Sample records for csf1po d3s1358 th01

  1. Second generation sequencing of three STRs D3S1358, D12S391 and D21S11 in Danes and a new nomenclature for sequenced STR alleles

    DEFF Research Database (Denmark)

    Gelardi, Chiara; Rockenbauer, Eszter; Dalsgaard, Sigrun


    Second generation sequencing (SGS) may revolutionize the field of forensic STR typing. Two of the essential requirements for implementation of an SGS based approach for forensic investigations are (1) establishment of adequate frequency databases and (2) adoption of a new STR nomenclature. We...... report the STR sequences and allele frequencies of three STR loci: D3S1358, D12S391 and D21S11 in 197 unrelated Danes. We used a new STR nomenclature that depicts the locus name used in forensic genetics, the length of the repeat region divided by the repeat length (typically 4 nucleotides) and detailed...

  2. Application of 9 STR loci in siblings identification%D3S1358等9个STR基因座在同胞鉴定中的应用

    Institute of Scientific and Technical Information of China (English)

    谢小虎; 周文华; 张富强; 刘惠芬; 陈为升; 庄丁丁; 张建兵


    目的 探讨D3S1358等9个常染色体STR基因座用于鉴定两个体间同胞亲缘关系的可行性.方法 用复合PCR扩增方法检测D3S1358等9个STR基因座的基因型,运用ITO法和IBS法两种分析方法计算两个体间的同胞亲权关系指数(paternity index,PI)和同胞亲权关系概率RCP(relative chance of paternity,RCP),并比较两个体间全相同、半相同和全不同的基因座数.结果 同胞个体间RCP值均值显著高于非同胞个体(P>0.05).同胞对全相同的基因座个数平均值>3,全不同的基因座个数平均值<2;而无关个体间全相同的基因座个数平均值<1,全不同的基因座个数平均值>3.结论 检测和分析D3S1358等9个STR基因座的基因型可以应用于同胞鉴定:以RCP≥95%或者以基因型全相同基因座数≥4或全不同基因座数≤1为肯定标准;以RCP≤5%或者以基因型全相同基因座数=0或全不同基因座数≥4为排除标准.

  3. Second generation sequencing of three STRs D3S1358, D12S391 and D21S11 in Danes and a new nomenclature for sequenced STR alleles. (United States)

    Gelardi, Chiara; Rockenbauer, Eszter; Dalsgaard, Sigrun; Børsting, Claus; Morling, Niels


    Second generation sequencing (SGS) may revolutionize the field of forensic STR typing. Two of the essential requirements for implementation of an SGS based approach for forensic investigations are (1) establishment of adequate frequency databases and (2) adoption of a new STR nomenclature. We report the STR sequences and allele frequencies of three STR loci: D3S1358, D12S391 and D21S11 in 197 unrelated Danes. We used a new STR nomenclature that depicts the locus name used in forensic genetics, the length of the repeat region divided by the repeat length (typically 4 nucleotides) and detailed sequence information of possible sub-repeats and SNPs within the amplified fragment.

  4. Population genetic data for 15 STR loci (Identifiler kit) in Bolivia. (United States)

    Rocabado, Omar; Taboada, Patricia; Inda, Francisco Javier; Yurrebaso, Inaki; García, Oscar


    Allele frequencies for 15 STR autosomal loci (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, VWA, TPOX, D18S51, D5S818 and FGA) were obtained from a sample of 200 unrelated individuals from Bolivia, South America.

  5. Meiosis study in a population sample from Nigeria: allele frequencies and mutation rates of 16 STR loci. (United States)

    Hohoff, Carsten; Schürenkamp, Marianne; Brinkmann, Bernd


    Allele frequencies for the 16 short tandem repeat (STR) loci D2S1338, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D19S433, D21S11, ACTBP2, CSF1PO, FGA, TH01, TPOX and VWA were determined for 337 immigrants from Nigeria. All loci were in Hardy-Weinberg equilibrium. More than 6,000 meiotic transfers were investigated and ten mutations were observed. Single mutations were observed in the STR systems D2S1338, D3S1358, D7S820, D8S1179, D16S539 and FGA, whereas two mutations were observed in the systems D21S11 and VWA.

  6. Population Genetic data for 15 Autosomal STR markers in Eastern Turkey. (United States)

    Tokdemir, Mehmet; Tunçez, Ferhat Turgut; Vicdanli, Nazif Harun


    The allelic frequency distribution and statistical genetic parameters of forensic relevance for 15 STR loci (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818 and FGA) in a population sample of 802 unrelated individuals in Eastern Turkey. The expected performance of these loci for personal identification and paternity testing in this population was estimated. Eastern Turkey and other 12 country population data were compared using allele frequencies.

  7. Genetic data on nine STRs (CSF1PO, TPOX, THO1, F13AO1, FESFPS, vWA, D16S539, D7S820 and D13S317) and two VNTRs (D1S80 and D17S5) in Rosario population, Santa Fe Argentine. (United States)

    Tenaglia, Mariano; Scollo, Adriana; Tripaldi, Regina; Grappiolo, Irene; Perichón, Armando M


    Allele frequencies for nine short tandem repeats (STRs) loci (CSF1PO, TPOX, THO1, F13AO1, FES/FPS, vWA, D16S539, D7S820 and D13S317) and two variable number tandem repeats (VNTRs) were obtained from a sample of 270 unrelated individuals born in the Rosario city, Santa Fe province of Argentina.

  8. Allele frequencies of 14 STR loci in the population of Malta. (United States)

    Cassar, M; Farrugia, C; Vidal, C


    Allele frequencies of 14 STR loci (D13S317, D16S539, D2S1338, vWA, TPOX, D18S51, D5S818, FGA, D8S1179, D21S11, D7S820, CSF1PO, TH01 and D3S1358) observed in the population of Malta are being reported. Polymerase chain reaction (PCR) amplification using the AmpFl STR Identifiler kit was performed in a random sample of 157 subjects (314 chromosomes). Markers D2S1338, D18S51 and FGA had the highest power of discrimination (PD) values while TPOX was the least informative marker. Allele frequencies observed in the Maltese population were also compared with those of other populations from the Mediterranean region, Europe and Africa. Our data is useful for anthropological and other comparative studies of populations and is powerful for forensic and paternity testing in the Maltese islands.

