNA microarray profiling.

  3. Characterization of a Novel Anti-Human HB-EGF Monoclonal Antibody Applicable for Paraffin-Embedded Tissues and Diagnosis of HB-EGF-Related Cancers.

    Science.gov (United States)

    Iwamoto, Ryo; Takagi, Mika; Akatsuka, Jun-Ichi; Ono, Ken-Ichiro; Kishi, Yoshiro; Mekada, Eisuke

    2016-04-01

    Heparin-binding EGF-like growth factor (HB-EGF) is a member of the EGF family of growth factors that bind to and activate the EGF receptor (EGFR/ErbB1) and ErbB4. HB-EGF plays pivotal roles in pathophysiological processes, including cancer. Thus, monoclonal antibodies (mAbs) for HB-EGF detection could be an important tool in the therapeutic diagnosis of HB-EGF-related cancers and other diseases. However, few mAbs, especially those applicable for immunohistochemistry (IHC), have been established to date. In this study, we generated a clone of hybridoma-derived mAb 2-108 by immunizing mice with recombinant human HB-EGF protein expressed by human cells. The mAb 2-108 specifically bound to human HB-EGF but not to mouse HB-EGF and was successful in immunoblotting, even under reducing conditions, immunoprecipitation, and immunofluorescence for unfixed as well as paraformaldehyde-fixed cells. Notably, this mAb was effective in IHC of paraffin-embedded tumor specimens. Epitope mapping analysis showed that mAb 2-108 recognized the N-terminal prodomain in HB-EGF. These results indicate that this new anti-HB-EGF mAb 2-108 would be useful in the diagnosis of HB-EGF-related cancers and would be a strong tool in both basic and clinical research on HB-EGF.

  4. MALDI imaging mass spectrometry profiling of N-glycans in formalin-fixed paraffin embedded clinical tissue blocks and tissue microarrays.

    Science.gov (United States)

    Powers, Thomas W; Neely, Benjamin A; Shao, Yuan; Tang, Huiyuan; Troyer, Dean A; Mehta, Anand S; Haab, Brian B; Drake, Richard R

    2014-01-01

    A recently developed matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI-IMS) method to spatially profile the location and distribution of multiple N-linked glycan species in frozen tissues has been extended and improved for the direct analysis of glycans in clinically derived formalin-fixed paraffin-embedded (FFPE) tissues. Formalin-fixed tissues from normal mouse kidney, human pancreatic and prostate cancers, and a human hepatocellular carcinoma tissue microarray were processed by antigen retrieval followed by on-tissue digestion with peptide N-glycosidase F. The released N-glycans were detected by MALDI-IMS analysis, and the structural composition of a subset of glycans could be verified directly by on-tissue collision-induced fragmentation. Other structural assignments were confirmed by off-tissue permethylation analysis combined with multiple database comparisons. Imaging of mouse kidney tissue sections demonstrates specific tissue distributions of major cellular N-linked glycoforms in the cortex and medulla. Differential tissue distribution of N-linked glycoforms was also observed in the other tissue types. The efficacy of using MALDI-IMS glycan profiling to distinguish tumor from non-tumor tissues in a tumor microarray format is also demonstrated. This MALDI-IMS workflow has the potential to be applied to any FFPE tissue block or tissue microarray to enable higher throughput analysis of the global changes in N-glycosylation associated with cancers.

  5. [Use of archival formalin-fixed, paraffin-embedded (FFPE) tissue samples for molecular genetic analysis in diffuse large B-cell lymphoma (DLBCL)].

    Science.gov (United States)

    Jarošová, Marie; Kučerová, Jana; Flodr, Patrik; Mikešová, Michaela; Procházka, Vít; Papajík, Tomáš

    2014-04-01

    The currently valid molecular genetic subclassification of patients with diffuse large B-cell lymphoma (DLBCL) into three prognostic subgroups based on expression profiling has been the objective of numerous genetic studies. In routine clinical practice, however, expression profiling technology remains unavailable for the most of centers. Apart from the technology, in some cases molecular genetic laboratories have problems obtaining high-quality material, i.e. fresh tissues, for RNA isolation to determine gene expression. One possibility is to determine the gene expression from RNA obtained by isolation from formalin-fixed, paraffin-embedded (FFPE) tissue. This pilot study aimed at isolating RNA from FFPE in patients diagnosed with DLBCL and verifying the potential use of such RNA for the expression analysis of 7 selected genes. Although the study showed that it is possible to isolate RNA and determine the expression of the selected genes from archival material, the values of relative expression of some genes in the set were too variable to be used for unambiguous prognostic classification. It was confirmed that retrospective analyses of selected genes may be performed with sufficient material obtained, and that properly archived blocks may be used for molecular biology analyses even after 8 years.

  6. Evaluation of positive Rift Valley fever virus formalin-fixed paraffin embedded samples as a source of sequence data for retrospective phylogenetic analysis.

    Science.gov (United States)

    Mubemba, B; Thompson, P N; Odendaal, L; Coetzee, P; Venter, E H

    2017-05-01

    Rift Valley fever (RVF), caused by an arthropod borne Phlebovirus in the family Bunyaviridae, is a haemorrhagic disease that affects ruminants and humans. Due to the zoonotic nature of the virus, a biosafety level 3 laboratory is required for isolation of the virus. Fresh and frozen samples are the preferred sample type for isolation and acquisition of sequence data. However, these samples are scarce in addition to posing a health risk to laboratory personnel. Archived formalin-fixed, paraffin-embedded (FFPE) tissue samples are safe and readily available, however FFPE derived RNA is in most cases degraded and cross-linked in peptide bonds and it is unknown whether the sample type would be suitable as reference material for retrospective phylogenetic studies. A RT-PCR assay targeting a 490 nt portion of the structural G N glycoprotein encoding gene of the RVFV M-segment was applied to total RNA extracted from archived RVFV positive FFPE samples. Several attempts to obtain target amplicons were unsuccessful. FFPE samples were then analysed using next generation sequencing (NGS), i.e. Truseq ® (Illumina) and sequenced on the Miseq ® genome analyser (Illumina). Using reference mapping, gapped virus sequence data of varying degrees of shallow depth was aligned to a reference sequence. However, the NGS did not yield long enough contigs that consistently covered the same genome regions in all samples to allow phylogenetic analysis. Copyright © 2017 Elsevier B.V. All rights reserved.

  7. Optimization and analysis of a quantitative real-time PCR-based technique to determine microRNA expression in formalin-fixed paraffin-embedded samples

    Directory of Open Access Journals (Sweden)

    Reis Patricia P

    2010-06-01

    Full Text Available Abstract Background MicroRNAs (miRs are non-coding RNA molecules involved in post-transcriptional regulation, with diverse functions in tissue development, differentiation, cell proliferation and apoptosis. miRs may be less prone to degradation during formalin fixation, facilitating miR expression studies in formalin-fixed paraffin-embedded (FFPE tissue. Results Our study demonstrates that the TaqMan Human MicroRNA Array v1.0 (Early Access platform is suitable for miR expression analysis in FFPE tissue with a high reproducibility (correlation coefficients of 0.95 between duplicates, p 35, we show that reproducibility between technical replicates, equivalent dilutions, and FFPE vs. frozen samples is best in the high abundance stratum. We also demonstrate that the miR expression profiles of FFPE samples are comparable to those of fresh-frozen samples, with a correlation of up to 0.87 (p Conclusion Our study thus demonstrates the utility, reproducibility, and optimization steps needed in miR expression studies using FFPE samples on a high-throughput quantitative PCR-based miR platform, opening up a realm of research possibilities for retrospective studies.

  8. Integrated and convenient procedure for protein extraction from formalin-fixed, paraffin-embedded tissues for LC-MS/MS analysis.

    Science.gov (United States)

    Lai, Xianyin; Schneider, Bryan P

    2014-11-01

    Because fresh-frozen tissue samples associated with long-term clinical data and of rare diseases are often unobtainable at the present time, formalin-fixed paraffin-embedded (FFPE) tissue samples are considered a highly valuable resource for researchers. However, protein extraction from FFPE tissues faces challenges of deparaffinization and cross-link reversion. Current procedures for protein extraction from FFPE tissue require separate steps and toxic solvents, resulting in inconvenience in protein extraction. To overcome these limitations, an integrated method was developed using nontoxic solvents in four types of FFPE tissues. The average amount of proteins from three replicates of bladder, kidney, liver, and lung FFPE tissues were 442.6, 728.9, 736.4, and 694.7 μg with CVs of 7.5, 5.8, 2.4, and 4.5%, respectively. Proteomic analysis showed that 348, 417, 607, and 304 unique proteins were identified and quantified without specification of isoform by a least two peptides from bladder, kidney, liver, and lung FFPE tissue samples, respectively. The analysis of individual protein CV demonstrated that 97-99% of the proteins were quantified with a CV ≤ 30%, verifying the reproducibility of the integrated protein extraction method. In summary, the developed method is high-yield, reproducible, convenient, simple, low cost, nonvolatile, nonflammable, and nontoxic. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. Gene Expression Analysis of Immunostained Endothelial Cells Isolated from Formaldehyde-fixated Paraffin Embedded Tumors Using Laser Capture Microdissection – a Technical Report

    Science.gov (United States)

    Kaneko, Tomoatsu; Okiji, Takashi; Kaneko, Reika; Suda, Hideaki; Nör, Jacques E.

    2009-01-01

    Laser capture microdissection (LCM) allows microscopic procurement of specific cell types from tissue sections that can then be used for gene expression analysis. In conventional LCM, frozen tissues stained with hematoxylin are normally used to the molecular analysis. Recent studies suggested that it is possible to carry out gene expression analysis of formaldehyde-fixated paraffin embedded (FFPE) tissues that were stained with hematoxylin. However, it is still unclear if quantitative gene expression analyses can be performed from LCM cells from FFPE tissues that were subjected to immunostaining to enhance identification of target cells. In this proof-of-principle study, we analyzed by RT-PCR and real time PCR the expression of genes in factor VIII immunostained human endothelial cells that were dissected from FFPE tissues by LCM. We observed that immunostaining should be performed at 4°C to preserve the mRNA from the cells. The expression of Bcl-2 in the endothelial cells was evaluated by RT-PCR and by real time PCR. GAPDH and 18S were used as house keeping genes for RT-PCR and real time PCR, respectively. This report unveils a method for quantitative gene expression analysis in cells that were identified by immunostaining and retrieved by LCM from FFPE tissues. This method is ideally suited for the analysis of relatively rare cell types within a tissue, and should improve on our ability to perform differential diagnosis of pathologies as compared to conventional LCM. PMID:19425073

  10. IN SITU IMMUNE RESPONSE EVALUATION VIA IMMUNOHISTOCHEMISTRY IN SKIN BIOPSIES FROM PATIENTS AFFECTED BY AUTOIMMUNE BLISTERING DISEASES

    Directory of Open Access Journals (Sweden)

    Ana Maria Abreu Velez

    2013-11-01

    Full Text Available Introduction: The in situ immune response in skin biopsies from patients affected by autoimmune skin blistering diseases (ABD is not well characterized. Aim: Our investigation attempts to immunophenotype cells in lesional skin in several ABD, utilizing immunohistochemistry (ICH. Methods: We tested by IHC for CD4, CD8, CD19, CD20, CD45, CD56/NCAM, PAX-5, granzyme B, myeloperoxidase, neutrophil elastase, LAT and ZAP-70 in patients affected by ABD. We tested 30 patients with endemic pemphigus foliaceus (EPF, 15 controls from the EPF endemic area, and 15 biopsies from healthy controls from the USA. We also tested archival biopsies from patients with selected ABD, including 30 patients with bullous pemphigoid, 20 with pemphigus vulgaris, 8 with pemphigus foliaceus and 14 with dermatitis herpetiformis. Results: We found a predominantly CD8 positive/CD45 positive T cell infiltrate in all ABD. Our skin biopsies demonstrated consistently positive staining for myeloperoxidase, but negative staining for neutrophil elastase. Most ABD biopsies displayed negative staining for CD4 and B cell markers; natural killer cell markers were also rarely seen. ZAP-70 and LAT were frequently detected. In El Bagre-EPF, a significant fragmentation of T cells in lesional skin was noted, as well as autoreactivity to lymph nodes. Conclusions: The documented T cell and myeloperoxidase staining are indicative of the role of T lymphocytes and neutrophils in lesional biopsies in patients with ABD, in addition to previously documented deposition of B cells, immunoglobulins and complement in situ. In El Bagre-EPF, T cells could also target lymph nodes; however, further studies are needed to confirm this possibility.

  11. Automated Extraction of Formalin-Fixed, Paraffin-Embedded Tissue for High-Risk Human Papillomavirus Testing of Head and Neck Squamous Cell Carcinomas Using the Roche Cobas 4800 System.

    Science.gov (United States)

    Kerr, Darcy A; Sweeney, Brenda; Arpin, Ronald N; Ring, Melissa; Pitman, Martha B; Wilbur, David C; Faquin, William C

    2016-08-01

    -Testing for high-risk human papillomavirus (HR-HPV) in head and neck squamous cell carcinomas (HNSCCs) is important for both prognostication and clinical management. Several testing platforms are available for HR-HPV; however, effective alternative automated approaches are needed. -To assess the performance of the automated Roche cobas 4800 HPV real-time polymerase chain reaction-based system on formalin-fixed, paraffin-embedded HNSCC specimens and compare results with standard methods of in situ hybridization (ISH) and p16 immunohistochemistry. -Formalin-fixed, paraffin-embedded samples of HNSCC were collected from archival specimens in the Department of Pathology, Massachusetts General Hospital (Boston), and prepared using the automated system by deparaffinization and dehydration followed by tissue lysis. Samples were integrated into routine cervical cytology testing runs by cobas. Corresponding formalin-fixed, paraffin-embedded samples were evaluated for HR-HPV by ISH and p16 by immunohistochemistry. Discrepant cases were adjudicated by polymerase chain reaction. -Sixty-two HNSCC samples were analyzed using the automated cobas system, ISH, and immunohistochemistry. Fifty-two percent (n = 32 of 62) of formalin-fixed, paraffin-embedded tumors were positive for HR-HPV by cobas. Eighty-eight percent (n = 28 of 32) of cases were the HPV 16 subtype and 12% (n = 4 of 32) were other HR-HPV subtypes. Corresponding testing with ISH was concordant in 92% (n = 57 of 62) of cases. Compared with the adjudication polymerase chain reaction standard, there were 3 false-positive cases by cobas. -Concordance in HNSCC HR-HPV status between cobas and ISH was more than 90%. The cobas demonstrated a sensitivity of 100% and a specificity of 91% for detection of HR-HPV. Advantages favoring cobas include its automation, cost efficiency, objective results, and ease of performance.

  12. Detection of a putative novel adenovirus by PCR amplification, sequencing and phylogenetic characterisation of two gene fragments from formalin-fixed paraffin-embedded tissues of a cat diagnosed with disseminated adenovirus disease.

    Science.gov (United States)

    Lakatos, Béla; Hornyák, Ákos; Demeter, Zoltán; Forgách, Petra; Kennedy, Frances; Rusvai, Miklós

    2017-12-01

    Adenoviral nucleic acid was detected by polymerase chain reaction (PCR) in formalin-fixed paraffin-embedded tissue samples of a cat that had suffered from disseminated adenovirus infection. The identity of the amplified products from the hexon and DNA-dependent DNA polymerase genes was confirmed by DNA sequencing. The sequences were clearly distinguishable from corresponding hexon and polymerase sequences of other mastadenoviruses, including human adenoviruses. These results suggest the possible existence of a distinct feline adenovirus.

  13. Immunohistochemical analysis of the distribution of desmoglein 1 and 2 in the skin of dogs and cats.

    Science.gov (United States)

    Miragliotta, Vincenzo; Coli, Alessandra; Ricciardi, Maria P; Podestà, Adriano; Abramo, Francesca

    2005-11-01

    To compare the distribution of desmoglein (Dsg) 1 and 2 in skin specimens obtained from dogs and cats to provide information about the possible role of the density of Dsg 1 and 2 in the localization of lesions attributable to pemphigus foliaceus in these 2 species. Skin biopsy specimens obtained from 4 dogs and 4 cats. Biopsy specimens were collected from the muzzle, bridge of the nose, ear, dorsum, abdomen, area adjacent to the teats, and footpads of each animal. Immunohistochemical analysis was performed on formalin-fixed, paraffin-embedded skin samples by use of a biotinylated mouse monoclonal anti-Dsg 1 and 2 antibody raised against bovine muzzle. Color development was performed by use of the streptavidin-biotin-peroxidase method with a chromogenic substrate. Immunohistochemical staining yielded a positive reaction in skin samples obtained from all anatomic sites. The intensity and distribution of staining were related to the number of layers of the stratum spinosum. No differences were detected between samples obtained from dogs and cats. No differences in intensity of Dsg 1 and 2 antigen were observed in the stratum spinosum between skin samples obtained from dogs and cats. Analysis of this result suggests that factors other than the distribution of Dsg may be responsible for the differences in localization of primary clinical lesions in dogs and cats with pemphigus foliaceus.

  14. Effects of a synthetic retinoid on skin structure, matrix metalloproteinases, and procollagen in healthy and high-risk subjects with diabetes.

    Science.gov (United States)

    Zeng, Wei; Tahrani, Abd; Shakher, Jayadave; Varani, James; Hughes, Sharon; Dubb, Kiran; Stevens, Martin J

    2011-01-01

    In diabetes, foot ulceration may result from increased skin fragility. Retinoids can reverse some diabetes-induced deficits of skin structure and function, but their clinical utility is limited by skin irritation. The effects of diabetes and MDI 301, a nonirritating synthetic retinoid, and retinoic acid have been evaluated on matrix metalloproteinases (MMPs), procollagen expression, and skin structure in skin biopsies from nondiabetic volunteers and diabetic subjects at risk of foot ulceration using organ culture techniques. Zymography and enzyme-linked immunosorbent assay were utilized for analysis of MMP-1, -2, and -9 and tissue inhibitor of metalloproteinase-1 (TIMP-1) and immunohistochemistry for type I procollagen protein abundance. Collagen structure parameters were assessed in formalin-fixed, paraffin-embedded tissue sections. The % of active MMP-1 and -9 was higher and TIMP-1 abundance was lower in subjects with diabetes. Type 1 procollagen abundance was reduced and skin structural deficits were increased in diabetes. Three μM MDI 301 reduced active MMP-1 and -9 abundance by 29% (P structural deficit scores. Two μM retinoic acid reduced MMP-1 but did not significantly affect skin structure. These data indicate that diabetic patients at risk of foot ulceration have deficits of skin structure and function. MDI 301 offers potential for repairing this skin damage complicating diabetes. Copyright © 2011 Elsevier Inc. All rights reserved.

  15. Nerve fibre studies in skin biopsies in peripheral neuropathies. I. Immunohistochemical analysis of neuropeptides in diabetes mellitus

    DEFF Research Database (Denmark)

    Lindberger, M; Schröder, H D; Schultzberg, M

    1989-01-01

    Standardised skin biopsies followed by immunohistochemical examination for the presence of terminal nerve fibres reacting for neuropeptides substance P (SP) and calcitonin gene-related peptide (CGRP) were evaluated. Healthy subjects regularly displayed free nerve endings of both fibre types in th...... a sensitive tool in evaluation of patients with peripheral neuropathies....

  16. Presence of non-fibrillar amyloid beta protein in skin biopsies of Alzheimer's disease (AD), Down's syndrome and non-AD normal persons

    DEFF Research Database (Denmark)

    Wen, G Y; Wisniewski, H M; Blondal, H

    1994-01-01

    A total of 66 skin biopsies from persons with Alzheimer's disease (AD) or Down's syndrome (DS) and from persons without AD were used in this study. The age range was from 7 to 89 years. Positive immunoreactivity of skin biopsies to monoclonal antibody 4G8, which is reactive to amino acid residue 17...

  17. Sonographically-guided vacuum-assisted biopsy with digital mammography-guided skin marking of suspicious breast microcalcifications: comparison of outcomes with stereotactic biopsy in Asian women.

    Science.gov (United States)

    Hahn, Soo Yeon; Shin, Jung Hee; Han, Boo-Kyung; Ko, Eun Young

    2011-02-01

    Management of suspicious microcalcifications in very thin breasts is problematic. To evaluate whether sonographically-guided vacuum-assisted biopsy (USVAB) with digital mammography-guided skin marking (DM) for the diagnosis of breast microcalcifications is comparable to stereotactic-guided vacuum-assisted biopsy (SVAB) in Asian women with thin breasts. Retrospective review was performed for 263 consecutive suspicious microcalcification lesions in 261 women who underwent USVAB with DM or SVAB using a prone table between January 2004 and December 2007. SVAB was performed for 190 lesions and USVAB for 73 lesions. Biopsy results were correlated with surgical pathology or followed up for at least 12 months. The diagnostic outcomes of SVAB and USVAB to diagnose microcalcifications were compared. Of 263 lesions, 104 (40%) underwent surgery and 159 (60%) were followed up. SVAB and USVAB groups showed similar final categories or the extent of microcalcifications. US visible lesions were 57 (78%) of 73 at USVAB and 14 (10%) of 140 at SVAB. Of 57 US visible lesions at USVAB, 29 (51%) were not found in initial US but were detectable with the help of DM. Specimen radiographs were negative in 2.1% of lesions at SVAB and in 4.1% at USVAB (p=0.4008). The under-estimation rate and false-negative rate were similar in SVAB and USVAB. US with DM facilitates US visibility of microcalcifications. USVAB with DM can produce acceptable biopsy results, as can SVAB, to diagnose breast microcalcifications in patients with thin breasts.

  18. Detection of SYT-SSX mutant transcripts in formalin-fixed paraffin-embedded sarcoma tissues using one-step reverse transcriptase real-time PCR.

    Science.gov (United States)

    Norlelawati, A T; Mohd Danial, G; Nora, H; Nadia, O; Zatur Rawihah, K; Nor Zamzila, A; Naznin, M

    2016-04-01

    Synovial sarcoma (SS) is a rare cancer and accounts for 5-10% of adult soft tissue sarcomas. Making an accurate diagnosis is difficult due to the overlapping histological features of SS with other types of sarcomas and the non-specific immunohistochemistry profile findings. Molecular testing is thus considered necessary to confirm the diagnosis since more than 90% of SS cases carry the transcript of t(X;18)(p11.2;q11.2). The purpose of this study is to diagnose SS at molecular level by testing for t(X;18) fusion-transcript expression through One-step reverse transcriptase real-time Polymerase Chain Reaction (PCR). Formalin-fixed paraffin-embedded tissue blocks of 23 cases of soft tissue sarcomas, which included 5 and 8 cases reported as SS as the primary diagnosis and differential diagnosis respectively, were retrieved from the Department of Pathology, Tengku Ampuan Afzan Hospital, Kuantan, Pahang. RNA was purified from the tissue block sections and then subjected to One-step reverse transcriptase real-time PCR using sequence specific hydrolysis probes for simultaneous detection of either SYT-SSX1 or SYT-SSX2 fusion transcript. Of the 23 cases, 4 cases were found to be positive for SYT-SSX fusion transcript in which 2 were diagnosed as SS whereas in the 2 other cases, SS was the differential diagnosis. Three cases were excluded due to failure of both amplification assays SYT-SSX and control β-2-microglobulin. The remaining 16 cases were negative for the fusion transcript. This study has shown that the application of One-Step reverse transcriptase real time PCR for the detection SYT-SSX transcript is feasible as an aid in confirming the diagnosis of synovial sarcoma.

  19. A methodological study of genome-wide DNA methylation analyses using matched archival formalin-fixed paraffin embedded and fresh frozen breast tumors.

    Science.gov (United States)

    Espinal, Allyson C; Wang, Dan; Yan, Li; Liu, Song; Tang, Li; Hu, Qiang; Morrison, Carl D; Ambrosone, Christine B; Higgins, Michael J; Sucheston-Campbell, Lara E

    2017-02-28

    DNA from archival formalin-fixed and paraffin embedded (FFPE) tissue is an invaluable resource for genome-wide methylation studies although concerns about poor quality may limit its use. In this study, we compared DNA methylation profiles of breast tumors using DNA from fresh-frozen (FF) tissues and three types of matched FFPE samples. For 9/10 patients, correlation and unsupervised clustering analysis revealed that the FF and FFPE samples were consistently correlated with each other and clustered into distinct subgroups. Greater than 84% of the top 100 loci previously shown to differentiate ER+ and ER- tumors in FF tissues were also FFPE DML. Weighted Correlation Gene Network Analyses (WCGNA) grouped the DML loci into 16 modules in FF tissue, with ~85% of the module membership preserved across tissue types. Restored FFPE and matched FF samples were profiled using the Illumina Infinium HumanMethylation450K platform. Methylation levels (β-values) across all loci and the top 100 loci previously shown to differentiate tumors by estrogen receptor status (ER+ or ER-) in a larger FF study, were compared between matched FF and FFPE samples using Pearson's correlation, hierarchical clustering and WCGNA. Positive predictive values and sensitivity levels for detecting differentially methylated loci (DML) in FF samples were calculated in an independent FFPE cohort. FFPE breast tumors samples show lower overall detection of DMLs versus FF, however FFPE and FF DMLs compare favorably. These results support the emerging consensus that the 450K platform can be employed to investigate epigenetics in large sets of archival FFPE tissues.

  20. Enhancement of Pathologist's Routine Practice: Reuse of DNA Extracted from Immunostained Formalin-fixed Paraffin-embedded (FFPE) Slides in Downstream Molecular Analysis of Cancer.

    Science.gov (United States)

    Al-Attas, Asmaa; Assidi, Mourad; Al-Maghrabi, Jaudah; Dallol, Ashraf; Schulten, Hans-Juergen; Abu-Elmagd, Muhammad; Chaudhary, Adeel; Abuzenadah, Adel; Budowle, Bruce; Buhmeida, Abdelbaset; Al-Qahtani, Mohammed

    To date, the conventional formalin-fixed, paraffin-embedded (FFPE) technique is the gold-standard for preserving histomorphology. Once FFPE tissues are stained, slides are routinely archived along with their blocks at biobanks/hospitals. However, the reuse of fixed and stained biospecimens as DNA source is not a common routine practice worldwide and, thus, indicates the need of studies to investigate the feasibility of extracting DNA from already immunohistochemistry (IHC) FFPE-stained slides and its possible reuse in subsequent downstream molecular analyses. FFPE IHC slides from colorectal cancer (CRC) patients were prepared and stored in the CEGMR Biobank. The workflow consists of digitalization of IHC stained slide's image, removing the slide cover-slip, crude dissection and DNA extraction. Following DNA quality assessment, mutation analysis of CTNNB1 and methylation profile of CDH1 were performed. High-quality DNA was obtained allowing 60% concordance between CDH1 methylation and membranous E-cadherin expression pattern. Clean CTNNB1 DNA chromatograms with evenly-spaced peaks were observed. This study is a proof of concept to recycle and reuse DNA from IHC stained slides with suitable concentration and integrity for further downstream molecular applications. These findings will enhance the pathologists' knowledge, attitudes and practices (KAP) towards the use of these biospecimens and support the implementation of this approach in clinical pathology practice. Therefore, the scientific community will benefit from the largest comprehensive database of human fully annotated FFPE biospecimens already available at their disposal in order to demystify the complexity and the heterogeneity of many challenging diseases and foster the transition towards precision medicine. Copyright© 2016, International Institute of Anticancer Research (Dr. John G. Delinasios), All rights reserved.

  1. A simple and cost-effective method of DNA extraction from small formalin-fixed paraffin-embedded tissue for molecular oncologic testing.

    Science.gov (United States)

    Snow, Anthony N; Stence, Aaron A; Pruessner, Jonathan A; Bossler, Aaron D; Ma, Deqin

    2014-01-01

    Extraction of DNA from formalin-fixed, paraffin-embedded (FFPE) tissue is a critical step in molecular oncologic testing. As molecular oncology testing becomes more important for prognostic and therapeutic decision making and tissue specimens become smaller due to earlier detection of suspicious lesions and the use of fine needle aspiration methods for tissue collection, it becomes more challenging for the typical molecular pathology laboratory to obtain reliable test results. We developed a DNA extraction method to obtain sufficient quantity and high quality genomic DNA from limited FFPE tissue for molecular oncology testing using a combination of H&E stained slides, a matrix capture method and the Qiagen DNA column. THREE DNA EXTRACTION METHODS WERE COMPARED: our standard procedure of manually scraping tissue from unstained slides followed by DNA extraction using the QIAamp FFPE column (Qiagen, Valencia, CA), a glue capture method (Pinpoint Solution, Zymo Research Corp, Inc) on H&E stained slides followed by DNA extraction using either the QIAamp column or the column included with the Pinpoint kit (Zymo Research). The DNA extraction protocol was optimized. Statistical analysis was performed using the paired two-sample student's t-test. The combination of the matrix capture method with the QIAamp column gave an equivalent amount of DNA as our standard extraction method using the unstained slides and a 4.6-fold higher DNA yield than using the Zymo column included in the Pinpoint Slide Solution kit. Several molecular tests were performed and DNA purified using the new method gave the same results as for the previous methods. Using H&E stained slides allows visual confirmation of tumor cells during microdissection. The Pinpoint solution made removal of specific tissue from the slides easier and reduced the risk of contamination and tissue loss. This DNA extraction method is simple, cost-effective, and blends with our current workflow requiring no additional equipment.

  2. Genome-wide massively parallel sequencing of formaldehyde fixed-paraffin embedded (FFPE tumor tissues for copy-number- and mutation-analysis.

    Directory of Open Access Journals (Sweden)

    Michal R Schweiger

    Full Text Available BACKGROUND: Cancer re-sequencing programs rely on DNA isolated from fresh snap frozen tissues, the preparation of which is combined with additional preservation efforts. Tissue samples at pathology departments are routinely stored as formalin-fixed and paraffin-embedded (FFPE samples and their use would open up access to a variety of clinical trials. However, FFPE preparation is incompatible with many down-stream molecular biology techniques such as PCR based amplification methods and gene expression studies. METHODOLOGY/PRINCIPAL FINDINGS: Here we investigated the sample quality requirements of FFPE tissues for massively parallel short-read sequencing approaches. We evaluated key variables of pre-fixation, fixation related and post-fixation processes that occur in routine medical service (e.g. degree of autolysis, duration of fixation and of storage. We also investigated the influence of tissue storage time on sequencing quality by using material that was up to 18 years old. Finally, we analyzed normal and tumor breast tissues using the Sequencing by Synthesis technique (Illumina Genome Analyzer, Solexa to simultaneously localize genome-wide copy number alterations and to detect genomic variations such as substitutions and point-deletions and/or insertions in FFPE tissue samples. CONCLUSIONS/SIGNIFICANCE: The application of second generation sequencing techniques on small amounts of FFPE material opens up the possibility to analyze tissue samples which have been collected during routine clinical work as well as in the context of clinical trials. This is in particular important since FFPE samples are amply available from surgical tumor resections and histopathological diagnosis, and comprise tissue from precursor lesions, primary tumors, lymphogenic and/or hematogenic metastases. Large-scale studies using this tissue material will result in a better prediction of the prognosis of cancer patients and the early identification of patients which

  3. Chromosomal aberrations in bladder cancer: fresh versus formalin fixed paraffin embedded tissue and targeted FISH versus wide microarray-based CGH analysis.

    Directory of Open Access Journals (Sweden)

    Elena Panzeri

    Full Text Available Bladder carcinogenesis is believed to follow two alternative pathways driven by the loss of chromosome 9 and the gain of chromosome 7, albeit other nonrandom copy number alterations (CNAs were identified. However, confirmation studies are needed since many aspects of this model remain unclear and considerable heterogeneity among cases has emerged. One of the purposes of this study was to evaluate the performance of a targeted test (UroVysion assay widely used for the detection of Transitional Cell Carcinoma (TCC of the bladder, in two different types of material derived from the same tumor. We compared the results of UroVysion test performed on Freshly Isolated interphasic Nuclei (FIN and on Formalin Fixed Paraffin Embedded (FFPE tissues from 22 TCCs and we didn't find substantial differences. A second goal was to assess the concordance between array-CGH profiles and the targeted chromosomal profiles of UroVysion assay on an additional set of 10 TCCs, in order to evaluate whether UroVysion is an adequately sensitive method for the identification of selected aneuploidies and nonrandom CNAs in TCCs. Our results confirmed the importance of global genomic screening methods, that is array based CGH, to comprehensively determine the genomic profiles of large series of TCCs tumors. However, this technique has yet some limitations, such as not being able to detect low level mosaicism, or not detecting any change in the number of copies for a kind of compensatory effect due to the presence of high cellular heterogeneity. Thus, it is still advisable to use complementary techniques such as array-CGH and FISH, as the former is able to detect alterations at the genome level not excluding any chromosome, but the latter is able to maintain the individual data at the level of single cells, even if it focuses on few genomic regions.

  4. Measurement of gene expression in archival paraffin-embedded tissues: development and performance of a 92-gene reverse transcriptase-polymerase chain reaction assay.

    Science.gov (United States)

    Cronin, Maureen; Pho, Mylan; Dutta, Debjani; Stephans, James C; Shak, Steven; Kiefer, Michael C; Esteban, Jose M; Baker, Joffre B

    2004-01-01

    Throughout the last decade many laboratories have shown that mRNA levels in formalin-fixed and paraffin-embedded (FPE) tissue specimens can be quantified by reverse transcriptase-polymerase chain reaction (RT-PCR) techniques despite the extensive RNA fragmentation that occurs in tissues so preserved. We have developed RT-PCR methods that are sensitive, precise, and that have multianalyte capability for potential wide use in clinical research and diagnostic assays. Here it is shown that the extent of fragmentation of extracted FPE tissue RNA significantly increases with archive storage time. Probe and primer sets for RT-PCR assays based on amplicons that are both short and homogeneous in length enable effective reference gene-based data normalization for cross comparison of specimens that differ substantially in age. A 48-gene assay used to compare gene expression profiles from the same breast cancer tissue that had been either frozen or FPE showed very similar profiles after reference gene-based normalization. A 92-gene assay, using RNA extracted from three 10- micro m FPE sections of archival breast cancer specimens (dating from 1985 to 2001) yielded analyzable data for these genes in all 62 tested specimens. The results were substantially concordant when estrogen receptor, progesterone receptor, and HER2 receptor status determined by RT-PCR was compared with immunohistochemistry assays for these receptors. Furthermore, the results highlight the advantages of RT-PCR over immunohistochemistry with respect to quantitation and dynamic range. These findings support the development of RT-PCR analysis of FPE tissue RNA as a platform for multianalyte clinical diagnostic tests.

  5. RT-PCR amplification of RNA extracted from formalin-fixed, paraffin-embedded oral cancer sections: analysis of p53 pathway.

    Science.gov (United States)

    Tachibana, Masatsugu; Shinagawa, Yasuhiro; Kawamata, Hitoshi; Omotehara, Fumie; Horiuchi, Hideki; Ohkura, Yasuo; Kubota, Keiichi; Imai, Yutaka; Fujibayashi, Takashi; Fujimori, Takahiro

    2003-01-01

    We present a new approach towards the detection of the mRNAs in formalin-fixed, paraffin-embedded samples using a reverse transcriptase (RT)-polymerase chain reaction (PCR). The total RNAs were extracted from 10-micron-thick sections and were reverse-transcribed, then the RT-products were subjected to PCR amplification of GAPDH mRNA for screening the mRNA degradation. Next, nested PCR was performed for examining the expression of p53-related genes, p21WAF1, MDM2, p33ING1 and p14ARF. GAPDH mRNA expression was detectable in 12 out of 21 oral squamous cell carcinoma (SCC) samples. p21WAF1 mRNA expression was detectable in 5 out of 12 SCC samples, MDM2 mRNA expression was detectable in 5 our of 12 SCC samples and p33ING1 mRNA expression was detectable in 6 out of 12 SCC samples. However, the expression of p14ARF mRNA was not detectable in any of the samples. Seven out of 12 oral SCC samples showed abnormal nuclear accumulation of p53 protein by immunohistochemical staining, whereas 5 out of 12 oral SCCs showed negative staining for p53 protein. Of of p33ING1 mRNA. One of these was a verrucous carcinoma in which the p53 gene products might be inactivated by the oncoprotein E6 of human papilloma virus. Thus, the p53 tumor suppressor pathway was disrupted in most oral SCCs at the cellular levels, due to either an abnormality in p53 itself or loss of expression of p53 regulatory factors. This method would assist in making diagnosis, determining therapeutic strategy and predicting the prognosis of various cancers including oral SCCs.

  6. High Quality Genomic Copy Number Data from Archival Formalin-Fixed Paraffin-Embedded Leiomyosarcoma: Optimisation of Universal Linkage System Labelling

    Science.gov (United States)

    Salawu, Abdulazeez; Ul-Hassan, Aliya; Hammond, David; Fernando, Malee; Reed, Malcolm; Sisley, Karen

    2012-01-01

    Most soft tissue sarcomas are characterized by genetic instability and frequent genomic copy number aberrations that are not subtype-specific. Oligonucleotide microarray-based Comparative Genomic Hybridisation (array CGH) is an important technique used to map genome-wide copy number aberrations, but the traditional requirement for high-quality DNA typically obtained from fresh tissue has limited its use in sarcomas. Although large archives of Formalin-fixed Paraffin-embedded (FFPE) tumour samples are available for research, the degradative effects of formalin on DNA from these tissues has made labelling and analysis by array CGH technically challenging. The Universal Linkage System (ULS) may be used for a one-step chemical labelling of such degraded DNA. We have optimised the ULS labelling protocol to perform aCGH on archived FFPE leiomyosarcoma tissues using the 180k Agilent platform. Preservation age of samples ranged from a few months to seventeen years and the DNA showed a wide range of degradation (when visualised on agarose gels). Consistently high DNA labelling efficiency and low microarray probe-to-probe variation (as measured by the derivative log ratio spread) was seen. Comparison of paired fresh and FFPE samples from identical tumours showed good correlation of CNAs detected. Furthermore, the ability to macro-dissect FFPE samples permitted the detection of CNAs that were masked in fresh tissue. Aberrations were visually confirmed using Fluorescence in situ Hybridisation. These results suggest that archival FFPE tissue, with its relative abundance and attendant clinical data may be used for effective mapping for genomic copy number aberrations in such rare tumours as leiomyosarcoma and potentially unravel clues to tumour origins, progression and ultimately, targeted treatment. PMID:23209738

  7. Revealing the Molecular Portrait of Triple Negative Breast Tumors in an Understudied Population through Omics Analysis of Formalin-Fixed and Paraffin-Embedded Tissues.

    Science.gov (United States)

    Vaca-Paniagua, Felipe; Alvarez-Gomez, Rosa María; Maldonado-Martínez, Hector Aquiles; Pérez-Plasencia, Carlos; Fragoso-Ontiveros, Veronica; Lasa-Gonsebatt, Federico; Herrera, Luis Alonso; Cantú, David; Bargallo-Rocha, Enrique; Mohar, Alejandro; Durand, Geoffroy; Forey, Nathalie; Voegele, Catherine; Vallée, Maxime; Le Calvez-Kelm, Florence; McKay, James; Ardin, Maude; Villar, Stéphanie; Zavadil, Jiri; Olivier, Magali

    2015-01-01

    Triple negative breast cancer (TNBC), defined by the lack of expression of the estrogen receptor, progesterone receptor and human epidermal receptor 2, is an aggressive form of breast cancer that is more prevalent in certain populations, in particular in low- and middle-income regions. The detailed molecular features of TNBC in these regions remain unexplored as samples are mostly accessible as formalin-fixed paraffin embedded (FFPE) archived tissues, a challenging material for advanced genomic and transcriptomic studies. Using dedicated reagents and analysis pipelines, we performed whole exome sequencing and miRNA and mRNA profiling of 12 FFPE tumor tissues collected from pathological archives in Mexico. Sequencing analyses of the tumor tissues and their blood pairs identified TP53 and RB1 genes as the most frequently mutated genes, with a somatic mutation load of 1.7 mutations/exome Mb on average. Transcriptional analyses revealed an overexpression of growth-promoting signals (EGFR, PDGFR, VEGF, PIK3CA, FOXM1), a repression of cell cycle control pathways (TP53, RB1), a deregulation of DNA-repair pathways, and alterations in epigenetic modifiers through miRNA:mRNA network de-regulation. The molecular programs identified were typical of those described in basal-like tumors in other populations. This work demonstrates the feasibility of using archived clinical samples for advanced integrated genomics analyses. It thus opens up opportunities for investigating molecular features of tumors from regions where only FFPE tissues are available, allowing retrospective studies on the search for treatment strategies or on the exploration of the geographic diversity of breast cancer.

  8. Detection of mucormycetes and other pathogenic fungi in formalin fixed paraffin embedded and fresh tissues using the extended region of 28S rDNA.

    Science.gov (United States)

    Gade, Lalitha; Hurst, Steven; Balajee, S Arunmozhi; Lockhart, Shawn R; Litvintseva, Anastasia P

    2017-06-01

    Molecular methods of detection based on DNA-sequencing of the internal transcribed spacer 1 and 2 (ITS1 and ITS2) or 5΄ end region of 28S (D1-D2 region) of ribosomal RNA gene (rDNA) have been used extensively for molecular identification and detection of fungal infections. However, these regions are not always informative for identification of mucormycetes and other rare fungal pathogens as they often contain large introns, heterogenic regions, and/or cannot be PCR-amplified using broad range fungal PCR primers. In addition, because of the difficulties of recovering intact fungal DNA from human specimens, smaller regions of DNA are more useful for the direct detection of fungal DNA in tissues and fluids. In this study, we investigated the utility of 12F/13R PCR primers targeting a 200-230 bp region of the extended 28S region of rDNA for molecular identification of fungal DNA in formalin fixed paraffin embedded tissues and other clinical specimens. We demonstrated that this region can be successfully used for identification of all genera and some species of clinically relevant mucormycetes, as well as other medically important fungi, such as Aspergillus, Fusarium, Coccidioides, and Cryptococcus. We also demonstrated that PCR amplification and direct sequencing of the extended 28S region of rDNA was more sensitive compared to targeting the ITS2 region, as we were able to detect and identify mucormycetes and other fungal pathogens in tissues from patients with histopathological and/or culture evidence of fungal infections that were negative with PCR using ITS-specific primers. Published by Oxford University Press on behalf of The International Society for Human and Animal Mycology 2016. This work is written by (a) US Government employee(s) and is in the public domain in the US.

  9. Technical reproducibility of single-nucleotide and size-based DNA biomarker assessment using DNA extracted from formalin-fixed, paraffin-embedded tissues.

    Science.gov (United States)

    Zhang, Shenli; Tan, Iain B; Sapari, Nur S; Grabsch, Heike I; Okines, Alicia; Smyth, Elizabeth C; Aoyama, Toru; Hewitt, Lindsay C; Inam, Imran; Bottomley, Dan; Nankivell, Matthew; Stenning, Sally P; Cunningham, David; Wotherspoon, Andrew; Tsuburaya, Akira; Yoshikawa, Takaki; Soong, Richie; Tan, Patrick

    2015-05-01

    DNA extracted from formalin-fixed, paraffin-embedded (FFPE) tissues has been used in the past to analyze genetic polymorphisms. We evaluated the technical reproducibility of different types of assays for gene polymorphisms using DNA extracted from FFPE material. By using the MassARRAY iPLEX system, we investigated polymorphisms in DPYD (rs1801159 and rs3918290), UMPS (rs1801019), ERCC1 (rs11615), ERCC1 (rs3212986), and ERCC2 (rs13181) in 56 FFPE DNA samples. By using PCR, followed by size-based gel electrophoresis, we also examined TYMS 5' untranslated region 2R/3R repeats and GSTT1 deletions in 50 FFPE DNA samples and 34 DNAs extracted from fresh-frozen tissues and cell lines. Each polymorphism was analyzed by two independent runs. We found that iPLEX biomarker assays measuring single-nucleotide polymorphisms provided consistent concordant results. However, by using FFPE DNA, size-based PCR biomarkers (GSTT1 and TYMS 5' untranslated region) were discrepant in 32.7% (16/49, with exact 95% CI, 19.9%-47.5%; exact binomial confidence limit test) and 4.2% (2/48, with exact 95% CI, 0.5%-14.3%) of cases, respectively, whereas no discrepancies were observed using intact genomic DNA. Our findings suggest that DNA from FFPE material can be used to reliably test single-nucleotide polymorphisms. However, results based on size-based PCR biomarkers, and particularly GSTT1 deletions, using FFPE DNA need to be interpreted with caution. Independent repeated assays should be performed on all cases to assess potential discrepancies. Copyright © 2015 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

  10. Simulators of Squamous Cell Carcinoma of the Skin: Diagnostic Challenges on Small Biopsies and Clinico pathological Correlation

    International Nuclear Information System (INIS)

    Tan, K. B.; Tan, S. H.; Lee, Y. S.; Wee Aw, D. C.; Jaffar, H.; Lim, T. C.; Lee, S. J.

    2013-01-01

    Squamous cell carcinoma (SCC) is a common and important primary cutaneous malignancy. On skin biopsies, SCC is characterized by significant squamous cell atypia, abnormal keratinisation, and invasive features. Diagnostic challenges may occasionally arise, especially in the setting of small punch biopsies or superficial shave biopsies, where only part of the lesion may be assessable by the pathologist. Benign mimics of SCC include pseudoepitheliomatous hyperplasia, eccrine squamous syringometaplasia, inverted follicular keratosis, and keratoacanthoma, while malignant mimics of SCC include basal cell carcinoma, melanoma, and metastatic carcinoma. The careful application of time-honored diagnostic criteria, close clinico pathological correlation and a selective request for a further, deeper, or wider biopsy remain the most useful strategies to clinch the correct diagnosis. This review aims to present the key differential diagnoses of SCC, to discuss common diagnostic pitfalls, and to recommend ways to deal with diagnostically challenging cases

  11. Increased expression of enhancer of Zeste Homolog 2 (EZH2) differentiates squamous cell carcinoma from normal skin and actinic keratosis.

    Science.gov (United States)

    Xie, Qiang; Wang, Hongbei; Heilman, Edward R; Walsh, Michael G; Haseeb, M A; Gupta, Raavi

    2014-01-01

    Enhancer of Zeste Homolog 2 (EZH2) is a polycomb group protein that has been shown to be involved in the progression of multiple human cancers including melanoma. The expression of EZH2 in normal skin and in pre-malignant and malignant cutaneous squamous cell carcinoma (SCC) has not been studied. We examined the expression of EZH2 in normal skin, actinic keratosis (AK), SCC in situ, well-differentiated (SCC-WD), moderately-differentiated (SCC-MD) and poorly-differentiated SCC (SCC-PD) to ascertain whether EZH2 expression differentiates these conditions. Immunohistochemical staining for EZH2 was performed on formalin-fixed paraffin-embedded biopsies and a tissue microarray containing normal skin, AK, SCC in situ, and SCC of different grades. In comparison to the normal skin, EZH2 expression in actinic keratosis was increased (p=0.03). Similarly, EZH2 expression in all of the neoplastic conditions studied (SCC in situ, SCC-WD, SCC-MD and SCC-PD) was greatly increased in comparison to both the normal skin and actinic keratosis (p≤0.001). EZH2 expression increases incrementally from normal skin to AK and further to SCC, suggesting a role for EZH2 in the progression and differentiation of SCC. EZH2 expression may be used as a diagnostic marker for differentiating SCC from AK or normal skin.

  12. Study to determine whether intraoperative frozen section biopsy improves surgical treatment of non-melanoma skin cancer.