  9. Allele frequencies of the 15 AmpF/Str Identifiler loci in the population of Metztitlán (Estado de Hidalgo), México. (United States)

    Gorostiza, A; González-Martín, A; Ramírez, C López; Sánchez, C; Barrot, C; Ortega, M; Huguet, E; Corbella, J; Gené, M


    The 15 AmpF/STR Identifiler loci (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818 and FGA) were analyzed in the sample of 180 unrelated autochthonous healthy adults born in Meztitlán City from the valley of Metztitlán (Estado de Hidalgo, México). The agreement with Hardy-Weinberg equilibrium was confirmed for all loci. From the forensic point of view, the heterozygosity value, power of discrimination and the a priori chance of exclusion were calculated.

  10. Population genetics of 15 AmpflSTR Identifiler loci in Macedonians and Macedonian Romani (Gypsy). (United States)

    Havas, Dubravka; Jeran, Nina; Efremovska, Ljudmila; Dordević, Dobrivoje; Rudan, Pavao


    Allele frequencies of 15 AmpFlSTR Identifiler STR loci (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818 and FGA) were analysed in a sample of 100 unrelated autochthonous Macedonian and 102 Macedonian Romani individuals, representing different ethnic groups residing within the same country of Former Yugoslav Republic of Macedonia. The interpopulation comparisons between Macedonians and Macedonian Romani with four south eastern European populations, Kosovo Albanians, Serbians from Vojvodina Province, western Romanians and northern Greeks were performed as well as comparison between Macedonian Romani and Assam population from Asia (India). Reported data point that Macedonian Romani, as an example of an endogamous population of Asian (Indian) origin, show significant allelic differences when compared to neighbouring south eastern European populations.

  11. Genetic Analysis of 15 STR Loci in Chinese Han Population from West China

    Institute of Scientific and Technical Information of China (English)

    Ya-Jun Deng; Jiang-Wei Yan; Xiao-Guang Yu; Yuan-Zhe Li; Hao-Fang Mu; Yan-Qing Huang; Xiao-Tie Shi; Wei-Min Sun


    Allele frequencies for 15 short tandem repeat (STR) loci (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818, and FGA) were obtained from 7,636 unrelated individuals of Chinese Han population living in Qinghai and Chongqing, China. Totally 206 alleles were observed, with the corresponding allele frequencies ranging from 0.0001-0.4982. Chi-square test showed that all of the STR loci agreed with the Hardy-Weinberg equilibrium. We also compared our data with previously published population data of other ethnics or areas. The results are valuable for human identification and paternity testing in Chinese Han population.

  12. Forensic Profiling of Javanese and Madurese Families in Malang and Madura, East Java Indonesia.

    Directory of Open Access Journals (Sweden)

    Nikmatul Iza


    Full Text Available Purpose: The aims of this study are to identify the heritability of fingerprint patterns among three generations of Javanese and Madurese families and to determine the similarities, genetic variability and allele patterns for paternity testing. Material and Methods: The methods used in this study were the identification of the fingerprint patterns, DNA extraction from blood samples by salting out, PCR amplification use 13 CODIS which consists of TPOX, D3S1358, FGA, D5S818, CSF1PO, D7S820, D8S1179, TH01, VWA, D13S317, D16S539, D18S51, D21S11, and visualized by 8% polyacrylamide gel. The allele of individual band profile was analyzed by using QuantityOne software. Results: The results of fingerprint patterns showed that the families of Javanese ethnic has specific in ulnar patterns on both the middle and little fingers, meanwhile the families of Madurese ethnic has a plain whorl patterns on the right thumb and left index fingers which were inherited from the first generation to the next generation. The similarities of profile DNA forensic in Javanese ethnic generally have the same band patterns were produced by using D7S820 and CSF1PO markers, whereas in Madurese ethnic by using VWA and D18S51 markers. The genetic variability in Javanese ethnic by using D3S1358 and D21S11 markers, meanwhile the Madurese ethnic by using TH01 and D21S11 markers. Conclusion: We can conclude that there are the different characteristic of the fingerprint pattern of Javanese and Madurese families and the similarities and genetic variability in families of Javanese were different with the families of Madurese on the some markers.

  13. Turkish population data with the CODIS multiplex short tandem repeat loci. (United States)

    Akbasak, B S; Budowle, B; Reeder, D J; Redman, J; Kline, M C


    Allele frequencies for 13 tetrameric short tandem repeat (STR) loci, CSF1PO, D18S51, D3S1358, D21S11, D5S818, FGA, D7S820, HUMTH01, D8S1179, TPOX, D13S317, VWA, and D16S539 were determined on 198 Turkish blood samples.

  14. Population data on the thirteen CODIS core short tandem repeat loci in African Americans, U.S. Caucasians, Hispanics, Bahamians, Jamaicans, and Trinidadians. (United States)

    Budowle, B; Moretti, T R; Baumstark, A L; Defenbaugh, D A; Keys, K M


    Allele distributions for 13 tetrameric short tandem repeat (STR) loci, CSF1PO, FGA, TH01, TPOX, VWA, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, and D21S11, were determined in African American, United States Caucasian, Hispanic, Bahamian, Jamaican, and Trinidadian sample populations. There was little evidence for departures from Hardy-Weinberg expectations (HWE) in any of the populations. Based on the exact test, the loci that departed significantly from HWE are: D21S11 (p = 0.010, Bahamians); CSF1PO (p = 0.014, Trinidadians); TPOX (p = 0.011, Jamaicans and p = 0.035, U.S. Caucasians); and D16S539 (p = 0.043, Bahamians). After employing the Bonferroni correction for the number of loci analyzed (i.e., 13 loci per database), these observations are not likely to be significant. There is little evidence for association of alleles between the loci in these databases. The allelic frequency data are similar to other comparable data within the same major population group.