    Science.gov (United States)

    Nicoletti, Giovanni; Brenta, Federica; Malovini, Alberto; Musumarra, Gaetano; Scevola, Silvia; Faga, Angela

    2013-03-01

    Skin cancers are the most common types of cancer and their incidence has shown an increase of ∼4 to 8% per year over the last 40 years. The majority of skin cancers (∼97%) are non-melanoma skin cancers, mainly represented by basal cell (80%) and squamous cell carcinomas (20%). The use of intra-operative frozen section remains controversial in the surgical treatment of non-melanoma skin cancer, being commonly considered an optional tool, the reliability and effectiveness of which remain questionable. A large retrospective study was conducted to examine 670 surgical excisions of non-melanoma skin cancers of the head and neck in 481 patients over a period of nine years, between May, 2002 and December, 2011, at the Plastic and Reconstructive Surgery Unit of the University of Pavia, Salvatore Maugeri Research and Care Institute, Pavia, Italy. Results demonstrated the paradoxical ineffectiveness of an intra-operative frozen section biopsy in pursuing higher rates of radical excision in non-melanoma skin cancers. Nevertheless, a more detailed analysis on the use of frozen sections focusing on the various anatomical sites of the body demonstrated a reverse trend in the eyelids and canthi, where a higher success rate (87.50 vs. 69.77%) in the surgical treatment of non-melanoma skin cancers was obtained with the use of an intra-operative frozen section biopsy. Results of the present study suggested that intra-operative frozen section biopsy be routinely used in the surgical treatment of nonmelanoma skin tumors involving the eyelids and canthi.

  13. Applying tattoo dye as a third-harmonic generation contrast agent for in vivo optical virtual biopsy of human skin

    Science.gov (United States)

    Tsai, Ming-Rung; Lin, Chen-Yu; Liao, Yi-Hua; Sun, Chi-Kuang

    2013-02-01

    Third-harmonic generation (THG) microscopy has been reported to provide intrinsic contrast in elastic fibers, cytoplasmic membrane, nucleus, actin filaments, lipid bodies, hemoglobin, and melanin in human skin. For advanced molecular imaging, exogenous contrast agents are developed for a higher structural or molecular specificity. We demonstrate the potential of the commonly adopted tattoo dye as a THG contrast agent for in vivo optical biopsy of human skin. Spectroscopy and microscopy experiments were performed on cultured cells with tattoo dyes, in tattooed mouse skin, and in tattooed human skin to demonstrate the THG enhancement effect. Compared with other absorbing dyes or nanoparticles used as exogenous THG contrast agents, tattoo dyes are widely adopted in human skin so that future clinical biocompatibility evaluation is relatively achievable. Combined with the demonstrated THG enhancement effect, tattoo dyes show their promise for future clinical imaging applications.

  14. Comparison of measured and estimated maximum skin doses during CT fluoroscopy lung biopsies

    Energy Technology Data Exchange (ETDEWEB)

    Zanca, F., E-mail: Federica.Zanca@med.kuleuven.be [Department of Radiology, Leuven University Center of Medical Physics in Radiology, UZ Leuven, Herestraat 49, 3000 Leuven, Belgium and Imaging and Pathology Department, UZ Leuven, Herestraat 49, Box 7003 3000 Leuven (Belgium); Jacobs, A. [Department of Radiology, Leuven University Center of Medical Physics in Radiology, UZ Leuven, Herestraat 49, 3000 Leuven (Belgium); Crijns, W. [Department of Radiotherapy, UZ Leuven, Herestraat 49, 3000 Leuven (Belgium); De Wever, W. [Imaging and Pathology Department, UZ Leuven, Herestraat 49, Box 7003 3000 Leuven, Belgium and Department of Radiology, UZ Leuven, Herestraat 49, 3000 Leuven (Belgium)

    2014-07-15

    Purpose: To measure patient-specific maximum skin dose (MSD) associated with CT fluoroscopy (CTF) lung biopsies and to compare measured MSD with the MSD estimated from phantom measurements, as well as with the CTDIvol of patient examinations. Methods: Data from 50 patients with lung lesions who underwent a CT fluoroscopy-guided biopsy were collected. The CT protocol consisted of a low-kilovoltage (80 kV) protocol used in combination with an algorithm for dose reduction to the radiology staff during the interventional procedure, HandCare (HC). MSD was assessed during each intervention using EBT2 gafchromic films positioned on patient skin. Lesion size, position, total fluoroscopy time, and patient-effective diameter were registered for each patient. Dose rates were also estimated at the surface of a normal-size anthropomorphic thorax phantom using a 10 cm pencil ionization chamber placed at every 30°, for a full rotation, with and without HC. Measured MSD was compared with MSD values estimated from the phantom measurements and with the cumulative CTDIvol of the procedure. Results: The median measured MSD was 141 mGy (range 38–410 mGy) while the median cumulative CTDIvol was 72 mGy (range 24–262 mGy). The ratio between the MSD estimated from phantom measurements and the measured MSD was 0.87 (range 0.12–4.1) on average. In 72% of cases the estimated MSD underestimated the measured MSD, while in 28% of the cases it overestimated it. The same trend was observed for the ratio of cumulative CTDIvol and measured MSD. No trend was observed as a function of patient size. Conclusions: On average, estimated MSD from dose rate measurements on phantom as well as from CTDIvol of patient examinations underestimates the measured value of MSD. This can be attributed to deviations of the patient's body habitus from the standard phantom size and to patient positioning in the gantry during the procedure.

  15. Evaluating low dose ionizing radiation effects on gene expression in human skin biopsy cores

    International Nuclear Information System (INIS)

    Goldberg, Z.; Schwietert, C.; Stern, R.L.; Lehnert, B.E.

    2003-01-01

    Significant biological effects can occur in animals, animal cells, immortalized human cell lines, and primary human cells after exposure to doses of ionizing radiation (IR) in the <1-10 cGy region. However it is unclear how these observations mimic or even pertain to the actual in vivo condition in humans, though such knowledge is required for reducing the uncertainty of assessing human risks due to low dose IR (LDIR) exposures. Further, low dose effects have increasing clinical relevance in the radiotherapeutic management of cancer as the volume of tissue receiving only LDIR increases as more targeted radiotherapy (i.e. IMRT) becomes more widely used. Thus, human translational data must be obtained with which to correlate in vitro experimental findings and evaluate their 'real-life' applicability. To evaluate LDIR effects in human tissue we have obtained freshly explanted full thickness human skin samples obtained from aesthetic surgery, and subjected them to ex vivo irradiation as a translational research model system of a complex human tissue. Ionizing radiation (IR) exposures were delivered at 1, 10, or 100 cGy. The temporal response to IR was assessed by harvesting RNA at multiple time points out to 24 hours post IR. Gene expression changes were assessed by real time PCR. We have shown that RNA can be reliably extracted with fidelity from 3 mm diameter punch biopsies of human tissue and provide good quality sample for the real time PCR evaluation. Genes of interest include those reported to have altered expression following LDIR from in vitro cell culture models. These include genes associated with cell cycle regulation, DNA repair and various cytokines. These feasibility studies in human skin irradiated ex vivo, have demonstrated that gene expression can be measured accurately from very small human tissue samples, thus setting the stage for biopsy acquisition of tissue irradiated in vivo from patients-volunteers. The clinical study has begun and the data from

  16. Comparison of measured and estimated maximum skin doses during CT fluoroscopy lung biopsies

    International Nuclear Information System (INIS)

    Zanca, F.; Jacobs, A.; Crijns, W.; De Wever, W.

    2014-01-01

    Purpose: To measure patient-specific maximum skin dose (MSD) associated with CT fluoroscopy (CTF) lung biopsies and to compare measured MSD with the MSD estimated from phantom measurements, as well as with the CTDIvol of patient examinations. Methods: Data from 50 patients with lung lesions who underwent a CT fluoroscopy-guided biopsy were collected. The CT protocol consisted of a low-kilovoltage (80 kV) protocol used in combination with an algorithm for dose reduction to the radiology staff during the interventional procedure, HandCare (HC). MSD was assessed during each intervention using EBT2 gafchromic films positioned on patient skin. Lesion size, position, total fluoroscopy time, and patient-effective diameter were registered for each patient. Dose rates were also estimated at the surface of a normal-size anthropomorphic thorax phantom using a 10 cm pencil ionization chamber placed at every 30°, for a full rotation, with and without HC. Measured MSD was compared with MSD values estimated from the phantom measurements and with the cumulative CTDIvol of the procedure. Results: The median measured MSD was 141 mGy (range 38–410 mGy) while the median cumulative CTDIvol was 72 mGy (range 24–262 mGy). The ratio between the MSD estimated from phantom measurements and the measured MSD was 0.87 (range 0.12–4.1) on average. In 72% of cases the estimated MSD underestimated the measured MSD, while in 28% of the cases it overestimated it. The same trend was observed for the ratio of cumulative CTDIvol and measured MSD. No trend was observed as a function of patient size. Conclusions: On average, estimated MSD from dose rate measurements on phantom as well as from CTDIvol of patient examinations underestimates the measured value of MSD. This can be attributed to deviations of the patient's body habitus from the standard phantom size and to patient positioning in the gantry during the procedure

  17. Should Skin Biopsies Be Performed in Patients Suspected of Having Parkinson’s Disease?

    Directory of Open Access Journals (Sweden)

    Timo Siepmann

    2017-01-01

    Full Text Available In patients with Parkinson’s disease (PD, the molecularly misfolded form of α-synuclein was recently identified in cutaneous autonomic nerve fibers which displayed increased accumulation even in early disease stages. However, the underlying mechanisms of synucleinopathic nerve damage and its implication for brain pathology in later life remain to be elucidated. To date, specific diagnostic tools to evaluate small fiber pathology and to discriminate neurodegenerative proteinopathies are rare. Recently, research has indicated that deposition of α-synuclein in cutaneous nerve fibers quantified via immunohistochemistry in superficial skin biopsies might be a valid marker of PD which could facilitate early diagnosis and monitoring of disease progression. However, lack of standardization of techniques to quantify neural α-synuclein deposition limits their utility in clinical practice. Additional challenges include the identification of potential distinct morphological patterns of intraneural α-synuclein deposition among synucleinopathies to facilitate diagnostic discrimination and determining the degree to which structural damage relates to dysfunction of nerve fibers targeted by α-synuclein. Answering these questions might improve our understanding of the pathophysiological role of small fiber neuropathy in Parkinson’s disease, help identify new treatment targets, and facilitate assessment of response to neuroprotective treatment.

  18. In vitro and in vivo MMP gene expression localisation by In Situ-RT-PCR in cell culture and paraffin embedded human breast cancer cell line xenografts

    International Nuclear Information System (INIS)

    Haupt, Larisa M; Thompson, Erik W; Trezise, Ann EO; Irving, Rachel E; Irving, Michael G; Griffiths, Lyn R

    2006-01-01

    Members of the matrix metalloproteinase (MMP) family of proteases are required for the degradation of the basement membrane and extracellular matrix in both normal and pathological conditions. In vitro, MT1-MMP (MMP-14, membrane type-1-MMP) expression is higher in more invasive human breast cancer (HBC) cell lines, whilst in vivo its expression has been associated with the stroma surrounding breast tumours. MMP-1 (interstitial collagenase) has been associated with MDA-MB-231 invasion in vitro, while MMP-3 (stromelysin-1) has been localised around invasive cells of breast tumours in vivo. As MMPs are not stored intracellularly, the ability to localise their expression to their cells of origin is difficult. We utilised the unique in situ-reverse transcription-polymerase chain reaction (IS-RT-PCR) methodology to localise the in vitro and in vivo gene expression of MT1-MMP, MMP-1 and MMP-3 in human breast cancer. In vitro, MMP induction was examined in the MDA-MB-231 and MCF-7 HBC cell lines following exposure to Concanavalin A (Con A). In vivo, we examined their expression in archival paraffin embedded xenografts derived from a range of HBC cell lines of varied invasive and metastatic potential. Mouse xenografts are heterogenous, containing neoplastic human parenchyma with mouse stroma and vasculature and provide a reproducible in vivo model system correlated to the human disease state. In vitro, exposure to Con A increased MT1-MMP gene expression in MDA-MB-231 cells and decreased MT1-MMP gene expression in MCF-7 cells. MMP-1 and MMP-3 gene expression remained unchanged in both cell lines. In vivo, stromal cells recruited into each xenograft demonstrated differences in localised levels of MMP gene expression. Specifically, MDA-MB-231, MDA-MB-435 and Hs578T HBC cell lines are able to influence MMP gene expression in the surrounding stroma. We have demonstrated the applicability and sensitivity of IS-RT-PCR for the examination of MMP gene expression both in vitro and in

  19. Early experience with formalin-fixed paraffin-embedded (FFPE) based commercial clinical genomic profiling of gliomas-robust and informative with caveats.

    Science.gov (United States)

    Movassaghi, Masoud; Shabihkhani, Maryam; Hojat, Seyed A; Williams, Ryan R; Chung, Lawrance K; Im, Kyuseok; Lucey, Gregory M; Wei, Bowen; Mareninov, Sergey; Wang, Michael W; Ng, Denise W; Tashjian, Randy S; Magaki, Shino; Perez-Rosendahl, Mari; Yang, Isaac; Khanlou, Negar; Vinters, Harry V; Liau, Linda M; Nghiemphu, Phioanh L; Lai, Albert; Cloughesy, Timothy F; Yong, William H

    2017-08-01

    Commercial targeted genomic profiling with next generation sequencing using formalin-fixed paraffin embedded (FFPE) tissue has recently entered into clinical use for diagnosis and for the guiding of therapy. However, there is limited independent data regarding the accuracy or robustness of commercial genomic profiling in gliomas. As part of patient care, FFPE samples of gliomas from 71 patients were submitted for targeted genomic profiling to one commonly used commercial vendor, Foundation Medicine. Genomic alterations were determined for the following grades or groups of gliomas; Grade I/II, Grade III, primary glioblastomas (GBMs), recurrent primary GBMs, and secondary GBMs. In addition, FFPE samples from the same patients were independently assessed with conventional methods such as immunohistochemistry (IHC), Quantitative real-time PCR (qRT-PCR), or Fluorescence in situ hybridization (FISH) for three genetic alterations: IDH1 mutations, EGFR amplification, and EGFRvIII expression. A total of 100 altered genes were detected by the aforementioned targeted genomic profiling assay. The number of different genomic alterations was significantly different between the five groups of gliomas and consistent with the literature. CDKN2A/B, TP53, and TERT were the most common genomic alterations seen in primary GBMs, whereas IDH1, TP53, and PIK3CA were the most common in secondary GBMs. Targeted genomic profiling demonstrated 92.3%-100% concordance with conventional methods. The targeted genomic profiling report provided an average of 5.5 drugs, and listed an average of 8.4 clinical trials for the 71 glioma patients studied but only a third of the trials were appropriate for glioma patients. In this limited comparison study, this commercial next generation sequencing based-targeted genomic profiling showed a high concordance rate with conventional methods for the 3 genetic alterations and identified mutations expected for the type of glioma. While it may not be feasible to

  20. The frequency of p53, Ki67, CD99 and Fli-1 protein expression in paraffin-embedded tissue blocks in Ewing’s sarcoma

    Directory of Open Access Journals (Sweden)

    Bagheri Hossein-Abadi Z

    2011-06-01

    Full Text Available "n Normal 0 false false false EN-US X-NONE AR-SA MicrosoftInternetExplorer4 /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-qformat:yes; mso-style-parent:""; mso-padding-alt:0in 5.4pt 0in 5.4pt; mso-para-margin:0in; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:11.0pt; font-family:"Calibri","sans-serif"; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-fareast-font-family:"Times New Roman"; mso-fareast-theme-font:minor-fareast; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:Arial; mso-bidi-theme-font:minor-bidi;} Background: Ewing sarcoma family tumors (ESFTs are among the most malignant tumors in children and young adults. ESFTs include Ewing sarcoma (ES and peripheral primitive neuroectodermal tumors (pPNETs. As there seemed to be few studies on the molecular biology of ESFTs, we investigated the frequency of CD99, Ki67, p53 and Fli-1 protein expression in 15 Iranian patients with ESFTs. In addition, the correlation between expression rate of these proteins and various clinical factors, including age, sex and survival was computed."n"nMethods: The expression of the aforesaid proteins was studied by immunohisto-chemistry in formalin-fixed and paraffin-embedded blocks of 15 ESFTs specimens. Stained sections were classified according to the percentage of stained tumor cells."n"nResults: The results showed the membrane expression of CD99 protein in all of the specimens. The nuclear expression of Fli-1 protein was observed in 86.7% and the over-expression of p53 nuclear protein was seen in 53.3% of the specimens. The expression rate of Ki67 protein was 60%. Although a significant correlation was not shown between the expression levels of Ki67, p53 or Fli-1 proteins with age, sex or survival of the patients, there was a significant

  1. SFN-SIQ, SFNSL and skin biopsy of 55 cases with small fibre involvement.

    Science.gov (United States)

    Sun, Bo; Li, Yifan; Liu, Lizhi; Chen, Zhaohui; Ling, Li; Yang, Fei; Liu, Jiexiao; Liu, Hong; Huang, Xusheng

    2018-05-01

    Purpose/aim of the study: To date, there are no validated screening scales for small fibre neuropathy. This study investigated the small-fibre neuropathy and the symptom inventory questionnaire as well as the small fibre neuropathy screening list for small fibre neuropathy diagnosis. Fifty-five patients were divided into small fibre neuropathy and mixed fibre damage groups. Relevant scales, nerve conduction studies and skin biopsies were performed. Relationships between the intraepidermal nerve fibre density and different scales as well as the diagnostic and cut-off values (score at which Youden's index is largest) were determined. Compared with healthy Chinese participants, 20 patients were diagnosed with small fibre neuropathy. Intraepidermal nerve fibre density was moderately and highly correlated with the small fibre neuropathy-symptom inventory questionnaire and small fibre neuropathy screening list, respectively. The diagnostic values were moderate and high for the small fibre neuropathy-symptom inventory questionnaire (cut-off value = 5, sensitivity = 80%, specificity = 81.8%) and small fibre neuropathy screening list (cut-off value = 8, sensitivity = 94.1%, specificity = 90.9%), respectively. There were no significant differences in the visual analogue scale between the small fibre neuropathy group, mixed small and large fibre neuropathy group, pure large fibre neuropathy group and the normal group. Small fibre neuropathy-symptom inventory questionnaire and small fibre neuropathy screening list represent potential small fibre neuropathy screening tools. Abbreviations EMG electromyography ENA anti-extractable nuclear antigens ESR erythrocyte sedimentation rate IENFD intraepidermal nerve fibre density IGT impaired glucose tolerance NCS nerve conduction studies NDS neuropathy disability score OGTT oral glucose tolerance test PGP protein gene product PN peripheral neuropathy ROC receiver operating characteristic curve ROC-AUC area under the ROC curve SFN small

  2. Alterations of the Human Skin N- and O-Glycome in Basal Cell Carcinoma and Squamous Cell Carcinoma

    Directory of Open Access Journals (Sweden)

    Uwe Möginger

    2018-03-01

    Full Text Available The glycome of one of the largest and most exposed human organs, the skin, as well as glycan changes associated with non-melanoma skin cancers have not been studied in detail to date. Skin cancers such as basal cell carcinoma (BCC and squamous cell carcinoma (SCC are among the most frequent types of cancers with rising incidence rates in the aging population. We investigated the healthy human skin N- and O-glycome and its changes associated with BCC and SCC. Matched patient samples were obtained from frozen biopsy and formalin-fixed paraffin-embedded tissue samples for glycomics analyses using two complementary glycomics approaches: porous graphitized carbon nano-liquid chromatography electro spray ionization tandem mass spectrometry and capillary gel electrophoresis with laser induced fluorescence detection. The human skin N-glycome is dominated by complex type N-glycans that exhibit almost similar levels of α2-3 and α2-6 sialylation. Fucose is attached exclusively to the N-glycan core. Core 1 and core 2 type O-glycans carried up to three sialic acid residues. An increase of oligomannose type N-glycans and core 2 type O-glycans was observed in BCC and SCC, while α2-3 sialylation levels were decreased in SCC but not in BCC. Furthermore, glycopeptide analyses provided insights into the glycoprotein candidates possibly associated with the observed N-glycan changes, with glycoproteins associated with binding events being the most frequently identified class.

  3. The localisation of treponemes and characterisation of the inflammatory infiltrate in skin biopsies from patients with primary or secondary syphilis, or early infectious yaws

    NARCIS (Netherlands)

    Engelkens, H. J.; ten Kate, F. J.; Judanarso, J.; Vuzevski, V. D.; van Lier, J. B.; Godschalk, J. C.; van der Sluis, J. J.; Stolz, E.

    1993-01-01

    To study the localisation of treponemes and to analyse the inflammatory infiltrate in biopsy specimens from patients with primary or secondary syphilis, or early infectious yaws. Skin biopsies originating from human lesions of primary (29x) or secondary (15x) syphilis (Rotterdam), or early yaws

  4. qPCR detection of Mycobacterium leprae in biopsies and slit skin smear of different leprosy clinical forms

    Directory of Open Access Journals (Sweden)

    Michelle de Campos Soriani Azevedo

    2017-01-01

    Full Text Available Leprosy, whose etiological agent is Mycobacterium leprae, is a chronic infectious disease that mainly affects the skin and peripheral nervous system. The diagnosis of leprosy is based on clinical evaluation, whereas histopathological analysis and bacilloscopy are complementary diagnostic tools. Quantitative PCR (qPCR, a current useful tool for diagnosis of infectious diseases, has been used to detect several pathogens including Mycobacterium leprae. The validation of this technique in a robust set of samples comprising the different clinical forms of leprosy is still necessary. Thus, in this study samples from 126 skin biopsies (collected from patients on all clinical forms and reactional states of leprosy and 25 slit skin smear of leprosy patients were comparatively analyzed by qPCR (performed with primers for the RLEP region of M. leprae DNA and routine bacilloscopy performed in histological sections or in slit skin smear. Considering clinical diagnostic as the gold standard, 84.9% of the leprosy patients were qPCR positive in skin biopsies, resulting in 84.92% sensitivity, with 84.92 and 61.22% positive (PPV and negative (NPV predictive values, respectively. Concerning bacilloscopy of histological sections (BI/H, the sensitivity was 80.15% and the PPV and NPV were 80.15 and 44.44%, respectively. The concordance between qPCR and BI/H was 87.30%. Regarding the slit skin smear, 84% of the samples tested positive in the qPCR. Additionally, qPCR showed 100% specificity, since all samples from different mycobacteria, from healthy individuals, and from other granulomatous diseases presented negative results. In conclusion, the qPCR technique for detection of M. leprae using RLEP primers proved to be specific and sensitive, and qPCR can be used as a complementary test to diagnose leprosy irrespective of the clinical form of disease.

  5. qPCR detection of Mycobacterium leprae in biopsies and slit skin smear of different leprosy clinical forms.

    Science.gov (United States)

    Azevedo, Michelle de Campos Soriani; Ramuno, Natália Mortari; Fachin, Luciana Raquel Vincenzi; Tassa, Mônica; Rosa, Patrícia Sammarco; Belone, Andrea de Faria Fernandes; Diório, Suzana Madeira; Soares, Cleverson Teixeira; Garlet, Gustavo Pompermaier; Trombone, Ana Paula Favaro

    Leprosy, whose etiological agent is Mycobacterium leprae, is a chronic infectious disease that mainly affects the skin and peripheral nervous system. The diagnosis of leprosy is based on clinical evaluation, whereas histopathological analysis and bacilloscopy are complementary diagnostic tools. Quantitative PCR (qPCR), a current useful tool for diagnosis of infectious diseases, has been used to detect several pathogens including Mycobacterium leprae. The validation of this technique in a robust set of samples comprising the different clinical forms of leprosy is still necessary. Thus, in this study samples from 126 skin biopsies (collected from patients on all clinical forms and reactional states of leprosy) and 25 slit skin smear of leprosy patients were comparatively analyzed by qPCR (performed with primers for the RLEP region of M. leprae DNA) and routine bacilloscopy performed in histological sections or in slit skin smear. Considering clinical diagnostic as the gold standard, 84.9% of the leprosy patients were qPCR positive in skin biopsies, resulting in 84.92% sensitivity, with 84.92 and 61.22% positive (PPV) and negative (NPV) predictive values, respectively. Concerning bacilloscopy of histological sections (BI/H), the sensitivity was 80.15% and the PPV and NPV were 80.15 and 44.44%, respectively. The concordance between qPCR and BI/H was 87.30%. Regarding the slit skin smear, 84% of the samples tested positive in the qPCR. Additionally, qPCR showed 100% specificity, since all samples from different mycobacteria, from healthy individuals, and from other granulomatous diseases presented negative results. In conclusion, the qPCR technique for detection of M. leprae using RLEP primers proved to be specific and sensitive, and qPCR can be used as a complementary test to diagnose leprosy irrespective of the clinical form of disease. Copyright © 2016 Sociedade Brasileira de Infectologia. Published by Elsevier Editora Ltda. All rights reserved.

  6. Southern blot analysis of skin biopsies for human papillomavirus DNA: renal allograft recipients in south-eastern Queensland.

    Science.gov (United States)

    Trenfield, K; Salmond, C A; Pope, J H; Hardie, I R

    1993-01-01

    The 104 skin biopsies from 34 patients who attended a Renal Transplant Unit in Brisbane over 12 months included 40 squamous cell carcinoma (SCC), 22 solar keratoses, 4 hyperkeratoses, 18 warts and 11 basal cell carcinoma (BCC). Human papillomavirus (HPV) DNA was identified by Southern blot hybridisation using, as individual probes, purified insert DNA from recombinant HPV 1, 2, 3 or 3/10, 4, 5 or 5/8, 7, 11, 16, 18 and 41 under relaxed conditions and characterised by restriction enzyme analysis and Southern blot hybridisation under more stringent conditions. Genomic HPV DNA was characterised in 7 skin biopsies from 4 renal allograft recipients (RARs): HPV 1A in a SCC (20 copies/cell) and a BCC (10 copies/cell) from the one patient, HPV 36 (20 copies/cell) in a SCC, HPV 1A [symbol: see text] 1000 copies/cell) in a wart and HPV 2B (200-800 copies/cell) in 3 warts from the one patient. Only HPV 1A in the SCC exhibited a significant degree of subtype variation. HPV DNA was identified in another 5 skin biopsies from another 4 RARs: HPV 3A in a wart and a hyperkeratosis, HPV 3/10-related DNA in 2 solar keratoses and HPV 5/8-related DNA in another (20-50 copies/cell). The incidence of HPV 5 (or 5-related HPVs) in RAR SCC was very low and that of HPV DNA in RAR warts was lower than that recorded elsewhere but this was not due to insensitivity of the assays. There was no evidence for a role for HPV in the aetiology of skin cancer in RARs in south-eastern Queensland but the possibility remains that as yet unidentified HPV types are involved.

  7. Stereotoracic skin biopsy in non-palpable woman mammary glands lesions

    International Nuclear Information System (INIS)

    Leborgne, Francisco; Mezzera, Julieta

    1999-01-01

    Seventy stereotactic breast biopsies in non palpable lesions were performed in asintomatic patients, studied with mammography, physical examination and high-resolution ultrasonography. A 14-gauge cutting needle was used with excursion of 2 and 20 mm. in high likelihood probably benign lesions and low likelihood probably malignant lesions, not snographical evident and not less than 4 mm. in diameter. Long term follow-up or surgical correlation is available in only 46 biopsies, with 35 negative results and 11 positive results for cancer. Follow-up mammography was recommended in 34 of 35 negative results and one case showed mammographic lesion progression, a false negative result, with sensitivity 90.9% and NPV 97%. Needle wire localization and open surgery was recommended in 11 positive results, with total agreement between stereotactic core biopsy and open surgery, with specificity 100% and PPV 100%. The indication of stereotactic biopsy in non palpable lesions as an alternative to surgical biopsy in order to decrease the number of surgical biopsies with negative results and in consequence lowering costs of diagnosis of asintomatic malignant lesions, with error of 2.1% and 2.8% minor complications

  8. Alterations of epidermal proliferation and cytokeratin expression in skin biopsies from heavy draught horses with chronic pastern dermatitis.

    Science.gov (United States)

    Geburek, Florian; Ohnesorge, Bernhard; Deegen, Eckehard; Doeleke, Renate; Hewicker-Trautwein, Marion

    2005-12-01

    We report the historical, clinical and histopathological characteristics of skin lesions in biopsies from 37 heavy draught horses with chronic pastern dermatitis. The skin lesions were divided into four macroscopic groups: scaling (group I, n=5), hyperkeratotic and hyperplastic plaque-like lesions (group II, n=14), nodular skin masses (group III, n=16) and verrucous skin lesions (group IV, n=2). The principal histological findings were hyperkeratosis and epidermal hyperplasia. There was a gradual increase in epidermal hyperplasia from groups I to IV, suggesting that the lesions represent different stages of disease. In all cases, there was perivascular dermatitis dominated by T lymphocytes with an increase in MHC class II-positive dendritic-like cells. Immunohistochemical labelling for cytokeratins CK5/6(4), CK10 and CK14 indicated a change in their expression pattern. This correlated with the degree of epidermal hyperplasia, indicating abnormal differentiation of keratinocytes. There was a statistically significant correlation between the severity of skin lesions and several other factors including increasing age, increasing cannon circumference, prominence of anatomical structures such as fetlock tufts of hairs, ergots and chestnuts, and bulges in the fetlock region.

  9. Quantification of small fiber pathology in patients with sarcoidosis and chronic pain using cornea confocal microscopy and skin biopsies

    Directory of Open Access Journals (Sweden)

    Oudejans LCJ

    2017-08-01

    Full Text Available Linda CJ Oudejans,1 Marieke Niesters,1 Michael Brines,2 Albert Dahan,1 Monique van Velzen1 1Department of Anesthesiology, Leiden University Medical Center, Leiden, the Netherlands; 2Araim Pharmaceuticals, Inc., Tarrytown, NY, USA Abstract: Small fiber pathology with concomitant chronic neuropathic pain is a common complication of sarcoidosis. The gold standard of diagnosis of small fiber neuropathy (SFN is the quantification of small nerve fibers in skin biopsies in combination with patient history and psychophysical tests; a new technique is the quantification of small nerve fibers in the cornea using cornea confocal microscopy (CCM. Here, we studied small fiber morphology in sarcoidosis patients with neuropathic pain using skin biopsies, CCM, and quantitative sensory testing (QST. Our aim was to construct specific phenotypes of neuropathic pain in sarcoidosis. Fifty-eight patients with a confirmed diagnosis of sarcoidosis and with moderate-to-severe neuropathic pain were tested. Decreased intraepidermal nerve fiber density (IENFD from skin biopsies was found in 28% of patients, and CCM abnormalities were observed in 45% of patients. There was no correlation between CCM and IENFD abnormalities. Eighty-three percent of patients had abnormal thermal detection thresholds, a sign of small fiber dysfunction. Based on the presence or absence of abnormalities in IENFD and CCM, four distinct phenotypes were identified with a distinct homogeneous pattern of somatosensory symptoms. We argue that these distinct phenotypes have a similar mechanistic construct with specific phenotype-specific treatment options. Additionally, our data suggest the presence of patients with length- and nonlength-dependent SFN within this population of sarcoidosis patients. Keywords: chronic pain, sarcoidosis, small fiber neuropathy

  10. Purpura fulminans mimicking toxic epidermal necrolysis - additional value of 16S rRNA sequencing and skin biopsy.

    Science.gov (United States)

    Dautzenberg, K H W; Polderman, F N; van Suylen, R J; Moviat, M A M

    2017-05-01

    Both purpura fulminans and toxic epidermal necrolysis (TEN) are rare and life-threatening disorders with a high mortality. We present a case of suspected rapidly progressive, severe pneumococcal sepsis-induced purpura fulminans complicated by multiple organ failure, severe epidermolysis and cutaneous necrosis. We show the diagnostic challenge to differentiate between purpura fulminans and TEN, as the extensive epidermolysis in purpura fulminans may mimic TEN and we highlight the additional value of repeated skin biopsies and 16S rRNA gene sequencing.

  11. Selection of reference genes for quantitative RT-PCR studies in striped dolphin (Stenella coeruleoalba skin biopsies

    Directory of Open Access Journals (Sweden)

    Casini Silvia

    2006-09-01

    Full Text Available Abstract Background Odontocete cetaceans occupy the top position of the marine food-web and are particularly sensitive to the bioaccumulation of lipophilic contaminants. The effects of environmental pollution on these species are highly debated and various ecotoxicological studies have addressed the impact of xenobiotic compounds on marine mammals, raising conservational concerns. Despite its sensitivity, quantitative real-time PCR (qRT-PCR has never been used to quantify gene induction caused by exposure of cetaceans to contaminants. A limitation for the application of qRT-PCR is the need for appropriate reference genes which allow the correct quantification of gene expression. A systematic evaluation of potential reference genes in cetacean skin biopsies is presented, in order to validate future qRT-PCR studies aiming at using the expression of selected genes as non-lethal biomarkers. Results Ten commonly used housekeeping genes (HKGs were partially sequenced in the striped dolphin (Stenella coeruleoalba and, for each gene, PCR primer pairs were specifically designed and tested in qRT-PCR assays. The expression of these potential control genes was examined in 30 striped dolphin skin biopsy samples, obtained from specimens sampled in the north-western Mediterranean Sea. The stability of selected control genes was determined using three different specific VBA applets (geNorm, NormFinder and BestKeeper which produce highly comparable results. Glyceraldehyde-3P-dehydrogenase (GAPDH and tyrosine 3-monooxygenase (YWHAZ always rank as the two most stably expressed HKGs according to the analysis with geNorm and Normfinder, and are defined as optimal control genes by BestKepeer. Ribosomal protein L4 (RPL4 and S18 (RPS18 also exhibit a remarkable stability of their expression levels. On the other hand, transferrin receptor (TFRC, phosphoglycerate kinase 1 (PGK1, hypoxanthine ribosyltransferase (HPRT1 and β-2-microglobin (B2M show variable expression

  12. TISSUE INHIBITOR OF METALLOPROTEINASE 1, MATRIX METALLOPROTEINASE 9, ALPHA-1 ANTITRYPSIN, METALLOTHIONEIN AND UROKINASE TYPE PLASMINOGEN ACTIVATOR RECEPTOR IN SKIN BIOPSIES FROM PATIENTS AFFECTED BY AUTOIMMUNE BLISTERING DISEASES

    Directory of Open Access Journals (Sweden)

    Ana Maria Abreu Velez

    2013-07-01

    Full Text Available Introduction: Proteinases and proteinase inhibitors have been described to play a role in autoimmune skin blistering diseases. We studied skin lesional biopsies from patients affected by several autoimmune skin blistering diseases for proteinases and proteinase inhibitors. Methods: We utilized immunohistochemistry to evaluate biopsies for alpha-1-antitrypsin, human matrix metalloproteinase 9 (MMP9, human tissue inhibitor of metalloproteinases 1 (TIMP-1, metallothionein and urokinase type plasminogen activator receptor (uPAR. We tested 30 patients affected by endemic pemphigus, 30 controls from the endemic area, and 15 normal controls. We also tested 30 biopsies from patients with bullous pemphigoid (BP, 20 with pemphigus vulgaris (PV, 8 with pemphigus foliaceus, and 14 with dermatitis herpetiformis (DH. Results: Contrary to findings in the current literature, most autoimmune skin blistering disease biopsies were negative for uPAR and MMP9. Only some chronic patients with El Bagre-EPF were positive to MMP9 in the dermis, in proximity to telocytes. TIMP-1 and metallothionein were positive in half of the biopsies from BP patients at the basement membrane of the skin, within several skin appendices, in areas of dermal blood vessel inflammation and within dermal mesenchymal-epithelial cell junctions.

  13. How accurate are measurements of skin-lesion depths on prebiopsy supine chest computed tomography for transthoracic needle biopsies?

    International Nuclear Information System (INIS)

    Cheung, Joo Yeon; Kim, Yookyung; Shim, Sung Shine; Lee, Jin Hwa; Chang, Jung Hyun; Ryu, Yon Ju; Lee, Rena J.

    2012-01-01

    Aim: To evaluate the accuracy of depth measurements on supine chest computed tomography (CT) for transthoracic needle biopsy (TNB). Materials and methods: We measured skin-lesion depths from the skin surface to nodules on both prebiopsy supine CT scans and CT scans obtained during cone beam CT-guided TNB in the supine (n = 29) or prone (n = 40) position in 69 patients, and analyzed the differences between the two measurements, based on patient position for the biopsy and lesion location. Results: Skin-lesion depths measured on prebiopsy supine CT scans were significantly larger than those measured on CT scans obtained during TNB in the prone position (p < 0.001; mean difference ± standard deviation (SD), 6.2 ± 5.7 mm; range, 0–18 mm), but the differences showed marginal significance in the supine position (p = 0.051; 3.5 ± 3.9 mm; 0–13 mm). Additionally, the differences were significantly larger for the upper (mean ± SD, 7.8 ± 5.7 mm) and middle (10.1 ± 6.5 mm) lung zones than for the lower lung zones (3.1 ± 3.3 mm) in the prone position (p = 0.011), and were larger for the upper lung zone (4.6 ± 5.0 mm) than for the middle (2.4 ± 2.0 mm) and lower (2.3 ± 2.3 mm) lung zones in the supine position (p = 0.004). Conclusions: Skin-lesion depths measured on prebiopsy supine chest CT scans were inaccurate for TNB in the prone position, particularly for nodules in the upper and middle lung zones.

  14. Improved clonality detection in Hodgkin lymphoma using a semi-nested modification of the BIOMED-2 PCR assay for IGH and IGK rearrangements: A paraffin-embedded tissue study.

    Science.gov (United States)

    Han, Shusen; Masaki, Ayako; Sakamoto, Yuma; Takino, Hisashi; Murase, Takayuki; Iida, Shinsuke; Inagaki, Hiroshi

    2018-05-01

    The BIOMED-2 PCR protocols targeting IGH and IGK genes may be useful for detecting clonality in Hodgkin lymphoma (HL). The clonality detection rates, however, have not been very high with these methods using paraffin-embedded tumor sections. We previously described the usefulness of the semi-nested BIOMED-2 IGH assay in B-cell malignancies. In this study, we devised a novel semi-nested BIOMED-2 IGK assay. Employing 58 cases of classical HL, we carried out the standard BIOMED-2, BIOMED-2 followed by BIOMED-2 re-amplification, and BIOMED-2 followed by semi-nested BIOMED-2, all targeting IGH and IGK, using paraffin-embedded tissues. In both IGH and IGK assays, semi-nested assays yielded significantly higher clonality detection rates than the standard assays and re-amplification assays. Clonality was detected in 13/58 (22.4%) classical HL cases using the standard IGH/IGK assays while it was detected in 38/58 (65.5%) cases using semi-nested IGH/IGK assays. The detection rates were not associated with the HL subtypes, CD30-positive cell density, CD20-positive cell density, or Epstein-Barr virus (EBV) positivity. In conclusion, tumor clonality was detected in nearly two-thirds of classical HL cases using semi-nested BIOMED-2 IGH/IGK assays using paraffin tumor sections. These semi-nested assays may be useful when the standard IGH/IGK assays fail to detect clonality in histopathologically suspected HLs. © 2018 Japanese Society of Pathology and John Wiley & Sons Australia, Ltd.

  15. The Impact of Quantitative Data Provided by a Multi-spectral Digital Skin Lesion Analysis Device on Dermatologists'Decisions to Biopsy Pigmented Lesions.

    Science.gov (United States)

    Farberg, Aaron S; Winkelmann, Richard R; Tucker, Natalie; White, Richard; Rigel, Darrell S

    2017-09-01

    BACKGROUND: Early diagnosis of melanoma is critical to survival. New technologies, such as a multi-spectral digital skin lesion analysis (MSDSLA) device [MelaFind, STRATA Skin Sciences, Horsham, Pennsylvania] may be useful to enhance clinician evaluation of concerning pigmented skin lesions. Previous studies evaluated the effect of only the binary output. OBJECTIVE: The objective of this study was to determine how decisions dermatologists make regarding pigmented lesion biopsies are impacted by providing both the underlying classifier score (CS) and associated probability risk provided by multi-spectral digital skin lesion analysis. This outcome was also compared against the improvement reported with the provision of only the binary output. METHODS: Dermatologists attending an educational conference evaluated 50 pigmented lesions (25 melanomas and 25 benign lesions). Participants were asked if they would biopsy the lesion based on clinical images, and were asked this question again after being shown multi-spectral digital skin lesion analysis data that included the probability graphs and classifier score. RESULTS: Data were analyzed from a total of 160 United States board-certified dermatologists. Biopsy sensitivity for melanoma improved from 76 percent following clinical evaluation to 92 percent after quantitative multi-spectral digital skin lesion analysis information was provided ( p quantitative data were provided. Negative predictive value also increased (68% vs. 91%, panalysis (64% vs. 86%, p data into physician evaluation of pigmented lesions led to both increased sensitivity and specificity, thereby resulting in more accurate biopsy decisions.

  16. The role of ultrasound and ultrasound-guided fine needle aspiration biopsy of lymph nodes in patients with skin tumours

    International Nuclear Information System (INIS)

    Solivetti, Francesco Maria; Elia, Fulvia; Santaguida, Maria Giulia; Guerrisi, Antonino; Visca, Paolo; Cercato, Maria Cecilia; Di Carlo, Aldo

    2014-01-01

    The primary aim of this study was to evaluate the diagnostic accuracy of ultrasound (US) in the study of superficial lymph nodes during the follow-up of patients surgically treated for skin tumours. The secondary objective was to compare positive cytological results with histological reports. From 2004 to 2011, 480 patients (male/female: 285/195; median age 57 years; prevalent skin tumour: melanoma) underwent US-guided fine-needle aspiration biopsy (FNAB) of suspicious recurrent lymph nodes. An expert radiologist first performed US testing of the lymph nodes, expressing either a negative or positive outcome of the test. Subsequently, US-guided FNAB was performed. FNAB positive patients were subjected to lymphadenectomy; the patients who tested negative underwent the follow-up. The size of lymph nodes was ≤ 2 cm in 90% of cases. Out of the 336 (70%) US “positive” patients, 231 (68.8%) were FNAB positives. Out of the 144 (30%) US “negatives”, 132 (91.7%) were FNAB negatives. The sensitivity and specificity of the US were 95% and 55.7%, respectively; the negative predictive value was 91.7% and the positive predictive value was 68.8%. Definitive histological results confirmed FNAB positivity in 97.5% of lymphadenectomies. US is a sensitive method in the evaluation of superficial lymph nodes during the follow-up of patients with skin tumours. High positive predictive value of cytology was confirmed

  17. Paraffin-based immunohistochemistry in the evaluation of glomerular diseases in renal biopsies

    International Nuclear Information System (INIS)

    Rathore, M.U.; Khadim, M.T.; Atique, M.

    2012-01-01

    Objective: To determine sensitivity and specificity of paraffin-based immunohistochemistry in the evaluation of glomerular diseases in renal biopsies using immunofluorescence as gold standard. Study Design: Cross-sectional analytical study. Place and Duration of Study: Department of Histopathology, Armed Forces Institute of Pathology, Rawalpindi, from August 2008 to August 2009. Methodology: Seventy renal biopsy specimens fulfilling the inclusion criteria for light microscopy and immuno-fluorescence during the study period were evaluated. Antibodies to immunoglobulins (IgG, IgA, and IgM) and components of complement system (C3) were applied on 70 formalin-fixed paraffin-embedded renal biopsy specimens previously classified by means of light microscopy and immunofluorescence (IF). Staining for these antibodies was recorded as positive and negative for immunohistochemistry (IHC) and IF in paired proportions presuming IF as gold standard test. The sensitivity, specificity, positive predictive value and negative predictive value of individual antibody were calculated. Results: Of 70 patients, mean age was 33 +- 18 years ranging from 2 to 80 years. Forty five (64%) were males and 25 (36%) were females. The sensitivity, specificity and predictive values of individual antibodies to IgG, IgA, IgM and C3 were very low and generally in the range of 40 - 60%. Conclusion: The sensitivity, specificity and predictive values of immunohistochemistry on formalin-fixed paraffin-embedded renal biopsy specimens were very low and therefore, not suitable for evaluation of renal biopsies in current circumstances. (author)

  18. Extraction of high-quality epidermal RNA after ammonium thiocyanate-induced dermo-epidermal separation of 4 mm human skin biopsies

    DEFF Research Database (Denmark)

    Clemmensen, Anders; Thomassen, Mads; Clemmensen, Ole

    2009-01-01

    To obtain a separation of the epidermal and dermal compartments to examine compartment specific biological mechanisms in the skin, we incubated 4 mm human skin punch biopsies in ammonium thiocyanate. We wanted to test (i) the histological quality of the dermo-epidermal separation obtained...... by different incubation times; (ii) the amount and quality of extractable epidermal RNA and (iii) its impact on sample RNA expression profiles assessed by large-scale gene expression microarray analysis in both normal and inflamed skin. At 30-min incubation, the split between dermis and epidermis...... and almost completely separated from the dermis of 4 mm skin biopsies by 30 min incubation in 3.8% ammonium thiocyanate combined with curettage of the dermal surface, producing high-quality RNA suitable for transcriptional analysis. Our refined method of dermo-epidermal separation will undoubtedly prove...

  19. Stenotrophomonas maltophila cellulitis in an immunocompromised patient presenting with purpura, diagnosed on skin biopsy.

    Science.gov (United States)

    Gao, Yi; Minca, Eugen C; Procop, Gary W; Bergfeld, Wilma F

    2016-11-01

    Stenotrophomas maltophilia is an opportunistic Gram-negative bacillus and an important cause of nosocomial infections, particularly in immunosuppressed individuals. Although infections with this organism are most often in the form of pneumonia, bacteremia and endocarditis, awareness of the impact of S. maltophilia skin infections has been increasing. Here we describe a case of S. maltophilia cellulitis in a 65-year-old man with severe neutropenia and purpuric skin lesions to highlight the critical histopathological findings and correlate them with the clinical manifestations of the skin infection with this organism. Because identification of S. maltophilia can be challenging and infections are difficult to manage, this case illustrates essential considerations regarding the multifaceted histopathological, dermatological, clinical and microbiological aspects of the diagnosis and treatment of S. maltophilia cellulitis in a severely immunocompromised patient. Cognizance of the increasing incidence of nosocomial infections with uncommon microorganisms such as S. maltophilia is necessary when presented with atypical cutaneous manifestations, particularly in immunocompromised patients. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  20. Assessment of tissue fibrosis in skin biopsies from patients with systemic sclerosis employing confocal laser scanning microscopy: an objective outcome measure for clinical trials?

    Science.gov (United States)

    Busquets, Joanna; Del Galdo, Francesco; Kissin, Eugene Y.

    2010-01-01

    Objectives. To obtain an objective, unbiased assessment of skin fibrosis in patients with SSc for use in clinical trials of SSc disease-modifying therapeutics. Methods. Skin biopsies from the dorsal forearm of six patients with diffuse SSc and six healthy controls, and skin biopsies from the forearm of one patient with diffuse SSc before and following 1 year treatment with mycophenolate mofetil were analysed by confocal laser scanning microscopy (CLSM) with specific antibodies against collagen types I and III or fibronectin. The integrated density of fluorescence (IDF) was calculated employing National Institutes of Health-ImageJ software in at least four different fields per biopsy spanning the full dermal thickness. Results. The intensities of collagen types I and III and fibronectin IDF were 174, 147 and 139% higher in SSc skin than in normal skin, respectively. All differences were statistically significant. The sum of the IDF values obtained for the three proteins yielded a comprehensive fibrosis score. The average fibrosis score for the six SSc samples was 28.3 × 106 compared with 18.6 × 106 for the six normal skin samples (P < 0.0001). Comparison of skin biopsies obtained from the same SSc patient before treatment and after 12 months of treatment with mycophenolate mofetil showed a reduction of 39% in total fibrosis score after treatment. Conclusions. CLSM followed by quantitative image analysis provides an objective and unbiased assessment of skin fibrosis in SSc and could be a useful end-point for clinical trials with disease-modifying agents to monitor the response or progression of the disease. PMID:20202926

  1. Examine Your Skin

    Medline Plus

    Full Text Available ... Suggestions Examine Your Skin Newly Diagnosed? Understanding Your Pathology Biopsy: The First Step Sentinel Node Biopsy Melanoma ... Suggestions Examine Your Skin Newly Diagnosed? Understanding Your Pathology Biopsy: The First Step Sentinel Node Biopsy Melanoma ...

  2. Small angle scattering polarization biopsy: a comparative analysis of various skin diseases

    Science.gov (United States)

    Zimnyakov, D. A.; Alonova, M. V.; Yermolenko, S. B.; Ivashko, P. V.; Reshetnikova, E. M.; Galkina, E. M.; Utz, S. R.

    2013-12-01

    An approach to differentiation of the morphological features of normal and pathological human epidermis on the base of statistical analysis of the local polarization states of laser light forward scattered by in-vitro tissue samples is discussed. The eccentricity and the azimuth angle of local polarization ellipses retrieved for various positions of the focused laser beam on the tissue surface, and the coefficient of collimated transmittance are considered as the diagnostic parameters for differentiation. The experimental data obtained with the psoriasis, discoid lupus erythematosus, alopecia, lichen planus, scabies, demodex, and normal skin samples are presented.

  3. Trench Foot or Non-Freezing Cold Injury As a Painful Vaso-Neuropathy: Clinical and Skin Biopsy Assessments

    Directory of Open Access Journals (Sweden)

    Praveen Anand

    2017-09-01

    Full Text Available BackgroundTrench foot, or non-freezing cold injury (NFCI, results from cold exposure of sufficient severity and duration above freezing point, with consequent sensory and vascular abnormalities which may persist for years. Based on observations of Trench foot in World War II, the condition was described as a vaso-neuropathy. While some reports have documented nerve damage after extreme cold exposure, sensory nerve fibres and vasculature have not been assessed with recent techniques in NFCI.ObjectiveTo assess patients with chronic sensory symptoms following cold exposure, in order to diagnose any underlying small fibre neuropathy, and provide insight into mechanisms of the persistent pain and cold hypersensitivity.MethodsThirty soldiers with cold exposure and persistent sensory symptoms (>4 months were assessed with quantitative sensory testing, nerve conduction studies, and skin biopsies. Immunohistochemistry was used to assess intraepidermal (IENF and subepidermal (SENF nerve fibres with a range of markers, including the pan-neuronal marker protein gene product 9.5 (PGP 9.5, regenerating fibres with growth-associated protein 43 (GAP43, and nociceptor fibres with transient receptor potential cation channel subfamily V member 1 (TRPV1, sensory neuron-specific receptor (SNSR, and calcitonin gene-related peptide (CGRP. von Willebrand factor (vWF, endothelial nitric oxide synthase (eNOS, and vascular endothelial growth factor (VEGF were used for assessing blood vessels, and transient receptor potential cation channel, subfamily A member 1 (TRPA1 and P2X purinoceptor 7 (P2X7 for keratinocytes, which regulate nociceptors via release of nerve growth factor.ResultsClinical examination showed pinprick sensation was abnormal in the feet of 20 patients (67%, and between 67 and 83% had abnormalities of thermal thresholds to the different modalities. 7 patients (23% showed reduced sensory action potential amplitude of plantar nerves. 27 patients (90% had

  4. Detection of MDM2/CDK4 amplification in lipomatous soft tissue tumors from formalin-fixed, paraffin-embedded tissue: comparison of multiplex ligation-dependent probe amplification (MLPA) and fluorescence in situ hybridization (FISH).

    Science.gov (United States)

    Creytens, David; van Gorp, Joost; Ferdinande, Liesbeth; Speel, Ernst-Jan; Libbrecht, Louis

    2015-02-01

    In this study, the detection of MDM2 and CDK4 amplification was evaluated in lipomatous soft tissue tumors using multiplex ligation-dependent probe amplification (MLPA), a PCR-based technique, in comparison with fluorescence in situ hybridization (FISH). These 2 techniques were evaluated in a series of 77 formalin-fixed, paraffin-embedded lipomatous tumors (27 benign adipose tumors, 28 atypical lipomatous tumors/well-differentiated liposarcomas, 18 dedifferentiated liposarcomas, and 4 pleomorphic liposarcomas). Using MLPA, with a cut-off ratio of >2, 36/71 samples (22 atypical lipomatous tumors/well-differentiated liposarcomas, and 14 dedifferentiated liposarcomas) showed MDM2 and CDK4 amplification. Using FISH as gold standard, MLPA showed a sensitivity of 90% (36/40) and a specificity of 100% (31/31) in detecting amplification of MDM2 and CDK4 in lipomatous soft tissue tumors. In case of high-level amplification (MDM2-CDK4/CEP12 ratio >5), concordance was 100%. Four cases of atypical lipomatous tumor/well-differentiated liposarcoma (4/26, 15%) with a low MDM2 and CDK4 amplification level (MDM2-CDK4/CEP12 ratio ranging between 2 and 2.5) detected by FISH showed no amplification by MLPA, although gain of MDM2 and CDK4 (ratios ranging between 1.6 and 1.9) was seen with MLPA. No amplification was detected in benign lipomatous tumors and pleomorphic liposarcomas. Furthermore, there was a very high concordance between the ratios obtained by FISH and MLPA. In conclusion, MLPA proves to be an appropriate and straightforward technique for screening MDM2/CDK4 amplification in lipomatous tumors, especially when a correct cut-off value and reference samples are chosen, and could be considered a good alternative to FISH to determine MDM2 and CDK4 amplification in liposarcomas. Moreover, because MLPA, as a multiplex technique, allows simultaneous detection of multiple chromosomal changes of interest, it could be in the future a very reliable and fast molecular analysis on

  5. Characterization and diagnostic evaluation of chronic polyneuropathies induced by oxaliplatin and docetaxel comparing skin biopsy to quantitative sensory testing and nerve conduction studies

    DEFF Research Database (Denmark)

    Krøigård, T; Schrøder, H D; Qvortrup, C

    2014-01-01

    was to characterize the neuropathies with regard to symptoms, neurological signs and objective evidence of damage to the structure and function of the peripheral nerves. Furthermore, the diagnostic values of skin biopsy, quantitative sensory testing (QST) and nerve conduction studies (NCS) were compared. METHODS......: Patients complaining of neuropathy symptoms at least 3 months after completion of treatment with oxaliplatin (n = 20) or docetaxel (n = 20) were recruited from the Department of Oncology or using hospital records. Neuropathy scores were determined along with the intraepidermal nerve fibre density in skin....... Mechanical detection threshold was most often affected in the QST. NCS, QTS and skin biopsy were abnormal in 11, 13 and 17 and 7, 11 and 15 of the oxaliplatin-treated patients and docetaxel-treated patients, respectively. CONCLUSIONS: Chemotherapy-induced peripheral neuropathy after oxaliplatin or docetaxel...

  6. Diagnostic sensitivity and specificity of in situ hybridization and immunohistochemistry for Eastern equine encephalitis virus and West Nile virus in formalin-fixed, paraffin-embedded brain tissue of horses.

    Science.gov (United States)

    Pennick, Kate E; McKnight, Christy A; Patterson, Jon S; Latimer, Kenneth S; Maes, Roger K; Wise, Annabel G; Kiupel, Matti

    2012-03-01

    Immunohistochemistry (IHC) and in situ hybridization (ISH) can be used either to detect or to differentiate between Eastern equine encephalitis virus (EEEV) and West Nile virus (WNV) within formalin-fixed, paraffin-embedded (FFPE) brain tissue of horses. To compare the diagnostic sensitivity and specificity of ISH and IHC, FFPE brain tissue from 20 EEEV-positive horses and 16 WNV-positive horses were tested with both EEEV and WNV oligoprobes and EEEV- and WNV-specific antibodies. Reverse transcription polymerase chain reaction (RT-PCR) for detection of EEEV and WNV was used as the gold standard to confirm infection. All horses that tested positive for EEEV by RT-PCR also tested positive by IHC and ISH, except for 1 case that was false-negative by ISH. In contrast, all horses that tested positive for WNV by RT-PCR tested negative by IHC and only 2 horses tested positive by ISH. No false-positives were detected with either method for both viruses. Both IHC and ISH are highly specific and sensitive diagnostic methods to detect EEEV in equine FFPE brain tissues, although neither appear effective for the diagnosis of WNV in equine neurologic cases.

  7. Clinical Usefulness of a One-Tube Nested Reverse Transcription Quantitative Polymerase Chain Reaction Assay for Evaluating Human Epidermal Growth Factor Receptor 2 mRNA Overexpression in Formalin-Fixed and Paraffin-Embedded Breast Cancer Tissue Samples.

    Science.gov (United States)

    Wang, Hye-Young; Ahn, Sungwoo; Park, Sunyoung; Kim, SeungIl; Lee, Hyeyoung

    2017-01-01

    Currently, the two main methods used to analyze human epidermal growth factor receptor 2 (HER2) amplification or overexpression have a limited accuracy and high costs. These limitations can be overcome by the development of complementary quantitative methods. In this study, we analyzed HER2 mRNA expression in clinical formalin-fixed and paraffin-embedded (FFPE) samples using a one-tube nested reverse transcription quantitative polymerase chain reaction (RT-qPCR) assay. We measured expression relative to 3 reference genes and compared the results to those obtained by conventional immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) assays with 226 FFPE breast cancer tissue samples. The one-tube nested RT-qPCR assay proved to be highly sensitive and specific based on comparisons with IHC (96.9 and 97.7%, respectively) and FISH (92.4 and 92.9%, respectively) obtained with the validation set. Comparisons with clinicopathological data revealed significant associations between HER2 overexpression and TNM stage (p < 0.01), histological type (p < 0.01), ER status (p < 0.001), PR status (p < 0.05), HER2 status (p < 0.001), and molecular subtypes (p < 0.001). Based on these findings, our one-tube nested RT-qPCR assay is a potentially useful and complementary screening tool for the detection of HER2 mRNA overexpression. © 2016 S. Karger AG, Basel.

  8. Nested-PCR for the detection of Mycoplasma hyopneumoniae in bronchial alveolar swabs, frozen tissues and formalin-fixed paraffin-embedded swine lung samples: comparative evaluation with immunohistochemical findings and histological features

    Directory of Open Access Journals (Sweden)

    Paula R. Almeida

    2012-08-01

    Full Text Available The diagnosis of Mycoplasma hyopneumoniae infection is often performed through histopathology, immunohistochemistry (IHC and polymerase chain reaction (PCR or a combination of these techniques. PCR can be performed on samples using several conservation methods, including swabs, frozen tissue or formalin-fixed and paraffin-embedded (FFPE tissue. However, the formalin fixation process often inhibits DNA amplification. To evaluate whether M. hyopneumoniae DNA could be recovered from FFPE tissues, 15 lungs with cranioventral consolidation lesions were collected in a slaughterhouse from swine bred in herds with respiratory disease. Bronchial swabs and fresh lung tissue were collected, and a fragment of the corresponding lung section was placed in neutral buffered formalin for 48 hours. A PCR assay was performed to compare FFPE tissue samples with samples that were only refrigerated (bronchial swabs or frozen (tissue pieces. M. hyopneumoniae was detected by PCR in all 15 samples of the swab and frozen tissue, while it was detected in only 11 of the 15 FFPE samples. Histological features of M. hyopneumoniae infection were presented in 11 cases and 7 of these samples stained positive in IHC. Concordance between the histological features and detection results was observed in 13 of the FFPE tissue samples. PCR was the most sensitive technique. Comparison of different sample conservation methods indicated that it is possible to detect M. hyopneumoniae from FFPE tissue. It is important to conduct further research using archived material because the efficiency of PCR could be compromised under these conditions.

  9. Improved clonality detection in B-cell lymphoma using a semi-nested modification of the BIOMED-2 PCR assay for IGH rearrangement: A paraffin-embedded tissue study.

    Science.gov (United States)

    Sakamoto, Yuma; Masaki, Ayako; Aoyama, Satsuki; Han, Shusen; Saida, Kosuke; Fujii, Kana; Takino, Hisashi; Murase, Takayuki; Iida, Shinsuke; Inagaki, Hiroshi

    2017-09-01

    The BIOMED-2 PCR protocol for targeting the IGH gene is widely employed for detecting clonality in B-cell malignancies. Unfortunately, the detection of clonality with this method is not very sensitive when paraffin sections are used as a DNA source. To increase the sensitivity, we devised a semi-nested modification of a JH consensus primer. The clonality detection rates of three assays were compared: the standard BIOMED-2, BIOMED-2 assay followed by BIOMED-2 re-amplification, and BIOMED-2 assay followed by semi-nested BIOMED-2. We tested more than 100 cases using paraffin-embedded tissues of various B-cell lymphomas, and found that the clonality detection rates with the above three assays were 63.9%, 79.6%, and 88.0%, respectively. While BIOMED-2 re-amplification was significantly more sensitive than the standard BIOMED-2, the semi-nested BIOMED-2 was significantly more sensitive than both the standard BIOMED-2 and BIOMED-2 re-amplification. An increase in sensitivity was observed in all lymphoma subtypes examined. In conclusion, tumor clonality may be detected in nearly 90% of B-cell lymphoma cases with semi-nested BIOMED-2. This ancillary assay may be useful when the standard BIOMED-2 fails to detect clonality in histopathologically suspected B-cell lymphomas. © 2017 Japanese Society of Pathology and John Wiley & Sons Australia, Ltd.

  10. Diagnostic multiplex polymerase chain reaction assay for the identification of Pseudomonas aeruginosa from the skin biopsy specimens in burn wound infections and detection of antibiotic susceptibility

    International Nuclear Information System (INIS)

    Mashouf, Rasoul Y.; Farahani, Hadi S.; Zamani, A.

    2008-01-01

    Objective was to identify Pseudomonas aeruginosa (P. aeruginosa) from the skin biopsy specimens in burn wound infections by multiplex polymerase chain reaction (M-PCR) and detection of antimicrobial susceptibility of isolates from culture. We conducted the cross-sectional study in 140 patients with wound infections who admitted to referral burn center of Motahari, Tehran, Iran, during a 12-month period from 2005-2006. Skin biopsy specimens were aseptically taken from each patient, one for PCR and one for bacterial culture. A M-PCR test based on simultaneous amplification of 2 lipoprotein genes: oprI and oprL, was used to directly detect fluorescent pseudomonades and P. aeruginosa in skin biopsy specimens. The susceptibility of P. aeruginosa isolates to 16 antibiotics was determined using the disc diffusion method. Out of 140 biopsy specimens, M-PCR detected 66 (47.2%) isolates, while culture detected 57 (40.7%) isolates as P. aeruginosa. Positive results for both genes which observed only for P. aeruginosa, while only one gene, oprI, was amplified from other fluorescent pseudomonades (n=12) and all other bacterial tested (n=62) were negative by the amplification test. The most effective antibiotics against isolate of P. aeruginosa were cefepime (79%), azetreonam (76%), ticarcillin-clavulanic acid (68%), tobramycin (62%) and amikacin (61%). Multiplex PCR assay appears promising for the rapid and sensitive detection of P. aeruginosa from the burned skin biopsy specimens. Simultaneous amplification of 2 lipoprotein genes: oprI and oprL could detect P. aeruginosa and oprI gene only for other fluorescent pseudomonades. (author)

  11. Utility of Fite-Faraco stain for both mast cell count and bacillary index in skin biopsies of leprosy patients.

    Science.gov (United States)

    Chatura, K R; Sangeetha, S

    2012-01-01

    To assess the utility of a single stain for both mast cell count and bacillary index (BI), 50 skin-biopsie patients were stained with Fite-Faraco (FF) stain, viewed under oil immersion and BI calculated using the Ridley's logarithmic scale, and mast cells counted as the number of cells per mm2. Mean mast cell count per mm2 at the tuberculoid pole was lowest in TT 7.9 and highest in BT 14.23. At the lepromatous end, it was highest in BL 9.21, while in LL it was 8.23. Highest counts were seen in the borderline types overall. The correlation coefficient between histopathological diagnosis and BI is 0.822 which is a positive correlation to a significant degree. The correlation coefficient between histopathological diagnosis and mast cell count was found to be -0.17, which is a negative correlation but not to a significant degree. FF stain was utilised to visualise both bacilli for estimation of BI and mast cells for mast cell count, a seldom attempted feature in literature.

  12. [Skin biopsy in diagnosis of chronic graft-versus-host disease in patients after allogeneic haematopoietic stem cell transplantation: pathologist's point of view on quantitative scoring system].

    Science.gov (United States)

    Grzanka, Dariusz; Styczyński, Jan; Debski, Robert; Krenska, Anna; Pacholska, Małgorzata; Prokurat, Andrzej I; Wysocki, Mariusz; Marszałek, Andrzej

    2008-01-01

    Pathology diagnosis of chronic graft-versus-host-disease (GVHD) after allogeneic haematopoietic stem cell transplantation (allo-HSCT) is an important issue in clinical follow-up, in spite of frequent difficulties in interpretation., related to dynamic changes occurring in the skin during the disease, as well as to sequelae of basic disease and immunosuppressive therapy. Recently presented Consensus NIH (National Health Institute, Bethesda, USA) of histopathologic (HP) analysis is still complex and intrinsically divergent, thus clinically difficult to implement. Analysis of clinical value of histological evaluation results of skin biopsy in children after allo-HSCT and its correlation with clinical status. Ten skin biopsies were taken from 7 patients (4 boys, 3 girls, age 3-15 years) after allo-HSCT (6 MFD, 1 MMUD) and analyzed after hematoxylin/eosine and immunohistochemical (CD3, CD45T, CD20) staining. Pathology analysis was based on commonly accepted criteria enabling simple and unambiguous interpretation. Results were compared with clinical data and indications for immunosuppressive therapy. It was found that reliable and coherent interpretation can be made when following parameters were taken into account: 1. in epithelium: the presence of apoptosis, archetypical changes and vacuolar degeneration in the basilar layer, presence of CD3/CD45 in the epidermis; 2. in the dermis: the extent of collagenization, presence of melanophages and lymphocyte infiltrations; 3. in the eccrine glands epithelium: eccrine glands atrophy and presence of lymphocytes. A new scoring system of skin biopsy analysis in patients with chronic GVHD based on the modified NIH Consensus was proposed. The preliminary clinical value of histological results was assessed. Skin biopsy evaluation based on limited qualitative and quantitative analysis of lymphocyte infiltrates together with studies on intensity of apoptosis, collagenization and archetypical changes is a valuable diagnostic method

  13. Hormone Receptor Expression Analyses in Neoplastic and Non-Neoplastic Canine Mammary Tissue by a Bead Based Multiplex Branched DNA Assay: A Gene Expression Study in Fresh Frozen and Formalin-Fixed, Paraffin-Embedded Samples.

    Directory of Open Access Journals (Sweden)

    Annika Mohr

    Full Text Available Immunohistochemistry (IHC is currently considered the method of choice for steroid hormone receptor status evaluation in human breast cancer and, therefore, it is commonly utilized for assessing canine mammary tumors. In case of low hormone receptor expression, IHC is limited and thus is complemented by molecular analyses. In the present study, a multiplex bDNA assay was evaluated as a method for hormone receptor gene expression detection in canine mammary tissues. Estrogen receptor (ESR1, progesterone receptor (PGR, prolactin receptor (PRLR and growth hormone receptor (GHR gene expressions were evaluated in neoplastic and non-neoplastic canine mammary tissues. A set of 119 fresh frozen and 180 formalin-fixed, paraffin-embedded (FFPE was comparatively analyzed and used for assay evaluation. Furthermore, a possible association between the hormone receptor expression in different histological subtypes of canine malignant mammary tumors and the castration status, breed and invasive growth of the tumor were analyzed. The multiplex bDNA assay proved to be more sensitive for fresh frozen specimens. Hormone receptor expression found was significantly decreased in malignant mammary tumors in comparison to non-neoplastic tissue and benign mammary tumors. Among the histological subtypes the lowest gene expression levels of ESR1, PGR and PRLR were found in solid, anaplastic and ductal carcinomas. In summary, the evaluation showed that the measurement of hormone receptors with the multiplex bDNA assay represents a practicable method for obtaining detailed quantitative information about gene expression in canine mammary tissue for future studies. Still, comparison with IHC or quantitative real-time PCR is needed for further validation of the present method.

  14. Chromogenic In Situ Hybridization and p16/Ki67 Dual Staining on Formalin-Fixed Paraffin-Embedded Cervical Specimens: Correlation with HPV-DNA Test, E6/E7 mRNA Test, and Potential Clinical Applications

    Directory of Open Access Journals (Sweden)

    Roberta Zappacosta

    2013-01-01

    Full Text Available Although HPV-DNA test and E6/E7 mRNA analyses remain the current standard for the confirmation of human papillomavirus (HPV infections in cytological specimens, no universally adopted techniques exist for the detection of HPV in formalin-fixed paraffin-embedded samples. Particularly, in routine laboratories, molecular assays are still time-consuming and would require a high level of expertise. In this study, we investigated the possible use of a novel HPV tyramide-based chromogenic in situ hybridization (CISH technology to locate HPV on tissue specimens. Then, we evaluate the potential usefulness of p16INK4a/Ki-67 double stain on histological samples, to identify cervical cells expressing HPV E6/E7 oncogenes. In our series, CISH showed a clear signal in 95.2% of the specimens and reached a sensitivity of 86.5%. CISH positivity always matched with HPV-DNA positivity, while 100% of cases with punctated signal joined with cervical intraepithelial neoplasia grade 2 or worse (CIN2+. p16/Ki67 immunohistochemistry gave an interpretable result in 100% of the cases. The use of dual stain significantly increased the agreement between pathologists, which reached 100%. Concordance between dual stain and E6/E7 mRNA test was 89%. In our series, both CISH and p16INK4a/Ki67 dual stain demonstrated high grade of performances. In particular, CISH would help to distinguish episomal from integrated HPV, in order to allow conclusions regarding the prognosis of the lesion, while p16INK4a/Ki67 dual stain approach would confer a high level of standardization to the diagnostic procedure.

  15. Chromogenic In Situ Hybridization and p16/Ki67 Dual Staining on Formalin-Fixed Paraffin-Embedded Cervical Specimens: Correlation with HPV-DNA Test, E6/E7 mRNA Test, and Potential Clinical Applications

    Science.gov (United States)

    Zappacosta, Roberta; Colasante, Antonella; Viola, Patrizia; D'Antuono, Tommaso; Lattanzio, Giuseppe; Capanna, Serena; Gatta, Daniela Maria Pia; Rosini, Sandra

    2013-01-01

    Although HPV-DNA test and E6/E7 mRNA analyses remain the current standard for the confirmation of human papillomavirus (HPV) infections in cytological specimens, no universally adopted techniques exist for the detection of HPV in formalin-fixed paraffin-embedded samples. Particularly, in routine laboratories, molecular assays are still time-consuming and would require a high level of expertise. In this study, we investigated the possible use of a novel HPV tyramide-based chromogenic in situ hybridization (CISH) technology to locate HPV on tissue specimens. Then, we evaluate the potential usefulness of p16INK4a/Ki-67 double stain on histological samples, to identify cervical cells expressing HPV E6/E7 oncogenes. In our series, CISH showed a clear signal in 95.2% of the specimens and reached a sensitivity of 86.5%. CISH positivity always matched with HPV-DNA positivity, while 100% of cases with punctated signal joined with cervical intraepithelial neoplasia grade 2 or worse (CIN2+). p16/Ki67 immunohistochemistry gave an interpretable result in 100% of the cases. The use of dual stain significantly increased the agreement between pathologists, which reached 100%. Concordance between dual stain and E6/E7 mRNA test was 89%. In our series, both CISH and p16INK4a/Ki67 dual stain demonstrated high grade of performances. In particular, CISH would help to distinguish episomal from integrated HPV, in order to allow conclusions regarding the prognosis of the lesion, while p16INK4a/Ki67 dual stain approach would confer a high level of standardization to the diagnostic procedure. PMID:24369532

  16. Validation of a Multiplex Allele-Specific Polymerase Chain Reaction Assay for Detection of KRAS Gene Mutations in Formalin-Fixed, Paraffin-Embedded Tissues from Colorectal Cancer Patients.

    Directory of Open Access Journals (Sweden)

    Sirirat Seekhuntod

    Full Text Available Patients with KRAS mutations do not respond to epidermal growth factor receptor (EGFR inhibitors and fail to benefit from adjuvant chemotherapy. Mutation analysis of KRAS is needed before starting treatment with monoclonal anti-EGFR antibodies in patients with metastatic colorectal cancer (mCRC. The objective of this study is to develop a multiplex allele-specific PCR (MAS-PCR assay to detect KRAS mutations.We developed a single-tube MAS-PCR assay for the detection of seven KRAS mutations (G12D, G12A, G12R, G12C, G12S, G12V, and G13D. We performed MAS-PCR assay analysis for KRAS on DNA isolated from 270 formalin-fixed paraffin-embedded (FFPE colorectal cancer tissues. Sequences of all 270 samples were determined by pyrosequencing. Seven known point-mutation DNA samples diluted with wild-type DNA were assayed to determine the limitation of detection and reproducibility of the MAS-PCR assay.Overall, the results of MAS-PCR assay were in good concordance with pyrosequencing, and only seven discordant samples were found. The MAS-PCR assay reproducibly detected 1 to 2% mutant alleles. The most common mutations were G13D in codon 13 (49.17%, G12D (25.83% and G12V (12.50% in codon 12.The MAS-PCR assay provides a rapid, cost-effective, and reliable diagnostic tool for accurate detection of KRAS mutations in routine FFPE colorectal cancer tissues.

  17. The storage period of the formalin-fixed paraffin-embedded tumor blocks does not influence the concentration and purity of the isolated DNA in a series of 83 renal and thyroid carcinomas.

    Science.gov (United States)

    Nechifor-Boilă, Adela Corina; Loghin, Andrada; Vacariu, Victor; Halaţiu, Vasile Bogdan; Borda, Angela

    2015-01-01

    Optimal recovery of nucleic acids from formalin-fixed paraffin-embedded (FFPE) tissues is highly dependent on a series of pre-extraction steps, mainly related (but not limited) to fixation. The aim of our study was to investigate if the storage period of the FFPE blocks had a significant effect on the isolated DNA. We examined the quantity and purity of the isolated DNA from 83 FFPE blocks, corresponding to malignant thyroid (n=28) and renal (n=55) carcinomas that had been stored in our department for up to eight years. The DNA extraction protocol was based on a precipitation method (MasterPure™ DNA Purification Kit, Epicentre), in accordance to the manufacturer instructions, optimized in our laboratory. A spectrophotometer was used to determine the yield (A260) and purity (A260/A280 ratio) of the isolated DNA. We successfully isolated good DNA quantity and purity from all our study cases (mean concentration: 223.4 ± 104.16 ng/μL; mean A260/A280 ratio: 1.68 ± 0.09). Moreover, no statistically significant differences were observed between tumor blocks stored for 2-3 years and 7-8 years, respectively, both in terms of DNA quantity (p=0.196) and purity (p=0.663). In conclusion, we successfully validated an efficient, reproducible DNA extraction technique that provided a good range of DNA concentrations and purity, regardless the type of tissue (thyroid or kidney). Moreover, we demonstrated that the storage period of the FFPE blocks does not have a significant influence on the DNA quantity and purity.

  18. In vitro propagation and dynamics of T cells from skin biopsies by methods using interleukins-2 and -4 or anti-CD3/CD28 antibody-coated microbeads

    DEFF Research Database (Denmark)

    Hashizume, Hideo; Hansen, Anker; Poulsen, Lars K

    2010-01-01

    In order to explore the mechanisms of inflammatory skin disorders, we established two methods of expanding skin-derived lymphocytes, one using high levels of interleukin (IL)-2 and IL-4 (method A) and the other using low levels of cytokines and anti-CD3/CD28 microbeads (method B). Both methods...... provide advantages for functional studies. With either of these two, we could obtain more than 10(7) cells/ from a 3 mm skin biopsy in 21 days from 23 out of 26 biopsies of various skin diseases. The relevance of these cells was confirmed by shifted T-cell receptor beta chain variable region (TCR......-Vbeta) repertoire and antigen-dependent proliferation in antigen-driven skin disorders. The propagation of skin-resident lymphocytes, seen especially in method A, seems to be mediated by a functional defect of regulatory T cells residing in skin sequentially expanding under the conditions of our methods....

  19. The Cadaveric Skin Biopsy Project: description and student evaluation of an innovative approach to dermatology instruction in the preclerkship medical school curriculum.

    Science.gov (United States)

    Baker, Mary Grace; Bradley, Elizabeth B; McCollum, Melanie A; Russell, Mark A

    2014-08-01

    Dermatology can develop creative ways of participating in the preclerkship medical school curriculum. We sought to describe and report student survey results of a novel collaborative learning activity for medical students, directed by dermatology, histology, and gross anatomy faculty, which used cadavers to replicate the process of skin lesion biopsy and provided a realistic setting in which to learn normal-appearing and abnormal skin histology. First-year medical students were surveyed regarding the impact of this activity on their understanding of skin histology and their appreciation of dermatology and dermatologic procedures. Students were appreciative of the opportunity to perform biopsies and discover the link between the clinical presentation of a lesion and its underlying histopathology. They were less impressed with the ability of the activity to improve their understanding of the characteristics of benign versus malignant lesions. This is an early feasibility trial at 1 institution. This project represents one approach to introducing students to dermatology and dermatologic procedures and achieves institutional, Liaison Committee on Medical Education, and Association of American Medical Colleges educational goals. Overall, students highly valued the opportunities to practice clinical procedures and found it aided their understanding and appreciation of dermatology. Copyright © 2014 American Academy of Dermatology, Inc. Published by Mosby, Inc. All rights reserved.

  20. Quality assessment of DNA derived from up to 30 years old formalin fixed paraffin embedded (FFPE) tissue for PCR-based methylation analysis using SMART-MSP and MS-HRM.

    Science.gov (United States)

    Kristensen, Lasse S; Wojdacz, Tomasz K; Thestrup, Britta B; Wiuf, Carsten; Hager, Henrik; Hansen, Lise Lotte

    2009-12-21

    The High Resolution Melting (HRM) technology has recently been introduced as a rapid and robust analysis tool for the detection of DNA methylation. The methylation status of multiple tumor suppressor genes may serve as biomarkers for early cancer diagnostics, for prediction of prognosis and for prediction of response to treatment. Therefore, it is important that methodologies for detection of DNA methylation continue to evolve. Sensitive Melting Analysis after Real Time - Methylation Specific PCR (SMART-MSP) and Methylation Sensitive - High Resolution Melting (MS-HRM) are two methods for single locus DNA methylation detection based on HRM. Here, we have assessed the quality of DNA extracted from up to 30 years old Formalin Fixed Paraffin Embedded (FFPE) tissue for DNA methylation analysis using SMART-MSP and MS-HRM. The quality assessment was performed on DNA extracted from 54 Non-Small Cell Lung Cancer (NSCLC) samples derived from FFPE tissue, collected over 30 years and grouped into five years intervals. For each sample, the methylation levels of the CDKN2A (p16) and RARB promoters were estimated using SMART-MSP and MS-HRM assays designed to assess the methylation status of the same CpG positions. This allowed for a direct comparison of the methylation levels estimated by the two methods for each sample. CDKN2A promoter methylation levels were successfully determined by SMART-MSP and MS-HRM in all 54 samples. Identical methylation estimates were obtained by the two methods in 46 of the samples. The methylation levels of the RARB promoter were successfully determined by SMART-MSP in all samples. When using MS-HRM to assess RARB methylation five samples failed to amplify and 15 samples showed a melting profile characteristic for heterogeneous methylation. Twenty-seven of the remaining 34 samples, for which the methylation level could be estimated, gave the same result as observed when using SMART-MSP. MS-HRM and SMART-MSP can be successfully used for single locus

  1. Analytic performance studies and clinical reproducibility of a real-time PCR assay for the detection of epidermal growth factor receptor gene mutations in formalin-fixed paraffin-embedded tissue specimens of non-small cell lung cancer

    International Nuclear Information System (INIS)

    O’Donnell, Patrick; Shieh, Felice; Wei, Wen; Lawrence, H Jeffrey; Wu, Lin; Schilling, Robert; Bloom, Kenneth; Maltzman, Warren; Anderson, Steven; Soviero, Stephen; Ferguson, Jane; Shyu, Johnny; Current, Robert; Rehage, Taraneh; Tsai, Julie; Christensen, Mari; Tran, Ha Bich; Chien, Sean Shih-Chang

    2013-01-01

    Epidermal growth factor receptor (EGFR) gene mutations identify patients with non-small cell lung cancer (NSCLC) who have a high likelihood of benefiting from treatment with anti-EGFR tyrosine kinase inhibitors. Sanger sequencing is widely used for mutation detection but can be technically challenging, resulting in longer turn-around-time, with limited sensitivity for low levels of mutations. This manuscript details the technical performance verification studies and external clinical reproducibility studies of the cobas EGFR Mutation Test, a rapid multiplex real-time PCR assay designed to detect 41 mutations in exons 18, 19, 20 and 21. The assay’s limit of detection was determined using 25 formalin-fixed paraffin-embedded tissue (FFPET)-derived and plasmid DNA blends. Assay performance for a panel of 201 specimens was compared against Sanger sequencing with resolution of discordant specimens by quantitative massively parallel pyrosequencing (MPP). Internal and external reproducibility was assessed using specimens tested in duplicate by different operators, using different reagent lots, instruments and at different sites. The effects on the performance of the cobas EGFR test of endogenous substances and nine therapeutic drugs were evaluated in ten FFPET specimens. Other tests included an evaluation of the effects of necrosis, micro-organisms and homologous DNA sequences on assay performance, and the inclusivity of the assay for less frequent mutations. A >95% hit rate was obtained in blends with >5% mutant alleles, as determined by MPP analysis, at a total DNA input of 150 ng. The overall percent agreement between Sanger sequencing and the cobas test was 96.7% (negative percent agreement 97.5%; positive percent agreement 95.8%). Assay repeatability was 98% when tested with two operators, instruments, and reagent lots. In the external reproducibility study, the agreement was > 99% across all sites, all operators and all reagent lots for 11/12 tumors tested. Test

  2. CD1a, HAM56, CD68 and S-100 are present in lesional skin biopsies from patients affected by autoimmune blistering diseases

    Directory of Open Access Journals (Sweden)

    Ana Maria Abreu Velez

    2014-04-01

    Full Text Available Introduction: Previous research on autoimmune skin blistering diseases (ABD has primarily focused on the humoral immune response; moreover, little attention has been given to the potential role of the antigen presenting cells (APCs in lesional skin. Aim: The purpose of our study was to immunophenotype selected APC in the lesional skin of ABDs, utilizing immunohistochemistry (IHC stains. Materials and Methods: We utilized IHC to stain for dendritic cells (DC, staining with CD1a, CD68, HAM56, and S-100 in lesional skin from 30 patients with endemic pemphigus foliaceus (EPF, 15 controls from the EPF endemic area, and 15 healthy controls from the USA. We also tested archival biopsies from patients with selected ABD, including 30 patients with bullous pemphigoid (BP, 20 with pemphigus vulgaris (PV, 8 with pemphigus foliaceus (PF and 14 with dermatitis herpetiformis (DH and 2 with epidermolysis bullosa acquisita (EBA. Results: Cells stained by CD68, HAM56 and S-100 were present in the majority of the ABD skin biopsies; these cells were located primarily in perivascular infiltrates surrounding dermal vessels subjacent to the blisters. However, these cells were also noted within the blisters, in vessels supplying dermal eccrine glands and ducts, and in areas of dermal endothelial-mesenchymal cell junction-like structures, especially in BP cases. In our CD1a staining, the number and location of positive staining cells varied with each disease, being abundant in most ABD in the epidermis suprajacent to the blisters, or in the epidermis surrounding the blister site if the blister site epidermis was missing. In the control biopsies, most did not display positive IHC staining, with the exception of a few CD1a positive cells in the epidermis Conclusion: Our findings confirm positive IHC staining for APCs in areas of the skin besides the disease blisters. Our findings suggest that the antigen presentation in ABD proceeds in areas distant from the blister site

  3. Study to determine whether intraoperative frozen section biopsy improves surgical treatment of non-melanoma skin cancer

    OpenAIRE

    NICOLETTI, GIOVANNI; BRENTA, FEDERICA; MALOVINI, ALBERTO; MUSUMARRA, GAETANO; SCEVOLA, SILVIA; FAGA, ANGELA

    2012-01-01

    Skin cancers are the most common types of cancer and their incidence has shown an increase of ∼4 to 8% per year over the last 40 years. The majority of skin cancers (∼97%) are non-melanoma skin cancers, mainly represented by basal cell (80%) and squamous cell carcinomas (20%). The use of intra-operative frozen section remains controversial in the surgical treatment of non-melanoma skin cancer, being commonly considered an optional tool, the reliability and effectiveness of which remain questi...

  4. KIT D816V mutation-positive cell fractions in lesional skin biopsies from adults with systemic mastocytosis

    DEFF Research Database (Denmark)

    Kielsgaard Kristensen, Thomas; Broesby-Olsen, Sigurd; Vestergaard, Hanne

    2013-01-01

    Most adults with systemic mastocytosis (SM) carry the somatic KIT D816V mutation, but the occurrence of the mutation in lesional skin remains to be characterized.......Most adults with systemic mastocytosis (SM) carry the somatic KIT D816V mutation, but the occurrence of the mutation in lesional skin remains to be characterized....

  5. Provider-to-provider communication in dermatology and implications of missing clinical information in skin biopsy requisition forms: a systematic review.

    Science.gov (United States)

    Comfere, Nneka I; Sokumbi, Olayemi; Montori, Victor M; LeBlanc, Annie; Prokop, Larry J; Murad, M Hassan; Tilburt, Jon C

    2014-05-01

    Various components of the skin biopsy requisition form (SBRF) may contribute to accurate dermatopathologic interpretation. A search of electronic databases, including those of Ovid MEDLINE In-Process & Other Non-Indexed Citations, Ovid MEDLINE, Ovid EMBASE, the Cochrane Database of Systematic Reviews, the Cochrane Central Register of Controlled Trials, and Scopus, was conducted from inception to October 2011. Two authors independently screened all articles for eligibility. Inclusion criteria required material to represent original studies on skin biopsy and pathology requisition forms. Data abstracted from each article that met the inclusion criteria included details of the study characteristics, including the study location, type of pathology practice, specimen type, type of dermatoses, medical specialty of the requesting provider, suggested clinical components, and format of the SBRF. Of 32 titles and abstracts reviewed, seven articles were included. From these, we determined that dermatologists, general practitioners and surgeons completed SBRFs. Commonly included components were patient demographics and requesting clinician characteristics. Clinical information and differential diagnosis were provided in 4% (two of 48 surgeons) to 36% (18 of 50 dermatologists) of requisitions. Most SBRFs did not include information on specimen type, clinical morphology, photographs or clinical history. The limited medical literature demonstrates variation in the content of SBRFs across clinicians and practices, and suggests an important target for improvement in the quality of communication and dermatologic care by requesting clinicians and pathologists. © 2013 The International Society of Dermatology.

  6. Genotyping of Mycobacterium leprae present on Ziehl-Neelsen-stained microscopic slides and in skin biopsy samples from leprosy patients in different geographic regions of Brazil

    Directory of Open Access Journals (Sweden)

    Amanda Nogueira Brum Fontes

    2012-12-01

    Full Text Available We analysed 16 variable number tandem repeats (VNTR and three single-nucleotide polymorphisms (SNP in Mycobacterium leprae present on 115 Ziehl-Neelsen (Z-N-stained slides and in 51 skin biopsy samples derived from leprosy patients from Ceará (n = 23, Pernambuco (n = 41, Rio de Janeiro (n = 22 and Rondônia (RO (n = 78. All skin biopsies yielded SNP-based genotypes, while 48 of the samples (94.1% yielded complete VNTR genotypes. We evaluated two procedures for extracting M. leprae DNA from Z-N-stained slides: the first including Chelex and the other combining proteinase and sodium dodecyl sulfate. Of the 76 samples processed using the first procedure, 30.2% were positive for 16 or 15 VNTRs, whereas of the 39 samples processed using the second procedure, 28.2% yielded genotypes defined by at least 10 VNTRs. Combined VNTR and SNP analysis revealed large variability in genotypes, but a high prevalence of SNP genotype 4 in the Northeast Region of Brazil. Our observation of two samples from RO with an identical genotype and seven groups with similar genotypes, including four derived from residents of the same state or region, suggest a tendency to form groups according to the origin of the isolates. This study demonstrates the existence of geographically related M. leprae genotypes and that Z-N-stained slides are an alternative source for M. leprae genotyping.

  7. Are whale sharks exposed to persistent organic pollutants and plastic pollution in the Gulf of California (Mexico)? First ecotoxicological investigation using skin biopsies.

    Science.gov (United States)

    Fossi, Maria Cristina; Baini, Matteo; Panti, Cristina; Galli, Matteo; Jiménez, Begoña; Muñoz-Arnanz, Juan; Marsili, Letizia; Finoia, Maria Grazia; Ramírez-Macías, Dení

    2017-09-01

    The whale shark (Rhincodon typus) is an endangered species that may be exposed to micro- and macro-plastic ingestion as a result of their filter-feeding activity, particularly on the sea surface. In this pilot project we perform the first ecotoxicological investigation on whale sharks sampled in the Gulf of California exploring the potential interaction of this species with plastic debris (macro-, micro-plastics and related sorbed contaminants). Due to the difficulty in obtaining stranded specimens of this endangered species, an indirect approach, by skin biopsies was used for the evaluation of the whale shark ecotoxicological status. The levels of organochlorine compounds (PCBs, DDTs), polybrominated diphenyl ethers (PBDEs) plastic additives, and related biomarkers responses (CYP1A) were investigated for the first time in the whale shark. Twelve whale shark skin biopsy samples were collected in January 2014 in La Paz Bay (BCS, Mexico) and a preliminary investigation on microplastic concentration and polymer composition was also carried out in seawater samples from the same area. The average abundance pattern for the target contaminants was PCBs>DDTs>PBDEs>HCB. Mean concentration values of 8.42ng/g w.w. were found for PCBs, 1.31ng/g w.w. for DDTs, 0.29ng/g w.w. for PBDEs and 0.19ng/g w.w. for HCB. CYP1A-like protein was detected, for the first time, in whale shark skin samples. First data on the average density of microplastics in the superficial zooplankton/microplastic samples showed values ranging from 0.00items/m 3 to 0.14items/m 3 . A focused PCA analysis was performed to evaluate a possible correlation among the size of the whale sharks, contaminants and CYP1A reponses. Further ecotoxicological investigation on whale shark skin biopsies will be carried out for a worldwide ecotoxicological risk assessment of this endangerd species. Copyright © 2017 Elsevier Inc. All rights reserved.

  8. The Role of Biopsy in Pediatric Dermatopathology

    Directory of Open Access Journals (Sweden)

    Fatma Şule Afşa

    2011-09-01

    Full Text Available Background and Design: Pediatric dermatology is characterized by skin disorders which have frequencies different from those in adults. Skin biopsies are necessary for differential diagnosis and clinicopathologic correlation is very important. The aim of this study was to evaluate retrospectively the pediatric dermatology cases in whom biopsy was performed for differential diagnosis and to investigate the contribution of biopsy to diagnosis of skin disorders. Material and Methods: The cases from whom biopsy was taken in the pediatric dermatology clinic during a three-year period were evaluated retrospectively for pre-diagnoses, biopsy diagnoses, and success of biopsies.Results: Two hundred thirteen (1.7% skin biopsies had been taken from a total of 12420 patients. Henoch-Schönlein purpura, psoriasis, pityriasis lichenoides, pityriasis rosea, lichen planus, pityriasis rubra pilaris, erythema multiforme, atopic dermatitis, granuloma annulare, and pigmented purpuric dermatosis were the most frequent skin disorders diagnosed dermatopathologically. In a total of 120 (56.3% cases, the biopsy diagnosis was within the pre-diagnosis and a biopsy consistency was present. In 25 (11.7% cases, biopsy had no contribution to the differential diagnosis. An absolutely different diagnosis which was incompatible with the pre-diagnosis had been reported in 10 (4.6% cases. Conclusion: In pediatric dermatology, skin biopsy is very helpful for the differential diagnosis. An easy biopsy procedure for the patient, an effective designation of biopsy indication, a good dermatopathologic correlation and an experienced team of pediatric dermatopathology increase the success of skin biopsies.

  9. Liver biopsy

    Science.gov (United States)

    Biopsy - liver; Percutaneous biopsy ... the biopsy needle to be inserted into the liver. This is often done by using ultrasound. The ... the chance of damage to the lung or liver. The needle is removed quickly. Pressure will be ...

  10. A three year study of metal levels in skin biopsies of whales in the Gulf of Mexico after the Deepwater Horizon oil crisis.

    Science.gov (United States)

    Wise, John Pierce; Wise, James T F; Wise, Catherine F; Wise, Sandra S; Gianios, Christy; Xie, Hong; Walter, Ron; Boswell, Mikki; Zhu, Cairong; Zheng, Tongzhang; Perkins, Christopher; Wise, John Pierce

    2018-02-01

    In response to the explosion of the Deepwater Horizon and the massive release of oil that followed, we conducted three annual research voyages to investigate how the oil spill would impact the marine offshore environment. Most investigations into the ecological and toxicological impacts of the Deepwater Horizon Oil crisis have mainly focused on the fate of the oil and dispersants, but few have considered the release of metals into the environment. From studies of previous oil spills, other marine oil industries, and analyses of oil compositions, it is evident that metals are frequently encountered. Several metals have been reported in the MC252 oil from the Deepwater Horizon oil spill, including the nonessential metals aluminum, arsenic, chromium, nickel, and lead; genotoxic metals, such as these are able to damage DNA and can bioaccumulate in organisms resulting in persistent exposure. In the Gulf of Mexico, whales are the apex species; hence we collected skin biopsies from sperm whales (Physeter macrocephalus), short-finned pilot whales (Globicephala macrorhynchus), and Bryde's whales (Balaenoptera edeni). The results from our three-year study of monitoring metal levels in whale skin show (1) genotoxic metals at concentrations higher than global averages previously reported and (2) patterns for MC252-relevant metal concentrations decreasing with time from the oil spill. Copyright © 2017 Elsevier Inc. All rights reserved.

  11. Quantification of Eosinophilic Granule Protein Deposition in Biopsies of Inflammatory Skin Diseases by Automated Image Analysis of Highly Sensitive Immunostaining

    Directory of Open Access Journals (Sweden)

    Peter Kiehl

    1999-01-01

    Full Text Available Eosinophilic granulocytes are major effector cells in inflammation. Extracellular deposition of toxic eosinophilic granule proteins (EGPs, but not the presence of intact eosinophils, is crucial for their functional effect in situ. As even recent morphometric approaches to quantify the involvement of eosinophils in inflammation have been only based on cell counting, we developed a new method for the cell‐independent quantification of EGPs by image analysis of immunostaining. Highly sensitive, automated immunohistochemistry was done on paraffin sections of inflammatory skin diseases with 4 different primary antibodies against EGPs. Image analysis of immunostaining was performed by colour translation, linear combination and automated thresholding. Using strictly standardized protocols, the assay was proven to be specific and accurate concerning segmentation in 8916 fields of 520 sections, well reproducible in repeated measurements and reliable over 16 weeks observation time. The method may be valuable for the cell‐independent segmentation of immunostaining in other applications as well.

  12. Prostate biopsy

    Science.gov (United States)

    ... give the cells a grade called a Gleason score . This helps predict how fast the cancer will ... TRUS); Stereotactic transperineal prostate biopsy (STPB) Images Male reproductive anatomy References Babayan RK, Katz MH. Biopsy prophylaxis, ...

  13. Kidney biopsy

    Science.gov (United States)

    ... the kidney (in rare cases, may require a blood transfusion) Bleeding into the muscle, which might cause soreness Infection (small risk) Alternative Names Renal biopsy; Biopsy - kidney Images Kidney anatomy ...