  15. Construction of a library of cloned short tandem repeat (STR) alleles as universal templates for allelic ladder preparation. (United States)

    Wang, Le; Zhao, Xing-Chun; Ye, Jian; Liu, Jin-Jie; Chen, Ting; Bai, Xue; Zhang, Jian; Ou, Yuan; Hu, Lan; Jiang, Bo-Wei; Wang, Feng


    Short tandem repeat (STR) genotyping methods are widely used for human identity testing applications, including forensic DNA analysis. Samples of DNA containing the length-variant STR alleles are typically separated and genotyped by comparison to an allelic ladder. Here, we describe a newly devised library of cloned STR alleles. The library covers alleles X and Y for the sex-determining locus Amelogenin and 259 other alleles for 22 autosomal STR loci (TPOX, D3S1358, FGA, D5S818, CSF1PO, D7S820, D8S1179, TH01, vWA, D13S317, D16S539, D18S51, D21S11, D2S1338, D6S1043, D12S391, Penta E, D19S433, D11S4463, D17S974, D3S4529 and D12ATA63). New primers were designed for all these loci to construct recombinant plasmids so that the library retains core repeat elements of STR as well as 5'- and 3'-flanking sequences of ∼500 base pairs. Since amplicons of commercial STR genotyping kits and systems developed in laboratories are usually distributed from 50 to STR alleles. The sequencing results showed all repeat structures we obtained for TPOX, CSF1PO, D7S820, TH01, D16S539, D18S51 and Penta E were the same as reported. However, we identified 102 unreported repeat structures from the other 15 STR loci, supplementing our current knowledge of repeat structures and leading to further understanding of these widely used loci.

  16. Mutations of microsatellite autosomal loci in paternity investigations of the Southern Poland population. (United States)

    Wojtas, Marta; Piniewska, Danuta; Polańska, Nina; Stawowiak, Agnieszka; Sanak, Marek


    In this study, germline mutations were analyzed for 26,040 parent-child allelic transfers among subjects referred to paternity testing and originating from the Slavonic population of the Southern Poland. Mutation rates were estimated for 15 autosomal microsatellite loci: D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818 and FGA. There were 35 mutation events observed at 11 from 15 analyzed loci. No mutations were found at TH01, D2S1338, D19S433 and TPOX loci. The mutation rate estimate was 0.0019 [0.0012-0.0028 95% CI] for paternal and 0.0004 [0.0002-0.0009] for maternal meiosis, while 25% mutations remained unassigned. The locus-specific mutation rate ranged from 0.0000 [0.0000-0.0014] to 0.0046 [0.0022-0.0087]. Mutations observed in male germlines were more frequent than in female germlines.

  17. Application of D3S1358 and other 8 STR loci amplification on identification if disputed paternity%复合扩增D3S1358等9个STR位点在亲子鉴定中的应用

    Institute of Scientific and Technical Information of China (English)

    谢小虎; 林锦锋; 王万旭; 张建兵; 许卫平; 周文华; 杨国栋


    @@人类基因组中约有50万个短串联重复序列位点(short tandem repeat, STR),其核心序列一般为2~6bp,片段长度为100~500bp,由于核心单位重复数目的变化,构成STR位点的高度多态性。

  18. The contribution of genetic diversity to subdivide populations living in the silk road of China. (United States)

    Zhang, Zhe; Wei, Shuguang; Gui, Hongsheng; Yuan, Zuyi; Li, Shengbin


    There are several indigenous ethnic populations along the silk road in the Northwest of China that display clear differences in culture and social customs, perhaps as a result of geographic isolation and different linguistic traditions. However, extensive trade and other interactions probably facilitated the admixture of different gene pools between these populations over the last two millennia. To further explore the evolutionary relationships of the 13 ethnic populations residing in Northwest China and to reveal the features of population admixture, the 9 most-commonly employed CODIS loci (D3S1358, TH01, D5S818, D13S317, D7S820, CSF1PO, vWA, TPOX, FGA) were selected for genotyping and further analysis. Phylogenetic tree and principal component analysis revealed clear pattern of population differentiation between 4 populations living in Sinkiang Uighur Autonomous Region and other 9 populations dwelled in the upper regions of Silk Road. R matrix regression showed high-level gene flow and population admixture dose exist among these ethic populations in the Northwest region of China. Furthermore, the Mantel test suggests that larger percent of genetic variance (21.58% versus 2.3%) can be explained by geographic isolation than linguistic barriers, which matched with the contribution of geographic factors to other world populations.

  19. Genetic polymorphism study at 15 autosomal locus in central Indian population. (United States)

    Shrivastava, Pankaj; Jain, Toshi; Trivedi, Veena Ben


    The analysis of 15 autosomal STR locus (TH01, D3S1358, vWA, D21S11, TPOX, D7S820, D19S433, D5S818, D2S1338, D16S539, CSF1PO, D13S317, FGA, D18S51, D8S1179) was done in 582 healthy unrelated individuals (Male-366, Female-216) originating from the various geographical regions of Madhya Pradesh, India. All locus fall under Hardy-Weinberg equilibrium except TPOX. These STR loci were highly informative and discriminating with combined power of discrimination (CPD) >0.99999. Locus wise allele frequencies of the studied population were compared with the other published populations. Also the Clustering pattern and genetic distance of studied populations is compared and presented with various populations. The studied population showed the genetic proximity with geographically close populations of India and significant genetic variation with distant populations which is also evident by clustering pattern of the NJ tree and the PCA plot.

  20. Analysis of short tandem repeat (STR polymorphisms by the powerplex 16 system and capillary electrophoresis: application to forensic practice.