  14. Concordance of DNA methylation profiles between breast core biopsy and surgical excision specimens containing ductal carcinoma in situ (DCIS).

    Science.gov (United States)

    Chen, Youdinghuan; Marotti, Jonathan D; Jenson, Erik G; Onega, Tracy L; Johnson, Kevin C; Christensen, Brock C

    2017-08-01

    The utility and reliability of assessing molecular biomarkers for translational applications on pre-operative core biopsy specimens assume consistency of molecular profiles with larger surgical specimens. Whether DNA methylation in ductal carcinoma in situ (DCIS), measured in core biopsy and surgical specimens are similar, remains unclear. Here, we compared genome-scale DNA methylation measured in matched core biopsy and surgical specimens from DCIS, including specific DNA methylation biomarkers of subsequent invasive cancer. DNA was extracted from guided 2mm cores of formalin fixed paraffin embedded (FFPE) specimens, bisulfite-modified, and measured on the Illumina HumanMethylation450 BeadChip. DNA methylation profiles of core biopsies exhibited high concordance with matched surgical specimens. Within-subject variability in DNA methylation was significantly lower than between-subject variability (all Pcore biopsy and surgical specimens, 15%, and a pathway analysis of these CpGs indicated enrichment for genes related with wound healing. Our results indicate that DNA methylation measured in core biopsies are representative of the matched surgical specimens and suggest that DCIS biomarkers measured in core biopsies can inform clinical decision-making. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

  15. Determination to genotypes of human papillomavirus and analysis with immunohistochemical marker Ki67 in biopsy with cervical dysplasia patients of Hospital Dr. Max Peralta in Cartago during 2013

    International Nuclear Information System (INIS)

    Blanco Chaves, Ana Lorely

    2014-01-01

    Cervical cancer is one of the leading causes of death among women worldwide, occupying in Costa Rica the fourth place. The human papillomavirus (HPV) is shown that is linked to at least 99.7% of cases, mainly associated with high risk genotypes. A study was conducted of type descriptive where were implemented molecular techniques such as: PCR, reverse hybridization for the determination of different HPV genotypes, and immunohistochemical detection of cell proliferation marker Ki67 in paraffin-embedded cervical biopsies from patients at the Hospital Dr. Max Peralta in Cartago, during the year 2013. The most frequent genotype that was determined among the study population has been 39, which was presented in 53% of cases. In addition, 65% of biopsies studied have showed mixed infections of HPV. (author) [es

  16. Cold knife cone biopsy

    Science.gov (United States)

    ... biopsy; Pap smear - cone biopsy; HPV - cone biopsy; Human papilloma virus - cone biopsy; Cervix - cone biopsy; Colposcopy - cone biopsy Images Female reproductive anatomy Cold cone biopsy Cold cone removal References Baggish ...

  17. Development and validation of a microRNA based diagnostic assay for primary tumor site classification of liver core biopsies

    DEFF Research Database (Denmark)

    Perell, Katharina; Vincent, Martin; Vainer, Ben

    2015-01-01

    for normal liver tissue contamination. Performance was estimated by cross-validation, followed by independent validation on 55 liver core biopsies with a tumor content as low as 10%. A microRNA classifier developed, using the statistical contamination model, showed an overall classification accuracy of 74...... on classification. MicroRNA profiling was performed using quantitative Real-Time PCR on formalin-fixed paraffin-embedded samples. 278 primary tumors and liver metastases, representing nine primary tumor classes, as well as normal liver samples were used as a training set. A statistical model was applied to adjust.......5% upon independent validation. Two-thirds of the samples were classified with high-confidence, with an accuracy of 92% on high-confidence predictions. A classifier trained without adjusting for liver tissue contamination, showed a classification accuracy of 38.2%. Our results indicate that surrounding...

  18. Nail biopsy: A user's manual

    Directory of Open Access Journals (Sweden)

    Chander Grover

    2018-01-01

    Full Text Available Nail biopsy is a procedure not routinely resorted to; but when indicated, it is often the only clue left for diagnosis. At such times, it pays to be conversant with it. It is an investigation that not only provides etiologic, diagnostic, and prognostic information but also aids in understanding the pathogenesis of nail diseases. It can be of therapeutic value, especially with respect to nail tumors. This article compiles the procedural techniques for nail biopsy of various types and attempts to summarize the evidence available in the literature. The objective of nail biopsy is to clinch a precise diagnosis of nail pathology with a simple and safe surgical procedure, avoiding pain or permanent nail damage. Patient selection is of utmost importance, wherein, the patient does not have typical skin lesions, yields inadequate information on routine nail investigations, and has no peripheral vascular compromise. The patient needs to be explained about the risks associated, the expected functional handicap, the time required for regrowth, a possibility of permanent nail dystrophy, and a possibility of not achieving a diagnosis even after the biopsy. Techniques and types of various nail biopsies are being discussed in this article. The specimen could be collected as an excision biopsy, punch biopsy, shave biopsy, or longitudinal biopsy. The trick lies in choosing the appropriate area for biopsy. Various biopsy types discussed in this article include nail plate biopsy (easiest and least scarring; nail bed biopsy (elliptical excision or punch; nail matrix biopsy (elliptical excision, punch excision (≤3 mm or tangential/shave excision; and nail fold biopsy. Complications reported along with means to minimize them are also discussed.

  19. Avaliação de dois métodos de extração de DNA de material parafinado para amplificação em PCR Evaluation of two methods of DNA extraction from paraffin-embedded material for PCR amplification

    Directory of Open Access Journals (Sweden)

    Luciana Estevam Simonato

    2007-04-01

    Full Text Available INTRODUÇÃO: Diversos métodos para extração de DNA a partir de tecidos biológicos inclusos em parafina encontram-se descritos na literatura, sendo o sucesso desse procedimento de grande importância para a realização de métodos moleculares de diagnóstico empregando a reação em cadeia da polimerase (PCR. OBJETIVO: Este estudo avaliou dois métodos de extração de DNA de material parafinado, visando à amplificação do DNA genômico pela técnica da PCR. MATERIAL E MÉTODO: Foram utilizadas 35 amostras de casos de carcinoma epidermóide de assoalho bucal diagnosticados e tratados no Centro de Oncologia Bucal da Universidade Estadual Paulista (Unesp. Os métodos de extração de DNA avaliados incluíram: 1. digestão com proteinase K seguida por purificação com Chelex 100® (BioRad; e 2. sistema QIAamp DNA minikit® (Qiagen. O DNA obtido foi quantificado por espectrofotometria e amplificado pela técnica da PCR, utilizando-se oligonucleotídeos iniciadores para betaglobina. RESULTADOS: A concentração de DNA obtido do material extraído com o primeiro método apresentou média de 120,62 ng/µl com razão entre as leituras das absorbâncias 260/280 variando de 0,8 a 1,41. Para as amostras extraídas com o segundo procedimento, o rendimento médio foi de 67,38 ng/µl, no entanto a razão 260/280 variou entre 1,11 e 2,53. O material foi submetido à PCR e, das 35 amostras extraídas com cada método, respectivamente, 29 e 30 apresentaram sinal positivo. CONCLUSÃO: Os dois métodos utilizados para obtenção de DNA de material parafinado apresentaram desempenho semelhante, revelando que ambos têm potencial para auxiliar na prática da biologia molecular diagnóstica, assim como no estudo diagnóstico retrospectivo em material parafinizado.BACKGROUND: There are several methods for DNA extraction from formalin-fixed paraffin-embedded tissues reported in the literature. High success rate on this procedure is important for the use of

  20. Skin

    International Nuclear Information System (INIS)

    Hunter, R.D.

    1985-01-01

    Malignant disease involving the skin represents a significant work load to the general radiotherapist and can involve interesting diagnostic and therapeutic decisions. Primary skin cancer is also relatively common and there is a need to provide an efficient service in which the first treatment is successful in the majority of patients. The reward for careful attention to technique is very considerable both in terms of clinical cancer control and functional results. Squamous cell carcinoma, basal cell carcinoma, and intra-epidermal carcinoma constitute the majority of the lesions dealt with clinically, but metastatic disease, lymphomas, and malignant melanomas are also referred regularly for opinions and may require radiotherapy. The general principle of the techniques of assessment and radiotherapeutic management to be described are equally applicable to any malignant skin tumour once the decision has been made to accept it for radiotherapy. Dosage and fractionation may have to be adjusted to allow for the nature of the disease process and the intent of the treatment

  1. Examine Your Skin

    Medline Plus

    Full Text Available ... Store In Memory Melanoma Info Melanoma Facts Melanoma Prevention Sunscreen Suggestions Examine Your Skin Newly Diagnosed? Understanding ... Biopsy: The First Step Sentinel Node Biopsy Melanoma Treatment: Stages I & II Melanoma Treatment: Stage III Melanoma ...

  2. Nerve Biopsy In The Diagnosis Of Leporsy

    OpenAIRE

    Hazra B; Banerjee P P; Bhattacharyya N K; Gupta P N; Barbhunia J N; Sanyal S

    1997-01-01

    Skin and nerve biopsies were done in 33 cases of different clinical types of leprosy selected from Dermatology OPD of Medical College and Hospitals, Calcutta during 1994-95. Histopathological results were compared with emphasis on the role of nerve biopsies in detection of patients with multibacillary leprosy. The evident possibility of having patients with multibacillary leprosy in peripheral leprosy with multiple drugs. It is found that skin and nerve biopsy are equally informative in borde...

  3. Proteins Annexin A2 and PSA in Prostate Cancer Biopsies Do Not Predict Biochemical Failure.

    Science.gov (United States)

    Lamb, David S; Sondhauss, Sven; Dunne, Jonathan C; Woods, Lisa; Delahunt, Brett; Ferguson, Peter; Murray, Judith; Nacey, John N; Denham, James W; Jordan, T William

    2017-12-01

    We previously reported the use of mass spectrometry and western blotting to identify proteins from tumour regions of formalin-fixed paraffin-embedded biopsies from 16 men who presented with apparently localized prostate cancer, and found that annexin A2 (ANXA2) appeared to be a better predictor of subsequent biochemical failure than prostate-specific antigen (PSA). In this follow-up study, ANXA2 and PSA were measured using western blotting of proteins extracted from biopsies from 37 men from a subsequent prostate cancer trial. No significant differences in ANXA2 and PSA levels were observed between men with and without biochemical failure. The statistical effect sizes were small, d=0.116 for ANXA2, and 0.266 for PSA. ANXA2 and PSA proteins measured from biopsy tumour regions are unlikely to be good biomarkers for prediction of the clinical outcome of prostate cancer presenting with apparently localized disease. Copyright© 2017, International Institute of Anticancer Research (Dr. George J. Delinasios), All rights reserved.

  4. Histological Spectrum of Idiopathic Noncirrhotic Portal Hypertension in Liver Biopsies From Dialysis Patients.

    Science.gov (United States)

    Lee, Hwajeong; Ainechi, Sanaz; Singh, Mandeep; Ells, Peter F; Sheehan, Christine E; Lin, Jingmei

    2015-09-01

    Liver biopsy is performed for various indications in dialysis patients. Being a less-common subset, the hepatic pathology in renal dialysis is not well documented. Idiopathic noncirrhotic portal hypertension (INCPH) is a clinical entity associated with unexplained portal hypertension and/or a spectrum of histopathological vascular changes in the liver. After encountering INCPH and vascular changes of INCPH in 2 renal dialysis patients, we sought to further investigate this noteworthy association. A random search for patients on hemodialysis or peritoneal dialysis with liver biopsy was performed. Hematoxylin and eosin, reticulin, trichrome, and CK7 stains were performed on formalin-fixed, paraffin-embedded tissue sections. Histopathological features were reviewed, and the results were correlated with clinical findings. In all, 13 liver biopsies were retrieved. The mean cumulative duration of dialysis was 50 months (range = 17 months to 11 years). All patients had multiple comorbidities. Indications for biopsy were a combination of abnormal liver function tests (6), portal hypertension (4), ascites (3), and possible cirrhosis (3). Two patients with portal hypertension underwent multiple liver biopsies for diagnostic purposes. All (100%) biopsies showed some histological features of INCPH, including narrowed portal venous lumen (9), increased portal vascular channels (8), shunt vessels (3), dilated sinusoids (9), regenerative nodule (5), and features of venous outflow obstruction (3). No cirrhosis was identified. Liver biopsies from patients on dialysis demonstrate histopathological vascular changes of INCPH. Some (31%) patients present with portal hypertension without cirrhosis. The histological changes may be reflective of underlying risk factors for INCPH in this group. © The Author(s) 2015.

  5. Biopsy in Musculoskeletal Tumors

    Directory of Open Access Journals (Sweden)

    Mohammad Gharehdaghi

    2014-09-01

    proximity to the skin incision, because this tract is also contaminated and must be excised with the surgical specimen. Imaging-guided core needle biopsy is a well-established technique for the diagnosis of bone and soft tissue tumors and tumor-like lesions in specialized orthopedic oncology centers. Although large lesions of the limbs can easily be biopsied without image guidance, lesions in the spine, para spinal area, and pelvis are difficult to target, therefore taking the advantage of C.T. guidance will improve the accuracy of targeting the lesion for biopsy purposes. We can benefit from image intensifiers for targeting limb lesions rather than C.T. guidance. Also sonographic guide can be applied for soft tissue lesions (Figure D, E, F. In soft tissue tumors, the results of percutaneous CNB are relatively inferior compared to open biopsy whereas almost equal results are expected for bony tumors except for low-grade chondrosarcoma. CNB is a safe, minimally invasive, and cost effective technique for the diagnosis of bone lesions if done by an experienced orthopedic oncologic surgeon and be evaluated by an experienced anatomical bone pathologist (1, 3. For soft tissue tumors, CNB results depend on the size of the lesion, its location and amount of tumor necrosis. Guided needle biopsy have become the standard technique in most orthopedic oncologic centers. The accuracy of this method in our center is more than 90% for bone tumors. Cores should be taken in different directions including areas of central necrotic tissues but from a single well planned entrance. The procedure is quick, especially for bone CNB or soft tissue FNA and CNB, and the diagnosis can be achieved within 24 – 48 hours. The material should be sufficient for immunohistochemistry evaluations as well (1-3. Because I have seen 3 cases of tumor implantation at the towel clips puncture site including 2 chondrosarcomas and a case of malignant schowanoma, so I highly suggest that never crush the skin by towel

  6. Mast cell concentration and skin wound contraction in rats treated with Brazilian pepper essential oil (Schinus terebinthifolius Raddi).

    Science.gov (United States)

    Estevão, Lígia Reis Moura; Medeiros, Juliana Pinto de; Simões, Ricardo Santos; Arantes, Rosa Maria Esteves; Rachid, Milene Alvarenga; Silva, Regildo Márcio Gonçalves da; Mendonça, Fábio de Souza; Evêncio-Neto, Joaquim

    2015-04-01

    To evaluate wound contraction and the concentration of mast cells in skin wounds treated with 5% BPT essential oil-based ointment in rats. Twenty rats, male, of adult age, were submitted to skin surgery on the right (RA) and left antimeres (LA) of the thoracic region. They were divided into two groups: control (RA - wounds receiving daily topical application of vaseline and lanolin) and treated (LA - wounds treated daily with the topical ointment). The skin region with wounds were collected at days 4, 7, 14 and 21 after surgery. Those were fixed in 10% formaldehyde and later processed for paraffin embedding. Sections were obtained and stained by H.E for histopathology analysis. The degree of epithelial contraction was measured and mast cell concentration were also evaluated. The treated group showed higher mast cell concentrations (poil increases mast cell concentration and promotes skin wound contraction in rats.

  7. SISH/CISH or qPCR as alternative techniques to FISH for determination of HER2 amplification status on breast tumors core needle biopsies: a multicenter experience based on 840 cases.

    Science.gov (United States)

    Jacquemier, Jocelyne; Spyratos, Frédérique; Esterni, Benjamin; Mozziconacci, Marie-Joëlle; Antoine, Martine; Arnould, Laurent; Lizard, Sarab; Bertheau, Philippe; Lehmann-Che, Jacqueline; Fournier, Cécile Blanc; Krieger, Sophie; Bibeau, Frédéric; Lamy, Pierre-Jean; Chenard, Marie Pierre; Legrain, Michèle; Guinebretière, Jean-Marc; Loussouarn, Delphine; Macgrogan, Gaëtan; Hostein, Isabelle; Mathieu, Marie Christine; Lacroix, Ludovic; Valent, Alexander; Robin, Yves Marie; Revillion, Françoise; Triki, Magali Lacroix; Seaume, Aline; Salomon, Anne Vincent; de Cremoux, Patricia; Portefaix, Geneviève; Xerri, Luc; Vacher, Sophie; Bièche, Ivan; Penault-Llorca, Frédérique

    2013-07-22

    Until now, FISH has been the gold standard technique to identify HER2 amplification status in ambiguous cases of breast cancer. Alternative techniques have been developed to increase the capacities of investigating HER2 amplification status. The aims of this multicenter study in a large series of breast cancer patients were to prospectively compare the level of performance of CISH, SISH, and qPCR alternative techniques on paraffin-embedded core biopsies with "gold standard FISH" for evaluation of HER2 amplification status. This study was performed on 840 cases scored by immunohistochemistry (IHC): 0=317 (38%), 1+=183 (22%), 2+=109 (13%), 3+=231 (27%). Each of the 15 French centers participating in the study analyzed 56 breast carcinoma cases diagnosed on fixed paraffin-embedded core biopsies. HER2 amplification status was determined by commercially available FISH used as the reference technique with determination of the HER2/CEN17 ratio or HER2 copy number status. The alternative techniques performed on the same cases were commercially available SISH or CISH and a common qPCR method especially designed for the study including a set of 10 primer pairs: 2 for HER2 (exons 8 and 26), 5 to evaluate chromosome 17 polysomy TAOK1, UTP6, MRM1, MKS1, SSTR2 and 3 for diploidy control TSN, LAP3 and ADAMTS16. The concordance between IHC and FISH was 96% to 95% based on the HER2/CEN17 ratio (n=766) or HER2 copy number (n=840), respectively. The concordance of the alternative techniques with FISH was excellent: 97% and 98% for SISH (498 and 587 cases), 98% and 75% for CISH (108 and 204 cases) and 95% and 93% (699 and 773 cases) for qPCR based on the HER2/CEN17 ratio or HER2 copy number, respectively. Similarly, sensitivity ranged from 99% to 95% for SISH, 100% to 99% for CISH and 89% to 80% for qPCR. The concordance with FISH (ratio) in the 2+ cases was 89% for SISH, 100% for CISH and 93% for qPCR. These alternative techniques showed an excellent concordance with FISH in core

  8. Comparação de três protocolos de extração de DNA a partir de tecido fixado em formol e incluído em parafina Comparison of three DNA extraction protocols from formaldehyde-fixed and paraffin-embedded tissues

    Directory of Open Access Journals (Sweden)

    José Veríssimo Fernandes

    2004-06-01

    Full Text Available OBJETIVO: Padronizar um método alternativo para extração de DNA a partir de tecido fixado em formol e conservado em arquivos de blocos de parafina, visando à realização de estudos retrospectivos. MÉTODOS: Comparou-se a eficiência de protocolos de extração de DNA a partir de tecido parafinado, para análise por reação em cadeia de polimerase (PCR, tomando-se como parâmetro um protocolo baseado em um kit comercial. Foram feitas extrações do DNA de 60 espécimes por três métodos: o protocolo A, baseado no kit GlassMAX; o B, utilizando-se o kit GFX TM; e o C, tendo como base o método de Banerjee et al.(2. A integridade e a suficiência do DNA presente na amostra foram avaliadas pela amplificação por PCR de um segmento de 110pb do gene da beta-globina humana, com visualização por meio de eletroforese em gel de poliacrilamida, corado pela prata. Resultados: Das 60 amostras analisadas, 45 apresentaram resultado positivo na PCR quando o DNA foi extraído por qualquer um dos três protocolos. Em seis amostras, a amplificação foi positiva apenas para o DNA extraído pelos protocolos A e C. Em três amostras, o resultado foi positivo apenas para o DNA extraído pelo protocolo A, e em duas, apenas para o DNA extraído pelo protocolo C. CONCLUSÕES: O protocolo C apresentou desempenho semelhante ao do protocolo A, com as vantagens de apresentar menor custo, dispensar o uso de kit comercial, além de não utilizar solventes orgânicos, revelando-se uma alternativa viável para a obtenção de DNA a partir de tecido fixado em formol e incluído em parafina.OBJECTIVE: To set up a method for DNA extraction from paraffin embedded cervical cancer specimens, previously formalin-fixed, aiming to accomplish retrospective analysis. METHODS: Sixty specimens were submitted to DNA extraction by three different methods. All of them involved digestion of the tissues by proteinase K, followed by DNA purification, based in three different approaches

  9. Microdissecção e captura a laser na investigação do gene TP53 em tecidos incluídos em parafina Laser-capture microdissection for TP53 gene analysis in paraffin-embedded tissues

    Directory of Open Access Journals (Sweden)

    Shadia Muhammad Ihlaseh

    2007-02-01

    characterize its enormous potential for diagnosis and research. OBJECTIVE: This study describes the standardization of LCM and DNA extraction from formalin fixed and paraffin-embedded tissues. MATERIAL AND METHOD: The gene TP53 exon 8 and the cyclophilin gene were studied in normal and neoplastic liver and kidney samples from a chemical carcinogenesis model in rat. DNA extraction was confirmed by nested-PCR. RESULTS: Histological sections preparation for LCM and the nested-PCR procedures were standardized; 48.3% amplifications of the gene TP53 exon 8 and 51.7% of the cyclophilin gene samples were obtained. When at least one of the gene segments was considered, 79.3% samples presented amplification. DISCUSSION AND CONCLUSION: Procedures for DNA extraction from formalin fixed and paraffin-embedded tissues collected by LCM were standardized. They can be useful for DNA collection for molecular studies.

  10. Nerve Biopsy In The Diagnosis Of Leporsy

    Directory of Open Access Journals (Sweden)

    Hazra B

    1997-01-01

    Full Text Available Skin and nerve biopsies were done in 33 cases of different clinical types of leprosy selected from Dermatology OPD of Medical College and Hospitals, Calcutta during 1994-95. Histopathological results were compared with emphasis on the role of nerve biopsies in detection of patients with multibacillary leprosy. The evident possibility of having patients with multibacillary leprosy in peripheral leprosy with multiple drugs. It is found that skin and nerve biopsy are equally informative in borderline and lepromatour leprosy and is the only means to diagnose polyneuritic leprosy. Nerve biopsy appears to be more informative in the diagnosis of all clinical types of leprosy.

  11. Latent and lytic HHV-8 mRNA expression in PBMCs and Kaposi's sarcoma skin biopsies of AIDS Kaposi's sarcoma patients

    NARCIS (Netherlands)

    Polstra, Abeltje M.; Goudsmit, Jaap; Cornelissen, Marion

    2003-01-01

    Human herpes virus 8 (HHV-8) is associated with all clinical forms of Kaposi's sarcoma. HHV-8 DNA is present in Kaposi's sarcoma biopsies and is observed regularly in saliva and less consistently in blood of Kaposi's sarcoma patients. The expression pattern of latent (ORF 73) and lytic (vGCR,

  12. Liver Biopsy

    Science.gov (United States)

    ... called if any of the following occur: ● Persistent abdominal or chest pain ● Vomiting ● Pallor, weakness or dizziness ● Bleeding from the site of the biopsy ● Passage of tarry black stools For more information or to locate a pediatric gastroen- terologist in your area please visit our ...

  13. A new technique for Gram staining paraffin-embedded tissue.

    Science.gov (United States)

    Engbaek, K; Johansen, K S; Jensen, M E

    1979-01-01

    Five techniques for Gram staining bacteria in paraffin sections were compared on serial sections of pulmonary tissues from eight bacteriological necropsies. Brown and Hopp's method was the most satisfactory for distinguishing Gram-positive and Gram-negative bacteria. However, this method cannot be recommended as the preparations were frequently overstained, and the Gram-negative bacteria were stained indistinctly. A modification of Brown and Hopps' method was developed which stains larger numbers of Gram-negative bacteria and differentiates well between different cell types and connective tissue, and there is no risk of overstaining. PMID:86548

  14. Improvised double-embedding technique of minute biopsies: a mega boon to histopathology laboratory.

    Science.gov (United States)

    Yadav, Lokendra; Thomas, Sarega; Kini, Usha

    2015-01-01

    Optimal orientation of minute mucosal biopsies is essential for a definite diagnosis in gastrointestinal pathology or to visualize neural plexuses in Hirschsprung disease. The problem of minute size of the biopsy and its orientation gets compounded when they are from neonates and mandates exhaustive strip cuts, thus delaying reporting. A modified agar-paraffin technique is aimed to make tissue embedding efficient and user-friendly by inking mapping biopsies (one or more) either fresh or fixed with surgical coloring inks followed by embedding first in agar after orientation and followed thereafter by processing, re-embedding in paraffin wax, sectioning and staining. The tissues in agar paraffin block were found to be well processed, firm, held secure and well preserved. The blocks were easy to cut, with serial sections of thickness 2-3 μ and easy to spread. The colored inks remained permanently on the tissues both in the block as well as on the sections which helped in easy identification of tissues. Agar did not interfere with any stain such as Hematoxylin and Eosin or with histochemical stains, enzyme histochemistry or immunohistochemistry. Inking biopsies and pooling them in a block when obtained from the same patient reduced the number of tissue blocks. The modified agar-paraffin embedding technique is a simple reliable user friendly method that can greatly improve the quality of diagnostic information from minute biopsies by optimal orientation, better quality of sections, faster turnaround time and cost-effectiveness by economizing on the number of paraffin blocks, manpower, chemical reagents and laboratory infrastructure.

  15. Improvised double-embedding technique of minute biopsies: A mega boon to histopathology laboratory

    Directory of Open Access Journals (Sweden)

    Lokendra Yadav

    2015-01-01

    Full Text Available Introduction: Optimal orientation of minute mucosal biopsies is essential for a definite diagnosis in gastrointestinal pathology or to visualize neural plexuses in Hirschsprung disease. The problem of minute size of the biopsy and its orientation gets compounded when they are from neonates and mandates exhaustive strip cuts, thus delaying reporting. Aim: A modified agar-paraffin technique is aimed to make tissue embedding efficient and user-friendly by inking mapping biopsies (one or more either fresh or fixed with surgical coloring inks followed by embedding first in agar after orientation and followed thereafter by processing, re-embedding in paraffin wax, sectioning and staining. Results: The tissues in agar paraffin block were found to be well processed, firm, held secure and well preserved. The blocks were easy to cut, with serial sections of thickness 2-3 μ and easy to spread. The colored inks remained permanently on the tissues both in the block as well as on the sections which helped in easy identification of tissues. Agar did not interfere with any stain such as Hematoxylin and Eosin or with histochemical stains, enzyme histochemistry or immunohistochemistry. Inking biopsies and pooling them in a block when obtained from the same patient reduced the number of tissue blocks. Conclusion: The modified agar-paraffin embedding technique is a simple reliable user friendly method that can greatly improve the quality of diagnostic information from minute biopsies by optimal orientation, better quality of sections, faster turnaround time and cost-effectiveness by economizing on the number of paraffin blocks, manpower, chemical reagents and laboratory infrastructure.

  16. Hepatitis E in liver biopsies from patients with acute hepatitis of clinically unexplained origin.

    Directory of Open Access Journals (Sweden)

    Uta eDrebber

    2013-12-01

    Full Text Available Hepatitis E virus (HEV is a small RNA virus and the infectious agent of hepatitis E that occurs worldwide either as epidemics in Asia caused by genotype 1 and 2 or as sporadic disease in industrialized countries induced by genotype 3 and 4. The frequency might be underestimated in central Europe as a cause of acute hepatitis. Therefore, we analyzed on liver biopsies, if cases of acute hepatitis with clinically unknown or obscure diagnosis were actually caused by the infection with HEV.We included 221 liver biopsies retrieved from the files of the institute of pathology during the years 2000 till 2010 that were taken from patients with acute hepatitis of obscure or doubtful diagnosis. From all biopsies RNA was extracted, prepared, and subjected to RT-PCR with specific primers. Amplified RNA was detected in 7 patients, sequenced and the genotype 3 could be determined in four of the seven of positive specimens from 221 samples. Histopathology of the biopsies revealed a classic acute hepatitis with cholestatic features and in some cases confluent necrosis in zone 3. Histology in a cohort of matched patients was less severe and showed more eosinophils. The analysis of the immune response by subtyping of liver infiltrating lymphocytes showed circumstantial evidence of adaptive immune reaction with CD 8 positive CTLs being the dominant lymphocyte population.In conclusion, in doubtful cases of acute hepatitis of unknown origine hepatitis E virus infection should be considered as etiology in central Europe. We demonstrate for the first time that the diagnosis can be made in paraffin-embedded liver biopsies reliably when no serum is available and also the genotype can be determined. The analysis of the immune response by subtyping of liver infiltrating lymphocytes indicates an adaptive mechanism suggesting in analogy with HAV, HBV and HCV that the virus itself is not cytopathic but liver damage is due to immune reaction.

  17. Low sensitivity of type VII collagen enzyme-linked immunosorbent assay in epidermolysis bullosa acquisita : serration pattern analysis on skin biopsy is required for diagnosis

    NARCIS (Netherlands)

    Terra, J. B.; Jonkman, M. F.; Diercks, G. F. H.; Pas, H. H.

    BackgroundThe type VII collagen (coll VII) enzyme-linked immunosorbent assay (ELISA) has been reported to have high sensitivity (>93%) and specificity (>96%) for diagnosing epidermolysis bullosa acquisita (EBA) in patients who are seropositive on indirect immunofluorescence on salt-split skin (SSS).

  18. Comparação de três protocolos distintos para extração de RNA de amostras fixadas em formalina e emblocadas em parafina Comparison of three different protocols for extracting RNA from formalin-fixed paraffin-embedded tissues

    Directory of Open Access Journals (Sweden)

    Gisele Rodrigues Gouveia

    2011-12-01

    Full Text Available INTRODUÇÃO: Tecidos fixados em formalina e emblocados em parafina (FFEP são importantes fontes de amostras para estudos retrospectivos. Apesar de sua capacidade de preservação de proteínas e morfologia celular, a formalina interfere negativamente em testes de biologia molecular por fragmentar e modificar quimicamente os ácidos nucleicos, particularmente o ácido ribonucleico (RNA. OBJETIVO: Comparar a eficiência de três diferentes protocolos de extração de RNA para análise de expressão gênica de tecidos FFEP. MATERIAL E MÉTODOS: Amostras de linfonodo humano FEEP foram submetidas à extração de RNA utilizando-se os kits Ambion e Arcturus Bioscience e o método clássico de Trizol. Após a extração, o RNA foi quantificado e testado quanto à sua capacidade de amplificaç��o pela reação em cadeia da polimerase em tempo real (RT-PCR utilizando primers do gene endógeno gliceraldeído-3 fosfato desidrogenase (GAPDH. DISCUSSÃO/CONCLUSÃO: Todos os protocolos testados produziram quantidades adequadas e suficientes de RNA total, entretanto, somente os protocolos com uso dos kits Ambion e Arcturus produziram RNA capaz de ser amplificado pela PCR.INTRODUCTION: Formalin fixed paraffin embedded (FFPE tissues are an important sample source for retrospective studies. Despite its ability to preserve proteins and cell morphology, formalin hinders Molecular Biology tests once it fragments and chemically modifies nucleic acids, particularly RNA. OBJECTIVE: To compare the efficiency of three different RNA extraction protocols for gene expression analysis of FFEP tissues. MATERIAL AND METHODS: RNA was extracted from FFPE samples of human lymph by means of Ambion and Arcturus Bioscience kits and the classical Trizol method. After extraction, RNA was quantified and tested for amplification through real time polymerase chain reaction (RT-PCR using glyceraldehydes-3 phosphate dehydrogenase (GAPDH endogenous gene primers. DISCUSSION

  19. Detecção molecular de herpesvírus bovino 1 e 5 em amostras de encéfalo conservadas em formol e emblocadas em parafina provenientes de bovinos com doença neurológica Molecular detection of bovine herpesvirus 1 and 5 in formalin-fixed, paraffin-embedded samples from cattle with neurological disease

    Directory of Open Access Journals (Sweden)

    Laura P. Arruda

    2010-08-01

    Full Text Available A infecção por herpesvírus bovino (BoHV é uma das principais causas de doença neurológica em bovinos na região Centro-Oeste do Brasil. O uso de técnicas moleculares de diagnóstico representa uma contribuição importante para o estudo dessa doença. Este trabalho descreve o uso de uma técnica específica de PCR multiplex para identificar BoHV-5 e BoHV-1 em 76 amostras de encéfalo de bovinos fixadas em formol e incluídas em parafina. Com base nas alterações histológicas, as amostras foram separadas em 2 grupos: o Grupo 1 era composto de 40 amostras de bovinos com meningoencefalite necrosante característica da infecção por BoHV; no Grupo 2 estavam 36 amostras de casos com encefalite não-supurativa inespecífica. Identificação de BoHV-5 foi constatada em 40% das amostras do grupo 1 e em 33% das amostras do grupo 2. Não houve amplificação de DNA de BoHV-1 em nenhuma amostra.Bovine herpesvirus (BoHV is an important cause of neurological disease in cattle in the Midwest Brazil. The application of molecular diagnostic techniques represents an important contribution for the study of BoHV. This paper describes the detection of BoHV-5 and BoHV-1 by a specific multiplex PCR assay in 76 paraffin-embedded samples from central nervous system (CNS of cattle with neurological disorders. The samples were divided into 2 groups according to the histological features: Group 1 was composed of 40 cases of necrotizing meningoencephalitis (characteristic of BoHV infection, and Group 2 was composed of 36 cases of nonspecific nonsuppurative meningoencephalitis. Positive results for BoHV-5 accounted for 40% of the samples in the group 1 and 33% in the group 2. No detection of BoHV-1 was recorded.

  20. Optimization of methods to assess mitochondrial DNA in archival paraffin-embedded tissues from mammary canine tumors Otimização dos métodos para avaliar o DNA mitocondrial obtido a partir de tumores mamários caninos incluídos em parafina

    Directory of Open Access Journals (Sweden)

    Angélica C. Bertagnolli

    2008-08-01

    Full Text Available In this study we describe the alterations used to extract and amplify mitochondrial desoxyribonucleic acid (DNA from formalin-fixed paraffin-embedded samples of canine mammary tumors. The epithelial and mesenchymal components (chondromyxoid and chondroid of each tumor, as well as the normal mammary gland tissues, were manually microdissected from 19 mixed canine mammary tumors (10 benign mixed tumors and nine carcinomas arising in mixed tumors. DNA was extracted by Invisorb® Spin Tissue Mini Kit, with protocol changes proposed by the manufacturer. A 273-bp fragment was amplified by polymerase chain reaction (PCR and submitted to automatic sequence analysis. The fragment was successfully analyzed in 100% of the samples. However, an additional lysis step, the reduction of volume in buffer solutions and PCR, a higher annealing temperature and an increase in the number of PCR cycles were required. The initial PCR products were diluted and re-amplified in six samples so that they could be successfully analyzed.A presente comunicação descreve as modificações usadas para extrair e amplificar o DNA mitocondrial obtido de amostras de tumores mamários caninos fixados em formol tamponado a 10% e incluídos em parafina. Os componentes epiteliais e mesenquimais (condromixóide e condróide, bem como a mama normal adjacente, foram microdissectados manualmente de 19 tumores mamários (10 tumores mistos benignos e nove carcinomas em tumores mistos. O DNA foi extraído utilizando-se o Invisorb® Spin Tissue Mini Kit com modificações do protocolo proposto pelo fabricante. Um fragmento de 273-pb foi amplificado por reação em cadeia da polimerase (PCR e seqüenciado em seqüenciador automático. O fragmento foi analisado em 100% das amostras, entretanto modificações como lise adicional, redução do volume das soluções de extração e PCR, aumento da temperatura de anelamento e do número de ciclos de amplificação foram necessárias. Em seis

  1. Punch Biopsy Results in Misdiagnosis of Pilomatrixoma

    Directory of Open Access Journals (Sweden)

    Metin Temel

    2017-03-01

    Full Text Available Punch biopsy results in misdiagnosis of clinically unsuspected giant pilomatrixoma located over the parotid gland. This study presents a case of pilomatrixoma that was misdiagnosed as a malignant epithelial tumor using punch biopsy. A 25-year-old male was admitted to our clinic for the evaluation of a mass measuring 7×8×8 cm located over the parotid gland. The patient had previously undergone punch biopsy at another clinic because of a lesion in the parotid gland. Punch biopsy revealed a malignant epithelial tumor. The patient underwent excisional biopsy at our clinic. After the biopsy, the residual skin defect was treated using full-thickness skin grafts. The facial nerve and parotid gland were preserved during the biopsy. Histopathological examination of the excisional biopsy material revealed pilomatrixoma. Punch biopsy may result in misdiagnosis of skin lesions in the parotid gland. A differential diagnosis for benign tumors such as pilomatrixoma is essential prior to an aggressive surgical intervention of the parotid gland.

  2. Oropharynx lesion biopsy

    Science.gov (United States)

    ... as papilloma) Fungal infections (such as candida) Histoplasmosis Oral lichen planus Precancerous sore (leukoplakia) Viral infections (such as Herpes simplex) Risks Risks of the procedure may ... Throat lesion biopsy; Biopsy - mouth or throat; Mouth lesion biopsy; Oral cancer - biopsy ...

  3. A tissue biopsy-based epigenetic multiplex PCR assay for prostate cancer detection

    Directory of Open Access Journals (Sweden)

    Van Neste Leander

    2012-06-01

    Full Text Available Abstract Background PSA-directed prostate cancer screening leads to a high rate of false positive identifications and an unnecessary biopsy burden. Epigenetic biomarkers have proven useful, exhibiting frequent and abundant inactivation of tumor suppressor genes through such mechanisms. An epigenetic, multiplex PCR test for prostate cancer diagnosis could provide physicians with better tools to help their patients. Biomarkers like GSTP1, APC and RASSF1 have demonstrated involvement with prostate cancer, with the latter two genes playing prominent roles in the field effect. The epigenetic states of these genes can be used to assess the likelihood of cancer presence or absence. Results An initial test cohort of 30 prostate cancer-positive samples and 12 cancer-negative samples was used as basis for the development and optimization of an epigenetic multiplex assay based on the GSTP1, APC and RASSF1 genes, using methylation specific PCR (MSP. The effect of prostate needle core biopsy sample volume and age of formalin-fixed paraffin-embedded (FFPE samples was evaluated on an independent follow-up cohort of 51 cancer-positive patients. Multiplexing affects copy number calculations in a consistent way per assay. Methylation ratios are therefore altered compared to the respective singleplex assays, but the correlation with patient outcome remains equivalent. In addition, tissue-biopsy samples as small as 20 μm can be used to detect methylation in a reliable manner. The age of FFPE-samples does have a negative impact on DNA quality and quantity. Conclusions The developed multiplex assay appears functionally similar to individual singleplex assays, with the benefit of lower tissue requirements, lower cost and decreased signal variation. This assay can be applied to small biopsy specimens, down to 20 microns, widening clinical applicability. Increasing the sample volume can compensate the loss of DNA quality and quantity in older samples.

  4. Operator dependent choice of prostate cancer biopsy has limited impact on a gene signature analysis for the highly expressed genes IGFBP3 and F3 in prostate cancer epithelial cells.

    Directory of Open Access Journals (Sweden)

    Zhuochun Peng

    Full Text Available BACKGROUND: Predicting the prognosis of prostate cancer disease through gene expression analysis is receiving increasing interest. In many cases, such analyses are based on formalin-fixed, paraffin embedded (FFPE core needle biopsy material on which Gleason grading for diagnosis has been conducted. Since each patient typically has multiple biopsy samples, and since Gleason grading is an operator dependent procedure known to be difficult, the impact of the operator's choice of biopsy was evaluated. METHODS: Multiple biopsy samples from 43 patients were evaluated using a previously reported gene signature of IGFBP3, F3 and VGLL3 with potential prognostic value in estimating overall survival at diagnosis of prostate cancer. A four multiplex one-step qRT-PCR test kit, designed and optimized for measuring the signature in FFPE core needle biopsy samples was used. Concordance of gene expression levels between primary and secondary Gleason tumor patterns, as well as benign tissue specimens, was analyzed. RESULTS: The gene expression levels of IGFBP3 and F3 in prostate cancer epithelial cell-containing tissue representing the primary and secondary Gleason patterns were high and consistent, while the low expressed VGLL3 showed more variation in its expression levels. CONCLUSION: The assessment of IGFBP3 and F3 gene expression levels in prostate cancer tissue is independent of Gleason patterns, meaning that the impact of operator's choice of biopsy is low.

  5. Stereotactic breast biopsy with a biopsy gun

    International Nuclear Information System (INIS)

    Parker, S.H.; Lovin, J.; Luethke, J.; Jobe, W.E.; Hopper, K.D.; Yakes, W.F.

    1989-01-01

    With the recent introduction of stereotactic mammographic localizing devices, the authors have been performing histologic core needle breast biopsies in which the Bard biopsy gun is used in conjunction with sterotactic guidance. The authors have performed 60 breast gun biopsies with 16-gauge and 18-gauge biopsy-cut needles. These biopsies were followed immediately by traditional surgical excision. Pathologic results correlated well in 52 of the 60 patients, including 10 of 13 cancers. Three of the eight negative correlations occurred when diagnosis was made on gun biopsy but not on surgical biopsy. The stereotactic- guided gun biopsies appear to approach the surgical gold standard, decrease patient discomfort and potential disfigurement, lower the cost of breast biopsy, and lower the threshold necessary to perform breast biopsy

  6. Influência do tempo e do meio de transporte no isolamento de fungos patogênicos de biópsias de pele Effects of time delay and transportation on isolation of pathogenic fungi from skin biopsies

    Directory of Open Access Journals (Sweden)

    Rafael Taglialegna

    2008-04-01

    Full Text Available FUNDAMENTOS: Não está definido como o meio de transporte e o intervalo de tempo até o processamento final interferem no isolamento de fungos patogênicos em material obtido de biópsias de pele. OBJETIVOS: Determinar o efeito da inoculação tardia de biópsias de pele, transportadas em diferentes meios líquidos, na taxa de isolamento de fungos patogênicos. MÉTODOS: De 47 pacientes com lesões cutâneas suspeitas de micoses invasivas obtiveram-se 278 biópsias das lesões. Cada biópsia foi transportada em frascos com caldo Sabouraud com cloranfenicol ou solução salina de cloreto de sódio e inoculada em ágar Sabouraud após 48-72 horas (precoce ou após 72 horas até sete dias (tardio, constituindo-se quatro grupos de estudo. RESULTADOS: As medianas das taxas de isolamento dos quatro grupos de esporotricose foram 100% e de paracoccidioidomicose foram 84% e 50% nos grupos precoces/solução salina ou caldo Sabouraud e 64% e 84% nos grupos tardios/solução salina ou caldo Sabouraud, respectivamente (p=0,88. Baixas taxas de contaminação resultaram em especificidade diagnóstica de 82% para doenças não fúngicas. CONCLUSÕES: Biópsias de pele podem ser transportadas em caldo Sabouraud ou solução salina por períodos de até sete dias, à temperatura ambiente, sem afetar a viabilidade dos fungos.BACKGROUND: It is not clear how culture media used during transport and the interval between the biopsy procedure and final processing can affect the successful isolation of fungi. OBJECTIVE: The aim of this study was to investigate the effects of late inoculation of skin biopsies, transported in different sterile fluids, on the isolation rate of pathogenic fungi. METHODS: A total of 278 punch biopsy specimens were collected from 47 patients with suspected lesions of invasive mycoses. Each biopsy was transported in vials with Sabouraud medium with chloramphenicol or saline solution and finally inoculated on Sabouraud agar and 2

  7. Fine-Needle Aspiration Biopsy of the Lymph Node: A Novel Tool for the Monitoring of Immune Responses after Skin Antigen Delivery.

    Science.gov (United States)

    Tatovic, Danijela; Young, Philippa; Kochba, Efrat; Levin, Yotam; Wong, F Susan; Dayan, Colin M

    2015-07-01

    Assessment of immune responses in lymph nodes (LNs) is routine in animals, but rarely done in humans. We have applied minimally invasive ultrasound-guided fine-needle aspiration of the LN to a before-and-after study of the immune response to intradermally delivered Ag in healthy volunteers (n = 25). By comparison with PBMCs from the same individual, LN cells (LNCs) were characterized by reduced numbers of effector memory cells, especially CD8(+) TEMRA cells (3.37 ± 1.93 in LNCs versus 22.53 ± 7.65 in PBMCs; p = 0.01) and a marked increased in CD69 expression (27.67 ± 7.49 versus 3.49 ± 2.62%, LNCs and PBMCs, respectively; p < 0.0001). At baseline, there was a striking absence of IFN-γ ELISPOT responses to recall Ags (purified protein derivative, Tetanus toxoid, or flu/EBV/CMV viral mix) in LN, despite strong responses in the peripheral blood. However, 48 h after tuberculin purified protein derivative administration in the ipsilateral forearm resulting in a positive skin reaction, a clear increase in IFN-γ ELISPOT counts was seen in the draining LN but not in PBMCs. This response was lost by 5 d. These data suggest that the low levels of effector memory cells in the LN may explain the low background of baseline ELISPOT responses in LNs as compared with PBMCs, and the appearance of a response after 48 h is likely to represent migration of effector memory cells from the skin to the LN. Hence, it appears that the combination of intradermal Ag administration and draining LN sampling can be used as a sensitive method to probe the effector memory T cell repertoire in the skin. Copyright © 2015 by The American Association of Immunologists, Inc.

  8. Isothermal multiple displacement amplification: a methodical approach enhancing molecular routine diagnostics of microcarcinomas and small biopsies.

    Science.gov (United States)

    Mairinger, Fabian D; Walter, Robert Fh; Vollbrecht, Claudia; Hager, Thomas; Worm, Karl; Ting, Saskia; Wohlschläger, Jeremias; Zarogoulidis, Paul; Zarogoulidis, Konstantinos; Schmid, Kurt W

    2014-01-01

    Isothermal multiple displacement amplification (IMDA) can be a powerful tool in molecular routine diagnostics for homogeneous and sequence-independent whole-genome amplification of notably small tumor samples, eg, microcarcinomas and biopsies containing a small amount of tumor. Currently, this method is not well established in pathology laboratories. We designed a study to confirm the feasibility and convenience of this method for routine diagnostics with formalin-fixed, paraffin-embedded samples prepared by laser-capture microdissection. A total of 250 μg DNA (concentration 5 μg/μL) was generated by amplification over a period of 8 hours with a material input of approximately 25 cells, approximately equivalent to 175 pg of genomic DNA. In the generated DNA, a representation of all chromosomes could be shown and the presence of elected genes relevant for diagnosis in clinical samples could be proven. Mutational analysis of clinical samples could be performed without any difficulty and showed concordance with earlier diagnostic findings. We established the feasibility and convenience of IMDA for routine diagnostics. We also showed that small amounts of DNA, which were not analyzable with current molecular methods, could be sufficient for a wide field of applications in molecular routine diagnostics when they are preamplified with IMDA.

  9. Stereotactic biopsy

    International Nuclear Information System (INIS)

    Mwangi, M.N.; Handa, A.

    2006-01-01

    This technology is capable of locating lesions precise detected by the mammography examinations. This devise allows the surgeon to position automatically the needle to perform the cytological/histological biopsy with maximum position accuracy. This is under sterile procedure. to position the lesion in the beam, two radiographic procedures are carried out: the first with the X-ray beam at an inclination of -15 degrees with respect to the position 0 degrees and the second at the inclination +15 degrees. After processing the film the lesion will appear on both radiographs but on light are of the negatoscope. With the cursor information is fed from four points. On the display the length of the needle will appear immediately. The length of the needle to be used in suction is chosen on the basis of the two values on the display. This information fed on the control panel will move the needle unit position where the lesion is. the needle is then introduced under local anaesthesia at the preselected length until it clicks into position. An exposure is made with needle in situ in position at +15 degrees and -15 degrees to ensure the needle is in position. the suction is then carried out and the needle removed. The machine is then reset to return at the initial position

  10. A gene-protein assay for human epidermal growth factor receptor 2 (HER2: brightfield tricolor visualization of HER2 protein, the HER2 gene, and chromosome 17 centromere (CEN17 in formalin-fixed, paraffin-embedded breast cancer tissue sections

    Directory of Open Access Journals (Sweden)

    Nitta Hiroaki

    2012-05-01

    Full Text Available Abstract Background The eligibility of breast cancer patients for human epidermal growth factor receptor 2 (HER2-directed therapies is determined by the HER2 gene amplification and/or HER2 protein overexpression status of the breast tumor as determined by in situ hybridization (ISH or immunohistochemistry (IHC, respectively. Our objective was to combine the US Food and Drug Administration (FDA-approved HER2 & chromosome 17 centromere (CEN17 brightfield ISH (BISH and HER2 IHC assays into a single automated HER2 gene-protein assay allowing simultaneous detection of all three targets in a single tissue section. Methods The HER2 gene-protein assay was optimized using formalin-fixed, paraffin-embedded (FFPE samples of the xenograft tumors MCF7 [HER2 negative (non-amplified gene, protein negative] and Calu-3 [HER2 positive (amplified gene, protein positive]. HER2 IHC was performed using a rabbit monoclonal anti-HER2 antibody (clone 4B5 and a conventional 3,3'-diaminobenzidine IHC detection. The HER2 & CEN17 BISH signals were visualized using horseradish peroxidase-based silver and alkaline phosphatase-based red detection systems, respectively with a cocktail of 2,4-dinitrophenyl-labeled HER2 and digoxigenin-labeled CEN17 probes. The performance of the gene-protein assay on tissue microarray slides containing 189 randomly selected FFPE clinical breast cancer tissue cores was compared to that of the separate HER2 IHC and HER2 & CEN17 BISH assays. Results HER2 protein detection was optimal when the HER2 IHC protocol was used before (rather than after the BISH protocol. The sequential use of HER2 IHC and HER2 & CEN17 BISH detection steps on FFPE xenograft tumor sections appropriately co-localized the HER2 protein, HER2 gene, and CEN17 signals after mitigating the silver background staining by using a naphthol phosphate-containing hybridization buffer for the hybridization step. The HER2 protein and HER2 gene status obtained using the multiplex HER2 gene

  11. Technical validation of an RT-qPCR in vitro diagnostic test system for the determination of breast cancer molecular subtypes by quantification of ERBB2, ESR1, PGR and MKI67 mRNA levels from formalin-fixed paraffin-embedded breast tumor specimens.

    Science.gov (United States)

    Laible, Mark; Schlombs, Kornelia; Kaiser, Katharina; Veltrup, Elke; Herlein, Stefanie; Lakis, Sotiris; Stöhr, Robert; Eidt, Sebastian; Hartmann, Arndt; Wirtz, Ralph M; Sahin, Ugur

    2016-07-07

    MammaTyper is a novel CE-marked in vitro diagnostic RT-qPCR assay which assigns routinely processed breast cancer specimens into the molecular subtypes Luminal A-like, Luminal B-like (HER2 positive or negative), HER2 positive (non-luminal) and Triple negative (ductal) according to the mRNA expression of ERBB2, ESR1, PGR and MKI67 and the St Gallen consensus surrogate clinical definition. Until now and regarding formalin-fixed, paraffin-embedded material (FFPE), this has been a task mostly accomplished by immunohistochemistry (IHC). However the discrepancy rates of IHC for the four breast cancer biomarkers are frequently under debate, especially for Ki-67 which carries the highest degree of inter- and even intra-observer variability. Herein we describe a series of studies in FFPE specimens which aim to fully validate the analytical performance of the MammaTyper assay, including the site to site reproducibility of the individual marker measurements. Tumor RNA was extracted with the novel RNXtract RNA extraction kit. Synthetic RNA was used to assess the sensitivity of the RNXtract kit. DNA and RNA specific qPCR assays were used so as to determine analyte specificity of RNXtract. For the assessment of limit of blank, limit of detection, analytical measurement range and PCR efficiency of the MammaTyper kit serial dilutions of samples were used. Analytical precision studies of MammaTyper were built around two different real time PCR platforms and involved breast tumor samples belonging to different subtypes analyzed across multiple sites and under various stipulated conditions. The MammaTyper assay robustness was tested against RNA input variations, alternative extraction methods and tumor cell content. Individual assays were linear up to at least 32.33 and 33.56 Cqs (quantification cycles) for the two qPCR platforms tested. PCR efficiency ranged from 99 to 109 %. In qPCR platform 1, estimates for assay specific inter-site standard deviations (SD) were between 0.14 and

  12. Technical validation of an RT-qPCR in vitro diagnostic test system for the determination of breast cancer molecular subtypes by quantification of ERBB2, ESR1, PGR and MKI67 mRNA levels from formalin-fixed paraffin-embedded breast tumor specimens

    International Nuclear Information System (INIS)

    Laible, Mark; Schlombs, Kornelia; Kaiser, Katharina; Veltrup, Elke; Herlein, Stefanie; Lakis, Sotiris; Stöhr, Robert; Eidt, Sebastian; Hartmann, Arndt; Wirtz, Ralph M.; Sahin, Ugur

    2016-01-01

    MammaTyper is a novel CE-marked in vitro diagnostic RT-qPCR assay which assigns routinely processed breast cancer specimens into the molecular subtypes Luminal A-like, Luminal B-like (HER2 positive or negative), HER2 positive (non-luminal) and Triple negative (ductal) according to the mRNA expression of ERBB2, ESR1, PGR and MKI67 and the St Gallen consensus surrogate clinical definition. Until now and regarding formalin-fixed, paraffin-embedded material (FFPE), this has been a task mostly accomplished by immunohistochemistry (IHC). However the discrepancy rates of IHC for the four breast cancer biomarkers are frequently under debate, especially for Ki-67 which carries the highest degree of inter- and even intra-observer variability. Herein we describe a series of studies in FFPE specimens which aim to fully validate the analytical performance of the MammaTyper assay, including the site to site reproducibility of the individual marker measurements. Tumor RNA was extracted with the novel RNXtract RNA extraction kit. Synthetic RNA was used to assess the sensitivity of the RNXtract kit. DNA and RNA specific qPCR assays were used so as to determine analyte specificity of RNXtract. For the assessment of limit of blank, limit of detection, analytical measurement range and PCR efficiency of the MammaTyper kit serial dilutions of samples were used. Analytical precision studies of MammaTyper were built around two different real time PCR platforms and involved breast tumor samples belonging to different subtypes analyzed across multiple sites and under various stipulated conditions. The MammaTyper assay robustness was tested against RNA input variations, alternative extraction methods and tumor cell content. Individual assays were linear up to at least 32.33 and 33.56 Cqs (quantification cycles) for the two qPCR platforms tested. PCR efficiency ranged from 99 to 109 %. In qPCR platform 1, estimates for assay specific inter-site standard deviations (SD) were between 0.14 and 0

  13. Effects of tissue handling and processing steps on PCR for detection of Mycobacterium tuberculosis in formalin-fixed paraffin-embedded samples Efeitos das etapas de tratamento e processamento do tecido na PCR para detecção de Mycobacterium tuberculosis em amostras fixadas em formalina e incluídas em parafina

    Directory of Open Access Journals (Sweden)

    Denise Barcelos

    2008-12-01

    Full Text Available Development and standardization of reliable methods for detection of Mycobacterium tuberculosis in clinical samples is an important goal in laboratories throughout the world. In this work, lung and spleen fragments from a patient who died with the diagnosis of miliary tuberculosis were used to evaluate the influence of the type of fixative as well as the fixation and paraffin inclusion protocols on PCR performance in paraffin embedded specimens. Tissue fragments were fixed for four h to 48 h, using either 10% non-buffered or 10% buffered formalin, and embedded in pure paraffin or paraffin mixed with bee wax. Specimens were submitted to PCR for amplification of the human beta-actin gene and separately for amplification of the insertion sequence IS6110, specific from the M. tuberculosis complex. Amplification of the beta-actin gene was positive in all samples. No amplicons were generated by PCR-IS6110 when lung tissue fragments were fixed using 10% non-buffered formalin and were embedded in paraffin containing bee wax. In conclusion, combined inhibitory factors interfere in the detection of M. tuberculosis in stored material. It is important to control these inhibitory factors in order to implement molecular diagnosis in pathology laboratories.O desenvolvimento e a padronização de métodos confiáveis para a detecção de Mycobacterium tuberculosis em amostras clínicas é um objetivo importante nos laboratórios de todo o mundo. Neste trabalho, fragmentos de pulmão e baço de paciente que morreu com o diagnóstico de tuberculose miliar foram usados para avaliar a influência do tipo de fixador e dos protocolos de fixação e inclusão em parafina na performance da PCR. Fragmentos de tecido foram fixados por quatro h a 48 h, usando formalina não tamponada a 10% ou formalina tamponada a 10% e incluídos em parafina pura ou misturada a cera de abelha. As amostras foram submetidas a PCR para amplificação do gene da beta-actina humana e

  14. Uncovering of melanin fluorescence in human skin tissue

    Science.gov (United States)

    Scholz, Matthias; Stankovic, Goran; Seewald, Gunter; Leupold, Dieter

    2007-07-01

    Due to its extremely low fluorescence quantum yield, in the conventionally (one-photon) excited autofluorescence of skin tissue, melanin fluorescence is masked by several other endogenous and possibly also exogenous fluorophores (e.g. NADH, FAD, Porphyrins). A first step to enhance the melanin contribution had been realized by two-photon fs-pulse excitation in the red/near IR, based on the fact that melanin can be excited by stepwise two-photon absorption, whereas all other fluorophores in this spectral region allow only simultaneous two-photon excitation. Now, the next and decisive step has been realized: Using an extremely sensitive detection system, for the first time twophoton fluorescence of skin tissue excited with pulses in the ns-range could be measured. The motivation for this step was based on the fact that the population density of the fluorescent level resulting from a stepwise excitation has a different dependence of the pulse duration than that from a simultaneous excitation (Δt2 vs. Δt). Due to this strong discrimination between the fluorophores, practically pure melanin fluorescence can be obtained. Examples for in-vivo, ex-vivo as well as paraffin embedded skin tissue will be shown. The content of information with respect to early diagnosis of skin deseases will be discussed.

  15. Intratumor microvessel density in biopsy specimens predicts local response of hypopharyngeal cancer to radiotherapy

    International Nuclear Information System (INIS)

    Zhang, Shi-Chuan; Miyamoto, Shin-ichi; Hasebe, Takahiro; Ishii, Genichiro; Ochiai, Atsushi; Kamijo, Tomoyuki; Hayashi, Ryuichi; Fukayama, Masashi

    2003-01-01

    The aim of this retrospective study was to identify reliable predictive factors for local control of hypopharyngeal cancer (HPC) treated by radiotherapy. A cohort of 38 patients with HPC treated by radical radiotherapy at the National Cancer Center Hospital East between 1992 and 1999 were selected as subjects for the present study. Paraffin-embedded pre-therapy biopsy specimens from these patients were used for immunostaining to evaluate the relationships between local tumor control and expression of the following previously reported predictive factors for local recurrence of head and neck cancer treated by radiotherapy: Ki-67, Cyclin D1, CDC25B, VEGF, p53, Bax and Bcl-2. The predictive power of microvessel density (MVD) in biopsy specimens and of clinicopathologic factors (age, gender and clinical tumor-node-metastasis stage) was also statistically analyzed. Twenty-five patients developed tumor recurrence at the primary site. Univariate analysis indicated better local control of tumors with high microvessel density [MVD≥median (39 vessels/field)] than with low MVD (< median, P=0.042). There were no significant associations between local control and expression of Ki-67 (P=0.467), Bcl-2 (P=0.127), Bax (P=0.242), p53 (P=0.262), Cyclin D1 (P=0.245), CDC25B (P=0.511) or VEGF (P=0.496). Clinicopathologic factors were also demonstrated to have no significant influence on local control (age, P=0.974; gender, P=0.372; T factor, P=0.602; N factor, P=0.530; Stage, P=0.499). MVD in biopsy specimens was closely correlated with local control of HPC treated by radiotherapy. (author)

  16. Open lung biopsy

    Science.gov (United States)

    Biopsy - open lung ... An open lung biopsy is done in the hospital using general anesthesia . This means you will be asleep and ... The open lung biopsy is done to evaluate lung problems seen on x-ray or CT scan .

  17. Bone lesion biopsy

    Science.gov (United States)

    Bone biopsy; Biopsy - bone ... the cut, then pushed and twisted into the bone. Once the sample is obtained, the needle is ... sample is sent to a lab for examination. Bone biopsy may also be done under general anesthesia ...

  18. Biopsy system for CT-guided biopsies

    International Nuclear Information System (INIS)

    Onik, G.; Cosman, E.; Wells, T.; Goldberg, H.I.; Moss, A.; Costello, P.; Kane, R.

    1987-01-01

    CT stereotaxic brain biopsies have made brain biopsies safe and minimally invasive. CT-guided biopsies of the body, however, have traditionally used a hand-guidance method. CT biopsy guidance systems for the body have recently become available that have similar capabilities as those of brain biopsy systems. To compare the clinical utility of stereotaxically guided biopsies with hand-guided biopsies, the authors prospectively compared 40 biopsies performed with each method. In the stereotaxic method, a localizor grid was placed on the patient to define a reference point, and a frame was used to guide the needle along the intended path. Computer software programs calculated complex paths from one scan plane to another. Although the results disclosed no significant differences in lesion size or path length between the two groups, the stereotaxically guided biopsies required 75% fewer needle manipulations to hit the intended target. Consequently, the stereotaxically guided biopsies required 40% less time and 80% fewer localization scans to find the biopsy needle than did the hand-guided biopsies

  19. The Expression of mRNA LMP1 Epstein-Barr Virus from FFPE Tumour Biopsy: a Potential Biomarker of Nasopharyngeal Carcinoma Diagnosis

    Directory of Open Access Journals (Sweden)

    Daniel Joko Wahyono

    2017-07-01

    Full Text Available Nasopharyngeal carcinoma (NPC is a multifactorial disease that is endemic geographically in the world. Indonesian population has a highly incidence rate that is 6.2/100,000 people year. The pathogenesis of NPC is more directly reflected by carcinoma-specific viral transcriptional activity at the site of primary tumour. Epstein-Barr virus (EBV infection in NPC is reflected by the expression of EBV latent and lytic gene. In fact, mRNA Latent Membrane Protein 1 (LMP1 EBV expression was an important latent infection biomarker. The aim of this study was to determine a potential use of relative expression of mRNA LMP1 EBV from formalin-fixed paraffin embedded (FFPE tumour biopsy in NPC as a tumour biomarker. This reseach design was a cross sectional study. The samples were the archived specimens of FFPE tumour biopsy from NPC WHO-3 patient which were collected from untreated patients from 2014 in the Department of Pathology Anatomy, Prof. dr. Margono Soekarjo Hospital, Purwokerto. The expression of mRNA LMP1 EBV expression was determined by RT-PCR technique. The positivity of mRNA LMP1 EBV expression was 51.9%, indicating a moderate positivity. The result proved that the expression of mRNA LMP1 EBV from FFPE NPC WHO-3 tumour biopsy was a potential biomarker of NPC diagnosis. The molecular methods would improved the management of NPC, particularly in the histopathological diagnosis of NPC.

  20. MR-guided biopsies

    International Nuclear Information System (INIS)

    Gehl, H.B.; Frahm, C.

    1998-01-01

    Biopsies were the first 'intervention' under MR guidance. After initial difficulties concerning ferromagnetic biopsy instruments and the design of MR scanners, the latest technological improvements rendered MR guidance for biopsies more feasible. In this article we illustrate present-day clinical experience in the field of abdominal, breast and bone biopsy. Important aspects regarding the different designs of 'interventional' MR scanners and the visualization of instruments for biopsy are discussed. (orig.) [de

  1. Isothermal multiple displacement amplification: a methodical approach enhancing molecular routine diagnostics of microcarcinomas and small biopsies

    Directory of Open Access Journals (Sweden)

    Mairinger FD

    2014-08-01

    Full Text Available Fabian D Mairinger,1 Robert FH Walter,2 Claudia Vollbrecht,3 Thomas Hager,1 Karl Worm,1 Saskia Ting,1 Jeremias Wohlschläger,1 Paul Zarogoulidis,4 Konstantinos Zarogoulidis,4 Kurt W Schmid1 1Institute of Pathology, 2Ruhrlandklinik, West German Lung Center, University Hospital Essen, Essen, 3Institute of Pathology, University Hospital Cologne, Cologne, Germany; 4Pulmonary Department, Oncology Unit, G Papanikolaou General Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece Background and methods: Isothermal multiple displacement amplification (IMDA can be a powerful tool in molecular routine diagnostics for homogeneous and sequence-independent whole-genome amplification of notably small tumor samples, eg, microcarcinomas and biopsies containing a small amount of tumor. Currently, this method is not well established in pathology laboratories. We designed a study to confirm the feasibility and convenience of this method for routine diagnostics with formalin-fixed, paraffin-embedded samples prepared by laser-capture microdissection. Results: A total of 250 µg DNA (concentration 5 µg/µL was generated by amplification over a period of 8 hours with a material input of approximately 25 cells, approximately equivalent to 175 pg of genomic DNA. In the generated DNA, a representation of all chromosomes could be shown and the presence of elected genes relevant for diagnosis in clinical samples could be proven. Mutational analysis of clinical samples could be performed without any difficulty and showed concordance with earlier diagnostic findings. Conclusion: We established the feasibility and convenience of IMDA for routine diagnostics. We also showed that small amounts of DNA, which were not analyzable with current molecular methods, could be sufficient for a wide field of applications in molecular routine diagnostics when they are preamplified with IMDA. Keywords: isothermal multiple displacement amplification, isothermal, whole

  2. Evaluation of 16S rRNA qPCR for detection of Mycobacterium leprae DNA in nasal secretion and skin biopsy samples from multibacillary and paucibacillary leprosy cases.

    Science.gov (United States)

    Marques, Lívia Érika Carlos; Frota, Cristiane Cunha; Quetz, Josiane da Silva; Bindá, Alexandre Havt; Mota, Rosa Maria Salane; Pontes, Maria Araci de Andrade; Gonçalves, Heitor de Sá; Kendall, Carl; Kerr, Ligia Regina Franco Sansigolo

    2017-12-26

    Mycobacterium leprae bacilli are mainly transmitted by the dissemination of nasal aerosols from multibacillary (MB) patients to susceptible individuals through inhalation. The upper respiratory tract represents the main entry and exit routes of M. leprae. Therefore, this study aimed to evaluate the sensitivity and specificity of real-time quantitative polymerase chain reaction (qPCR) in detecting M. leprae in nasal secretion (NS) and skin biopsy (SB) samples from MB and paucibacillary (PB) cases. Fifty-four NS samples were obtained from leprosy patients at the Dona Libânia National Reference Centre for Sanitary Dermatology in Ceará, Brazil. Among them, 19 MB cases provided both NS and SB samples. Bacilloscopy index assays were conducted and qPCR amplification was performed using specific primers for M. leprae 16S rRNA gene, generating a 124-bp fragment. Primer specificity was verified by determining the amplicon melting temperature (T m  = 79.5 °C) and detection limit of qPCR was 20 fg of M. leprae DNA. Results were positive for 89.7 and 73.3% of NS samples from MB and PB cases, respectively. SB samples from MB patients were 100% positive. The number of bacilli detected in NS samples were 1.39 × 10 3 -8.02 × 10 5 , and in SB samples from MB patients were 1.87 × 10 3 -1.50 × 10 6 . Therefore, qPCR assays using SYBR Green targeting M. leprae 16S rRNA region can be employed in detecting M. leprae in nasal swabs from leprosy patients, validating this method for epidemiological studies aiming to identify healthy carriers among household contacts or within populations of an endemic area.

  3. Salivary gland biopsy

    Science.gov (United States)

    ... also be performed to diagnose diseases such as Sjogren syndrome . How to Prepare for the Test There is ... few days after the biopsy. The biopsy for Sjogren syndrome requires an injection of the anesthetic in the ...

  4. Validation of morphometric analyses of small-intestinal biopsy readouts in celiac disease.

    Directory of Open Access Journals (Sweden)

    Juha Taavela

    Full Text Available BACKGROUND: Assessment of the gluten-induced small-intestinal mucosal injury remains the cornerstone of celiac disease diagnosis. Usually the injury is evaluated using grouped classifications (e.g. Marsh groups, but this is often too imprecise and ignores minor but significant changes in the mucosa. Consequently, there is a need for validated continuous variables in everyday practice and in academic and pharmacological research. METHODS: We studied the performance of our standard operating procedure (SOP on 93 selected biopsy specimens from adult celiac disease patients and non-celiac disease controls. The specimens, which comprised different grades of gluten-induced mucosal injury, were evaluated by morphometric measurements. Specimens with tangential cutting resulting from poorly oriented biopsies were included. Two accredited evaluators performed the measurements in blinded fashion. The intraobserver and interobserver variations for villus height and crypt depth ratio (VH:CrD and densities of intraepithelial lymphocytes (IELs were analyzed by the Bland-Altman method and intraclass correlation. RESULTS: Unevaluable biopsies according to our SOP were correctly identified. The intraobserver analysis of VH:CrD showed a mean difference of 0.087 with limits of agreement from -0.398 to 0.224; the standard deviation (SD was 0.159. The mean difference in interobserver analysis was 0.070, limits of agreement -0.516 to 0.375, and SD 0.227. The intraclass correlation coefficient in intraobserver variation was 0.983 and that in interobserver variation 0.978. CD3(+ IEL density countings in the paraffin-embedded and frozen biopsies showed SDs of 17.1% and 16.5%; the intraclass correlation coefficients were 0.961 and 0.956, respectively. CONCLUSIONS: Using our SOP, quantitative, reliable and reproducible morphometric results can be obtained on duodenal biopsy specimens with different grades of gluten-induced injury. Clinically significant changes were

  5. Biopsying southern right whales : Their reactions and effects on reproduction

    NARCIS (Netherlands)

    Best, PB; Reeb, D; Rew, MB; Palsboll, PJ; Schaeff, C; Brandao, A

    Collecting skin biopsies from large whales for genetic analysis is often subject to national permit, and in the case of cow-calf pairs, it may be prohibited. We present results of 906 biopsy attempts on southern fight whales (Eubalaena australis) in South African waters between 1995 and 1997,

  6. Abdominal wall fat pad biopsy

    Science.gov (United States)

    Amyloidosis - abdominal wall fat pad biopsy; Abdominal wall biopsy; Biopsy - abdominal wall fat pad ... is the most common method of taking an abdominal wall fat pad biopsy . The health care provider cleans the ...

  7. Chronic ultraviolet exposure-induced p53 gene alterations in sencar mouse skin carcinogenesis model

    International Nuclear Information System (INIS)

    Tong, Ying; Smith, M.A.; Tucker, S.B.

    1997-01-01

    Alterations of the tumor suppressor gene p53 have been found in ultraviolet radiation (UVR) related human skin cancers and in UVR-induced murine skin tumors. However, links between p53 gene alterations and the stages of carcinogenesis induced by UVR have not been clearly defined. We established a chronic UVR exposure-induced Sencar mouse skin carcinogenesis model to determine the frequency of p53 gene alterations in different stages of carcinogenesis, including UV-exposed skin, papillomas, squamous-cell carcinomas (SCCs), and malignant spindle-cell tumors (SCTs). A high incidence of SCCs and SCTs were found in this model. Positive p53 nuclear staining was found in 10137 (27%) of SCCs and 12124 (50%) of SCTs, but was not detected in normal skin or papillomas. DNA was isolated from 40 paraffin-embedded normal skin, UV-exposed skin, and tumor sections. The p53 gene (exons 5 and 6) was amplified from the sections by using nested polymerase chain reaction (PCR). Subsequent single-strand conformation polymorphism (SSCP) assay and sequencing analysis revealed one point mutation in exon 6 (coden 193, C → A transition) from a UV-exposed skin sample, and seven point mutations in exon 5 (codens 146, 158, 150, 165, and 161, three C → T, two C → A, one C → G, and one A → T transition, respectively) from four SCTs, two SCCs and one UV-exposed skin sample. These experimental results demonstrate that alterations in the p53 gene are frequent events in chronic UV exposure-induced SCCs and later stage SCTs in Sencar mouse skin. 40 refs., 5 figs., 1 tab

  8. New Image-Based Techniques for Prostate Biopsy and Treatment

    Science.gov (United States)

    2012-04-01

    correspondence between the pathology slices and the MR image slices. The processing and paraffin embedding were carried out in a routine manner, except using...results (Mor- ris et al., 2009). In this treatment, 40-150 small radioactive seeds (Iodine-125 or Palladium-103) are inserted through the perineum and...creating the VE images. Any out of plane motion, including the lat- eral motions caused by the slippage between the protective sheath on the probe and the

  9. La biopsie prostatique

    OpenAIRE

    DJEDOUI, MERIEM

    2013-01-01

    La preuve d'un cancer de la prostate est apportée par la biopsie prostatique. Malheureusement, une biopsie négative, bien que rassurante, ne suffit pas à exclure un noyau cancéreux à côté duquel l'aiguille est passée. L'urologue peut être amené à proposer une nouvelle biopsie, en augmentant, s'il le faut, le nombre de prélèvements de tissu prostatique. Ayant connu Le but d'une biopsie prostatique, le patient pourrait maintenant décider d'entrer dans d'autres alternatives qui...

  10. Immunolocalization of lactoferrin in surgically resected pigmented skin lesions

    Directory of Open Access Journals (Sweden)

    G Tuccari

    2009-06-01

    Full Text Available Lactoferrin (Lf expression was determined immunohistochemically in 57 formalin-fixed paraffin-embedded bioptic samples obtained from an equal number of patients treated by surgery to remove pigmented skin lesions (nevi = 23; melanoma = 12; vulgaris and seborrhoeic warts = 12; basal cell carcinoma = 10; in addition, 10 specimens of normal skin were studied as control. On 3 ?m thick sections, depigmentation and antigen retrieval procedures were performed. The Lf immunoreactivity was revealed by a rabbit anti-human Lf. Quantification of Lf immunoreactivity was performed using an intensity-distribution (ID score. Melanocytic cells, regardless of their benign or malignant nature, were consistently stained, with no significant differences in the Lf IDscore between melanomas or nevi. A different intensity of Lf immunoreactivity was encountered in superficial portions of warts, exclusively inside squamous epithelial cells arranged in sheets or whorls of keratin. On the contrary, basal cell carcinomas were always unstained, while a slight Lf positivity was found in focal keratinized areas present in two tumours showing baso-squamous differentiation. The Lf immunoreactivity was localized in the cytoplasm and only occasionally in the nucleus. The biological meaning of Lf in these cases of human skin specimens remains unexplained, although it cannot be ruled out that Lf might be involved in the defense system against tumours, or alternatively, may be used by cells requiring iron availability for their turnover. Moreover, the immunohistochemical expression of Lf in melanocytic lesions might be also related to a Lf-melanin interaction. Finally, the involvement of Lf in skin squamous non-neoplastic elements could be related to its role as one of the molecules modulating an unspecific inflammatory or anti-oxidant response.

  11. Biopsy - Multiple Languages

    Science.gov (United States)

    ... Biopsy - العربية (Arabic) Bilingual PDF Health Information Translations Breast Biopsy - العربية (Arabic) Bilingual PDF Health Information Translations Colposcopy - العربية (Arabic) Bilingual PDF ...

  12. Examination of the skin barrier repair/wound healing process using a living skin equivalent model and matrix-assisted laser desorption-ionization-mass spectrometry imaging.

    Science.gov (United States)

    Lewis, E E L; Barrett, M R T; Freeman-Parry, L; Bojar, R A; Clench, M R

    2018-04-01

    Examination of the skin barrier repair/wound healing process using a living skin equivalent (LSE) model and matrix-assisted laser desorption/ionization-mass spectrometry imaging (MALDI-MSI) to identify lipids directly involved as potential biomarkers. These biomarkers may be used to determine whether an in vivo wound is going to heal for example if infected. An in vitro LSE model was wounded with a scalpel blade and assessed at day 4 post-wounding by histology and MALDI-MSI. Samples were sectioned at wound site and were either formalin-fixed paraffin-embedded (FFPE) for histology or snapped frozen (FF) for MSI analysis. The combination of using an in vitro wounded skin model with MSI allowed the identification of lipids involved in the skin barrier repair/wound healing process. The technique was able to highlight lipids directly in the wound site and distinguish differences in lipid distribution between the epidermis and wound site. This novel method of coupling an in vitro LSE with MSI allowed in-depth molecular analysis of the skin barrier repair/wound healing process. The technique allowed the identification of lipids directly involved in the skin barrier repair/wound healing process, indicating these biomarkers may be potentially be used within the clinic. These biomarkers will help to determine, which stage of the skin barrier repair/wound healing process the wound is in to provide the best treatment. © 2018 Society of Cosmetic Scientists and the Société Française de Cosmétologie.

  13. Demonstration of the proliferation marker Ki-67 in renal biopsies: correlation to clinical findings.

    Science.gov (United States)

    Nabokov, A; Waldherr, R; Ritz, E

    1997-07-01

    Assessment of cell proliferation in renal biopsy samples is a potentially promising analytical tool to evaluate disease activity. So far no information is available on the correlation between proliferative activity in different anatomic compartments of the kidney and clinical symptoms. To elucidate this issue, we examined renal biopsy specimens from 20 patients with systemic vasculitis (15 Wegener's granulomatosis, five microscopic polyangiitis), 20 patients with immunoglobulin (Ig) A nephropathy (IgAN), 13 patients with minimal-change disease (MCD), 11 patients with tubulointerstitial nephritis, and five patients with diabetes mellitus. The streptavidin-biotin-peroxidase complex technique was applied to autoclave-pretreated, formalin-fixed, paraffin-embedded tissue sections to label different cell types with the antibody MIB1 directed against the Ki-67 antigen. Proliferation index (PI) was estimated as the number of positively stained nuclei per glomerular cross-section or per square millimeter section area. The interstitial cells were discriminated by additional staining of Ki-67-processed samples with specific immune markers. In patients with vasculitis, PI was considerably elevated in the extracapillary glomerular compartment (0.86), in proximal tubules (6.24), and in the interstitium (8.62). High proliferative activity was also noted in interstitium (3.98) and proximal tubules (1.35) of patients with IgAN. Of particular interest was the increased interstitial proliferative activity (15.0) in diabetic patients. Resident renal cells, but not infiltrating cells, seemed to constitute the majority of the proliferating cell population in the interstitium. In systemic vasculitis, clinical disease activity was significantly correlated to endocapillary (r(s) = 0.58), extracapillary (r(s) = 0.67), proximal tubular (r(s) = 0.67), and interstitial PI (r(s) = 0.61). By multiple linear regression analysis, proximal tubular PI was correlated to the presence of hematuria

  14. Improved transvenous liver biopsy needle

    DEFF Research Database (Denmark)

    Henriksen, Jens Henrik Sahl; Matzen, P; Christoffersen, P

    1979-01-01

    A modified type of the standard transvenous cholangiography biopsy needle is described. The modified tranvenous liver biopsy needle caused only minimal artefactual changes of the liver biopsy specimens. The new type of biopsy needle is a modified Menghini needle. The conventional Menghini needle...... should be avoided for transvenous catheter biopsies because of risk of leaving catheter fragments in the liver....

  15. No need for biopsies

    DEFF Research Database (Denmark)

    Gjødsbøl, Kristine; Skindersoe, Mette E; Christensen, Jens Jørgen

    2011-01-01

    The aim of the study was to compare three sampling techniques used in routine diagnostics to identify the microbiota in chronic venous leg ulcers. A total of 46 patients with persisting venous leg ulcers were included in the study. At inclusion, swab, biopsy and filter paper pad samples were...... collected. After 4 weeks, additional biopsy and filter paper pad samples were collected. Bacteria were isolated and identified at species level by standard methods. The most common bacterial species detected was Staphylococcus aureus found in 89% of the ulcers. No methicillin-resistant S. aureus isolates...... species present in chronic wounds, thus avoiding complications during and after biopsy sampling....

  16. The biopsy of the boar testes using ultrasonographic examination

    Directory of Open Access Journals (Sweden)

    Laima Liepa

    2014-03-01

    Full Text Available The biopsy of live animal testes is an important clinical manipulation to control spermatogenesis and reproductive system pathologies. The aim was to develop a method of boar testes biopsy using a biopsy gun with ultrasound guidance and to investigate the influence of this procedure on the boar testes parenchyma and quality of ejaculate. The biopsy was carried out in six 8-month-old boars. Fourteen days prior to and 21 days after biopsy, the quality of ejaculate was examined (weight of ejaculate; concentration and motility of spermatozoa with a seven-day intervals. Ultrasound images of the testes parenchyma were recorded three times: directly before and 15 minutes after the biopsy, then 21 days after the procedure. The testes biopsies of generally anesthetized boars were performed with the biopsy gun for needle biopsy with a 12cm long, disposable 16-gauge needle 1.8mm in diameter (Vitesse through 1cm skin incision in the depth of 1.2-1.6cm of parenchyma. Fifteen minutes after the biopsy, macroscopic injures of the parenchyma of all the boar testes were not detected in the ultrasound image. Twenty one days after biopsy, the hyperechogenic line 0.1-0.2cm in diameter was seen in the testes parenchyma of six boars in the depth of 1.2-1.6cm. The biopsy of boar testes did not influence the quality of boars ejaculate. The ultrasonographic examination of boar testicles before the biopsy reduced possibilities to traumatize large blood vessels of the testes. A perfect boar testicular biopsy was easy to perform using ultrasonographic examination in the pigsty conditions.

  17. Breast biopsy -- stereotactic

    Science.gov (United States)

    ... org/-/media/ACR/Files/Practice-Parameters/stereo-breast.pdf . Updated 2016. Accessed March 14, 2017. Parker C, Umphrey H, Bland K. The role of stereotactic breast biopsy in the management of breast disease. In: Cameron ...

  18. Breast biopsy -- ultrasound

    Science.gov (United States)

    ... org/-/media/ACR/Files/Practice-Parameters/us-guidedbreast.pdf . Updated 2016. Accessed March 14, 2017. Torrente J, Brem RF. Minimally invasive image-guided breast biopsy and ablation. In: Mauro MA, Murphy KPJ, Thomson ...

  19. Pleural needle biopsy

    Science.gov (United States)

    ... own. Sometimes, a chest tube is needed to drain the air and expand the lung. There is also a chance of excessive blood loss. Considerations If a closed pleural biopsy is not enough to make a diagnosis, ...

  20. Colposcopy - directed biopsy

    Science.gov (United States)

    ... squamous cells - colposcopy; Pap smear - colposcopy; HPV - colposcopy; Human papilloma virus - colposcopy; Cervix - colposcopy; Colposcopy ... also called cervical dysplasia) Cervical warts (infection with human papilloma virus , or HPV) If the biopsy does not ...

  1. Liver biopsy under hypnosis.

    Science.gov (United States)

    Adams, P C; Stenn, P G

    1992-09-01

    Two patients underwent outpatient percutaneous liver biopsy under hypnosis without complications. One patient had severe anxiety about the procedure because of a previous adverse experience with liver biopsy and the other had a history of severe allergy to local anesthesia. Both patients had undergone a session of hypnosis at least once prior to the biopsy. One received no local anesthetic and the other received 1% lidocaine as a local anesthetic. Both patients were completely cooperative during the procedure with the required respiratory maneuvers. Both patients stated that they were aware of the procedure under hypnosis but described no pain and would be most willing to have the procedure done under hypnosis in the future. Hypnosis can be a useful method of preparing carefully selected patients for percutaneous liver biopsy.

  2. Corpus vitreum, retina og chorioidea biopsi

    DEFF Research Database (Denmark)

    Scherfig, Erik Christian Høegh

    2002-01-01

    oftalmology, biopsy, choroid, corpus vitreum, retina, malignant melanoma, biopsy technic, retinoblastoma......oftalmology, biopsy, choroid, corpus vitreum, retina, malignant melanoma, biopsy technic, retinoblastoma...

  3. Skin graft

    Science.gov (United States)

    Skin transplant; Skin autografting; FTSG; STSG; Split thickness skin graft; Full thickness skin graft ... donor site. Most people who are having a skin graft have a split-thickness skin graft. This takes ...

  4. Evaluation of an endoscopic liver biopsy technique in green iguanas.

    Science.gov (United States)

    Hernandez-Divers, Stephen J; Stahl, Scott J; McBride, Michael; Stedman, Nancy L

    2007-06-15

    To establish a safe and effective endoscopic technique for collection of liver biopsy specimens from lizards by use of a 2.7-mm rigid endoscope system that is commonly available in zoologic veterinary practice. Prospective study. 11 subadult male green iguanas (Iguana iguana). Each lizard was anesthetized, and right-sided coelioscopic examination of the right liver lobe and gallbladder was performed. Three liver biopsy specimens were collected from each lizard by use of a 2.7-mm rigid endoscope and 1.7-mm (5-F) biopsy forceps. Biopsy samples were evaluated histologically for quality and crush artifact. Ten days following surgery, all iguanas were euthanatized and underwent full necropsy examination. For all 11 iguanas, the right liver lobe and gallbladder were successfully examined endoscopically, and 3 biopsy specimens of the liver were collected without complications. Mean +/- SD durations of anesthesia and surgery were 24 +/- 7 minutes and 6.8 +/- 1.0 minutes, respectively. At necropsy, there was no evidence of trauma or disease associated with the skin or muscle entry sites, liver, or any visceral structures in any iguana. All 33 biopsy specimens were considered acceptable for histologic interpretation; in most samples, the extent of crush artifact was considered minimal. By use of a 2.7-mm rigid endoscope, liver biopsy procedures can be performed safely, swiftly, and easily in green iguanas. Biopsy specimens obtained by this technique are suitable for histologic examination. For evaluation of the liver and biopsy specimen collection in lizards, endoscopy is recommended.

  5. Ultraviolet-fluorescent tattoo location of cutaneous biopsy site.

    Science.gov (United States)

    Chuang, Gary S; Gilchrest, Barbara A

    2012-03-01

    Cutaneous biopsies often heal with little or no scarring. Prior studies have shown an alarming percentage of patients who incorrectly identify biopsy sites at the time of surgery. To investigate the safety and utility of an ultraviolet (UV)-fluorescent tattoo for biopsy site identification. A preclinical proof of concept was established with skin culture. An UV-fluorescent tattoo was applied to discarded neonatal foreskin in culture medium. The stability of the tattooed skin was examined clinically and histologically. One patient with a recurrent basal cell carcinoma in a difficult-to-identify location underwent tattoo application at the time of biopsy to demarcate the site. The patient was monitored for tattoo reaction and referred for surgical excision. The cultured tissue exhibited stable UV fluorescence with daily washing. Tissue histology demonstrated tattoo particles lining the skin edge under fluorescent microscopy. The patient was reluctant to undergo another surgical procedure and instead returned to our clinic at 3 months and 17 months after the biopsy for management of other tumors. The patient had no symptoms of allergic reaction to the tattoo dye. The fluorescent tattoo remains invisible under visible light and visible only under Wood's light. The present study documents the utility of an UV-fluorescent tattoo to locate a biopsy site. © 2011 by the American Society for Dermatologic Surgery, Inc. Published by Wiley Periodicals, Inc.

  6. Skin Diseases: Skin Health and Skin Diseases

    Science.gov (United States)

    Skip Navigation Bar Home Current Issue Past Issues Skin Diseases Skin Health and Skin Diseases Past Issues / Fall 2008 Table of Contents ... acne to wrinkles Did you know that your skin is the largest organ of your body? It ...

  7. Lung needle biopsy

    Science.gov (United States)

    ... if you have certain lung diseases such as emphysema. Usually, a collapsed lung after a biopsy does not need treatment. But ... any type Bullae (enlarged alveoli that occur with emphysema) Cor pulmonale (condition ... of the lung High blood pressure in the lung arteries Severe ...

  8. Closed Pericardial Biopsy

    African Journals Online (AJOL)

    1974-09-28

    Sep 28, 1974 ... The instrument used is a hook biopsy needle (Fig. I). manufactured by Becton, Dickinson and Co., Rutherford,. New Jersey, USA. The instrument' and technique' will be reviewed. The instrument consists of an ll-gauge needle with a sharp cutting edge into which fits, interchangeably, a 13-gauge needle or a ...

  9. CONE BIOPSY IN PREGNANCY*

    African Journals Online (AJOL)

    1 Mei 1971. S.-A. TYDSKRIF VIR OBSTETRIE EN GINEKOLOGIE. CONE BIOPSY ... of the abnormal cervix in pregnancy is also no longer in question following the .... the concept of cancer prophylaxis to the majority of women, many of whom ...

  10. Demonstration of Hepatitis C Virus RNA with In Situ Hybridization Employing a Locked Nucleic Acid Probe in Humanized Liver of Infected Chimeric Mice and in Needle-Biopsied Human Liver

    Directory of Open Access Journals (Sweden)

    Kazuya Shiogama

    2013-01-01

    Full Text Available Background. In situ hybridization (ISH with high sensitivity has been requested to demonstrate hepatitis C virus (HCV RNA in formalin-fixed, paraffin-embedded (FFPE sections of the liver. Methods. ISH employing a locked-nucleic-acid- (LNA-modified oligonucleotide probe and biotin-free catalyzed signal amplification system (CSAII was applied to HCV-RNA detection in the liver tissue. Nested reverse-transcription polymerase chain reaction (RT-PCR was performed for HCV genotyping using total RNA extracted from FFPE sections. The target tissues included FFPE tissue sections of humanized livers in HCV-infected chimeric mice (HCV genotypes 1a, 1b, and 2a and noninfected and of needle-biopsied livers from HCV-infected patients. Results. HCV-RNA was demonstrated with the ISH technique in HCV-infected liver tissues from both chimeric mice and 9 (82% of 11 patients with HCV infection. The HCV signals were sensitive to RNase. Nested RT-PCR confirmed the genotype in 8 (73% of 11 livers (type 1b: 6 lesions and type 2a: 2 lesions. HCV-RNA was not identified in chronic hepatitis B lesions, fatty liver, autoimmune hepatitis, and hepatocellular carcinoma. Conclusion. ISH using the LNA-modified oligonucleotide probe and CSAII was applicable to detecting HCV-RNA in routinely prepared FFPE liver specimens.

  11. Does Prebiopsy, Nonsterile Ultrasonography Gel Affect Biopsy-Site Asepsis?

    International Nuclear Information System (INIS)

    Gurel, Kamil; Karabay, Oguz; Gurel, Safiye; Hildebolt, Charles

    2008-01-01

    Purpose. The purpose of this study was to determine the extent to which the use of nonsterile gel, prior to antiseptic procedures in ultrasonography (US)-guided percutaneous biopsies, results in contamination of the biopsy site. Materials and Methods. Patients referred for US-guided percutaneous biopsies were included in this study. Transmission material used for US evaluation before biopsy-site antiseptic procedures were performed was either nonsterile gel or sterile saline. Patients were randomly assigned to two groups: nonsterile gel (n = 30) and sterile saline (n = 30). Before the transmission material was used and after antiseptic procedures were performed, microbial swabs of a 10-cm 2 -diameter area were obtained at the biopsy site. Swabs were also obtained from the gel, saline, and povidine-iodine. Inoculated specimen plates were incubated at 37 o C under aerobic conditions, and the numbers of colony-forming units recorded. Nominal logistic regression analysis was used to calculate the odds of postantisepsis bacterial growth (after antiseptic procedures were performed) based on group, gender, coincidental disease (diabetes, chronic renal failure, and malignancy), biopsy-site location (head and neck or breast and abdomen), and local factors (skin fold, skin tag, and hair). Results. The following odds ratios (adjusted for the other variables) and their 95% confidence intervals were calculated: (1) group (2.9 [0.8-11.1]; p = 0.10); (2) gender (1.2 [0.3-5.2]; p = 0.78); (3) coincidental disease (7.6 [0.9-166.7]; p = 0.09); (4) biopsy site location (6.2 [1.4-31.3]; p = 0.02); and (5) local factors (7.0 [1.6-36.0]; p = 0.01). No bacterial growth occurred with swabs obtained from gel, povidine-iodine, or saline. Conclusion. We conclude that nonsterile gel used prior to percutaneous biopsy does not affect biopsy-site asepsis

  12. Sonographically guided percutaneous muscle biopsy in diagnosis of neuromuscular disease: a useful alternative to open surgical biopsy.

    Science.gov (United States)

    O'Sullivan, Paul J; Gorman, Grainne M; Hardiman, Orla M; Farrell, Michael J; Logan, P Mark

    2006-01-01

    The purpose of this study was to evaluate the feasibility of sonographically guided percutaneous muscle biopsy in the investigation of neuromuscular disorders. Sonographically guided percutaneous needle biopsy of skeletal muscle was performed with a 14-gauge core biopsy system in 40 patients over a 24-month period. Patients were referred from the Department of Neurology under investigation for neuromuscular disorders. Sonography was used to find suitable tissue and to avoid major vascular structures. A local anesthetic was applied below skin only. A 3- to 4-mm incision was made. Three 14-gauge samples were obtained from each patient. All samples were placed on saline-dampened gauze and sent for neuropathologic analysis. As a control, we retrospectively assessed results of the 40 most recent muscle samples acquired via open surgical biopsy. With the use of sonography, 32 (80%) of 40 patients had a histologic diagnosis made via percutaneous needle biopsy. This included 26 (93%) of 28 patients with acute muscular disease and 6 (50%) of 12 patients with chronic disease. In the surgical group (all acute disease), 38 (95%) of 40 patients had diagnostic tissue attained. Sonographically guided percutaneous 14-gauge core skeletal muscle biopsy is a useful procedure, facilitating diagnosis in acute muscular disease. It provides results comparable with those of open surgical biopsy in acute muscular disease. It may also be used in chronic muscular disease but repeated or open biopsy may be needed.

  13. Endogenous and radiation-induced expression of γH2AX in biopsies from patients treated for carcinoma of the uterine cervix

    International Nuclear Information System (INIS)

    Olive, Peggy L.; Banuelos, C. Adriana; Durand, Ralph E.; Kim, Joo-Young; Aquino-Parsons, Christina

    2010-01-01

    Background and purpose: The possibility of using γH2AX foci as a marker of DNA damage and as a potential predictor of tumour response to treatment was examined using biopsies from 3 sets of patients with advanced carcinoma of the cervix. The relation between endogenous γH2AX expression and hypoxia was also examined. Materials and methods: Set 1 consisted of 26 biopsies that included pre-treatment and 24 h post-radiation treatment samples. Pre-treatment biopsies from 12 patients in Set 2 were used to develop image analysis software while pre-treatment biopsies from 33 patients in Set 3 were examined for the relation between staining for the hypoxia marker pimonidazole and endogenous γH2AX expression. Formalin-fixed paraffin-embedded sections were analyzed after antigen retrieval and fluorescence antibody labeling for the hypoxia markers CAIX or pimonidazole in combination with γH2AX staining. Results: Before treatment, 24 ± 19% of cells contained γH2AX foci, with most positive cells containing fewer than 5 foci per nucleus. Twenty-four hours after exposure to the first fraction of 1.8-2.5 Gy, 38 ± 19% contained foci. CAIX positive cells were 1.4 times more likely to exhibit endogenous γH2AX foci, and pimonidazole-positive cells were 2.8 times more likely to contain γH2AX foci. For 18 patients for whom both pre-treatment and 24 h post-irradiation biopsies were available, local control was unrelated to the fraction of cells that retained γH2AX foci. However, 24 h after irradiation, tumours that had received 2.5 Gy showed a significantly higher fraction of cells with residual γH2AX foci than tumours given 1.8 Gy. Conclusions: Endogenous γH2AX foci are enriched in hypoxic tumour regions. Small differences in delivered dose can produce quantifiable differences in residual DNA damage that can overshadow inter-tumour differences in response.