    Directory of Open Access Journals (Sweden)

    Okamoto O


    Full Text Available Allele and genotype frequencies for 15 short tandem repeat (STR polymorphisms--D3S1358, TH01, D21S11, D18S51, Penta E, D5S818, D13S317, D7S820, D16S539, CSF1PO, Penta D, vWA, D8S1179, TPOX and FGA--in a Japanese population were estimated. No deviations of the observed allele frequency from Hardy-Weinberg equilibrium expectations were found for any of the systems studied. Between 2 new pentanucleotide STR loci, Penta E and Penta D, for which there is only limited data regarding the allelic distribution in Japanese, the Penta E locus was found to be highly polymorphic and exhibited a tri- or tetra-modal distribution pattern having allelic peaks with 5, 11, 15 and 20 repeats. The distribution was significantly different from that of the other ethnic groups. Statistical parameters of forensic importance, the power of discrimination (PD, observed and expected heterozygosity values (H, polymorphism information content (PIC, power of discrimination (PD, matching probability (pM, power of exclusion (PE, and typical paternity index (PI, were calculated for the loci. These parameters indicated the usefulness of the loci in forensic personal identification and paternity testing among Japanese. The systems Penta E, FGA, D18S51 and D8S1179 were the most informative. This method was successfully applied to forensic personal identification and paternity testing among Japanese, thereby confirming its efficacy for forensic practice.

  1. Developmental validation of the PowerPlex(®) Fusion System for analysis of casework and reference samples: A 24-locus multiplex for new database standards. (United States)

    Oostdik, Kathryn; Lenz, Kristy; Nye, Jeffrey; Schelling, Kristin; Yet, Donald; Bruski, Scott; Strong, Joshua; Buchanan, Clint; Sutton, Joel; Linner, Jessica; Frazier, Nicole; Young, Hays; Matthies, Learden; Sage, Amber; Hahn, Jeff; Wells, Regina; Williams, Natasha; Price, Monica; Koehler, Jody; Staples, Melisa; Swango, Katie L; Hill, Carolyn; Oyerly, Karen; Duke, Wendy; Katzilierakis, Lesley; Ensenberger, Martin G; Bourdeau, Jeanne M; Sprecher, Cynthia J; Krenke, Benjamin; Storts, Douglas R


    The original CODIS database based on 13 core STR loci has been overwhelmingly successful for matching suspects with evidence. Yet there remain situations that argue for inclusion of more loci and increased discrimination. The PowerPlex(®) Fusion System allows simultaneous amplification of the following loci: Amelogenin, D3S1358, D1S1656, D2S441, D10S1248, D13S317, Penta E, D16S539, D18S51, D2S1338, CSF1PO, Penta D, TH01, vWA, D21S11, D7S820, D5S818, TPOX, DYS391, D8S1179, D12S391, D19S433, FGA, and D22S1045. The comprehensive list of loci amplified by the system generates a profile compatible with databases based on either the expanded CODIS or European Standard Set (ESS) requirements. Developmental validation testing followed SWGDAM guidelines and demonstrated the quality and robustness of the PowerPlex(®) Fusion System across a number of variables. Consistent and high-quality results were compiled using data from 12 separate forensic and research laboratories. The results verify that the PowerPlex(®) Fusion System is a robust and reliable STR-typing multiplex suitable for human identification.

  2. Developmental validation of the GlobalFiler(®) Express PCR Amplification Kit: A 6-dye multiplex assay for the direct amplification of reference samples. (United States)

    Wang, Dennis Y; Gopinath, Siddhita; Lagacé, Robert E; Norona, Wilma; Hennessy, Lori K; Short, Marc L; Mulero, Julio J


    In order to increase the power of discrimination, reduce the possibility of adventitious matches, and expand global data sharing, the CODIS Core Loci Working Group made a recommendation to expand the CODIS core loci from the "required" 13 loci to 20 plus three additional "highly recommended" loci. The GlobalFiler(®) Express Kit was designed to incorporate all 20 required and 3 highly recommended loci along with a novel male-specific Y insertion/deletion marker. The GlobalFiler(®) Express Kit allows simultaneous amplification of the following loci: D3S1358, vWA, D16S539, CSF1PO, TPOX, Yindel, AMEL, D8S1179, D21S11, D18S51, DYS391, D2S441, D19S433, TH01, FGA, D22S1045, D5S818, D13S317, D7S820, SE33, D10S1248, D1S1656, D12S391, and D2S1338. The kit enables direct amplification from blood and buccal samples stored on paper or swab and the chemistry features an optimized PCR protocol that yields time to results in less than an hour. Developmental validation testing followed SWGDAM guidelines and demonstrated the quality and robustness of the GlobalFiler(®) Express Kit over a number of variables. The validation results demonstrate that the 24-locus multiplex kit is a robust and reliable identification assay as required for forensic DNA typing and databasing.

  3. Developmental validation of a single-tube amplification of the 13 CODIS STR loci, D2S1338, D19S433, and amelogenin: the AmpFlSTR Identifiler PCR Amplification Kit. (United States)

    Collins, Patrick J; Hennessy, Lori K; Leibelt, Craig S; Roby, Rhonda K; Reeder, Dennis J; Foxall, Paul A


    Analysis of length polymorphism at short tandem repeat (STR) loci utilizing the polymerase chain reaction (PCR) process has proven to be an ideal assay for human identification purposes. The short length of STR loci coupled with the amplification of target sequence through PCR allows for a robust, sensitive, and specific assay for highly polymorphic markers. A multiplex containing fifteen STR loci plus the gender-determining locus Amelogenin was developed to provide a single amplification/detection of all CODIS (Combined DNA Index System) STR loci (CSF1PO, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D21S11, FGA, TH01, TPOX, and vWA) as well as two internationally-accepted STRs (D2S1338 and D19S433). By incorporating five-dye fragment analysis technology and non-nucleotide linkers, previously optimized AmpFlSTR kit primer sequences have been maintained. This kit has been developed in accordance with the standards of the forensic community as defined by the DNA Advisory Board. Validation studies were performed to include developmental validation, and the results support the use of the AmpFlSTR Identifiler PCR Amplification Kit for human identity and parentage testing.