  14. Identification of proteins from 4200-year-old skin and muscle tissue biopsies from ancient Egyptian mummies of the first intermediate period shows evidence of acute inflammation and severe immune response.

    Science.gov (United States)

    Jones, Jana; Mirzaei, Mehdi; Ravishankar, Prathiba; Xavier, Dylan; Lim, Do Seon; Shin, Dong Hoon; Bianucci, Raffaella; Haynes, Paul A

    2016-10-28

    We performed proteomics analysis on four skin and one muscle tissue samples taken from three ancient Egyptian mummies of the first intermediate period, approximately 4200 years old. The mummies were first dated by radiocarbon dating of the accompany-\\break ing textiles, and morphologically examined by scanning electron microscopy of additional skin samples. Proteins were extracted, separated on SDS-PAGE (sodium dodecyl sulfate polyacrylamide gel electrophoresis) gels, and in-gel digested with trypsin. The resulting peptides were analysed using nanoflow high-performance liquid chromatography-mass spectrometry. We identified a total of 230 unique proteins from the five samples, which consisted of 132 unique protein identifications. We found a large number of collagens, which was confirmed by our microscopy data, and is in agreement with previous studies showing that collagens are very long-lived. As expected, we also found a large number of keratins. We identified numerous proteins that provide evidence of activation of the innate immunity system in two of the mummies, one of which also contained proteins indicating severe tissue inflammation, possibly indicative of an infection that we can speculate may have been related to the cause of death.This article is part of the themed issue 'Quantitative mass spectrometry'. © 2016 The Author(s).

  15. Image-Guided percutaneous biopsies with a biopsy gun

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Kyung Hwan; Lim, Hyo Keun; Kim, Eun Ah; Yun, Ku Sub; Bae, Sang Hoo; Shin, Hyung Sik [Hallym University College of Medicine, Seoul (Korea, Republic of)

    1994-07-15

    We report the results of image-guided percutaneous biopsies with a biopsy gun and evaluate the clinical usefulness. One hundred and five biopsies under ultrasonographic or fluoroscopic guidance were performed. Various anatomic sites were targeted(liver; 50, chest; 22, kidney; 12, pancreas; 8, intraperitoeum; 7, retroperitoneum; ). Obtained tissue was diagnostic in 98 of the 105 biopsies(93%). In each instance, representative core tissue specimens were obtained. Evaluation of the core tissue by pathologist revealed consistent, uniform specimens that contained significant crush artifact in no case. Five biopsies yielded inadequate tissue which were too small for histopathologic interpretation or were composed of necrotic debris. Two biopsies yielded adequate tissues, but tissues were not of the target. The diagnoses were malignancy in 77 biopsies and benign disease in 21 biopsies. No complications other than mild, localized discomfort were encountered except a transient hemoptysis and pneumothorax which was observed in two patients. Cutting biopsy with a biopsy gun provided sufficient amount of target tissue for an accurate diagnosis of malignant and benign disease. It was a safe and useful procedure for percutaneous biopsy.

  16. Radiologically Guided Bone Biopsy: Results of 502 Biopsies

    International Nuclear Information System (INIS)

    Ng, Chaan S.; Salisbury, Jonathan R.; Darby, Alan J.; Gishen, Philip

    1998-01-01

    Purpose: To analyze the results of 502 biopsies over a 19-year period for the purpose of highlighting the results that can be expected from such a large study, with emphasis on needle choice and anesthetic methods. Methods: The histological, cytological, and microbiological results of 477 patients who had 502 bone biopsies carried out between July 1977 and March 1996 were studied. Less than 5% of patients required second biopsies. There were almost equal numbers of males and females in the group. The lesions were visible radiologically and most of the biopsies were carried out by a single operator. The lesions were classified on their histopathological, cytopathological, and microbiological findings. Results: Tumors accounted for 40% of the biopsies, and infection for 16%. Biopsies which did not yield a 'positive' diagnosis accounted for 31%; these included specimens reported as normal, or as showing reactive changes, repair, remodelling, non-specific features, inflammation (but not clearly infective), or no evidence of malignancy or inflammation. Less than 4% of biopsies were incorrect, and some of these were re-biopsied. Conclusion: Bone biopsy is a valuable technique for positive diagnosis of malignancy or infection, as it enables a definitive plan for treatment and management of patients to be established. Exclusion of serious pathology is almost equally important. In principle, any osseous site can be biopsied using fluoroscopic or computed tomographic guidance. Care in the biopsy technique and selection of the bone needle is required

  17. US-guided percutaneous biopsies with a biopsy gun

    International Nuclear Information System (INIS)

    Ahn, In Oak; Kim, Hyung Jin; Kim, Jae Hyung; Lee, Goo; Jung, Sung Hoon

    1993-01-01

    Core tissue for histologic study is believed by many pathologist to be more diagnostic than material from needle aspiration. Recently introduced automatched biopsy gun simplifies core biopsies with increased quantity and quality of samples. Authors performed 38 percutaneous biopsies from 38 patients with 18G automated biopsy guns under US guide. Diagnostic target tissues were obtained in 33 biopsies(87%), inadequate tissues in 4(11%), and adequate but not of target tissue in 1(3%). There was no major complication requiring treatment, but pain needing analgesics and pain with nausea/vomiting were experienced in 2 and 1 biopsies respectively. Average number of needle passes was 1.5. We concluded that US guided gun biopsy was a easy and safe way to obtain tissue samples of good quantity and quality, especially useful in hospitals without constant availability of specialist in cytopathology

  18. The comparison of nuclear ubiquitous casein and cyclin-dependent kinases substrate (NUCKS) with Ki67 proliferation marker expression in common skin tumors.

    Science.gov (United States)

    Zduniak, Krzysztof; Agrawal, Siddarth; Symonowicz, Krzysztof; Jurczyszyn, Kamil; Ziółkowski, Piotr

    2014-03-01

    Nuclear ubiquitous casein and cyclin-dependent kinases substrate (NUCKS) is a chromosomal protein of unknown function. Its amino acid composition and structure of its DNA binding domain resemble those of high mobility group A (HMGA) proteins which are associated with various malignancies. Since changes in expression of HMGA are considered as a marker of tumor progression, it is possible that similar changes in expression of NUCKS could be a useful tool in diagnosis of malignant skin tumors. To investigate this assumption we used specific antibodies against NUCKS for immunohistochemistry of squamous (SCC) and basal cell carcinoma (BCC) as well as keratoacanthoma (KA). We found high expression of NUCKS in nuclei of SCC and BCC cells which exceeded expression of the well-known proliferation marker Ki67. Expression of NUCKS in benign KA was much below that of malignant tumors. With the present study and based on our previous experience we would like to suggest the NUCKS protein as a novel proliferation marker for immunohistochemical evaluation of formalin-fixed and paraffin-embedded skin tumor specimens. We would like to emphasize that NUCKS abundance in malignant skin tumors is higher than that of the well-known proliferation marker Ki67, thus allowing more precise assessment of tumor proliferation potential.

  19. Diagnostic accuracy of confocal microscopy imaging vs. punch biopsy for diagnosing and subtyping basal cell carcinoma

    NARCIS (Netherlands)

    Kadouch, D. J.; Leeflang, M. M.; Elshot, Y. S.; Longo, C.; Ulrich, M.; van der Wal, A. C.; Wolkerstorfer, A.; Bekkenk, M. W.; de Rie, M. A.

    2017-01-01

    BackgroundIn vivo reflectance confocal microscopy (RCM) is a promising non-invasive skin imaging technique that could facilitate early diagnosis of basal cell carcinoma (BCC) instead of routine punch biopsies. However, the clinical value and utility of RCM vs. a punch biopsy in diagnosing and

  20. Breast skin calcifications: Mammographic recognition and confirmation

    International Nuclear Information System (INIS)

    Berkowitz, J.E.; Gatewood, O.M.B.; Gayler, B.W.

    1987-01-01

    The authors found microcalcifications in the skin of the breast to occur in 8% of patients undergoing mammography, a prevalence much higher than what has been previously reported. Usually in incidental finding, breast skin calcifications are readily recognized when they are multiple, bilateral, coarse, or polygonal with a central radiolucency; when they are located in a peripheral portion of the breast on at least one view, or when they are serendipitously imaged within the skin. One hundred patients with breast skin calcifications were studied. In 15 patients in whom clustered dermal calcifications simulated parenchymal microcalcifications, template-guided tangential views permitted precise skin localization. Three of those patients had been referred for needle localization before biopsy and four after failed biopsy for clustered microcalcifications. Dermal calcifications can pose a vexing problem in the management of microcalcifications of the breast. A high index of suspicion is warrented in order to forestall unnecessary or unsuccessful biopsies

  1. Your Skin

    Science.gov (United States)

    ... Safe Videos for Educators Search English Español Your Skin KidsHealth / For Kids / Your Skin What's in this ... body) are really dead skin cells. Bye-Bye Skin Cells These old cells are tough and strong, ...

  2. Usefulness of automated biopsy guns in image-guided biopsy

    International Nuclear Information System (INIS)

    Lee, Jung Hyung; Rhee, Chang Soo; Lee, Sung Moon; Kim, Hong; Woo, Sung Ku; Suh, Soo Jhi

    1994-01-01

    To evaluate the usefulness of automated biopsy guns in image-guided biopsy of lung, liver, pancreas and other organs. Using automated biopsy devices, 160 biopsies of variable anatomic sites were performed: Biopsies were performed under ultrasonographic(US) guidance in 95 and computed tomographic (CT) guidance in 65. We retrospectively analyzed histologic results and complications. Specimens were adequate for histopathologic diagnosis in 143 of the 160 patients(89.4%)-Diagnostic tissue was obtained in 130 (81.3%), suggestive tissue obtained in 13(8.1%), and non-diagnostic tissue was obtained in 14(8.7%). Inadequate tissue was obtained in only 3(1.9%). There was no statistically significant difference between US-guided and CT-guided percutaneous biopsy. There was no occurrence of significant complication. We have experienced mild complications in only 5 patients-2 hematuria and 2 hematochezia in transrectal prostatic biopsy, and 1 minimal pneumothorax in CT-guided percutaneous lung biopsy. All of them were resolved spontaneously. The image-guided biopsy using the automated biopsy gun was a simple, safe and accurate method of obtaining adequate specimen for the histopathologic diagnosis

  3. Usefulness of automated biopsy guns in image-guided biopsy

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Jung Hyung; Rhee, Chang Soo; Lee, Sung Moon; Kim, Hong; Woo, Sung Ku; Suh, Soo Jhi [School of Medicine, Keimyung University, Daegu (Korea, Republic of)

    1994-12-15

    To evaluate the usefulness of automated biopsy guns in image-guided biopsy of lung, liver, pancreas and other organs. Using automated biopsy devices, 160 biopsies of variable anatomic sites were performed: Biopsies were performed under ultrasonographic(US) guidance in 95 and computed tomographic (CT) guidance in 65. We retrospectively analyzed histologic results and complications. Specimens were adequate for histopathologic diagnosis in 143 of the 160 patients(89.4%)-Diagnostic tissue was obtained in 130 (81.3%), suggestive tissue obtained in 13(8.1%), and non-diagnostic tissue was obtained in 14(8.7%). Inadequate tissue was obtained in only 3(1.9%). There was no statistically significant difference between US-guided and CT-guided percutaneous biopsy. There was no occurrence of significant complication. We have experienced mild complications in only 5 patients-2 hematuria and 2 hematochezia in transrectal prostatic biopsy, and 1 minimal pneumothorax in CT-guided percutaneous lung biopsy. All of them were resolved spontaneously. The image-guided biopsy using the automated biopsy gun was a simple, safe and accurate method of obtaining adequate specimen for the histopathologic diagnosis.

  4. Telepathology and Optical Biopsy

    Directory of Open Access Journals (Sweden)

    Olga Ferrer-Roca

    2009-01-01

    Full Text Available The ability to obtain information about the structure of tissue without taking a sample for pathology has opened the way for new diagnostic techniques. The present paper reviews all currently available techniques capable of producing an optical biopsy, with or without morphological images. Most of these techniques are carried out by physicians who are not specialized in pathology and therefore not trained to interpret the results as a pathologist would. In these cases, the use of telepathology or distant consultation techniques is essential.

  5. No need for biopsies

    DEFF Research Database (Denmark)

    Gjødsbøl, Kristine; Skindersoe, Mette E; Christensen, Jens Jørgen

    2011-01-01

    collected. After 4 weeks, additional biopsy and filter paper pad samples were collected. Bacteria were isolated and identified at species level by standard methods. The most common bacterial species detected was Staphylococcus aureus found in 89% of the ulcers. No methicillin-resistant S. aureus isolates...... were found. We did not find any significant differences regarding the bacterial species isolated between the three sampling techniques. However, using multiple techniques led to identification of more species. Our study suggests that it is sufficient to use swab specimens to identify the bacterial...

  6. Non-hazardous organic solvents in the paraffin-embedding technique

    DEFF Research Database (Denmark)

    Holm, Inger Lindebo; Lyon, Hans; Prentø, Poul

    1995-01-01

    The aim of this study was to substitute hazardous compounds, used in tissue processing and dewaxing, with compounds having lowest possible toxicity and inflammability without impairing the morphology, staining characteristics, or diagnostic value of the tissue sections. All aromatic compounds...... and aliphatic hydrocarbons (e.g. alkanes, isoparaffins, petroleum distillates, etc.) were rejected, primarily due to their high vapour pressure. Based on a theoretical study of compounds used for clearing, a number of non-hazardous potential substitutes were chosen. The following experimental study narrowed...... the group to three unbranched, saturated, aliphatic monoesters containing 12-14 carbon atoms. On large-scale testing of these compounds, we found butyldecanoate to be the closest to an ideal substitute for aromatic and aliphatic hydrocarbons in the histology department: the section quality is at least equal...

  7. Proposals for best-quality immunohistochemical staining of paraffin-embedded brain tissue slides in forensics.

    Science.gov (United States)

    Trautz, Florian; Dreßler, Jan; Stassart, Ruth; Müller, Wolf; Ondruschka, Benjamin

    2018-01-03

    Immunohistochemistry (IHC) has become an integral part in forensic histopathology over the last decades. However, the underlying methods for IHC vary greatly depending on the institution, creating a lack of comparability. The aim of this study was to assess the optimal approach for different technical aspects of IHC, in order to improve and standardize this procedure. Therefore, qualitative results from manual and automatic IHC staining of brain samples were compared, as well as potential differences in suitability of common IHC glass slides. Further, possibilities of image digitalization and connected issues were investigated. In our study, automatic staining showed more consistent staining results, compared to manual staining procedures. Digitalization and digital post-processing facilitated direct analysis and analysis for reproducibility considerably. No differences were found for different commercially available microscopic glass slides regarding suitability of IHC brain researches, but a certain rate of tissue loss should be expected during the staining process.

  8. MicroRNA Expression in Formalin-fixed Paraffin-embedded Cancer Tissue

    DEFF Research Database (Denmark)

    Boisen, Mogens Karsbøl; Dehlendorff, Christian; Linnemann, Dorte

    2015-01-01

    of miRNA expression in FFPE tissue samples from patients with colorectal (CRC) and pancreatic (PC) cancer and to quantify the variability associated with sample age and fixation. METHODS: High-throughput miRNA profiling results from 203 CRC and 256 PC FFPE samples as well as from 37 paired frozen....../FFPE samples from nine other CRC tumors (methodological samples) were used. Candidate reference miRNAs were identified by their correlation with global mean expression. The stability of reference genes was analyzed according to published methods. The association between sample age and global mean mi...... to global mean expression in each cancer type. Nine of these miRNAs were present in both lists, and miR-103a-3p was the most stable reference miRNA for both CRC and PC FFPE tissue. The optimal number of reference miRNAs was 4 in CRC and 10 in PC. Sample age had a significant effect on global mi...

  9. Fluorescence in situ hybridization on formalin-fixed and paraffin-embedded tissue

    DEFF Research Database (Denmark)

    Laub Petersen, Bodil; Zeuthen, Mette Christa; Pedersen, Sanni

    2004-01-01

    Fluorescence in situ hybridization (FISH) is widely used to study numerical and structural genetic abnormalities in both metaphase and interphase cells. The technique is based on the hybridization of labeled probes to complementary sequences in the DNA or RNA of the cells. Interphase FISH is most...... in time lapse between removal of tissue and fixation, duration of fixation, enzymatic pretreatment, hybridization conditions, and posthybridization washing conditions are important factors in the hybridization. In this study, we have listed the results of a systematic approach to improve FISH on isolated...

  10. In situ hybridization for the detection of rust fungi in paraffin embedded plant tissue sections

    Science.gov (United States)

    Rust fungi infect a wide range of plant species making them of particular interest to plant pathologists. In order to study the interactions between these important pathogenic fungi and their host plants it is useful to be able to differentiate fungal tissue from plant tissue. This can be accomplish...

  11. Cellular localization of 2-[3H]deoxy-D-glucose from paraffin-embedded brains

    International Nuclear Information System (INIS)

    Durham, D.; Woolsey, T.A.; Kruger, L.

    1981-01-01

    Results of experiments in which regional neuronal activity is revealed by a 2-[ 3 H]deoxy-D-glucose ( 3 H-2-DG)-paraffin section-emulsion autoradiography method are described. The trigeminal pathway of freely behaving mice was activated differentially by selective patterns of whisker removal. One hour after injection of concentrated 3 H-2-DG, the animals were perfused systemically with a periodate/lysine/paraformaldehyde mixture the brains were embedded in paraffin, and serial sections were taken and coated with emulsion for autoradiography. Diffusion of the isotope out of the tissue was assessed visually and by liquid scintillation counting. While substantial loss of 3 H isotope into the embedding fluids (about 95%) was found, the scintillation counts and the autoradiograms showed good fixation of the isotope in situ, no evidence of isotope movement into the emulsion, and no gradients of diffusion in the sectioned material. Patterns of regional labeling were similar to those reported from brains prepared by conventional 2-[ 14 C]deoxy-D-glucose ( 14 C-2-DG) autoradiography; Trigeminal structures associated with the intact (stimulated) whiskers were labeled relatively heavily, indicating that label uptake is specific with respect to neuronal activity. In the cortex, the patterns of label corresponded directly and precisely to those barrels known to receive inputs from the intact whiskers. Distribution of silver grains in the cortex and in the brainstem was correlated directly with neuronal profiles. Clearly, this approach offers considerable technical advantages, in particular, the ease with which the histological material is prepared. The resolution of the autoradiograms and the quality of the histology are excellent

  12. Diagnostic accuracy of pre-treatment biopsy for grading cutaneous mast cell tumours in dogs.

    Science.gov (United States)

    Shaw, T; Kudnig, S T; Firestone, S M

    2018-06-01

    Mast cell tumours (MCTs) are common tumours of the canine skin, and are estimated to represent up to 20% of all skin tumours in dogs. Tumour grade has a major impact on the incidence of local recurrence and metastatic potential. In addition to helping the clinician with surgical planning, knowledge of the tumour grade also assists in proper prognostication and client education. For pre-treatment biopsies to be useful, there must exist a high level of correlation between the histopathological grade obtained from the pre-treatment biopsy and the actual histopathological grade from the excisional biopsy. The aim of this study was to determine concordance of tumour grade between various biopsy techniques (wedge, punch, needle core) and the "gold standard" excisional biopsy method. We found an overall concordance rate of 96% based on the Patnaik grading system, and an overall concordance rate of 92% based on the Kiupel grading system. The accuracy of the various biopsy techniques (wedge, punch and needle core) when compared with excisional biopsy was 92%, 100% and 100%, respectively, based on the Patnaik grading system, and 90%, 95% and 100%, respectively, based on the Kiupel grading system. Of the cases with discordant results, the pre-treatment biopsies tended to underestimate the grade of the tumour. Based on these results, we conclude that pre-treatment biopsies are sufficiently accurate for differentiating low-grade from high-grade MCTs, regardless of biopsy technique or tumour location. © 2017 John Wiley & Sons Ltd.

  13. Utilization of Cell-Transfer Technique for Molecular Testing on Hematoxylin-Eosin-Stained Sections: A Viable Option for Small Biopsies That Lack Tumor Tissues in Paraffin Block.

    Science.gov (United States)

    Wu, Howard H; Jovonovich, Stephen M; Randolph, Melissa; Post, Kristin M; Sen, Joyashree D; Curless, Kendra; Cheng, Liang

    2016-12-01

    - In some instances the standard method of doing molecular testing from formalin-fixed, paraffin-embedded block is not possible because of limited tissue. Tumor cell-enriched cell-transfer technique has been proven useful for performing immunocytochemistry and molecular testing on cytologic smears. - To establish the cell-transfer technique as a viable option for isolating tumor cells from hematoxylin-eosin (H&E)-stained slides. - Molecular testing was performed by using the cell-transfer technique on 97 archived H&E-stained slides from a variety of different tumors. Results were compared to the conventional method of molecular testing. - Polymerase chain reaction-based molecular testing via the cell-transfer technique was successfully performed on 82 of 97 samples (85%). This included 39 of 47 cases for EGFR, 10 of 11 cases for BRAF, and 33 of 39 cases for KRAS mutations. Eighty-one of 82 cell-transfer technique samples (99%) showed agreement with previous standard method results, including 4 mutations and 35 wild-type alleles for EGFR, 4 mutations and 6 wild-type alleles for BRAF, and 11 mutations and 21 wild-type alleles for KRAS. There was only 1 discrepancy: a cell-transfer technique with a false-negative >KRAS result (wild type versus G12C). - Molecular testing performed on H&E-stained sections via cell-transfer technique is useful when tissue from cell blocks and small surgical biopsy samples is exhausted and the only available material for testing is on H&E-stained slides.

  14. Presence of human papilloma virus, herpes simplex virus and Epstein-Barr virus DNA in oral biopsies from Sudanese patients with regard to toombak use.

    Science.gov (United States)

    Jalouli, Jamshid; Ibrahim, Salah O; Sapkota, Dipak; Jalouli, Miranda M; Vasstrand, Endre N; Hirsch, Jan M; Larsson, Per-Anders

    2010-09-01

    Using PCR/DNA sequencing, we investigated the prevalence of human papillomavirus (HPV), herpes simplex virus (HSV) and Epstein-Barr virus (EBV) DNA in brush biopsies obtained from 150 users of Sudanese snuff (toombak) and 25 non-users of toombak in formalin-fixed paraffin-embedded tissue samples obtained from 31 patients with oral dysplasias (25 toombak users and 6 non-users), and from 217 patients with oral cancers (145 toombak users and 72 non-users). In the brush tissue samples from toombak users, HPV was detected in 60 (40%), HSV in 44 (29%) and EBV in 97 (65%) of the samples. The corresponding figures for the 25 samples from non-users were 17 (68%) positive for HPV, 6 (24%) positive for HSV and 21 (84%) for EBV. The formalin-fixed samples with oral dysplasias were all negative for HPV. In the 145 oral cancer samples from toombak users, HPV was detected in 39 (27%), HSV in 15 (10%) and EBV in 53 (37%) of the samples. The corresponding figures for the samples from non-users were 15 (21%) positive for HPV, 5 (7%) for HSV and 16 (22%) for EBV. These findings illustrate that prevalence of HSV, HPV and EBV infections are common and may influence oral health and cancer development. It is not obvious that cancer risk is increased in infected toombak users. These observations warrant further studies involving toombak-associated oral lesions, to uncover the possible mechanisms of these viral infections in the development of oral cancer, and the influence of toombak on these viruses. © 2010 John Wiley & Sons A/S.

  15. The use of droplet digital PCR in liquid biopsies: A highly sensitive technique for MYD88 p.(L265P) detection in cerebrospinal fluid.

    Science.gov (United States)

    Hiemcke-Jiwa, Laura S; Minnema, Monique C; Radersma-van Loon, Joyce H; Jiwa, N Mehdi; de Boer, Mirthe; Leguit, Roos J; de Weger, Roel A; Huibers, Manon M H

    2018-04-01

    The gold standard for diagnosis of central nervous system lymphomas still regards a stereotactic brain biopsy, with the risk of major complications for the patient. As tumor cells can be detected in cerebrospinal fluid (CSF), CSF analysis can be used as an alternative. In this respect, mutation analysis in CSF can be of added value to other diagnostic parameters such a cytomorphology and clonality analysis. A well-known example of targeted mutation analysis entails MYD88 p.(L265P) detection, which is present in the majority of Bing Neel syndrome and primary central nervous system lymphoma (PCNSL) patients. Unfortunately, tumor yield in CSF can be very low. Therefore, use of the highly sensitive droplet digital PCR (ddPCR) might be a suitable analysis strategy for targeted mutation detection. We analyzed 26 formalin fixed paraffin embedded (FFPE) samples (8 positive and 18 negative for MYD88 p.(L265P) mutation) by ddPCR, of which the results were compared with next generation sequencing (NGS). Subsequently, 32 CSF samples were analyzed by ddPCR. ddPCR and NGS results on FFPE material showed 100% concordance. Among the 32 CSF samples, 9 belonged to patients with lymphoplasmacytic lymphoma (LPL) and clinical suspicion of Bing Neel syndrome, and 3 belonged to patients with PCNSL. Nine of these samples tested positive for MYD88 p.(L265P) (8 LPL and 1 PCNSL). This study shows that sensitive MYD88 mutation analysis by ddPCR in CSF is highly reliable and can be applied even when DNA input is low. Therefore, ddPCR is of added value to current diagnostic parameters, especially when the available amount of DNA is limited. Copyright © 2017 John Wiley & Sons, Ltd.

  16. Eosinophils are rare in biopsy specimens of psoriasis vulgaris.

    Science.gov (United States)

    Rosa, Gabriela; Fernandez, Anthony P; Schneider, Sarah; Billings, Steven D

    2017-12-01

    Histological features of lesional biopsies can be helpful in distinguishing psoriasis subtypes from disease mimickers. However, occasionally, classic histological features are not sufficient for distinction, and additional clues would be useful. There is a common belief that the presence of eosinophils in skin biopsies argues against psoriasis, but actual literature is scant. Skin biopsies with a diagnosis of psoriasis from 2013 to 2016 were reviewed. For inclusion, both histological and clinical features were required to be consistent with psoriasis. For biopsies meeting inclusion criteria, a detailed evaluation for typical histological parameters of psoriasis, as well as presence of dermal eosinophils, was performed. Of 85 cases meeting inclusion criteria, all had either individual or grouped intracorneal neutrophils and dilated papillary blood vessels. Diminished or complete loss of the granular cell layer was seen in 83 cases (98%), and parakeratosis was seen in 84 cases (99%). Alternatively, dermal eosinophils were seen in only 15 cases (18%). Of cases with eosinophils, none had more than 3 eosinophils upon examination of the entire dermis. Active treatment did not appear to impact presence/absence or numbers of eosinophils. Eosinophils are uncommon in psoriasis biopsies, and when present, they are found in small numbers. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  17. Cutaneous lesions in pet rabbits following subcutaneous administration of a novel bivalent vaccine against myxomatosis and rabbit haemorrhagic disease.

    Science.gov (United States)

    Selleri, Paolo; Di Girolamo, Nicola; Vögtlin, Andrea; Fileccia, Ivan; Hoop, Richard; Bongiovanni, Laura

    2014-12-01

    A novel bivalent vaccine to protect against myxomatosis and rabbit haemorrhagic disease is commercially available for pet rabbits. To describe the appearance of cutaneous lesions arising in pet rabbits positive for myxoma virus (MV) by RT-PCR evaluation shortly after vaccination. Four pet rabbits presenting with papular, crusting skin lesions ~10 days after vaccination. Histological evaluation of formalin-fixed skin biopsies obtained from lesional skin (case 1). Real-time polymerase chain reaction (RT-PCR) evaluation of paraffin-embedded tissue from skin biopsies (case 1) and crusts obtained from the lesion surface (cases 2-4) for myxoma virus are reported as cycle threshold (Ct ) values. Lesions affecting the ear pinna, dorsal aspect of the nose, vulva and/or conjunctiva are reported. Histopathological findings included severe ulcerative, necrotizing dermatitis and intralesional cytoplasmic inclusion bodies in myxoma cells. DNA was amplified from all the paraffin-embedded skin biopsies (Ct  = 34-35) and crusts (Ct  = 20-24). Although a wild virus challenge cannot be definitively excluded, veterinarians and pet-owners should be aware that cutaneous lesions have been observed after vaccination with this novel vaccine in low numbers of rabbits. © 2014 ESVD and ACVD.

  18. Oral Biopsy: A Dental Gawk

    African Journals Online (AJOL)

    Sir,. Dermatologists are often confronted with neoplasms and diseases of the oral cavity. Although many may be reluctant to perform oral surgical procedures, a biopsy is often needed to establish a definitive diagnosis, and biopsy of the oral cavity is a safe and useful technique that can be easily employed by dermatologists.

  19. The accuracy of colposcopic biopsy

    DEFF Research Database (Denmark)

    Stoler, Mark H; Vichnin, Michelle D; Ferenczy, Alex

    2011-01-01

    We evaluated the overall agreement between colposcopically directed biopsies and the definitive excisional specimens within the context of three clinical trials. A total of 737 women aged 16-45 who had a cervical biopsy taken within 6 months before their definitive therapy were included. Per-prot...

  20. Skin Conditions

    Science.gov (United States)

    Your skin is your body's largest organ. It covers and protects your body. Your skin Holds body fluids in, preventing dehydration Keeps harmful ... it Anything that irritates, clogs, or inflames your skin can cause symptoms such as redness, swelling, burning, ...

  1. Liquid biopsy for brain tumors

    Science.gov (United States)

    Shankar, Ganesh M.; Balaj, Leonora; Stott, Shannon L.; Nahed, Brian; Carter, Bob S.

    2018-01-01

    Introduction Minimally invasive methods will augment the clinical approach for establishing the diagnosis or monitoring treatment response of central nervous system tumors. Liquid biopsy by blood or cerebrospinal fluid sampling holds promise in this regard. Areas covered In this literature review, the authors highlight recent studies describing the analysis of circulating tumor cells, cell free nucleic acids, and extracellular vesicles as strategies to accomplish liquid biopsy in glioblastoma and metastatic tumors. The authors then discuss the continued efforts to improve signal detection, standardize the liquid biopsy handling and preparation, develop platforms for clinical application, and establish a role for liquid biopsies in personalized medicine. Expert commentary As the technologies used to analyze these biomarkers continue to evolve, we propose that there is a future potential to precisely diagnose and monitor treatment response with liquid biopsies. PMID:28875730

  2. Reoperative sentinel lymph node biopsy after previous mastectomy.

    Science.gov (United States)

    Karam, Amer; Stempel, Michelle; Cody, Hiram S; Port, Elisa R

    2008-10-01

    Sentinel lymph node (SLN) biopsy is the standard of care for axillary staging in breast cancer, but many clinical scenarios questioning the validity of SLN biopsy remain. Here we describe our experience with reoperative-SLN (re-SLN) biopsy after previous mastectomy. Review of the SLN database from September 1996 to December 2007 yielded 20 procedures done in the setting of previous mastectomy. SLN biopsy was performed using radioisotope with or without blue dye injection superior to the mastectomy incision, in the skin flap in all patients. In 17 of 20 patients (85%), re-SLN biopsy was performed for local or regional recurrence after mastectomy. Re-SLN biopsy was successful in 13 of 20 patients (65%) after previous mastectomy. Of the 13 patients, 2 had positive re-SLN, and completion axillary dissection was performed, with 1 having additional positive nodes. In the 11 patients with negative re-SLN, 2 patients underwent completion axillary dissection demonstrating additional negative nodes. One patient with a negative re-SLN experienced chest wall recurrence combined with axillary recurrence 11 months after re-SLN biopsy. All others remained free of local or axillary recurrence. Re-SLN biopsy was unsuccessful in 7 of 20 patients (35%). In three of seven patients, axillary dissection was performed, yielding positive nodes in two of the three. The remaining four of seven patients all had previous modified radical mastectomy, so underwent no additional axillary surgery. In this small series, re-SLN was successful after previous mastectomy, and this procedure may play some role when axillary staging is warranted after mastectomy.

  3. Skin abscess

    Science.gov (United States)

    Abscess - skin; Cutaneous abscess; Subcutaneous abscess; MRSA - abscess; Staph infection - abscess ... Skin abscesses are common and affect people of all ages. They occur when an infection causes pus ...

  4. In vitro culture of skin-homing T lymphocytes from inflammatory skin diseases

    DEFF Research Database (Denmark)

    Bang, Karen; Lund, Marianne; Mogensen, Søren C

    2005-01-01

    We, in this study, describe how T lymphocytes in a skin biopsy can proliferate in vitro for up to 3 months by using T-cell growth factors - interleukin-2 (IL-2) and IL-4 yielding approximately 100-160 million T lymphocytes within 1 month. We established cell lines from three tuberculin skin tests......, four positive patch tests, 15 of 16 biopsies from atopic dermatitis (AD), 15 of 19 biopsies from mycosis fungoides (MF), 12 of 24 biopsies from psoriasis vulgaris, which was significantly less than AD (P lymphocytes (P ... to immediate halt of proliferation. Blood mononuclear cells from patients and biopsies from healthy persons never gave cell lines. All cells were T lymphocytes expressing CD45RO+, HLA-DR+ and CD150. The CD7 expression was significantly increased in cell lines from AD (P

  5. Mammographic scar for stereotaxic biopsy

    International Nuclear Information System (INIS)

    Guzman Tattis; Hincapie U, Ana Lucia; Patino P, Jairo Hernando

    1997-01-01

    It is reported the case of 56 years old woman who underwent a stereotactic biopsy because of having a circumscribed breast nodule. The histologic diagnosis was benign. After six months, during the mammographic control, it was noticed that the nodule showed irregular contours, because of that a surgical biopsy was performed. The histopathology was reported as benign. it is considered then, that the mammographic changes observed in the mammographic control are due to scar phenomenon after stereotactic biopsy. This findings has not been reported previously

  6. Skin Cancer.

    Science.gov (United States)

    Linares, Miguel A; Zakaria, Alan; Nizran, Parminder

    2015-12-01

    Skin cancer accounts for most malignancies across the globe. They are primarily divided into melanoma and nonmelanoma skin malignancies. Nonmelanoma skin cancer includes basal cell carcinoma and squamous cell carcinoma. Fair skin and chronic ultraviolet B exposure are the most important risk factors. Primary prevention is achieved by avoiding sun exposure and tanning beds. Copyright © 2015 Elsevier Inc. All rights reserved.

  7. HER2 testing on core needle biopsy specimens from primary breast cancers: interobserver reproducibility and concordance with surgically resected specimens

    Directory of Open Access Journals (Sweden)

    Yamamoto Sohei

    2010-10-01

    Full Text Available Abstract Background Accurate evaluation of human epidermal growth factor receptor type-2 (HER2 status based on core needle biopsy (CNB specimens is mandatory for identification of patients with primary breast cancer who will benefit from primary systemic therapy with trastuzumab. The aim of the present study was to validate the application of HER2 testing with CNB specimens from primary breast cancers in terms of interobserver reproducibility and comparison with surgically resected specimens. Methods A total of 100 pairs of archival formalin-fixed paraffin-embedded CNB and surgically resected specimens of invasive breast carcinomas were cut into sections. All 100 paired sections were subjected to HER2 testing by immunohistochemistry (IHC and 27 paired sections were subjected to that by fluorescence in situ hybridization (FISH, the results being evaluated by three and two observers, respectively. Interobserver agreement levels in terms of judgment and the concordance of consensus scores between CNB samples and the corresponding surgically resected specimens were estimated as the percentage agreement and κ statistic. Results In CNB specimens, the percentage interobserver agreement of HER2 scoring by IHC was 76% (κ = 0.71 for 3 × 3 categories (0-1+ versus 2+ versus 3+ and 90% (κ = 0.80 for 2 × 2 categories (0-2+ versus 3+. These levels were close to the corresponding ones for the surgically resected specimens: 80% (κ = 0.77 for 3 × 3 categories and 92% (κ = 0.88 for 2 × 2 categories. Concordance of consensus for HER2 scores determined by IHC between CNB and the corresponding surgical specimens was 87% (κ = 0.77 for 3 × 3 categories, and 94% (κ = 0.83 for 2 × 2 categories. Among the 13 tumors showing discordance in the mean IHC scores between the CNB and surgical specimens, the results of consensus for FISH results were concordant in 11. The rate of successful FISH analysis and the FISH positivity rate in cases with a HER2 IHC score of

  8. HER2 testing on core needle biopsy specimens from primary breast cancers: interobserver reproducibility and concordance with surgically resected specimens

    International Nuclear Information System (INIS)

    Tsuda, Hitoshi; Kurosumi, Masafumi; Umemura, Shinobu; Yamamoto, Sohei; Kobayashi, Takayuki; Osamura, Robert Yoshiyuki

    2010-01-01

    Accurate evaluation of human epidermal growth factor receptor type-2 (HER2) status based on core needle biopsy (CNB) specimens is mandatory for identification of patients with primary breast cancer who will benefit from primary systemic therapy with trastuzumab. The aim of the present study was to validate the application of HER2 testing with CNB specimens from primary breast cancers in terms of interobserver reproducibility and comparison with surgically resected specimens. A total of 100 pairs of archival formalin-fixed paraffin-embedded CNB and surgically resected specimens of invasive breast carcinomas were cut into sections. All 100 paired sections were subjected to HER2 testing by immunohistochemistry (IHC) and 27 paired sections were subjected to that by fluorescence in situ hybridization (FISH), the results being evaluated by three and two observers, respectively. Interobserver agreement levels in terms of judgment and the concordance of consensus scores between CNB samples and the corresponding surgically resected specimens were estimated as the percentage agreement and κ statistic. In CNB specimens, the percentage interobserver agreement of HER2 scoring by IHC was 76% (κ = 0.71) for 3 × 3 categories (0-1+ versus 2+ versus 3+) and 90% (κ = 0.80) for 2 × 2 categories (0-2+ versus 3+). These levels were close to the corresponding ones for the surgically resected specimens: 80% (κ = 0.77) for 3 × 3 categories and 92% (κ = 0.88) for 2 × 2 categories. Concordance of consensus for HER2 scores determined by IHC between CNB and the corresponding surgical specimens was 87% (κ = 0.77) for 3 × 3 categories, and 94% (κ = 0.83) for 2 × 2 categories. Among the 13 tumors showing discordance in the mean IHC scores between the CNB and surgical specimens, the results of consensus for FISH results were concordant in 11. The rate of successful FISH analysis and the FISH positivity rate in cases with a HER2 IHC score of 2+ differed among specimens processed at

  9. Skin tightening.

    Science.gov (United States)

    Woolery-Lloyd, Heather; Kammer, Jenna N

    2011-01-01

    Skin tightening describes the treatment of skin laxity via radiofrequency (RF), ultrasound, or light-based devices. Skin laxity on the face is manifested by progressive loss of skin elasticity, loosening of the connective tissue framework, and deepening of skin folds. This results in prominence of submandibular and submental tissues. Genetic factors (chronological aging) and extrinsic factors (ultraviolet radiation) both contribute to skin laxity. There are many RF, ultrasound, and light-based devices directed at treating skin laxity. All of these devices target and heat the dermis to induce collagen contraction. Heating of the dermis causes collagen denaturation and immediate collagen contraction in addition to long-term collagen remodeling. Via RF, light, or ultrasound, these skin tightening devices deliver heat to the dermis to create new collagen and induce skin tightening. This chapter will provide an overview of the various skin tightening devices. Copyright © 2011 S. Karger AG, Basel.

  10. Ultrasound-Guided Breast Biopsy

    Science.gov (United States)

    ... over time. top of page What are the benefits vs. risks? Benefits The procedure is less invasive than surgical biopsy, ... risk of infection. The chance of infection requiring antibiotic treatment appears to be less than one in ...

  11. X-ray guided biopsy

    International Nuclear Information System (INIS)

    Casanova, R.; Lezana, A.H.; Pedrosa, C.S.

    1980-01-01

    Fine needle aspiration biopsy (FNAB) is now a routine procedure in many X-ray Departments. This paper presents the authors' experience with this technique in chest, abdominal and skeletal lesions. (Auth.)

  12. Stereotactic (Mammographically Guided) Breast Biopsy

    Science.gov (United States)

    ... over time. top of page What are the benefits vs. risks? Benefits The procedure is less invasive than surgical biopsy, ... risk of infection. The chance of infection requiring antibiotic treatment appears to be less than one in ...

  13. Testicular biopsy in prepubertal boys

    DEFF Research Database (Denmark)

    Faure, Alice; Bouty, Aurore; O'Brien, Mike

    2016-01-01

    No consensus exists regarding the precise role of testicular biopsy in prepubertal boys, although it is considered useful for assessing the potential consequences of undescended testes on fertility. Current scientific knowledge indicates that surgeons should broaden indications for this procedure...... for the preservation of fertility after gonadotoxic chemotherapy - even for prepubertal boys - are emerging. Cryopreservation of testicular tissue samples for the preservation of fertility - although still an experimental method at present - is appealing in this context. In our opinion, testicular biopsy...

  14. Optical Biopsy of Human Skin in Conjunction With Laser Treatment

    Science.gov (United States)

    2017-02-08

    Malignant Melanoma; Merkel Cell Carcinoma; Basal Cell Carcinoma; Squamous Cell Carcinoma; Atypical Nevi; Congenital Nevi; Seborrheic Keratosis; Paget's Disease; Dermatofibroma; Kaposi's Sarcoma; Port Wine Stain; Hemangioma; Tattoos; Scleroderma; Burns

  15. Association of Diet With Skin Histological Features in UV-B-Exposed Mice.

    Science.gov (United States)

    Bhattacharyya, Tapan K; Hsia, Yvonne; Weeks, David M; Dixon, Tatiana K; Lepe, Jessica; Thomas, J Regan

    2017-09-01

    Long-term exposure to solar radiation produces deleterious photoaging of the skin. It is not known if diet can influence skin photoaging. To study the influence of a calorie-restricted diet and an obesity diet in mice exposed to long-term UV-B irradiation to assess if there is an association between diet and histopathological response to UV-B irradiation. In this animal model study in an academic setting, the dorsal skin of SKH1 hairless mice receiving normal, calorie-restricted, and obesity diets was exposed to UV-B irradiation 3 times a week for 10 weeks and were compared with corresponding controls. The mice were placed in the following groups, with 8 animals in each group: (1) intact control (C) with regular diet and no UV-B exposure, (2) intact control with UV-B exposure (CR), (3) calorie-restricted diet (CrC), (4) calorie-restricted diet with UV-B exposure (CrR), (5) obesity diet (OC), and (6) obesity diet with UV-B exposure (OR). The experiment was conducted during October through December 2013. Tissue processing and histological analysis were completed in 2016. Histomorphometric analysis was performed on paraffin-embedded skin sections stained by histological and immunohistochemical methods for estimation of epidermal thickness, epidermal proliferating cell nuclear antigen index, collagen I, elastic fibers, fibroblasts, mast cells, dermal cellularity, and adipose layer ratio. Changes in wrinkles were noted. Hairless female mice (age range, 6-8 weeks) were obtained. With a normal diet, changes from UV-B irradiation occurred in epidermal thickness, epidermal proliferating cell nuclear antigen index, collagen I, elastic fibers, fibroblasts, and mast cells, which were modestly influenced by an obesity diet. Calorie restriction influenced the skin in nonirradiated control animals, with higher values for most variables. After UV-B exposure in animals with calorie restriction, epidermal thickness was increased, but other variables were unaffected. Animals

  16. Skin manifestations in a case of trisomy 16 mosaicism

    DEFF Research Database (Denmark)

    Ousager, Lilian Bomme; Brandrup, Flemming; Andersen, Charlotte Brasch

    2006-01-01

    We present a 48-year-old man with unilateral dermatological manifestations including hypertrichosis, telangiectasia, hyperkeratosis and hyperpigmentation. Additional findings included skeletal abnormalities and left-sided hearing loss. Skin biopsies showed changes characteristic of porokeratosis....

  17. Screening for skin cancer.

    Science.gov (United States)

    Helfand, M; Mahon, S M; Eden, K B; Frame, P S; Orleans, C T

    2001-04-01

    of referrals, types of suspected skin cancers, biopsies, confirmed skin cancers, and stages and thickness of skin cancers. For studies that reported test performance, we recorded the definition of a suspicious lesion, the "gold-standard" determination of disease, and the number of true positive, false positive, true negative, and false negative test results. When possible, positive predictive values, likelihood ratios, sensitivity, and specificity were recorded. No randomized or case-control studies have been done that demonstrate that routine screening for melanoma by primary care providers reduces morbidity or mortality. Basal cell carcinoma and squamous cell carcinoma are very common, but detection and treatment in the absence of formal screening are almost always curative. No controlled studies have shown that formal screening programs will improve this already high cure rate. While the efficacy of screening has not been established, the screening procedures themselves are noninvasive, and the follow-up test, skin biopsy, has low morbidity. Five studies from mass screening programs reported the accuracy of skin examination as a screening test. One of these, a prospective study, tracked patients with negative results to determine the number of patients with false-negative results. In this study, the sensitivity of screening for skin cancer was 94% and specificity was 98%. Several recent case-control studies confirm earlier evidence that risk of melanoma rises with the presence of atypical moles and/or many common moles. One well-done prospective study demonstrated that risk assessment by limited physical exam identified a relatively small (fair. We found no studies that assessed the effectiveness of periodic skin examination by a clinician in reducing melanoma mortality. Both self-assessment of risk factors or clinician examination can classify a small proportion of patients as at highest risk for melanoma. Skin cancer screening, perhaps using a risk

  18. Ultrasound-guided forceps for pleural biopsy

    Directory of Open Access Journals (Sweden)

    Gamal Agmy

    2014-04-01

    Clinical implications: Ultrasound-guided forceps for pleural biopsy can overcome many of the limitations of the conventional needle biopsy procedures, provides multiple biopsy specimens of the parietal pleura that are inaccessible to the biopsy needle, and can be carried out easily and safely even in sick and obese patients. The diagnostic yield is nearly similar to thoracoscopy.

  19. Exame imuno-histoquímico na biópsia de medula óssea: uma importante ferramenta complementar à morfologia Immunohistochemistry in bone marrow biopsy: an important complementary tool for morphology

    Directory of Open Access Journals (Sweden)

    Maria Cláudia Nogueira Zerbini

    2011-12-01

    Full Text Available Por razões técnicas e históricas, a utilização da imuno-histoquímica (IHQ em biópsias de medula óssea (BMO levou algum tempo a ocupar espaço na avaliação diagnóstica desse tipo de material. Entretanto, esse cenário vem se modificando graças ao crescimento exponencial do número de anticorpos disponíveis para a utilização em material incluído em parafina, além do aperfeiçoamento das técnicas de recuperação antigênica e descalcificação do material. Este texto tem a finalidade de auxiliar o patologista na seleção/ interpretação de painéis de anticorpos utilizados nos laboratórios de rotina, de acordo com a experiência do autor, assim como de enumerar referências da literatura de grande utilidade para a prática diagnóstica.Due to historical and technical reasons, the use of immunohistochemistry (IHC in bone marrow biopsies (BMB has not till recently been introduced in diagnostic evaluation. However, this scenario has changed owing to the exponential growth in the number of antibodies available for paraffin-embedded material and the development of techniques for antigen retrieval and material decalcification. Not only does this text aim to assist pathologists in the selection/interpretation of antibody panels used in routine laboratories, but it also lists literature references highly useful for diagnostic practice in accordance with the author's experience.

  20. Skin Complications

    Science.gov (United States)

    ... Text Size: A A A Listen En Español Skin Complications Diabetes can affect every part of the ... lipoidica diabeticorum, diabetic blisters, and eruptive xanthomatosis. General Skin Conditions Bacterial Infections Several kinds of bacterial infections ...