  4. Infrared fluorescent automated detection of thirteen short tandem repeat polymorphisms and one gender-determining system of the CODIS core system. (United States)

    Ricci, U; Sani, I; Guarducci, S; Biondi, C; Pelagatti, S; Lazzerini, V; Brusaferri, A; Lapini, M; Andreucci, E; Giunti, L; Giovannucci Uzielli, M L


    We used an infrared (IR) automated fluorescence monolaser sequencer for the analysis of 13 autosomal short tandem repeat (STR) systems (TPOX, D3S1358, FGA, CSF1PO, D5S818, D7S820, D8S1179, TH01, vWA, D13S317, D16S359, D18S51, D21S11) and the X-Y homologous gene amelogenin system. These two systems represent the core of the combined DNA index systems (CODIS). Four independent multiplex reactions, based on the polymerase chain reaction (PCR) technique and on the direct labeling of the forward primer of every primer pair, with a new molecule (IRDye800), were set up, permitting the exact characterization of the alleles by comparison with ladders of specific sequenced alleles. This is the first report of the whole analysis of the STRs of the CODIS core using an IR automated DNA sequencer. The protocol was used to solve paternity/maternity tests and for population studies. The electrophoretic system also proved useful for the correct typing of those loci differing in size by only 2 bp. A sensibility study demonstrated that the test can detect an average of 10 pg of undegraded human DNA. We also performed a preliminary study analyzing some forensic samples and mixed stains, which suggested the usefulness of using this analytical system for human identification as well as for forensic purposes.

  5. The Contribution of Genetic Diversity to Subdivide Populations Living in the Silk Road of China (United States)

    Gui, Hongsheng; Yuan, Zuyi; Li, Shengbin


    There are several indigenous ethnic populations along the silk road in the Northwest of China that display clear differences in culture and social customs, perhaps as a result of geographic isolation and different linguistic traditions. However, extensive trade and other interactions probably facilitated the admixture of different gene pools between these populations over the last two millennia. To further explore the evolutionary relationships of the 13 ethnic populations residing in Northwest China and to reveal the features of population admixture, the 9 most-commonly employed CODIS loci (D3S1358, TH01, D5S818, D13S317, D7S820, CSF1PO, vWA, TPOX, FGA) were selected for genotyping and further analysis. Phylogenetic tree and principal component analysis revealed clear pattern of population differentiation between 4 populations living in Sinkiang Uighur Autonomous Region and other 9 populations dwelled in the upper regions of Silk Road. R matrix regression showed high-level gene flow and population admixture dose exist among these ethic populations in the Northwest region of China. Furthermore, the Mantel test suggests that larger percent of genetic variance (21.58% versus 2.3%) can be explained by geographic isolation than linguistic barriers, which matched with the contribution of geographic factors to other world populations. PMID:24828511

  6. The contribution of genetic diversity to subdivide populations living in the silk road of China.

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    Zhe Zhang

    Full Text Available There are several indigenous ethnic populations along the silk road in the Northwest of China that display clear differences in culture and social customs, perhaps as a result of geographic isolation and different linguistic traditions. However, extensive trade and other interactions probably facilitated the admixture of different gene pools between these populations over the last two millennia. To further explore the evolutionary relationships of the 13 ethnic populations residing in Northwest China and to reveal the features of population admixture, the 9 most-commonly employed CODIS loci (D3S1358, TH01, D5S818, D13S317, D7S820, CSF1PO, vWA, TPOX, FGA were selected for genotyping and further analysis. Phylogenetic tree and principal component analysis revealed clear pattern of population differentiation between 4 populations living in Sinkiang Uighur Autonomous Region and other 9 populations dwelled in the upper regions of Silk Road. R matrix regression showed high-level gene flow and population admixture dose exist among these ethic populations in the Northwest region of China. Furthermore, the Mantel test suggests that larger percent of genetic variance (21.58% versus 2.3% can be explained by geographic isolation than linguistic barriers, which matched with the contribution of geographic factors to other world populations.

  7. Genetic admixture and diversity estimations in the Mexican Mestizo population from Mexico City using 15 STR polymorphic markers. (United States)

    Juárez-Cedillo, Teresa; Zuñiga, Joaquín; Acuña-Alonzo, Victor; Pérez-Hernández, Nonanzit; Rodríguez-Pérez, José Manuel; Barquera, Rodrigo; Gallardo, Guillermo J; Sánchez-Arenas, Rosalinda; García-Peña, Maria Del Carmen; Granados, Julio; Vargas-Alarcón, Gilberto


    The 15 AmpFlSTR Identifiler loci D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818 and FGA were analyzed in a sample of 378 unrelated individuals from Mexico City, Mexico. Significant deviations from HW equilibrium in 14/15 STR loci alleles were not detected. The D18S51 locus had the highest power of discrimination (0.970). Genetic admixture estimations revealed a 69% of Amerindian, 26% of European and 5% of African contribution. Comparative analyses between Mexicans and other neighboring populations reveal significant differences in genetic diversity. Our results are important for future comparative genetic studies in different Latin American ethnic groups, particularly Mexican Mestizos and Amerindians. They should also be helpful in genetics, population evolution, forensic and paternity testing.

  8. STR allele sequence variation: Current knowledge and future issues. (United States)

    Gettings, Katherine Butler; Aponte, Rachel A; Vallone, Peter M; Butler, John M


    This article reviews what is currently known about short tandem repeat (STR) allelic sequence variation in and around the twenty-four loci most commonly used throughout the world to perform forensic DNA investigations. These STR loci include D1S1656, TPOX, D2S441, D2S1338, D3S1358, FGA, CSF1PO, D5S818, SE33, D6S1043, D7S820, D8S1179, D10S1248, TH01, vWA, D12S391, D13S317, Penta E, D16S539, D18S51, D19S433, D21S11, Penta D, and D22S1045. All known reported variant alleles are compiled along with genomic information available from GenBank, dbSNP, and the 1000 Genomes Project. Supplementary files are included which provide annotated reference sequences for each STR locus, characterize genomic variation around the STR repeat region, and compare alleles present in currently available STR kit allelic ladders. Looking to the future, STR allele nomenclature options are discussed as they relate to next generation sequencing efforts underway.