  1. Cryotherapy - skin

    Science.gov (United States)

    Cryosurgery - skin; Warts - freezing; Warts - cryotherapy; Actinic keratosis - cryotherapy; Solar keratosis - cryotherapy ... may be used to: Remove warts Destroy precancerous skin lesions (actinic keratoses or solar keratoses) In rare ...

  2. Skin Cancer

    Science.gov (United States)

    Skin cancer is the most common form of cancer in the United States. The two most common types ... face, neck, hands, and arms. Another type of skin cancer, melanoma, is more dangerous but less common. Anyone ...

  3. Sagging Skin

    Science.gov (United States)

    ... turkey neck,” this occurs as skin loses its elasticity and in cases where individuals have lost a ... technique or procedure is appropriate for my skin type? Did the doctor show me before-and-after ...

  4. Performing MR-guided biopsies in clinical routine: factors that influence accuracy and procedure time

    International Nuclear Information System (INIS)

    Hoffmann, Ruediger; Thomas, Christoph; Rempp, Hansjoerg; Schmidt, Diethard; Claussen, Claus D.; Clasen, Stephan; Pereira, Philippe L.

    2012-01-01

    To assess the accuracy, the duration and factors that influence the duration of MRI-guided liver or soft-tissue biopsies. Nineteen liver biopsies and 19 soft-tissue biopsies performed using 1.5T-MRI guidance were retrospectively analysed. Diagnostic performance and complications were assessed. Intervention time was subdivided into preparation period, puncture period and control period. Correlation between procedure time and target size, skin-to-target-distance, used sequences and interventionalists' experience were analysed. Overall sensitivity, specificity and accuracy were 0.86, 1.0 and 0.92, respectively. Two minor complications occurred. Overall median procedure time was 103.5 min. Liver biopsies lasted longer than soft-tissue biopsies (mean [soft-tissue] : 73.0 min, mean [liver] : 134.1 min, P [liver] = 0.048, P [soft-tissue] = 0.005) was significantly prolonged for longer skin-to-target-distances. Lower numbers of image acquisitions (P [liver] = 0.0007, P [soft-tissue] = 0.0012) and interventionalists' experience reduces the procedure duration significantly (P < 0.05), besides all false-negative results appeared during the first five biopsies of each individual radiologist. The interventionalists' experience, skin-to-target-distances and number of image acquisition influence the procedure time significantly. (orig.)

  5. Skin Graft

    OpenAIRE

    Shimizu, Ruka; Kishi, Kazuo

    2012-01-01

    Skin graft is one of the most indispensable techniques in plastic surgery and dermatology. Skin grafts are used in a variety of clinical situations, such as traumatic wounds, defects after oncologic resection, burn reconstruction, scar contracture release, congenital skin deficiencies, hair restoration, vitiligo, and nipple-areola reconstruction. Skin grafts are generally avoided in the management of more complex wounds. Conditions with deep spaces and exposed bones normally require the use o...

  6. The Incidence of Malignant Infiltration in the Biopsy Tract of Osteosarcoma

    Directory of Open Access Journals (Sweden)

    R Mohana

    2007-11-01

    Full Text Available Biopsy is a crucial step in the management of musculoskeletal sarcoma. The surgical approach to the biopsy site is important, as the tract must be removed en bloc with the tumour during limb sparing surgery so as to reduce the risk of local recurrence. The biopsy tracts of 26 osteosarcoma patients were evaluated histologically for tumour infiltration. Horizontal sections of 1 mm thickness with 2 cm radius from were evaluated from each excised biopsy tract. Five out of 26 cases (19.2% showed positive tumour infiltration. One case (3.85% had tumour infiltration in the pseudocapsule, two cases (7.69% had tumour infiltration into the muscle and two other cases (7.69% had tumour infiltration into the subcutaneous tissue. None had skin infiltration. We conclude that resection of the entire biopsy tract is indeed mandatory for surgical treatment of osteosarcoma.

  7. Novel Growth Factor as Prognostic Marker for Estrogen-Independence in Breast Cancer

    National Research Council Canada - National Science Library

    Serrero, Ginette

    2002-01-01

    ...-independence and tamoxifen resistance. Here, wave conducted a study with 206 paraffin embedded human breast cancer biopsies and measured PCDGF expression by immunohistochemistry using an anti-PCDGF developed in our laboratory...

  8. Tissue Biopsies in Diabetes Research

    DEFF Research Database (Denmark)

    Højlund, Kurt; Gaster, Michael; Beck-Nielsen, Henning

    2007-01-01

    resistance of glucose disposal and glycogen synthesis in this tissue are hallmark features of type 2 diabetes in humans (2,3). During the past two decades, we have carried out more than 1200 needle biopsies of skeletal muscle to study the cellular mechanisms underlying insulin resistance in type 2 diabetes....... Together with morphological studies, measurement of energy stores and metabolites, enzyme activity and phosphorylation, gene and protein expression in skeletal muscle biopsies have revealed a variety of cellular abnormalities in patients with type 2 diabetes and prediabetes. The possibility to establish...... and gene expression profiling on skeletal muscle biopsies have pointed to abnormalities in mitochondrial oxidative phosphorylation in type 2 diabetes. These novel insights will inevitably cause a renewed interest in studying skeletal muscle. This chapter reviews our experience to date and gives a thorough...

  9. Skin Aging

    Science.gov (United States)

    Your skin changes as you age. You might notice wrinkles, age spots and dryness. Your skin also becomes thinner and loses fat, making it ... heal, too. Sunlight is a major cause of skin aging. You can protect yourself by staying out ...

  10. Biopsy techniques for intraocular tumors

    Directory of Open Access Journals (Sweden)

    Pukhraj Rishi

    2016-01-01

    Full Text Available Biopsy involves the surgical removal of a tissue specimen for histopathologic evaluation. Most intraocular tumors are reliably diagnosed based on the clinical evaluation or with noninvasive diagnostic techniques. However, accurately diagnosing a small percentage of tumors can be challenging. A tissue biopsy is thus needed to establish a definitive diagnosis and plan the requisite treatment. From fine-needle aspiration biopsy (FNAB to surgical excision, all tissue collection techniques have been studied in the literature. Each technique has its indications and limitations. FNAB has been reported to provide for 88-95% reliable and safe ophthalmic tumor diagnosis and has gained popularity for prognostic purposes and providing eye conserving treatment surgeries. The technique and instrumentation for biopsy vary depending upon the tissue involved (retina, choroid, subretinal space, vitreous, and aqueous, suspected diagnosis, size, location, associated retinal detachment, and clarity of the media. The cytopathologist confers a very important role in diagnosis and their assistance plays a key role in managing and planning the treatment for malignancies.

  11. Gastric tissue biopsy and culture

    Science.gov (United States)

    ... symptoms may include: Loss of appetite or weight loss Nausea and vomiting Pain in the upper part of the belly Black stools Vomiting blood or coffee ground-like material A gastric tissue biopsy and culture can help detect: Cancer Infections, most commonly Helicobacter ...

  12. Retroperitoneoscopic renal biopsy in children

    Directory of Open Access Journals (Sweden)

    Carlos M. Jesus

    2007-08-01

    Full Text Available OBJECTIVE: We present our experience in a series of 17 consecutive pediatric patients submitted to retroperitoneal laparoscopic renal biopsy. MATERIALS AND METHODS: Retroperitoneal laparoscopic renal biopsy (LRB was performed in 5 boys and 12 girls. Mean age was 8.1 years and age range from 2 to 12. Two or three trocars were used to expose the inferior pole of the kidney, remove enough cortical parenchymal specimen and fulgurate the biopsy site. Assessment included surgical time, estimated blood loss, hospitalization period, analgesia requirements, complications and number of glomeruli present in the specimen. RESULTS: LRB was successfully performed in all 15 patients (88%. In two cases, LRB was not possible to be performed. One patient was converted to a transperitoneal laparoscopy due to tear in the peritoneum. The other patient had had previous abdominal surgery and, during retroperitoneal balloon dilation, the peritoneum was opened and the open biopsy was performed. A third patient had postoperatively a perirenal hematoma, which was solved spontaneously. Complication rate was 17.6% (3/17 cases. Mean operative time was 65 minutes, while mean estimated blood loss was 52 mL, mean hospital stay was 2.2 days and mean analgesic requirement was 100 mg of tramadol. The mean number of glomeruli present in the specimen was 60. CONCLUSION: Retroperitoneal laparoscopic renal biopsy in children is a simple, safe. Bleeding is still the most common complication. However, direct vision usually allows a safe control of this drawback. In our institution, laparoscopic approach is the chosen procedure in pediatric patients older than one - year - old.

  13. CT-guided biopsies and drainage

    International Nuclear Information System (INIS)

    Scheppers, I.; Wollschlaeger, D.

    2011-01-01

    Following the implementation of computed tomography (CT) or ultrasound-guided biopsy of solid tumors and the puncture and drainage of liquid processes, the number of surgical open biopsies and curative operations for abscess drainage has declined. Such CT-guided interventions are performed in nearly every organ. Instead of aspiration biopsies, more and more core biopsies are being performed to allow histopathological evaluation and thus allowing targeted therapy. This article is intended to give a general overview of techniques, materials, indications and contraindications. Ultrasound-guided biopsies as well as large bore vacuum biopsies of the breast are not included in this review. (orig.) [de

  14. Freehand biopsy guided by electromagnetic needle tracking

    DEFF Research Database (Denmark)

    Ewertsen, C; Nielsen, Marie Kristina Rue; Nielsen, M Bachmann

    2011-01-01

    To evaluate the overall accuracy and time spent on biopsy guided by electromagnetic needle tracking in a phantom compared with the standard technique of US-guided biopsy with an attached steering device. Furthermore, to evaluate off-plane biopsy guided by needle tracking.......To evaluate the overall accuracy and time spent on biopsy guided by electromagnetic needle tracking in a phantom compared with the standard technique of US-guided biopsy with an attached steering device. Furthermore, to evaluate off-plane biopsy guided by needle tracking....

  15. Ultrasound guided percutaneous fine needle aspiration biopsy ...

    African Journals Online (AJOL)

    )-guided percutaneous fine needle aspiration biopsy (PFNAB)/US-guided percutaneous needle core biopsy (PNCB) of abdominal lesions is efficacious in diagnosis, is helpful in treatment choice, to evaluate whether various other investigations ...

  16. Right Ventricular Pseudoaneurysm Following Endomyocardial Biopsy.

    Science.gov (United States)

    Pita; Santos; Manteiga; Rodriguez; Beiras

    1996-03-01

    Ventricular perforation is an unusual complication after endomyocardial biopsy in heart transplanted patients. We report a case of asymptomatic right ventricular perforation and pseudoaneurysm formation, secondary to endomyocardial biopsy, diagnosed by angiography. The spontaneous obliteration of the pseudoaneurysm was observed.

  17. Superficial skin ulcers

    International Nuclear Information System (INIS)

    Samaila, Modupeola O.; Rafindadi, Abdulmumini H.; Oluwole, Olabode P.; Adewuyi, Sunday A.

    2007-01-01

    Objective was to determine the underlying cause of superficial skin ulcers over a 15-year period. A retrospective histopathological analysis of 670 cases of superficial skin ulcers diagnosed in the Dept. of Pathology, Ahmadu Bello University Teaching Hospital, Zaria, Nigeria from January 1991 to December 2005. A total of 670 superficial skin ulcers were analyzed. The mail to female gender ratio was 409:261(1.5:1.0) and a peakage frequency of 44.3 %( 297) in the 5th and 6th decades. Spectrum of lesions encountered was categorized into inflammatory, infections, benign and malignant diseases. The malignant lesions were 309 (46.1%), non-specific inflammation 302 (45.1%), granulation tissue 25 (3.7%) and pseudoepitheliomatous hyperplasia 14 (2.1%). A total of 18(2.7%) specific infections were encountered, which included bacterial, fungal and viral infection. Benign lesions were 2(0.3%), comprising of neurofibroma and Bowen's disease. The most common malignant lesion was squamous cell carcinoma 203 (30.3%) with a male to female ratio of 128:75 (1.7:1.0). Of these 161 were well differentiated tumors. The lower limb was the prevalent site distribution of all the ulcers. Superficial ulcers may be harbinger of malignant diseases. Squamous cell carcinoma remains the most common malignant lesion arising from chronic superficial ulcers from our setting. Adequate tissue biopsy and early diagnosis may reduce the attendant morbidity of these ulcers. (author)

  18. Dry Skin Relief

    Science.gov (United States)

    ... on a budget Skin care products Skin care secrets Skin lighteners Skin of color Summer skin problems ... condition, such as eczema. Additional related information Dermatologists' top tips for relieving dry skin FIND A DERMATOLOGIST ...

  19. Neuronavigator-guided cerebral biopsy.

    Science.gov (United States)

    Koivukangas, J; Louhisalmi, Y; Alakuijala, J; Oikarinen, J

    1993-01-01

    Neuronavigators are new dynamic interactive instruments that use on-line computers to orient imaging data to the surgical field and guide the neurosurgeon to his target. We have been working since 1987 on a neuronavigator that serves not only as a precise pointer, but also as a dynamic arm that can be used to hold instruments, such as biopsy guides. The neuronavigator arm consists of six joints with optical encoders and is attached to the Mayfield headholder. The arm is connected to a workstation running customized 3D image graphics software. Special instruments and surgical technique have been developed. Here, we report on early clinical experience with ten biopsy procedures: 4 low-grade and 3 high-grade astrocytomas, one craniopharyngioma and one chronic intracerebral haematoma and intracerebral cyst, both of the latter with surrounding tumour suspect tissue. In all glioma cases serial biopsies were taken from optimal sites under ultrasound imaging control. Eight cases showed representative tumour tissue, while in two cases neoplasia was ruled out. The neuronavigator proved to be versatile, allowing comprehensive imaging data to be adapted to the surgical field.

  20. Aortography following subdiaphragmal aortic biopsy

    International Nuclear Information System (INIS)

    Schimmler, J.

    1982-01-01

    A juxtaposition of the subdiaphragmal and infrarenal translumbar aortic biopsy sites showed decisive advantages in favour of the higher site: a more stable position because of better anatomic fixation and rarer incidence of vascular alterations, a wider vascular lumen. Disadvantages lie in the fact that the large visceral arteries (especially Tr. coeliacus) branch off nearly and in the close anatomic relationship to large abdominal organs and the thoracal region. Evaluation of the radiographical image of the vascular tree after subdiaphragmal aortic biopsy showed an average 82% of the vessels to the area of the Knees to be assessable (renal arteries approximately 93%, popliteal arteries approximately 70%). Beyong, the method proved unsatisfactory: 52% of the vessels could not, or not safety, be evaluated. A relatively broad spectrum of indications by comparison with transfemoral catheter aortography had no influence on the rate of complications with reference to either method. A comparison of the topographic conditions shows the need for even more scrupulons observation of the technique in subdiaphragmal biopsy than in the infrarenal one. To sum up the results obtained, subdiaphregmal translumbar aortography is to be preferred to the infrarenal one where transfemoral catheter aortography is contra-indicated, within the limits mentioned. (orig.) [de

  1. Freehand biopsy guided by electromagnetic needle tracking

    DEFF Research Database (Denmark)

    Ewertsen, C; Nielsen, Marie Kristina Rue; Nielsen, M Bachmann

    2011-01-01

    To evaluate the overall accuracy and time spent on biopsy guided by electromagnetic needle tracking in a phantom compared with the standard technique of US-guided biopsy with an attached steering device. Furthermore, to evaluate off-plane biopsy guided by needle tracking....

  2. 20 CFR 718.106 - Autopsy; biopsy.

    Science.gov (United States)

    2010-04-01

    ... 20 Employees' Benefits 3 2010-04-01 2010-04-01 false Autopsy; biopsy. 718.106 Section 718.106... PNEUMOCONIOSIS Criteria for the Development of Medical Evidence § 718.106 Autopsy; biopsy. (a) A report of an autopsy or biopsy submitted in connection with a claim shall include a detailed gross macroscopic and...

  3. Malakoplakia of the prostate diagnosed by elevated PSA level and transrectal prostate biopsy

    Directory of Open Access Journals (Sweden)

    Sacit Nuri Görgel

    2011-04-01

    Full Text Available Malakoplakia is an inflammation which is thought to develop secondary to chronic Escherichia coli infections. Although often seen in the genitourinary tract, it can also be seen in colon, stomach, lung, liver, bone, uterus, and skin. In this case report, we present prostatic malakoplakia diagnosed by elevated prostate-specific antigen level and transrectal prostate biopsy.

  4. Skin cancer

    International Nuclear Information System (INIS)

    Yamada, Michiko

    1992-01-01

    This chapter reviews the development of skin cancer associated with radiation, focusing on the knowledge of A-bomb radiation-induced skin cancer. Since the discovery of X radiation in 1895, acute and chronic radiation dermatitis has been the first matter of concern. Then, in 1902, skin cancer found among radiological personnel has posed a social problem. In earlier study determining the relationship between skin cancer and A-bomb radiation, there is no increase in the incidence of either skin cancer or precancerous condition during the first 20 years after A-bombing. More recent studies have showed that there is a significant correlation between the incidence of skin cancer and distance from the hypocenter; and the incidence of skin cancer is found to be remarkably increased since 1975 in the group exposed at ≤2,000 m. Excess relative risk is 2.2 at one Gy dose. The incidence of skin cancer is also found to be extremely increased with aging. Relative risk is high in younger A-bomb survivors at the time of exposure. Histologically, basal cell carcinoma is more senstitive to ionizing radiation than squamous cell carcinoma. (N.K.)

  5. Comparison of sonoelastography guided biopsy with systematic biopsy: impact on prostate cancer detection

    International Nuclear Information System (INIS)

    Pallwein, Leo; Struve, Peter; Aigner, Friedrich; Gradl, Johann; Schurich, Matthias; Frauscher, Ferdinand; Mitterberger, Michael; Horninger, Wolfgang; Bartsch, Georg; Pedross, Florian

    2007-01-01

    A prospective study was performed to determine the value of sonoelastography (SE) targeted biopsy for prostate cancer (PCa) detection. A series of 230 male screening volunteers was examined. Two independent examiners evaluated each subject. One single investigator performed ≤5 SE targeted biopsies into suspicious regions in the peripheral zone only. The stiffness of the lesion was displayed by SE and color-coded from red (soft) to blue (hard). Hard lesions were considered as malignant and targeted by biopsy. Subsequently, another examiner performed ten systematic biopsies. Cancer detection rates of the two techniques were compared. Cancer was detected in 81 of the 230 patients (35%), including 68 (30%) by SE targeted biopsy and in 58 (25%) by systematic biopsy. Cancer was detected by targeted biopsy alone in 23 patients (10%) and by systematic biopsy alone in 13 patients (6%). The detection rate for SE targeted biopsy cores (12.7% or 135 of 1,109 cores) was significantly better than for systematic biopsy cores (5.6% or 130 of 2,300 cores, P < 0.001). SE targeted biopsy in a patient with cancer was 2.9-fold more likely to detect PCa than systematic biopsy. SE targeted biopsy detected more cases of PCa than systematic biopsy, with fewer than half the number of biopsy cores in this prostate-specific antigen screening population. (orig.)

  6. Evaluation of The Value of Core Needle Biopsy in The Diagnosis of a Breast Mass

    Directory of Open Access Journals (Sweden)

    Asieh Sadat Fattahi

    2016-06-01

    Full Text Available Background: Core needle biopsy (CNB with histological findings is regarded as one of the most important diagnostic measures that make preoperative assessment and planning for appropriate treatment possible. The aim of this study was to determine the sensitivity and specificity of core biopsy results in our patients with benign and malignant breast lumps, especially for borderline breast lesions, by using a classification method.Methods: In this study, 116 patients who were referred to the Surgery Clinic of Ghaem Hospital, Mashhad University of Medical Sciences, Mashhad, Iran with breast lump and underwent diagnostic procedures such as mammography and ultrasound were selected. Core needle biopsy (Tru-cut #14 or 16 was performed. After that, excisional biopsy was done. The benign, malignant and unspecified samples obtained by core needle biopsy were evaluated with the samples of the surgical and pathological findings. Then, false positive, false negative, sensitivity, specificity, and diagnostic accuracy of the core needle biopsy method were calculated. Also, the National Health Service Breast Screening Program (NHSBSP classification was employed.Results: The mean age of the participants in this study was 39±13.13 years and the mean tumor size was 2.7 cm. An average of 3.35 biopsies was taken from all patients. Most of the pathology samples taken from CNB and excisional biopsy were compatible with invasive ductal carcinoma. Of the B type classifications, B5 was the most frequent in both methods. Borderline lesions B3 and B4 had a change in their category after surgery. About 2.5% of the samples in core biopsy were inadequate. Skin bruising was the most common core biopsy complication reported. While, the most common complication of excisional biopsy was hematoma. Accuracy, sensitivity, specificity, positive and negative predictive values of the core needle biopsy procedure compared with excisional biopsy was 95.5%, 92.6%, 100%, 100%, and 91

  7. Skin Dictionary

    Science.gov (United States)

    ... Registration General information Housing & travel Education Exhibit hall Mobile app 2019 Annual Meeting Derm Exam Prep Course ... SkinPAC State societies Scope of practice Truth in advertising NP/PA laws Action center Public and patients ...

  8. Hyperelastic skin

    Science.gov (United States)

    ... is most often seen in people who have Ehlers-Danlos syndrome. People with this disorder have very elastic skin. ... any member of your family been diagnosed with Ehlers-Danlos syndrome? What other symptoms are present? Genetic counseling may ...

  9. Skin Cancer

    Science.gov (United States)

    ... sunlamps. There are 2 types of UV rays: UVA rays (long-wave) – UVA rays penetrate clouds and glass. They penetrate the ... to cancer. But studies have shown that both UVA and UVB damage the skin and can cause ...

  10. Fluoroscopy-guided transnasal biopsy of nasopharyngeal carcinoma using a flexible bronchoscopic biopsy forcep

    International Nuclear Information System (INIS)

    Kim, Jai Keun; Chung, Tae Sub; Kim, Dong Ik; Suh, Jung Ho

    1996-01-01

    Otolaryngoscopic biopsy of nasopharyngeal carcinoma is a generalized method which may be associated with inadequate sampling of tissue and patient discomfort. So, we tried fluoroscopy-guided transnasal biopsy using bronchoscopic biopsy forcep and evaluated its safety and efficacy. Prospectively we performed fluoroscopy-guided transnasal biopsy in 11 patients who were radiographically suspected of nasopharyngeal carcinoma. The posterior wall of the nasopharynx was coated with barium sulfate under fluoroscopy. A flexible bronchoscopic biopsy forcep with a steerable guiding catheter which was used in removal of intrahepatic duct stones was inserted through the nare. After localization of the tip of the biopsy forcep at tumor site with fluoroscopy, a tissue specimen was obtained. We also tried CT guided biopsy in initial 2cases. Each patient had otolaryngoscopic biopsy to compare the biopsy result and patient discomfort. We could have sufficient amount of tissue for pathological evaluation in 10 of 11 patients by the first pass with the fluoroscopic technique. Contrarily, otolaryngoscopic biopsy was successful in 7 of 11 patients on single passage. Additionally, 2 patients had complaint in our method comparing with 9 patients in otolaryngoscopic biopsy. Fluoroscopy-guided transnasal biopsy of nasopharyngeal carcinoma using the bronchoscopic biopsy forcep is safe and accurate. It can be a appropriate method competing otolaryngoscopic biopsy

  11. Skin Cancer Screening

    Science.gov (United States)

    ... Genetics of Skin Cancer Skin Cancer Screening Research Skin Cancer Screening (PDQ®)–Patient Version What is screening? ... These are called diagnostic tests . General Information About Skin Cancer Key Points Skin cancer is a disease ...

  12. The relative test performance characteristics of two commercial assays for the detection of Mycobacterium tuberculosis complex in paraffin-fixed human biopsy specimens

    Directory of Open Access Journals (Sweden)

    Broukhanski George

    2008-09-01

    Full Text Available Abstract The Seeplex™ TB Detection-2 assay (Rockville, MD is a nested endpoint PCR for the Mycobacterium tuberculosis complex (MTBC targets IS6110 and MPB64 that utilizes dual priming oligonucleotide technology. When used to detect the presence of MTBC DNA in formalin-fixed paraffin-embedded tissue specimens, the sensitivity and specificity of this assay is equivalent to a labor-intensive traditional endpoint PCR assay and is more sensitive than a commercial real-time PCR assay.

  13. Ultrasound-guided renal biopsy: experience using an automated core biopsy system.

    Science.gov (United States)

    Chan, R; Common, A A; Marcuzzi, D

    2000-04-01

    To assess the safety and efficacy of ultrasound-guided percutaneous renal biopsy using an automated core biopsy system, and to determine radiologists' accuracy in predicting sample adequacy. Ninety-five biopsies were performed on 25 native kidneys and 70 renal allografts using a 16-gauge automated, spring-loaded core biopsy device under real-time sonographic guidance. Radiologists performing the biopsy estimated the number of core samples needed to obtain an adequate specimen, based on visual inspection of each core. The final determination of the number of samples was made by a pathology technologist who attended each biopsy, based on preliminary microscopic examination of tissue cores. After each biopsy, an ultrasonographic examination was performed to search for biopsy-related hemorrhage, and a questionnaire was given to the patient to determine biopsy-related complications, which were categorized as either minor or major. The main indication for biopsy was acute renal failure (in 43.2% of biopsies). An average of 3 tissue cores per biopsy were obtained. Of the 94 patients in whom a biopsy was conducted to exclude diffuse renal disease, a mean of 12.5 glomeruli were present in each specimen. Overall, adequate tissue for diagnosis was obtained in 98.9% of cases. The radiologists' estimate of the number of core samples needed concurred with the pathology technologists' determination of sample adequacy in 88.4% of cases. A total of 26 complications occurred (in 27.4% of biopsies), consisting of 23 minor (24.2%) and 3 major (3.2%) complications. Real-time sonographic guidance in conjunction with an automated core biopsy system is a safe and accurate method of performing percutaneous renal biopsy. Routine use of sonographic examinations to search for biopsy-related complications is not indicated. Radiologists are accurate in estimating sample adequacy in most cases; however, the presence of a pathology technologist at the biopsy procedure virtually eliminates the

  14. 'Microerosions' in rectal biopsies in Crohn's disease

    DEFF Research Database (Denmark)

    Poulsen, Steen Seier

    1984-01-01

    Small (less than 1 mm), superficial erosions ('microerosions') have been observed stereo-microscopically in surface-stained rectal biopsies in Crohn's disease (CD). Biopsy specimens from 97 patients with CD, 225 with ulcerative colitis (UC), and a control material of 161 patients were investigated....... Granulomas were identified in 62% of the biopsies with microerosions and by examination of two consecutive biopsies from each of these patients, in 85% indicating a positive correlation. In patients with microerosions and a primary diagnosis of UC, granulomas were found in 38% and by examination of two...... biopsies in 54%. Patients with granulomas and a few other patients were reclassified as CD, but there still remained some patients with microerosions, who most probably had UC. In conclusion, microerosions are observed mainly in CD with colonic involvement. There is a high incidence of granulomas in biopsy...

  15. Detection of Hepatitis B Virus Antigens in Paraffin-embedded Liver Specimens from the Amazon Region, Brazil

    Directory of Open Access Journals (Sweden)

    Simonetti SRR

    2002-01-01

    Full Text Available Hepatic viscerotomy of paraffin-preserved old specimens, collected in the period from 1934 to 1967, were analyzed by immunohistochemical assays to detect hepatitis B, hepatitis D, dengue and yellow fever virus antigens. The material belongs to the Yellow Fever Collection, Department of Pathology, Instituto Oswaldo Cruz, Rio de Janeiro, Brazil and the cases were diagnosed at that time according to clinical aspects and histopathological findings reporting viral hepatitis, yellow fever, focal necrosis and hepatic atrophy. From the 79 specimens, 69 were collected at the Labrea Region and the other 10 in different other localities in the Amazon Region. The five micra thick histological slices were analyzed for the presence of hepatitis B surface antigen (HBsAg and hepatitis B core antigen (HBcAg by immunoperoxidase technique. An immunofluorescence assay was applied to the detection of hepatitis D, yellow fever and dengue virus antigens. Nine (11.4% histological samples were HBsAg reactive and 5 (6.3% were HBcAg reactive. The oldest reactive sample was from 1934. Viral antigens related to the other pathologies were not detected in this study. Our results confirm that the methodology described may be used to elucidate the aetiology of hepatitis diseases even after a long time of conservation of the specimens.

  16. The isolation of nucleic acids from fixed, paraffin-embedded tissues-which methods are useful when?

    DEFF Research Database (Denmark)

    Gilbert, M Thomas P; Haselkorn, Tamara; Bunce, Michael

    2007-01-01

    . Cross-linking not only complicates isolation of nucleic acid but also introduces polymerase "blocks" during PCR. A wide variety of methods exists for the recovery of DNA and RNA from archival tissues, and although a number of previous studies have qualitatively compared the relative merits....... These include methods of pre-treating the samples prior to extraction, extraction and nucleic acid purification methods themselves, and a post-extraction enzymatic repair technique. We find that although many of the published methods have distinct positive effects on some characteristics of the nucleic acids...

  17. Antibody validation and scoring guidelines for ABCG2 immunohistochemical staining in formalin-fixed paraffin-embedded colon cancer tissue

    DEFF Research Database (Denmark)

    Cederbye, Camilla Natasha; Palshof, Jesper Andreas; Hansen, Tine Plato

    2016-01-01

    cancer (CRC), probably because of the use of different antibodies and scoring approaches. In this study, we systematically studied six commercially available anti-ABCG2 antibodies, using cell lines with up-regulation of ABCG2, and selected one antibody for validation in CRC tissue. Furthermore, we...... sections, especially when more than one core was used. In conclusion, here, we provide validated results to guide future studies on the associations between ABCG2 immunoreactivity in tumor cells and the benefits of chemotherapeutic treatment in patients with CRC...

  18. RNA Sequencing of Formalin-Fixed, Paraffin-Embedded Specimens for Gene Expression Quantification and Data Mining

    Directory of Open Access Journals (Sweden)

    Yan Guo

    2016-01-01

    Full Text Available Background. Proper rRNA depletion is crucial for the successful utilization of FFPE specimens when studying gene expression. We performed a study to evaluate two major rRNA depletion methods: Ribo-Zero and RNase H. RNAs extracted from 4 samples were treated with the two rRNA depletion methods in duplicate and sequenced (N=16. We evaluated their reducibility, ability to detect RNA, and ability to molecularly subtype these triple negative breast cancer specimens. Results. Both rRNA depletion methods produced consistent data between the technical replicates. We found that the RNase H method produced higher quality RNAseq data as compared to the Ribo-Zero method. In addition, we evaluated the RNAseq data generated from the FFPE tissue samples for noncoding RNA, including lncRNA, enhancer/super enhancer RNA, and single nucleotide variation (SNV. We found that the RNase H is more suitable for detecting high-quality, noncoding RNAs as compared to the Ribo-Zero and provided more consistent molecular subtype identification between replicates. Unfortunately, neither method produced reliable SNV data. Conclusions. In conclusion, for FFPE specimens, the RNase H rRNA depletion method performed better than the Ribo-Zero. Neither method generates data sufficient for SNV detection.

  19. Investigation of Epstein-Barr virus DNA in formalin-fixed and paraffin- embedded breast cancer tissues.

    Science.gov (United States)

    Kalkan, Ahmet; Ozdarendeli, Aykut; Bulut, Yasemin; Yekeler, Hayrettin; Cobanoglu, Bengu; Doymaz, Mehmet Z

    2005-01-01

    To investigate etiological role of Epstein-Barr virus (EBV) DNA in breast cancer. The presence of EBV DNA in 57 breast cancer tissues was investigated with a sensitive PCR assay. The breast cancer tissues were from invasive ductular (n=28), lobular (n=20) and other miscellaneous carcinomas (n=9). Tissues from normal breasts and patients with various benign breast diseases (n=55): fibrocystic disease (n=34), fibroadenoma (n=16), hyperplasia, and granulomatous mastitis (n=5), were used as control samples. EBV DNA was detected in 13 (23%) cancerous tissues (7 ductular, 4 lobular, 2 other carcinoma) and 19 (35%) in the control tissues. The difference between EBV presence in malignant and benign tissues was not statistically significant (p>0.05). The presence of EBV DNA was detected almost equally in both breast cancer and normal tissues, which indicates no etiological role for EBV in breast cancer. We suggest further etiological studies. Copyright (c) 2005 S. Karger AG, Basel.

  20. The Effectiveness of Mapping Biopsy in Patients with Extramammary Paget's Disease

    Directory of Open Access Journals (Sweden)

    Byung Jun Kim

    2014-11-01

    Full Text Available BackgroundExtramammary Paget's disease (EMPD is an intraepithelial carcinoma usually occurring on the skin or mucosa of the perineum. Clinically, it resembles eczema or dermatitis, and misdiagnosis and treatment delays are common. The treatment of choice for EMPD is a wide excision with adequate margins. Wide excision with intraoperative frozen biopsy and Mohs micrographic surgery are common methods; however, these are associated with a high recurrence rate and long operation time, respectively.MethodsBetween January 2010 and June 2013, 21 patients diagnosed with EMPD underwent mapping biopsy. Biopsy specimens were collected from at least 10 areas, 2 cm from the tumor margin. When the specimens were positive for malignancy, additional mapping biopsy was performed around the biopsy site of the positive result, and continued until no cancer cells were found. Based on the results, excision margins and reconstruction plans were established preoperatively.ResultsThe patients (18 male, 3 female had a mean age of 66.5 years (range, 50-82 years. Almost all cases involved in the perineal area, except one case of axillary involvement. Permanent biopsy revealed one case (4.8% of positive cancer cells on the resection margin, in which additional mapping biopsy and re-operation was performed. At the latest follow-up (mean, 27.4 months; range, 12-53 months, recurrence had not occurred.ConclusionsPreoperative mapping biopsy enables accurate resection margins and a preoperative reconstructing plan. Additionally, it reduces the operation time and risk of recurrence. Accordingly, it represents an effective alternative to Mohs micrographic surgery and wide excision with intraoperative frozen biopsy.

  1. Infective endocarditis with spondylodiscitis after prostate biopsy

    Directory of Open Access Journals (Sweden)

    Fernando Pivatto Júnior

    2014-04-01

    Full Text Available Transrectal ultrasonography-guided prostate needle biopsy is the ideal method to obtain prostate specimens for histological analysis and is therefore frequently used in clinical practice. In the majority of the studies, prostate biopsy is considered a safe procedure with few major complications. In the present report, we describe a case of endocarditis with spondylodiscitis, two very rare complications of prostate biopsy.

  2. Biopsy-proven childhood glomerulonephritis in Johor.

    Science.gov (United States)

    Khoo, J J; Pee, S; Thevarajah, B; Yap, Y C; Chin, C K

    2004-06-01

    There has been no published study of biopsy-proven childhood glomerulonephritis in Malaysia. To determine the pattern of childhood glomerulonephritis in Johor, Malaysia from a histopathological perspective and the various indications used for renal biopsy in children. Retrospective study was done of all renal biopsies from children under 16 years of age, received in Sultanah Aminah Hospital, Johor between 1994 and 2001. The histopathological findings were reviewed to determine the pattern of biopsy-proven glomerulonephritis. The indications for biopsy, mode of therapy given after biopsy and the clinical outcome were studied. 122 adequate biopsies were received, 9 children had repeat biopsies. Of the 113 biopsies, minimal change disease formed the most common histopathological diagnosis (40.7%) while lupus nephritis formed the most common secondary glomerulonephritis (23.0%). The main indications for biopsy were nephrotic syndrome (50.8%), lupus nephritis (25.4%) and renal impairment (13.1%). The mode of therapy was changed in 59.8% of the children. Of 106 patients followed-up, 84 children were found to have normal renal function in remission or on treatment. 4 patients developed chronic renal impairment and 16 reached end stage renal disease. Five of the 16 children with end stage disease had since died while 11 were on renal replacement therapy. Another 2 patients died of other complications. The pattern of childhood GN in our study tended to reflect the more severe renal parenchymal diseases in children and those requiring more aggressive treatment. This was because of our criteria of selection (indication) for renal biopsy. Renal biopsy where performed appropriately in selected children may not only be a useful investigative tool for histological diagnosis and prognosis but may help clinicians plan the optimal therapy for these children.

  3. Sentinel lymph node biopsy: clinical relevance

    International Nuclear Information System (INIS)

    Howman-Giles, R.

    2002-01-01

    Sentinel lymph node biopsy (SLNB) has become an important technique in the management of patients with intermediate level melanoma, clinical operable breast cancer and some other cancers. The technique relies on lymphatic mapping to define the lymph drainage from a primary tumour with the premise that the lymph nodes, which directly drain from that area, will reflect the tumour status of the remainder of the node field. Current techniques use lymphoscintigraphy where a radioactive labelled particle and / or blue dye are injected intradermally or intraparenchymally to map the lymph drainage, often in conjunction with a radioactive gamma probe at surgery. In patients with melanoma the SLNB has improved the staging and prognostic information by more accurate determination of whether regional lymph nodes have metastatic spread. This has a major impact on patient management as those patients with negative nodes do not require regional lymph node dissection and have a significantly better prognosis. In our experience of over 3000 patients the combined sentinel node biopsy technique localised accurately 98% of sentinel lymph nodes. Lymphoscintigraphy in patients with melanoma to locate the sentinel lymph nodes involves the intradermal injection of a radiocolloid around the melanoma site or the excision biopsy site. Injections of 5 -10 MBq in 0.05-0.1ml/inj are used and typically 4 injections are usually required. Following tracer injection dynamic imaging is performed to follow the lymphatic collecting vessels until they reach the draining sentinel nodes. An image should be acquired as the vessels reach the node field so that the sentinel nodes directly receiving the channels can be identified and distinguished from any second tier nodes which may sometimes be seen. Delayed scans are performed 2 hours later at which time all regions which can possible drain the primary melanoma site are examined with 5-10 minute static images. The surface location of all sentinel nodes is

  4. Hypoxia marker labeling in tumor biopsies: quantification of labeling variation and criteria for biopsy sectioning

    International Nuclear Information System (INIS)

    Thrall, Donald E.; Rosner, Gary L.; Azuma, Chieko; McEntee, Margaret C.; Raleigh, James A.

    1997-01-01

    Background and purpose: The error associated with using biopsy-based methods for assessing parameters reflective of the tumor microenvironment depends on the variability in distribution of the parameter throughout the tumor and the biopsy sample. Some attention has been given to intratumoral distribution of parameters, but little attention has been given to their intrabiopsy distribution. We evaluated the intrabiopsy distribution of CCI-103F, a 2-nitroimidazole hypoxia marker. Materials and methods: The hypoxia marker CCI-103F was studied in dogs bearing spontaneous solid tumors. Two biopsies were taken from each of seven tumors, for a total of 14 biopsies. Biopsies were serially sectioned and four to six contiguous slides from each 100-150 μm of the biopsy were used to formulate the best estimate of CCI-103F labeled area throughout the biopsy sample. One, two or four slides were then randomly selected from each biopsy and the labeled area, based on this limited sample, was compared to the estimate obtained from counting all available slides. Random sampling of slides was repeated 1000 times for each biopsy sample. Results: CCI-103F labeling variance throughout the biopsy decreased as the estimated overall labeled area in the biopsy decreased. The error associated with estimating the overall labeled area in a biopsy from a randomly selected subset of slides decreased as the number of slides increased, and as the overall labeled area in the biopsy decreased. No minimally labeled biopsy was classified as unlabeled based on limited sampling. Conclusion: With regard to CCI-103F labeling, quantification of the labeled area in four randomly selected slides from a biopsy can provide, in most biopsies, an estimate of the labeled area in the biopsy within an absolute range of ±0.05

  5. When size matters: diagnostic value of kidney biopsy according to the gauge of the biopsy needle.

    Science.gov (United States)

    Roth, Rachel; Parikh, Samir; Makey, Dayanand; Foster, Jamison; Rozenblit, Grigory; Satoskar, Anjali; Nadasdy, Gyongyi; Von Visger, Jon; Hebert, Lee; Rovin, Brad H; Nadasdy, Tibor; Brodsky, Sergey V

    2013-01-01

    Kidney biopsy is a vital tool in the diagnosis of kidney disease. Although it has become a routine procedure, it is not complication-free. Some serious complications of percutaneous kidney biopsy include retroperitoneal hemorrhage and death. There is an increased belief that smaller biopsy needle size results in a lower complication rate. As renal pathologists, we witness an increased number of kidney biopsies performed with a small needle size (as low as gauge 22), which results in inadequate tissue sampling and often non-diagnostic biopsy results. Herein we report the diagnostic value of kidney biopsies according to the size of the biopsy needles. We performed kidney biopsies from nephrectomy specimens using biopsy needles of different sizes. Morphologic parameters were analyzed. We found that biopsies performed by small needles (gauges 20 and 22) contain significantly lower numbers of glomeruli and blood vessels, which limits pathologic evaluation. Data from our institution do not show differences in kidney biopsy complication rates between 16- and 18-gauge needles. Our data indicate that small biopsy needles do not provide sufficient material for diagnosis, and they increase the likelihood for a repeat biopsy. Copyright © 2013 S. Karger AG, Basel.

  6. Surface staining of small intestinal biopsies

    DEFF Research Database (Denmark)

    Poulsen, Steen Seier

    1977-01-01

    Small intestinal biopsies are most often by routine examined under a stereo-microscope, prior to embedding for histological examination. This is done in order to get a view of the appearance of the mucosal pattern, especially villus configuration. The distinctness of the surface pattern however......, is improved considerably if the biopsies are stained with Alcian Green and/or PAS before they are examined. In the present paper a detailed description is given of staining of small intestinal biopsies as whole mounts. The difference between the unstained and the stained biopsies is illustrated by a few...

  7. Robotic Prostate Biopsy in Closed MRI Scanner

    National Research Council Canada - National Science Library

    Fischer, Gregory

    2008-01-01

    .... This work enables prostate brachytherapy and biopsy procedures in standard high-field diagnostic MRI scanners through the development of a robotic needle placement device specifically designed...

  8. Needle muscle biopsy and its application

    Directory of Open Access Journals (Sweden)

    Meng-long CHEN

    2015-07-01

    Full Text Available Needle muscle biopsy is a straightforward and reliable minimally-invasive technique. During the past century, the needle biopsy can provide adequate samples and the technique has gradually gained wider acceptance. Compared with open biopsy, needle biopsy is less traumatic, with low rate of complications, and is suitable for the identifications and evaluations of muscular dystrophy, inflammatory myopathies and systemic diseases involving muscles, specially for infants and young children. Domestic insiders should be encouraged to apply this technique. DOI: 10.3969/j.issn.1672-6731.2015.06.003 

  9. Skin decontamination

    International Nuclear Information System (INIS)

    Moehrle, G.

    1975-01-01

    A general survey of skin decontamination is given. The success of every decontamination treatments depends mainly on the speed, but also on the care, with which the action is taken. The best way to remove the skin contaminants is thorough washing under lukewarm running water with mild soap and a soft brush. This washing is to be repeated several times for a period of several minutes. If results are not satisfactory, light duty detergents and wetting agents available commercially may also be used. Some solutions which have proved useful are mentioned. The decontamination solutions are best used in the order given. When one has no satisfactory decontamination effect, the next one is to be used. If necessary, these agents must be used several times in the stated order as long as this does not involve too much strain for the skin. All the decontamination measures mentioned refer, of course, to intact healthy skin. After decontamination has been completed, the skin should be treated with a protective cream

  10. Adult dementia: history, biopsy, pathology.

    Science.gov (United States)

    Torack, R M

    1979-05-01

    The historical events in the evolution of Alzheimer's disease are reviewed, including the initial description by Alois Alzheimer and the subsequent controversy regarding the nosological specificity of this entity. The similarity of senile dementia and Alzheimer's disease is emphasized. The basis for the modern concept of Alzheimer's disease as premature or accelerated aging is included in the review. The pathological correlates of the major categories of adult dementia have been described. The traditional criteria of neurofibrillary tangles and senile plaques have been re-evaluated using the current insight into these changes afforded by electron microscopy and biochemistry. The significance of amyloid has been described because it occurs within the senile plaque and also as the essential component of congophilic angiopathy. The new information regarding neuronal cell counts and the loss of choline acetyltransferase has been evaluated in terms of an indication of a pathogenic mechanism of Alzheimer's disease. The current understanding of normal pressure hydrocephalus, Creutzfeldt-Jakob disease, and multi-infarct dementia has been described. Brain biopsy in dementia has been described as having diagnostic, research, pathogenic, and prognostic value. The precautions involving the performance and handling of the biopsy have been stressed, particularly because these procedures involve conditions of possible slow virus etiology. The polemic for Alzheimer's disease as aging or slow virus infection has been summarized. At this time a consideration seems justified that Alzheimer's disease is an age-related, slow virus disease due to a hitherto unknown immune defect. Aging as an etiological agent must be clarified before Alzheimer's disease, in any form, can be considered to be an inevitable consequence of longevity.

  11. Newly recognized Leptospira species ("Leptospira inadai" serovar lyme) isolated from human skin.

    OpenAIRE

    Schmid, G P; Steere, A C; Kornblatt, A N; Kaufmann, A F; Moss, C W; Johnson, R C; Hovind-Hougen, K; Brenner, D J

    1986-01-01

    Leptospira strain 10, which represents a new Leptospira species, was isolated from a skin biopsy of a patient with Lyme disease. Although pathogenic for laboratory animals, the organism was not considered to have a significant role in the patient's illness.

  12. Immunohistopathological appearance of three different types of injury in human skin

    NARCIS (Netherlands)

    van der Laan, N; de Leij, LFMH; ten Duis, HJ

    Objective and design: To determine whether underlying mechanisms of inflammation, like cellular infiltrates, expression of adhesion molecule and cytokine patterns are similar under different conditions of injury. Skin biopsies were taken of three different groups of patients in which local

  13. Mast cells and atopic dermatitis. Stereological quantification of mast cells in atopic dermatitis and normal human skin

    DEFF Research Database (Denmark)

    Damsgaard, T E; Olesen, A B; Sørensen, Flemming Brandt

    1997-01-01

    Stereological quantification of mast cell numbers was applied to sections of punch biopsies from lesional and nonlesional skin of atopic dermatitis patients and skin of healthy volunteers. We also investigated whether the method of staining and/or the fixative influenced the results...... of the determination of the mast cell profile numbers. The punch biopsies were taken from the same four locations in both atopic dermatitis patients and normal individuals. The locations were the scalp, neck and flexure of the elbow (lesional skin), and nates (nonlesional skin). Clinical scoring was carried out...... at the site of each biopsy. After fixation and plastic embedding, the biopsies were cut into 2 microns serial sections. Ten sections, 30 microns apart, from each biopsy were examined and stained alternately with either toluidine blue or Giemsa stain and mast cell profile numbers were determined. The study...

  14. Is Lack of Sleep Capable of Inducing DNA Damage in Aged Skin?

    OpenAIRE

    Kahan, Vanessa [UNIFESP; Ribeiro, Daniel Araki [UNIFESP; Egydio, Flavia [UNIFESP; Barros, L. A. [UNIFESP; Tomimori, Jane [UNIFESP; Tufik, Sergio [UNIFESP; Andersen, Monica Levy [UNIFESP

    2014-01-01

    Skin naturally changes with age, becoming more fragile. Various stimuli can alter skin integrity. the aim of this study was to evaluate whether sleep deprivation affects the integrity of DNA in skin and exacerbates the effects of aging. Fifteen-month old female Hairless mice underwent 72 h of paradoxical sleep deprivation or 15 days of chronic sleep restriction. Punch biopsies of the skin were taken to evaluate DNA damage by single cell gel (comet) assay. Neither paradoxical sleep deprivation...

  15. Cellularized Bilayer Pullulan-Gelatin Hydrogel for Skin Regeneration.

    Science.gov (United States)

    Nicholas, Mathew N; Jeschke, Marc G; Amini-Nik, Saeid

    2016-05-01

    Skin substitutes significantly reduce the morbidity and mortality of patients with burn injuries and chronic wounds. However, current skin substitutes have disadvantages related to high costs and inadequate skin regeneration due to highly inflammatory wounds. Thus, new skin substitutes are needed. By combining two polymers, pullulan, an inexpensive polysaccharide with antioxidant properties, and gelatin, a derivative of collagen with high water absorbency, we created a novel inexpensive hydrogel-named PG-1 for "pullulan-gelatin first generation hydrogel"-suitable for skin substitutes. After incorporating human fibroblasts and keratinocytes onto PG-1 using centrifugation over 5 days, we created a cellularized bilayer skin substitute. Cellularized PG-1 was compared to acellular PG-1 and no hydrogel (control) in vivo in a mouse excisional skin biopsy model using newly developed dome inserts to house the skin substitutes and prevent mouse skin contraction during wound healing. PG-1 had an average pore size of 61.69 μm with an ideal elastic modulus, swelling behavior, and biodegradability for use as a hydrogel for skin substitutes. Excellent skin cell viability, proliferation, differentiation, and morphology were visualized through live/dead assays, 5-bromo-2'-deoxyuridine proliferation assays, and confocal microscopy. Trichrome and immunohistochemical staining of excisional wounds treated with the cellularized skin substitute revealed thicker newly formed skin with a higher proportion of actively proliferating cells and incorporation of human cells compared to acellular PG-1 or control. Excisional wounds treated with acellular or cellularized hydrogels showed significantly less macrophage infiltration and increased angiogenesis 14 days post skin biopsy compared to control. These results show that PG-1 has ideal mechanical characteristics and allows ideal cellular characteristics. In vivo evidence suggests that cellularized PG-1 promotes skin regeneration and may

  16. [Muscle biopsy in children: Usefulness in 2012].

    Science.gov (United States)

    Cuisset, J-M; Maurage, C-A; Carpentier, A; Briand, G; Thévenon, A; Rouaix, N; Vallée, L

    2013-01-01

    Muscle biopsy is a mainstay diagnostic tool for investigating neuromuscular disorders in children. We report the yield of pediatric muscle biopsy in a population of 415 children by a retrospective study of 419 biopsies performed between 1/01/2000 and 31/12/2009 in a neuropediatric department, including mitochondrial respiratory chain analysis for 87 children. Two hundred and fifty-five biopsies were from boys (61%) 164 from girls (39%). Their mean age at biopsy was 6.5years; 155 (37%) biopsies were obtained before the child was 5years old. Final histopathological diagnoses were: congenital myopathy (n=193, including 15 structural congenital myopathies); progressive muscular dystrophy (n=75 [18%] including 57 dystrophinopathies); congenital muscular dystrophy (n=17, including six primary merosinopathies); dermatomyositis (n=11); spinal muscular atrophy (n=9, including six atypical spinal muscular atrophies); metabolic myopathy (n=32, including 19 mitochondrial myopathies); encephalomyopathy (n=53 [13%], including 27 with a mitochondrial respiratory chain defect). Pathological diagnosis remained undetermined in 16 cases. In 184 patients (44%), the muscle biopsy revealed specific histopathological anomalies (dystrophic process; specific ultrastructural abnormalities; perifascicular atrophy; neurogenic atrophy; metabolic anomalies) enabling a precise etiological diagnosis. For 85% of progressive muscular dystrophies, the biopsy resulted in a genetic diagnosis after identification of the protein defect. In 15% of the congenital myopathies, histopathological anomalies focused attention on one or several genes. Concerning dystrophinopathies, quantification of dystrophin deficiency on the biopsy specimen contributed to the definition of the clinical phenotype: Duchenne, or Becker. In children with a myopathy, muscle biopsy is often indispensable to establish the etiological diagnosis. Based on the results from this series, muscle biopsy can provide a precise

  17. Outcomes of ultrasound guided renal mass biopsies.

    Science.gov (United States)

    Sutherland, Edward L; Choromanska, Agnieszka; Al-Katib, Sayf; Coffey, Mary

    2018-06-01

    The purpose of this study was to evaluate the rate of nondiagnostic ultrasound-guided renal mass biopsies (RMBs) at our institution and to determine what patient, procedural, and focal renal mass (FRM) factors were associated with nondiagnostic ultrasound-guided RMBs. Eighty-two ultrasound-guided renal mass biopsies performed between January 2014 and October 2016 were included in our study. Biopsy outcomes (diagnostic vs. nondiagnostic) and patient, procedural, and FRM characteristics were retrospectively reviewed and recorded. Univariate statistical analyses were performed to identify biopsy characteristics that were indicative of nondiagnostic biopsy. Ultrasound-guided RMBs were diagnostic in 70 out of 82 cases (85%) and non-diagnostic in 12 cases (15%). Among the diagnostic biopsies, 54 (77%) were malignant cases, 94% of which were renal cell carcinoma (RCC). Of the 12 nondiagnostic cases, the final diagnosis was RCC in 4 cases and angiomyolipoma in one case; seven of the nondiagnostic cases were lost to follow-up. A weak association (p = 0.04) was found between the number of needle passes and the biopsy outcome. None of the remaining collected RMB characteristics showed a significant correlation with a diagnostic or nondiagnostic RMB. Six patients (7%) experienced complications. Ultrasound-guided renal mass biopsy is a safe and effective method for the diagnosis of renal masses with a low rate of nondiagnostic outcomes. A nondiagnostic biopsy should not be treated as a surrogate for a diagnosis since a significant number of patients with nondiagnostic biopsies have subsequently been shown to have renal malignancies. Repeat biopsy should be considered in such cases.

  18. Prostate biopsy after ano-rectal resection: value of CT-guided trans-gluteal biopsy

    International Nuclear Information System (INIS)

    Cantwell, Colin P.; Hahn, Peter F.; Gervais, Debra A.; Mueller, Peter R.

    2008-01-01

    We describe our single-institutional experience with computed tomography (CT)-guided percutaneous transgluteal biopsy of the prostate in patients in whom transrectal ultrasound-guided biopsy is precluded by prior ano-rectal resection. Between March 1995 and April 2007, 22 patients had 34 prostate biopsies (mean age 68; mean PSA 29 ng/ml; mean follow-up 6.1 years). The charts of patients who had transgluteal biopsy were reviewed for demographic, complications and pathology. Ninety-five percent (21/22) of primary biopsies were diagnostic. Of the 21 diagnostic biopsies, 11 were positive for prostate cancer and ten were definitive benign samples. Seventy-three percent (8/11) of the patients had progressive PSA elevation that mandated 11 further prostate biopsies. Six patients had a second biopsy, one patient had a third and one patient had a fourth biopsy. Among patients who had serial biopsies, 38% (3/8) had prostate cancer. No complications or death occurred. A malignant biopsy was not significantly associated with core number (P = 0.58) or a high PSA level (P 0.15). CT-guided transgluteal biopsy of the prostate is safe and effective. (orig.)

  19. Comparison between endobronchial forceps-biopsy and cryo-biopsy by flexible

    Directory of Open Access Journals (Sweden)

    Sami El-Dahdouh

    2016-01-01

    Conclusions: We concluded that cryoprobe biopsies were more successful than forceps biopsies in the diagnosis of lung cancer. Nevertheless, further investigations are warranted to determine an efficacy of cryoprobe biopsy procedures and a rationale to use as a part of routine flexible bronchoscopy.

  20. Ultrasound guided synovial biopsy of the wrist

    NARCIS (Netherlands)

    van Vugt, R. M.; van Dalen, A.; Bijlsma, J. W.

    1997-01-01

    Seven patients (4 female and 3 male, mean age 46) with arthritis of the wrist (n = 7) without known etiology were evaluated. High-definition ultrasound equipment was used for localization of synovial hypertrophy, suitable for ultrasound guided biopsy without risk. A 18-gauge diameter Tru-cut biopsy

  1. Squamous cell skin cancer

    Science.gov (United States)

    ... that reflect light more, such as water, sand, concrete, and areas that are painted white. The higher ... - skin - squamous cell; Skin cancer - squamous cell; Nonmelanoma skin cancer - squamous ...

  2. Histopathologic quality of prostate core biopsy specimens: comparison of an MR-compatible biopsy needle and a ferromagnetic biopsy needle used for ultrasound-guided prostate biopsy

    International Nuclear Information System (INIS)

    Franiel, T.; Hamm, B.; Beyersdorff, D.; Fritzsche, F.; Staack, A.; Rost, J.

    2006-01-01

    Purpose: The histopathologic quality of core biopsy specimens obtained via MRI-guided prostate biopsy using a 16G MR-compatible needle was compared to that of biopsies obtained via ultrasound-guided biopsy using a conventional 18G stainless steel biopsy needle. Material and Methods: A retrospective analysis was performed for a total of 247 transrectal prostate biopsy specimens obtained from 32 patients. A total of 117 tissue cores were obtained from 15 patients (PSA of 10.8 ng/ml, age 64 years) who underwent an MRI-guided prostate biopsy using a 16G (1.7 mm) MR-compatible biopsy needle made of titanium alloy. The remaining 130 tissue cores were obtained from 17 patients (PSA of 6.7 ng/ml, age 68 years) who underwent a transrectal ultrasound-guided prostate biopsy using an 18G (1.3 mm) ferromagnetic stainless steel biopsy needle. The length and width of the histologic sections prepared from the tissue cores were measured to calculate the area. The histopathologic quality of the specimens was assessed microscopically using tissue fragmentation, the presence of crush artifacts, and the overall assessability as criteria. Each of these features was assigned a score from 0 to 3. All 3 features contributed equally to the overall score which ranged from 0 (no tissue) to 9 (optimal quality). Results: The overall quality scores assigned to the biopsies obtained with a 16G MR-compatible needle and an 18G ferromagnetic needle can be considered to be equivalent to a mean difference between patient related median scores of the specimens of -0.05 (95% confidence interval [-0.46; 0.36]) and a given equivalence limit of 1. The MRI biopsies showed more tissue fragmentation (p=0.001) but fewer crush artifacts (p=0.022) while the assessability did not differ significantly between the two needle types (p=0.064). There was also no significant difference in the calculated areas of the tissue cores (p=0.236). According to the different calibers of the biopsy needles, the lengths (p=0

  3. Coeliac disease: to biopsy or not?

    Science.gov (United States)

    Reilly, Norelle R; Husby, Steffen; Sanders, David S; Green, Peter H R

    2018-01-01

    Coeliac disease is increasingly recognized as a global problem in both children and adults. Traditionally, the findings of characteristic changes of villous atrophy and increased intraepithelial lymphocytosis identified in duodenal biopsy samples taken during upper gastrointestinal endoscopy have been required for diagnosis. Although biopsies remain advised as necessary for the diagnosis of coeliac disease in adults, European guidelines for children provide a biopsy-sparing diagnostic pathway. This approach has been enabled by the high specificity and sensitivity of serological testing. However, these guidelines are not universally accepted. In this Perspective, we discuss the pros and cons of a biopsy-avoiding pathway for the diagnosis of coeliac disease, especially in this current era of the call for more biopsies, even from the duodenal bulb, in the diagnosis of coeliac disease. In addition, a contrast between paediatric and adult guidelines is presented.

  4. Usefulness of CT fluoroscopy-guided percutaneous needle biopsy in the presence of pneumothorax during biopsy

    International Nuclear Information System (INIS)

    O, Dong Hyun; Cho, Young Jun; Park, Yong Sung; Hwang, Cheol Mok; Kim, Keum Won; Kim, Ji Hyung

    2006-01-01

    When pneumothorax occurs during a percutaneous needle biopsy, the radiologist usually stops the biopsy. We evaluated the usefulness of computed tomographic (CT) fluoroscopy-guided percutaneous needle biopsy in the presence of pneumothorax during biopsy. We performed 288 CT fluoroscopy guided percutaneous needle biopsies to diagnose the pulmonary nodules. Twenty two of these patients had pneumothorax that occurred during the biopsy without obtaining an adequate specimen. After pneumothorax occurred, we performed immediate CT fluoroscopy guided percutaneous needle biopsies using an 18-gauge cutting needle. We evaluated the success rate of the biopsies and also whether or not the pneumothorax progressed. We classified these patients into two groups according to whether the pneumothorax progressed (Group 2) or not (Group 1) by measuring the longest distance between the parietal pleura and the visceral pleura both in the early and late pneumothorax. Additionally, we analyzed the relationship between the progression of pneumothorax after biopsy and 1) the depth of the pulmonary nodule; 2) the number of biopsies; 3) the presence or absence of emphysema at the biopsy site; and 4) the size of the pulmonary nodule. Biopsy was successful in 19 of 22 nodules (86.3%). Of the 19 nodules, 12 (63.2%) were malignant and 7 (36.8%) were benign. Twelve patients (54.5%) were classified as group 1 and 10 patients (45.4%) as group 2. The distance between the lung lesion and pleura showed a statistically significant difference between these two groups: ≤ 1 cm in distance for group 1 (81.8%) and group 2 (18.2%), and > 1 cm in distance for group 1 (30%) and group 2 (70%), ρ 0.05). When early pneumothorax occurs during a biopsy, CT fluoroscopy guided percutaneous needle biopsy is an effective and safe procedure. Aggravation of pneumothorax after biopsy is affected by the depth of the pulmonary nodule

  5. Findings of skin and bones in mastocytosis

    International Nuclear Information System (INIS)

    Rohner, H.G.; Bartl, R.; Koischwitz, D.; Rodermund, O.E.

    1982-01-01

    The syndrome of mastocytosis can include isolated urticaria pigmentosa, systemic mastocytosis, or the extremely rare form of mast cell leucemia. Our investigations of many patients have shown more frequently than earlier suspected, that the mastocytosis is a systemic disease. The frequency of attacked bone marrow is noteworthy. Because of the inflammatorygranulomatous manifestation in bone marrow, considerations of the pathogenesis of an immune and reactive event are taken into account. The mast cell granulomas are mostly found in the endosteal region, which is the reason for frequenctly occurring bone lesions (half on all patients show bone lesions). The bone changes can develop generalized (osteoporosis-osteosclerosis) or localized (osteolytic-osteosclerotic foci). In clinical work bone biopsies and skeletal radiology are supplementing each other: bone biopsy and skin biopsy give the first diagnosis of mastocytosis and reveal the systemic disease; X-ray pictures give information of shape and dimension of the induced osteopathy. (orig.)

  6. Findings of skin and bones in mastocytosis

    Energy Technology Data Exchange (ETDEWEB)

    Rohner, H.G.; Bartl, R.; Koischwitz, D.; Rodermund, O.E.

    1982-12-01

    The syndrome of mastocytosis can include isolated urticaria pigmentosa, systemic mastocytosis, or the extremely rare form of mast cell leucemia. Our investigations of many patients have shown more frequently than earlier suspected, that the mastocytosis is a systemic disease. The frequency of attacked bone marrow is noteworthy. Because of the inflammatory granulomatous manifestation in bone marrow, considerations of the pathogenesis of an immune and reactive event are taken into account. The mast cell granulomas are mostly found in the endosteal region, which is the reason for frequently occurring bone lesions (half of all patients show bone lesions). The bone changes can develop generalized (osteoporosis-osteosclerosis) or localized (osteolytic-osteosclerotic foci). In clinical work bone biopsies and skeletal radiology are supplementing each other: bone biopsy and skin biopsy give the first diagnosis of mastocytosis and reveal the systemic disease; X-ray pictures give information of shape and dimension of the induced osteopathy.

  7. Breast carcinoma in radiosurgery biopsy

    International Nuclear Information System (INIS)

    Cohen, Leonard O.; Brito, Pablo E.; Coppolecchia, German L.; Giarmana, Maria J.; Delle Ville, Rodolfo E.; Cortese, Eduardo M.

    2006-01-01

    Purpose: To report our experience on the detection of breast cancer (BC) through guided radiosurgical biopsies (GRSB) in the Gynecology Department of the Hospital Aeronautico Central (SGHAC). Materials and method: We retrospectively analyzed 622 GRSBs performed at the SGHAC between 1 January 1995 and 31 December 2004. We took into account single or associated lesions found in mammograms, which we subdivided into four types: 1) Non-palpable mammographic nodules; 2) Microcalcifications; 3) Structural distortions; 4) Mammographic asymmetries. Results: We found 332 non-palpable nodules (53.4%), 214 microcalcifications (34.4%), 40 structural distortions (6.4%), and 36 mammographic asymmetries (5.8%). Out of the 622 GRSBs performed during the above period, 152 BCs were diagnosed, that is, an incidence of 24.4% detected through this method. Out of the 152 BCs, 110 (72.4%) were invasive and 42 (27.6%) were noninvasive. Conclusions: Although 24.4% of BCs were identified through GRSBs, our tea m considers this to be the standard method for early detection of breast cancer. (author) [es

  8. Simplifying Skin Disease Diagnosis with Topical Nanotechnology.

    Science.gov (United States)

    Yeo, David C; Xu, Chenjie

    2018-05-01

    A new study published in the journal Nature Biomedical Engineering 1 documents a novel diagnostic technology that exploits topically applied nanotechnology to detect skin tissue biomarkers for diagnosis. This concept is demonstrated by noninvasively imaging connective tissue growth factor (CTGF) mRNA in abnormal scar cells, whole tissue, and animal models. In this commentary, we highlight the main findings and discuss their implications. Successful implementation in the clinic could give rise to self-applied, biopsy-free diagnostic technology and significantly reduce healthcare burden. Crucially, noninvasive visualization of disease biomarkers, mobile device signal acquisition, and Internet-enabled transmission could significantly transform the diagnosis of skin disease and other superficial tissues.

  9. Navigated MRI-guided liver biopsies in a closed-bore scanner: experience in 52 patients.

    Science.gov (United States)

    Moche, Michael; Heinig, Susann; Garnov, Nikita; Fuchs, Jochen; Petersen, Tim-Ole; Seider, Daniel; Brandmaier, Philipp; Kahn, Thomas; Busse, Harald

    2016-08-01

    To evaluate clinical effectiveness and diagnostic efficiency of a navigation device for MR-guided biopsies of focal liver lesions in a closed-bore scanner. In 52 patients, 55 biopsies were performed. An add-on MR navigation system with optical instrument tracking was used for image guidance and biopsy device insertion outside the bore. Fast control imaging allowed visualization of the true needle position at any time. The biopsy workflow and procedure duration were recorded. Histological analysis and clinical course/outcome were used to calculate sensitivity, specificity and diagnostic accuracy. Fifty-four of 55 liver biopsies were performed successfully with the system. No major and four minor complications occurred. Mean tumour size was 23 ± 14 mm and the skin-to-target length ranged from 22 to 177 mm. In 39 cases, access path was double oblique. Sensitivity, specificity and diagnostic accuracy were 88 %, 100 % and 92 %, respectively. The mean procedure time was 51 ± 12 min, whereas the puncture itself lasted 16 ± 6 min. On average, four control scans were taken. Using this navigation device, biopsies of poorly visible and difficult accessible liver lesions could be performed safely and reliably in a closed-bore MRI scanner. The system can be easily implemented in clinical routine workflow. • Targeted liver biopsies could be reliably performed in a closed-bore MRI. • The navigation system allows for image guidance outside of the scanner bore. • Assisted MRI-guided biopsies are helpful for focal lesions with a difficult access. • Successful integration of the method in clinical workflow was shown. • Subsequent system installation in an existing MRI environment is feasible.

  10. US-guided biopsy of renal allografts using 18G biopsy gun: analysis of 200 cases

    International Nuclear Information System (INIS)

    Kim, Eun Kyung; Lee, Jong Tae; Kim, Myeong Jin; Yoo, Hyung Sik; Kim, Ki Whang; Park, Ki Ill; Chung, Hyun Joo

    1995-01-01

    We evaluated the effectiveness and safety of 18G biopsy gun with US guidance in the transplanted kidneys. We performed 200 US-guided percutaneous biopsies using 18G biopsy gun. Diagnostic efficacy and complication of the biopsy in these patients were analyzed. Biopsy specimens were adequate for histologic diagnoses in 193 patients(96.5%). The mean of the biopsy frequency was 3, the mean of total glomerular number was 21.64 and the mean glomerular number per one biopsy was 6.93. Major complications occurred in 3 (1.5%) of the 200 biopsies; hematuria developed in two patients, AV fistula in one. These complications were successfully controlled either by only transfusion or by coil embolization. There were no statistical differences in blood pressure, hemoglobin, BUN/Cr between pre-and post-renal biopsies. US-guided percutaneous biopsy of renal allograft with 18G biopsy gun is simple, safe, and accurate method in evaluating the renal allograft dysfunction

  11. Electromagnetic-Tracked Biopsy under Ultrasound Guidance: Preliminary Results

    International Nuclear Information System (INIS)

    Hakime, Antoine; Deschamps, Frederic; Marques De Carvalho, Enio Garcia; Barah, Ali; Auperin, Anne; Baere, Thierry De

    2012-01-01

    Purpose: This study was designed to evaluate the accuracy and safety of electromagnetic needle tracking for sonographically guided percutaneous liver biopsies. Methods: We performed 23 consecutive ultrasound-guided liver biopsies for liver nodules with an electromagnetic tracking of the needle. A sensor placed at the tip of a sterile stylet (18G) inserted in a coaxial guiding trocar (16G) used for biopsy was localized in real time relative to the ultrasound imaging plane, thanks to an electromagnetic transmitter and two sensors on the ultrasound probe. This allows for electronic display of the needle tip location and the future needle path overlaid on the real-time ultrasound image. Distance between needle tip position and its electronic display, number of needle punctures, number of needle pull backs for redirection, technical success (needle positioned in the target), diagnostic success (correct histopathology result), procedure time, and complication were evaluated according to lesion sizes, depth and location, operator experience, and “in-plane” or “out-of-plane” needle approach. Results: Electronic display was always within 2 mm from the real position of the needle tip. The technical success rate was 100%. A single needle puncture without repuncture was used in all patients. Pull backs were necessary in six patients (26%) to obtain correct needle placement. The overall diagnostic success rate was 91%. The overall true-positive, true-negative, false-negative, and failure rates of the biopsy were 100% (19/19) 100% (2/2), 0% (0/23), and 9% (2/23). The median total procedure time from the skin puncture to the needle in the target was 30 sec (from 5–60 s). Lesion depth and localizations, operator experience, in-plane or out-of-plane approach did not affect significantly the technical, diagnostic success, or procedure time. Even when the tumor size decreased, the procedure time did not increase. Conclusions: Electromagnetic-tracked biopsy is accurate to

  12. Refining criteria for diagnosis of cutaneous infections caused by herpes viruses through correlation of morphology with molecular pathology

    Directory of Open Access Journals (Sweden)

    Böer Almut

    2006-01-01

    Full Text Available BACKGROUND: Infections of the skin by herpes viruses do not always present themselves in typical fashion. Early diagnosis, however, is crucial for appropriate treatment. Polymerase chain reaction (PCR allows diagnosis and differential diagnosis of herpes virus infections, but the method is not yet available in large parts of the world, where diagnosis is made based on morphology alone. AIM: To refine criteria for the diagnosis of herpes virus infections of the skin by way of correlation of clinical and histopathologic findings with results of PCR studies. METHODS: We studied 75 clinically diagnosed patients of "zoster," "varicella," and "herpes simplex", to correlate clinical and histopathological findings with results of PCR studies on paraffin embedded biopsy specimens. RESULTS: Clinical suspicion of infection by herpes viruses was confirmed by histopathology in 37% of the cases and by PCR studies in 65% of the cases. Zoster was frequently misdiagnosed as infection with herpes simplex viruses (30%. When diagnostic signs of herpes virus infection were encountered histopathologically, PCR confirmed the diagnosis in 94%. By way of correlation with results of PCR studies, initial lesions of herpes virus infections could be identified to have a distinctive histopathological pattern. Herpetic folliculitis appeared to be a rather common finding in zoster, it occurring in 28% of the cases. CONCLUSION: We conclude that correlation of clinical and histopathological features with results of PCR studies on one and the same paraffin embedded specimen permits identification of characteristic morphologic patterns and helps to refine criteria for diagnosis both clinically and histopathologically.

  13. HLA-DPDQDR is expressed in all lesional skin from patients with autoimmune skin diseases

    Directory of Open Access Journals (Sweden)

    Ana Maria Abreu Velez

    2014-04-01

    Full Text Available Introduction: Human genes responsible for human antigen presentation and transplant rejection functions are located on the short arm of Chromosome 6 and are called the Major Histocompatibility Complex (MHC. Moreover, the primary physiologic function of MHC molecules is to present peptides to T lymphocytes. MHC molecules are integral components of the ligands that most T cells recognize, since the T cell receptor (TCR has specificity for complexes of foreign antigenic peptides, as well as self-MHC molecules. Aim: Our investigation attempts to investigate the presence of HLA-DPDQDR within lesional skin biopsies from patients affected by autoimmune skin blistering diseases (ABDs. Materials and Methods: We utilized immunohistochemistry (IHC to evaluate the presence of HLA-DPDQDR in lesional skin biopsies of patients affected by ABDs. We tested 30 patients with endemic pemphigus foliaceus (EPF, 15 controls from the EPF endemic area, and 15 biopsies from healthy controls from the USA. We also tested archival biopsies from patients with selected ABDs, including 30 patients with bullous pemphigoid (BP, 20 with pemphigus vulgaris (PV, 8 with pemphigus foliaceus (PF, 14 with dermatitis herpetiformis (DH and 2 with epidermolysis bullosa acquisita (EBA. Results: Most ABD biopsies stained positive for HLA-DPDQDR in the lesional blisters and/or inflamed neurovascular plexus in the superficial dermis, and also at mesenchymal-endothelial like-cell junctions in the dermis. In BP, EBA and EPF, the HLA-DPDQDR staining was also seen in the dermal eccrine sweat gland coils and and ducts. Conclusion: Here, we document that HLA-DPDQDR is expressed in several anatomic areas of lesional skin in patients with ABDs. Notably, HLA-DPDQDR positivity was also consistently present in areas of the classic immune response in pemphigus epidermal keratinocytic intercellular junctions, and at basement membrane sites in bullous pemphigoid and other subepidermal blistering diseases.

  14. Koebner phenomenon of the ear canal skin.

    LENUS (Irish Health Repository)

    Young, O

    2012-02-01

    The Koebner phenomenon originally described the appearance of psoriatic lesions in the uninvolved skin of patients with psoriasis as a consequence of trauma. We describe a case of concurrent lichen planus and sarcoidosis in the auditory canal, which represents an unusual manifestation of the Koebner phenomenon. This is the first case of concurrent lichen planus and sarcoidosis in the head and neck region and highlights the need for biopsy to allow accurate histopathological diagnosis and treatment.

  15. Koebner phenomenon of the ear canal skin.

    LENUS (Irish Health Repository)

    Young, O

    2009-02-01

    The Koebner phenomenon originally described the appearance of psoriatic lesions in the uninvolved skin of patients with psoriasis as a consequence of trauma. We describe a case of concurrent lichen planus and sarcoidosis in the auditory canal, which represents an unusual manifestation of the Koebner phenomenon. This is the first case of concurrent lichen planus and sarcoidosis in the head and neck region and highlights the need for biopsy to allow accurate histopathological diagnosis and treatment.

  16. Skin Pigmentation Disorders

    Science.gov (United States)

    Pigmentation means coloring. Skin pigmentation disorders affect the color of your skin. Your skin gets its color from a pigment called melanin. Special cells in the skin make melanin. When these cells become damaged or ...

  17. Skin Cancer Foundation

    Science.gov (United States)

    ... Host a Fundraising Event | About Us | Store The Skin Cancer Foundation The Skin Cancer Foundation is the ... Handbook A "Sunscreen Gene"? Skin Cancer Facts & Statistics Skin Cancer Treatment Glossary Information on medications and procedures ...

  18. Skin Cancer Treatment

    Science.gov (United States)

    ... Unusual Cancers of Childhood Treatment Genetics of Skin Cancer Skin color and being exposed to sunlight can increase ... is based on the type of nonmelanoma skin cancer or other skin condition diagnosed: Basal cell carcinoma Enlarge Basal cell ...

  19. Stages of Skin Cancer

    Science.gov (United States)

    ... Unusual Cancers of Childhood Treatment Genetics of Skin Cancer Skin color and being exposed to sunlight can increase ... is based on the type of nonmelanoma skin cancer or other skin condition diagnosed: Basal cell carcinoma Enlarge Basal cell ...

  20. Diagnostic yield and complications of transthoracic computed tomography-guided biopsies

    DEFF Research Database (Denmark)

    Vagn-Hansen, Chris Aksel; Pedersen, Malene Roland Vils; Rafaelsen, Søren Rafael

    2016-01-01

    , the tissue material was found to be sufficient. In 32% of the biopsies, a complication arose, mostly pneumothorax (30%), but chest drainage was needed in only 15% of the 520 cases. Patients with more than ten cigarette pack-years had a complication risk that was twice as high at that of patients with fewer...... packyears. We found that the risk of pneumothorax increased the further the lesion was from the skin surface, the smaller the lesions were and when the patient was biopsied in a lateral position. We also found a higher risk of complications in females than in males. CONCLUSIONS: CT-guided biopsy...... is an excellent tool for analysing pulmonary lesions. The present study clearly shows that the risk of developing a pneumothorax is significantly increased among smokers and former smokers with more than ten pack-years....

  1. Transvenous liver biopsy via the femoral vein

    International Nuclear Information System (INIS)

    Khosa, F.; McNulty, J.G.; Hickey, N.; O'Brien, P.; Tobin, A.; Noonan, N.; Ryan, B.; Keeling, P.W.N.; Kelleher, D.P.; McDonald, G.S.A.

    2003-01-01

    AIM: To study the safety, effectiveness and diagnostic value of transvenous forceps biopsy of the liver in 54 patients with coagulopathy, gross ascites or morbid obesity and suspected liver disease in whom percutaneous liver biopsy was contraindicated. MATERIAL AND METHODS: Forceps biopsy of the liver via the femoral vein was attempted in 54 adult patients with advanced liver disease of unknown aetiology who had coagulation disorders (41 cases), gross ascites (11 cases) or morbid obesity (two cases). In each patient two to six biopsies (average four) were taken using a radial jaw forceps inserted via the right or left femoral vein. RESULTS: The procedure was successful in 53 cases. Hepatic vein catheterization failed in one patient. Adequate liver tissue for diagnosis was obtained in 84% of cases. One patient developed delayed haemorrhage at 12 h from a capsular leak that was undetected during the biopsy procedure. This patient required blood transfusions and laparotomy to control bleeding. There were no deaths in the 53 patients studied. Transient minor chest and shoulder pain was encountered during sheath insertion into a hepatic vein in 23 patients. Three patients developed a femoral vein haematoma, which resolved with conservative treatment. CONCLUSION: Transvenous liver biopsy via the femoral vein is another safe, effective, simple alternative technique of biopsy when the percutaneous route is contraindicated

  2. Relationship between skin color and solar elastosis in aged Asian skin: A colorimetric-pathologic correlation.

    Science.gov (United States)

    Kim, Dai Hyun; Oh, Ga Na; Kwon, In Hyuk; Seo, Soo Hong; Kye, Young Chul; Ahn, Hyo Hyun

    2017-10-01

    Aged skin is reported to be associated with unattractive skin color changes and solar elastosis. However, comparative studies have not documented the possible correlation between the two factors. This study investigated the plausible relationship between the facial skin color of elderly Asians and solar elastosis. A total of 22 skin specimens were collected from 22 Korean patients who underwent cheek skin biopsies. Skin color was quantitatively measured using colorimetric photography techniques to produce CIE L*a*b* values; the degree of solar elastosis was quantifiably assessed using a histologic grading scale. These values were used to investigate a correlation between the CIE L*a*b* coordinates and solar elastosis grade. The solar elastosis grade increased according to patient age (r = 0.67, p = .0006). However, the extent of solar elastosis was not statistically correlated with the CIE L*a*b* values, including L*, a*, and b* (r = 0.02, p = .95; r = 0.15, p = 0.50; r = -0.07, p = 0.76, respectively). The results showed that the solar elastosis grade increased, according to patient age, because of cumulative actinic damage. However, colorimetric skin color data did not correlate with the degree of solar elastosis. Therefore, cutaneous color changes and solar elastosis are separate, age-related phenomena. Physicians should be aware of the possible histologic changes in actinically damaged facial skin, regardless of the skin color. © 2017 Wiley Periodicals, Inc.

  3. Cutaneous skin tag

    Science.gov (United States)

    Skin tag; Acrochordon; Fibroepithelial polyp ... have diabetes. They are thought to occur from skin rubbing against skin. ... The tag sticks out of the skin and may have a short, narrow stalk connecting it to the surface of the skin. Some skin tags are as long as ...

  4. Axillary web syndrome following sentinel node biopsy for breast cancer.

    Science.gov (United States)

    Nieves Maldonado, S M; Pubul Núñez, V; Argibay Vázquez, S; Macías Cortiñas, M; Ruibal Morell, Á

    2016-01-01

    A 49 year-old woman diagnosed with infiltrating lobular breast carcinoma, underwent a right mastectomy and sentinel node biopsy (SLNB). The resected sentinel lymph nodes were negative for malignancy, with an axillary lymphadenectomy not being performed. In the early post-operative period, the patient reported an axillary skin tension sensation, associated with a painful palpable cord. These are typical manifestations of axillary web syndrome (AWS), a poorly known axillary surgery complication, from both invasive and conservative interventions. By presenting this case we want to focus the attention on a pathological condition, for which its incidence may be underestimated by not including it in SLNB studies. It is important for nuclear medicine physicians to be aware of AWS as a more common complication than infection, seroma, or lymphoedema, and to discuss this possible event with the patient who is consenting to the procedure. Copyright © 2016 Elsevier España, S.L.U. y SEMNIM. All rights reserved.

  5. Die Biopsie von Knochen- und Weichteiltumoren

    OpenAIRE

    Fuchs, B

    2008-01-01

    Technisch stellt die Biopsie von Knochen- und Weichteiltumoren einen simplen Akt dar, intellektuell aber ist die Planung einer Biopsie höchst anspruchsvoll. Zu häufig werden heutzutage immer noch Biopsien unsachgemäss durchgeführt, so dass die Behandlung - im besten Fall - erschwert wird. Eine unsachgemäss durchgeführte Biopsie führt häufig zu negativen funktionellen Konsequenzen für den Patienten, im schlimmsten Fall kann es die Prognose direkt beeinträchtigen. Aus diesem Grund soll...

  6. Acral peeling skin syndrome: a case of two brothers.

    Science.gov (United States)

    Wakade, Oojwala; Adams, Beth; Shwayder, Tor

    2009-01-01

    We report two brothers of Middle Eastern descent with consanguineous parents who present with numerous fragile, flaccid blisters on the hands and feet. In addition to spontaneous peeling, they can manually peel skin from acral areas without pain. The symptoms worsen with warm temperatures, excessive water exposure, and perspiration. Two biopsies from flaccid blisters on the feet were taken from the older brother, which revealed cleavage at the level of the stratum corneum. A diagnosis of acral peeling skin syndrome was made.

  7. Ultrasound-Guided Fine Needle Aspiration Biopsy of the Thyroid

    Science.gov (United States)

    ... Physician Resources Professions Site Index A-Z Ultrasound-Guided Fine Needle Aspiration Biopsy of the Thyroid An ... Aspiration Biopsy of the Thyroid? What is Ultrasound-Guided Fine Needle Aspiration Biopsy of the Thyroid? During ...

  8. Ultrasound guided pleural biopsy in undiagnosed exudative pleural effusion patients

    Directory of Open Access Journals (Sweden)

    Adel S. Ahmed

    2016-04-01

    In conclusion: Thoracic ultrasound (TUS guided pleural biopsy had a diagnostic yield which was slightly lower but comparable to both CT guided pleural biopsy and medical thoracoscopic pleural biopsy (MT.

  9. Clinical application of Lin's biopsy grasper for intrauterine targeted biopsy and polypectomy during office hysteroscopy.

    Science.gov (United States)

    Cheng, Hsin-Yi; Lin, Bao-Liang; Tseng, Jen-Yu; Ueno, Kazunori; Nakada, Sakura

    2018-06-01

    Hysteroscopy has widely been used for diagnosis of the uterine cavity; however, target biopsy has often been difficult in part to the inherent limitations of ancillary instruments. Lin's biopsy grasper was specifically designed to work in conjunction with a flexible hysteroscope to obtain intrauterine biopsy under transabdominal sonography. Herein, we share our clinical experience in the management of endometrial abnormalities with the use of Lin's biopsy grasper during office-based hysteroscopy. From February 2006 to November 2016, the use of Lin's biopsy grasper for tissue biopsy was attempted on 126 cases. We retrospectively recorded and analyzed the patients' preoperative characteristics and biopsy outcomes to demonstrate the feasibility and efficacy of Lin's biopsy grasper. Out of the one hundred and twenty-six enrolled patients, satisfactory targeted biopsies were achieved; including high diagnostic rate (92.1%, with 116 cases confirmed histologically) and adequate tissue retrieval (77.8%, with 98 cases obtaining optimal specimen volume). All patients tolerated the procedure without analgesics or anesthesia. Diagnostic flexible hysteroscopy combined with the use of Lin's biopsy grasper has proven to be an effective tool for intrauterine evaluation and obtaining tissue sample. Copyright © 2018. Published by Elsevier B.V.

  10. Biopsy diagnoses of clinically atypical pigmented lesions of the head and neck in adults.

    Science.gov (United States)

    Udovenko, Olga; Griffin, John R; Elston, Dirk M

    2014-10-01

    A subset of facial melanoma in situ has histological features that overlap with those of "dysplastic" nevi. The authors evaluated this important diagnostic pitfall by assessing the frequency of melanoma as the final diagnosis in skin biopsies submitted over a 1-year period with a clinical impression of "atypical" or dysplastic nevus from the head or neck of adults. A total of 1998 biopsies met inclusion criteria. Final diagnoses included both melanocytic and nonmelanocytic processes. Clear trends were noted based on the age of the patient with benign nevi encompassing nearly 70% of specimens in patients aged 21-29 years and jawline; and 3, temple), a location not traditionally associated with atypical nevi. Facial atypical nevi were found in all age groups. Malignant melanoma accounted for 1.8% of all specimens increasing from 0% in the patients aged 21-29 years to 5% in patients aged 70 years and above. Caution is warranted when evaluating skin biopsies from sun-damaged skin of the head or neck of an older adult submitted with a clinical diagnosis of atypical nevus. However, the authors' findings suggest that atypical nevi with histological features of dysplastic nevi occur on the head and neck of adults, including elderly adults. The incidence of such lesions decreases with age as the incidence of melanoma increases, and careful clinicopathologic correlation is vital.

  11. Skin Findings in Renal Transplantation Patients

    Directory of Open Access Journals (Sweden)

    Demet Kartal

    2013-03-01

    Full Text Available Objective: It was aimed to identify skin findings those were seen in patients who undergone renal transplantation. Methods: Patients who have been followed in Erciyes University Nephrology Hospital renal transplantation outpatient clinic were included in the study. They were evaluated for dermatologic findings during routine controls. Age, gender, transplantation date, identity of organ donor, history of medications, dermatological history and dermatological findings during examination were recorded. Biopsy was performed when needed. Results: In total 94 patients, 25 female (26.6% and 69 male (73.4%, were recruited to the study. Mean age was 36±10 years. The most frequent skin finding was drug-related acne (n=20. Most common infectious disease was verruca (n=17. There were viral disease other than verruca such as herpes zoster (n=3, superficial mycosis such as onychomycosis (n=5, tinea versicolor, tinea pedis and bacterial skin disease (n=2, and paronychia (n=1 and pre-malign lesions such as actinic cheilitis and bowenoid papulosis. Besides these, stria (n=3, kserosis (n=2, cornu cutaneum, café-au-lait spots, sebaceous hyperplasia and seborrheic dermatitis, skin tag, hypertrichosis, unguis incarinatus and calcinosis were other skin findings those were seen. No malign skin lesion was observed in any of patients. Conclusion: Miscellaneous skin lesions should develop in patients those undergone renal transplantation due to long-term utilization of various immunosuppressive drugs.

  12. Sentinel node biopsy in penile cancer

    DEFF Research Database (Denmark)

    Jakobsen, J. K.; Krarup, K. P.; Sommer, P.

    2015-01-01

    INTRODUCTION & OBJECTIVES: Nodal involvement is a strong prognosticator in penile cancer and lymph node staging is crucial. Sentinel node biopsy (SNB) has proven a useful staging tool with few complications, but evidence rely mostly on single institution publications with a short follow-up. In th......INTRODUCTION & OBJECTIVES: Nodal involvement is a strong prognosticator in penile cancer and lymph node staging is crucial. Sentinel node biopsy (SNB) has proven a useful staging tool with few complications, but evidence rely mostly on single institution publications with a short follow...... died from complications. CONCLUSIONS: To our knowledge, this is the first complete national study on sentinel node biopsy. Penile cancer sentinel node biopsy with a close follow-up is a reliable lymph node staging and has few complications in a national multicentre setting. Inguinal lymph node...

  13. Computed tomography guidance for skeletal biopsy

    International Nuclear Information System (INIS)

    Frager, D.H.; Goldman, M.J.; Elkin, C.M.; Cynamon, J.; Leeds, N.E.; Seimon, L.P.; Habermann, E.T.; Schreiber, K.; Freeman, L.M.

    1987-01-01

    Computed tomographic (CT) guided biopsy and abscess drainage of multiple organ systems have been well described. Reports of spinal and skeletal applications have been less common. This study describes the use of CT guidance in the biopsy of various skeletal lesions in 46 patients. Forty-one patients had skinny needle aspirations (18 or 22 gauge) and 23 patients had trephine core biopsies. Sites of the lesions included: thoracic spine - 15 patients, lumbosacral spine - 17 patients, bony pelvis - 6 patients, rib - 2 patients, and long bones - 6 patients. Fast scanners capable of rapid image reconstruction have overcome many constraints. With CT guidance, the physician who performs the procedure receives virtually no ionizing radiation. The exact location of the needle tip is accurately visualized in relation to the lesion being biopsied and to the vital organs. (orig.)

  14. Magnetic Resonance (MR)-Guided Breast Biopsy

    Science.gov (United States)

    ... over time. top of page What are the benefits vs. risks? Benefits The procedure is less invasive than surgical biopsy, ... risk of infection. The chance of infection requiring antibiotic treatment appears to be less than one in ...

  15. GoM Coastal Biopsy Surveys - NRDA

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Small vessel surveys were conducted within estuarine and nearshore coastal waters of Barataria Bay, LA and Mississippi Sound, MS to collect tissue biopsy samples...

  16. morphological pattern of endometrial biopsies in south

    African Journals Online (AJOL)

    Method: A retrospective study was undertaken to review all cases of endometrial biopsies ... MATERIALS AND METHODS. A retrospective ... tumours, 10 (0.4%) mixed tumours, 14 (0.6%) ..... accurate and concise clinical information on the.

  17. Examine Your Skin

    Medline Plus

    Full Text Available ... Biopsy: The First Step Sentinel Node Biopsy Melanoma Treatment: Stages I & II Melanoma Treatment: Stage III Melanoma Treatment: Stage IV Finding the Right Doctor Glossary of ...

  18. Outpatient percutaneous renal biopsy in adult patients

    International Nuclear Information System (INIS)

    Al-Hweish, Abdulla K.; Abdul-Rehman, I. Saeed

    2007-01-01

    To study the safety and efficacy of performing percutanaeous renal biopsy in the outpatient department compared to the traditional inpatient policy, we studied 44 consecutive patients with proteinuria and other urinary sediment abnormalities, at King Fahd Hospital of the University, Al-Khobar, Saudi Arabia, during the period from September 2004 to August 2006. The patients were divided into two groups: group I, in whom kidney biopsy was performed and followed by 1-day hospital admission; and group II, in whom renal biopsy was performed in the outpatient department and followed by 6 hours observation period and then by regular outpatient visits. All biopsies were performed with the use of real-time ultrasound and automated biopsy needle. Patients with a history of bleeding diathesis or abnormal coagulation profile and those receiving warfarin, heparin, aspirin or nonsteroidal anti-inflammatory drugs were excluded from the study. Only minor biopsy-related complications such as gross hematuria, perinephric hematoma that resolved without the need for blood transfusion or surgical intervention occurred in three (13.6%) patients in group I and in two (9.1%) patients in group II. The complications were apparent within 6 hours in all but one patient (97.7%). Overall, hematuria was identified in 52% of patients at <-72 hours, 85% at <-4 hours and 97.7% at <- 6 hours. The 24-hour hematocrit levels were not significantly different between the study groups. One (4.5%) patient from group II had a small perinephric hematoma, which was detected by ultrasound examination at 24 hours but not at 6 hours post biopsy period; it resolved spontaneously without intervention. We conclude that in selected patients, same day discharge after 6 hours of renal biopsy may be given safety without increased risk of complications. (author)

  19. Transbronchial biopsies safely diagnose amyloid lung disease

    Science.gov (United States)

    Govender, Praveen; Keyes, Colleen M.; Hankinson, Elizabeth A.; O’Hara, Carl J.; Sanchorawala, Vaishali; Berk, John L.

    2018-01-01

    Background Autopsy identifies lung involvement in 58–92% of patients with the most prevalent forms of systemic amyloidoses. In the absence of lung biopsies, amyloid lung disease often goes unrecognized. Report of a death following transbronchial biopsies in a patient with systemic amyloidosis cautioned against the procedure in this patient cohort. We reviewed our experience with transbronchial biopsies in patients with amyloidosis to determine the safety and utility of bronchoscopic lung biopsies. Methods We identified patients referred to the Amyloidosis Center at Boston Medical Center with lung amyloidosis diagnosed by transbronchial lung biopsies (TBBX). Amyloid typing was determined by immunohistochemistry or mass spectrometry. Standard end organ assessments, including pulmonary function test (PFT) and chest tomography (CT) imaging, and extra-thoracic biopsies established the extent of disease. Results Twenty-five (21.7%) of 115 patients with lung amyloidosis were diagnosed by TBBX. PFT classified 33.3% with restrictive physiology, 28.6% with obstructive disease, and 9.5% mixed physiology; 9.5% exhibited isolated diffusion defects while 19% had normal pulmonary testing. Two view chest or CT imaging identified focal opacities in 52% of cases and diffuse interstitial disease in 48%. Amyloid type and disease extent included 68% systemic AL disease, 16% localized (lung limited) AL disease, 12% ATTR disease, and 4% AA amyloidosis. Fluoroscopy was not used during biopsy. No procedure complications were reported. Conclusions Our case series of 25 patients supports the use of bronchoscopic transbronchial biopsies for diagnosis of parenchymal lung amyloidosis. Normal PFTs do not rule out the histologic presence of amyloid lung disease. PMID:28393574

  20. CT guided biopsies as a part of the investigations in findings in the lung and thorax wall

    DEFF Research Database (Denmark)

    Vagn-Hansen, Chris Aksel; Pedersen, Malene Roland Vils; Rafaelsen, Søren Rafael

    was performed. Results: In 86 % of the biopsies, the tissue material was found sufficient. In 32 % of the biopsies there was a complication, mostly pneumothorax (30%), but in only 15 % of the 520 cases chest drainage was needed. There was one death in a known cancer patient with severe reduced lung and cardiac...... function. Patients with more than 10 cigarette pack years had a complication risk twice as high compared to patients with less pack years. We found that the risk of pneumothorax rises the further the lesion is from the skin surface, the smaller the lesions are and when the patient is biopsied in a lateral...... position. We found a higher risk of complications in females. Conclusion: CT guided biopsy is an excellent tool in the analysis of lesions in the lungs. This study clearly shows that the risk of developing a pneumothorax is significantly higher among smokers and former smokers with more than 10 pack years....