  9. Microsatellite data support subpopulation structuring among Basques. (United States)

    Pérez-Miranda, Ana M; Alfonso-Sánchez, Miguel A; Kalantar, Arif; García-Obregón, Susana; de Pancorbo, Marian M; Peña, José A; Herrera, Rene J


    Genomic diversity based on 13 short tandem repeat (STR) loci (D3S1358, vWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, D7S820, D16S539, TH01, TPOX, and CSF1PO) is reported for the first time in Basques from the provinces of Guipúzcoa and Navarre (Spain). STR data from previous studies on Basques from Alava and Vizcaya provinces were also examined using hierarchal analysis of molecular variance (AMOVA) and genetic admixture estimations to ascertain whether the Basques are genetically heterogeneous. To assess the genetic position of Basques in a broader geographic context, we conducted phylogenetic analyses based on F(ST) genetic distances [neighbor-joining trees and multidimensional scaling (MDS)] using data compiled in previous publications. The genetic profile of the Basque groups revealed distinctive regional partitioning of short tandem repeat (STR) diversity. Consistent with the above, native Basques clearly segregated from other populations from Europe (including Spain), North Africa, and the Middle East. The main line of genetic discontinuity inferred from the spatial variability of the microsatellite diversity in Basques significantly overlapped the geographic distribution of the Basque language. The genetic heterogeneity among native Basque groups correlates with the peculiar geography of peopling and marital structure in rural Basque zones and with language boundaries resulting from the uneven impact of Romance languages in the different Basque territories.

  10. Mutation analysis of 24 short tandem repeats in Chinese Han population. (United States)

    Lu, Dejian; Liu, Qiuling; Wu, Weiwei; Zhao, Hu


    Germline mutations of 24 short tandem repeat (STR) loci (TPOX, D3S1358, FGA, D5S818, CSF1PO, D7S820, D8S1179, TH01, vWA, D13S317, Penta E, D16S539, D18S51, Penta D, D21S11, D2S1772, D6S1043, D7S3048, D8S1132, D11S2368, D12S391, D13S325, D18S1364, and GATA198B05) were studied for 6,441 parent-child meioses taken from the paternity testing cases in Chinese Han population. In total, 195 mutations were identified at 22 of the 24 loci. Among them, 189 (96.92%) mutations were one step, five mutations (2.56%) were two step, and one mutation (0.51%) was three step. No mutation was found at the TH01 and TPOX loci. The overall mutation rate estimated was 0.0013 (95% CI 0.0011-0.0015), and the locus-specific mutation rate estimated ranged from 0 to 0.0034. There was a bias in the STR mutations that repeat gains were more common than losses (∼1.7:1). Mutation events in the male germline were more frequent than in the female germline (∼4.3:1). Furthermore, loci with a larger heterozygosity tended to have a higher mutation rate. Mutation in short alleles was biased towards expansion, whereas mutation in long alleles favored contraction. The long alleles have a higher allelic mutational probability than short alleles.

  11. Introduction of the Python script STRinNGS for analysis of STR regions in FASTQ or BAM files and expansion of the Danish STR sequence database to 11 STRs. (United States)

    Friis, Susanne L; Buchard, Anders; Rockenbauer, Eszter; Børsting, Claus; Morling, Niels


    This work introduces the in-house developed Python application STRinNGS for analysis of STR sequence elements in BAM or FASTQ files. STRinNGS identifies sequence reads with STR loci by their flanking sequences, it analyses the STR sequence and the flanking regions, and generates a report with the assigned SNP-STR alleles. The main output file from STRinNGS contains all sequences with read counts above 1% of the total number of reads per locus. STR sequences are automatically named according to the nomenclature used previously and according to the repeat unit definitions in STRBase ( The sequences are named with (1) the locus name, (2) the length of the repeat region divided by the length of the repeat unit, (3) the sequence(s) of the repeat unit(s) followed by the number of repeats and (4) variations in the flanking regions. Lower case letters in the main output file are used to flag sequences with previously unknown variations in the STRs. SNPs in the flanking regions are named by their "rs" numbers and the nucleotides in the SNP position. Data from 207 Danes sequenced with the Ion Torrent™ HID STR 10-plex that amplified nine STRs (CSF1PO, D3S1358, D5S818, D7S820, D8S1179, D16S539, TH01, TPOX, vWA), and Amelogenin was analysed with STRinNGS. Sequencing uncovered five common SNPs near four STRs and revealed 20 new alleles in the 207 Danes. Three short homopolymers in the D8S1179 flanking regions caused frequent sequencing errors. In 29 of 3726 allele calls (0.8%), sequences with homopolymer errors were falsely assigned as true alleles. An in-house developed script in R compensated for these errors by compiling sequence reads that had identical STR sequences and identical nucleotides in the five common SNPs. In the output file from the R script, all SNP-STR haplotype calls were correct. The 207 samples and six additional samples were sequenced for D3S1358, D12S391, and D21S11 using the 454 GS Junior platform in this and a

  12. Second generation sequencing of three STRs D3S1358, D12S391 and D21S11 in Danes and a new nomenclature for sequenced STR alleles

    DEFF Research Database (Denmark)

    Gelardi, Chiara; Rockenbauer, Eszter; Dalsgaard, Sigrun;


    Second generation sequencing (SGS) may revolutionize the field of forensic STR typing. Two of the essential requirements for implementation of an SGS based approach for forensic investigations are (1) establishment of adequate frequency databases and (2) adoption of a new STR nomenclature. We...

  13. 云南汉族15个短串联重复序列基因座遗传多态性特征及分析%Analysis on characteristics of fifteen short tandem repeat genetic polymorphisms in Yunnan Han population

    Institute of Scientific and Technical Information of China (English)

    靳婵婵; 贺静; 王蕾; 陈鹏; 杨继青; 李秀玲; 苏洁; 朱宝生


    目的::调查云南地区汉族的D8S1179、D21S11、D7S820、CSF1PO、D3S1358TH01、D13S317、D16S539、D2S1338、D19S433、VWA、TPOX、D18S51、D5S818、FGA 15个短串联重复序列( Short tandem repeat,STR)基因座的遗传多态性。方法:收集云南汉族313名无关个体血样,提取DNA,PCR复合扩增并利用ABI-3130型基因分析仪进行毛细管电泳检测每个样本各基因座的等位基因大小,分别统计每个STR基因座各基因型的频率,并进行Hardy-Weinberg遗传平衡检验。结果:云南汉族这15个STR基因座各基因型频率分布符合Hardy-Weinberg平衡(P>0.05),杂合度在0.636~0.901,匹配概率在0.034~0.220,单一STR位点的个体识别率在0.780~0.966、非父排除率在0.336~0.797、多态性信息总量在0.555~0.860,联合使用这15个位点所产生的累积个体识别率大于0.99999999,累积非父排除率等于0.999998408。与中国其他地区汉族群体这15个STR基因座等位基因频率分布相比有较高的相似性,但也有轻微的地区差异。结论:云南汉族的D8S1179、D21S11、D7S820、CSF1PO、D3S1358TH01、D13S317、D16S539、D2S1338、D19S433、VWA、TPOX、D18S51、D5S818、FGA这15个STR基因座具有高度的多态性,与中国其他地区汉族群体有较高的相似性,在法医学中的亲子鉴定和个人识别方面具有较高应用价值。%Objective:To research on the genetic polymorphism distributions of fifteen short tandem repeat ( STR ) loci (D8S1179,D21S11,D7S820,CSF1PO,D3S1358,TH01,D13S317,D16S539,D2S1338,D19S433,VWA,TPOX,D18S51,D5S818, FGA) in Han race of Yunnan. Methods:A total of 313 specimens were collected from the unrelated individuals in Yunnan Han popu-lation. Genome DNA was extracted and amplified by multiplex PCR technique,the PCR products were analyzed by ABI-3130 genetic analyzer capillary electrophoresis detection, collected statistics of each STR loci genotypic frequency, and carried out the Hardy-Weinberg Genetic balance

  14. Trace samples of human blood in mosquitoes as a forensic investigation tool. (United States)

    Rabêlo, K C N; Albuquerque, C M R; Tavares, V B; Santos, S M; Souza, C A; Oliveira, T C; Oliveira, N C L; Crovella, S


    Investigations of any type of crime invariably starts at the crime scene by collecting evidence. Thus, the purpose of this research was to collect and analyze an entomological trace from an environment that is similar to those of indoor crime scenes. Hematophagous mosquitoes were collected from two residential units; saliva of volunteers that were residents in the units was also collected for genetic analysis as reference samples. We examined the allele frequencies of 15 short tandem repeat loci (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818, and FGA) and amelogenin. A total of 26 female hematophagous mosquitoes were identified as Aedes aegypti, Aedes albopictus, and Culex quinquefasciatus; we were able to obtain 11 forensically valid genetic profiles, with a minimum of 0.028203 ng/μL of human DNA. Thus, the results of this study showed that it was possible to correlate human genetic information from mosquitoes with the volunteer reference samples, which validates the use of this information as forensic evidence. Furthermore, we observed mixed genetic profiles from one mosquito. Therefore, it is clearly important to collect these insects indoors where crimes were committed, because it may be possible to find intact genetic profiles of suspects in the blood found in the digestive tract of hematophagous mosquitoes for later comparison to identify an offender and/or exclude suspects.

  15. Germline mutations of STR-alleles include multi-step mutations as defined by sequencing of repeat and flanking regions. (United States)

    Dauber, Eva-Maria; Kratzer, Adelgunde; Neuhuber, Franz; Parson, Walther; Klintschar, Michael; Bär, Walter; Mayr, Wolfgang R


    Well defined estimates of mutation rates are a prerequisite for the use of short tandem repeat (STR-) loci in relationship testing. We investigated 65 isolated genetic inconsistencies, which were observed within 50,796 allelic transfers at 23 STR-loci (ACTBP2 (SE33), CD4, CSF1PO, F13A1, F13B, FES, FGA, vWA, TH01, TPOX, D2S1338, D3S1358, D5S818, D7S820, D8S1132, D8S1179, D12S391, D13S317, D16S539, D17S976, D18S51, D19S433, D21S11) in Caucasoid families residing in Austria and Switzerland. Sequencing data of repeat and flanking regions and the median of all theoretically possible mutational steps showed valuable information to characterise the mutational events with regard to parental origin, change of repeat number (mutational step size) and direction of mutation (losses and gains of repeats). Apart from predominant single-step mutations including one case with a double genetic inconsistency, two double-step and two apparent four-step mutations could be identified. More losses than gains of repeats and more mutations originating from the paternal than the maternal lineage were observed (31 losses, 22 gains, 12 losses or gains and 47 paternal, 11 maternal mutations and 7 unclear of parental origin). The mutation in the paternal germline was 3.3 times higher than in the maternal germline. The results of our study show, that apart from the vast majority of single-step mutations rare multi-step mutations can be observed. Therefore, the interpretation of mutational events should not rigidly be restricted to the shortest possible mutational step, because rare but true multi-step mutations can easily be overlooked, if haplotype analysis is not possible.

  16. Developmental validation of the PowerPlex(®) 21 System. (United States)

    Ensenberger, Martin G; Hill, Carolyn R; McLaren, Robert S; Sprecher, Cynthia J; Storts, Douglas R


    The PowerPlex(®) 21 System is a STR multiplex that has been optimized for casework samples while still being capable of database workflows including direct amplification. The loci included in the multiplex offer increasing overlap with core loci used in different countries and regions throughout the world. The PowerPlex(®) 21 System contains D1S1656, D2S1338, D3S1358, D5S818, D6S1043, D7S820, D8S1179, D12S391, D13S317, D16S539, D18S51, D19S433, D21S11, Amelogenin, CSF1PO, FGA, Penta D, Penta E, TH01, TPOX, and vWA. These loci represent all 13 core CODIS loci in addition to loci commonly used in Asia and Europe. A developmental validation study was completed to document performance capabilities and limitations of the PowerPlex(®) 21 System. Data from this validation work served as the basis for the following conclusions: genotyping of single-source samples was reliable across a range of template DNA concentrations with >95% alleles called at 50 pg. Direct amplification of samples from FTA(®) storage cards was successfully performed using the reagents provided with the system and modified cycling protocols provided in the technical manual. Mixture analysis showed that over 95% of minor alleles were detected at 1:9 ratios. Reaction conditions including volume and annealing temperature as well as the concentrations of primers, DNA polymerase, magnesium, and Master Mix were shown to be optimal and able to withstand moderate variations without affecting system performance. Reproducible results were generated by different users at different sites. Finally, concordance studies showed consistent results when comparing the PowerPlex(®) 21 System with other commercially available STR-genotyping systems.

  17. Evaluation of the Early Access STR Kit v1 on the Ion Torrent PGM™ platform. (United States)

    Guo, Fei; Zhou, Yishu; Liu, Feng; Yu, Jiao; Song, He; Shen, Hongying; Zhao, Bin; Jia, Fei; Hou, Guangwei; Jiang, Xianhua


    The Early Access STR Kit v1 is designed to detect 25-plex loci with next generation sequencing (NGS) technology on the Ion Torrent PGM™ platform, including 16 of 20 expanded Combined DNA Index System (CODIS) core loci (CSF1PO, D1S1656, D2S1338, D2S441, D3S1358, D5S818, D7S820, D8S1179, D10S1248, D13S317, D16S539, D19S433, D21S11, TH01, TPOX and vWA), 8 non-CODIS core loci (D1S1677, D2S1776, D4S2408, D5S2500.AC008791, D6S1043, D6S474, D9S2157 and D14S1434) and Amelogenin. In this study, we compared the Early Access STR Kit v1 with the Ion Torrent™ HID STR 10-plex to find out its improvements and explored an appropriate analytical threshold to enhance the performance. In addition, seven experiments were conducted to evaluate the Early Access STR Kit v1 such as studies of repeatability, concordance, sensitivity, mixtures, degraded samples, case-type samples and pedigrees. Other than a little discordance (0.95%) with CE-STR results observed at D21S11, NGS-STR results correctly reflected the sample being tested. Repeatable results were obtained from both initial PCRs and emPCRs aside from a few variations of allele coverage. Full profiles could be obtained from 100pg input DNA and >48.84% profiles from 10pg input DNA. Mixtures were easily detected at 9:1 and 1:9 ratios. This system could be adapted to case-type samples and degraded samples. As a whole, the Early Access STR Kit v1 is a robust, reliable and reproducible assay for NGS-STR typing and a potential tool for human identification.

  18. 亲权鉴定中TH01基因座丢失现象分析%Analysis of allele dropout at TH01 locus in paternity testing

    Institute of Scientific and Technical Information of China (English)

    赖力; 沈晓丽; 薛士杰; 胡洁


    目的 对亲权鉴定中TH01基因座丢失现象进行分析,以确定基因型.方法 应用两套短串联重复序列基因座分型系统对TH01基因座异常分型进行重复验证,并设计TH01单基因座引物进行基因分型,产物经克隆测序分析.结果 在TH01基因座检出稀有等位基因5.2,该稀有基因型在PowerPlex 21分型系统中无法检出,呈现基因座丢失现象,而在Identifiler分型系统中可以准确分型.结论 基因变异可导致稀有等位基因的出现以及基因座丢失现象的产生,严重影响鉴定结果的准确判断,实验室应具备多种检测手段对基因座丢失现象进行分析,以避免错判发生.%Objective To analyze allele dropout at TH01 locus in paternity testing in order to determine the accurate genotype.Methods To use a two STR loci genotyping system to verify an abnormal genotype for the TH01 locus with PCR using specific primers,cloning and DNA sequencing.Results A rare allele at TH01 locus named 5.2,which was undetectable with PowerPlex 21 system,was detected with an Identifiler system.Conclusion Genetic variations may result in rare alleles and loci loss.To avoid misjudgment,laboratories shall have a variety of methods for detecting loci loss.

  19. 云南傣族与广西侗族18个STR基因座的遗传多态性%Genetic polymorphisms of 18 STR loci in Dai population of Yunnan and Dong population of Guangxi

    Institute of Scientific and Technical Information of China (English)

    王玮; 孙启凡; 张涛; 王英元; 程宝文; 赵兴春; 李彩霞; 叶健


    目的 调查云南傣族和广西侗族无关个体18个STR基因座(D18S51、D21S11、D3S1358、FGA、D8S1179、vWA、CSF1PO、D16S539、D7S820、D13S317、D5S818、D2S1338、D19S433、D12S391、TPOX、TH01、Penta E和D6S1043)的遗传多态性并研究其法医学应用价值. 方法 采用DNA TyperTM 19试剂盒对100名云南傣族和70名广西侗族的无关个体血样进行复合扩增,用遗传分析仪3130XL对扩增产物检测,用GeneMapper ID v3. 2软件进行基因分型,并计算群体遗传学参数. 结果 在100名云南傣族和70名广西侗族的无关个体中,云南傣族共发现185种等位基因,广西侗族共发现162种等位基因. 傣族单个等位基因频率分布在0. 005-0. 600、侗族在0. 007-0. 493;傣族与侗族累计个人识别能力均大于99. 999 999 999 999 999 999 99%.结论 这18个 STR基因座在云南傣族和广西侗族地区具有高度多态性,可满足对这两个群体的个体识别和亲权鉴定.%Objective To investigate the genetic polymorphisms of 18 STR loci(D18S51, D21S11, D3S1358, FGA, D8S1179, vWA, CSF1PO, D16S539, D7S820, D13S317, D5S818, D2S1338, D19S433, D12S391, TPOX, TH01, Penta E and D6S1043) in unre-lated Dai individuals in Yunnan and Dong individuals in Guangxi and to explore its application value in forensic practice. Methods Blood samples from unrelated 100 Dai and 70 Dong individuals were amplified using DNA TyperTM 19 kit. The amplified products were detected using 3130XL Genetic Analyzer, and the genotyping was done using GeneMapper ID v3. 2, and the population genetics param-eters were calculated. Results Of 100 Dai and 70 Dong unrelated individuals, 185 alleles were detected in Dai population and 162 alleles were detected in Dong population. The allele frequency was 0. 005-0. 600 for Dai population and 0. 007-0. 493 for Dong pop-ulation. The TDP of both Dai and Dong population was more than 99. 999 999 999 999 999 999 99%. Conclusion The 18 STR loci in Dai population of Yunnan and

  20. Genetic Polymorphism Study on 15 STR Loci of Han Population in Hunan%湖南省汉族人群15个STR基因座多态性分析

    Institute of Scientific and Technical Information of China (English)

    欧阳曙明; 殷照初; 江源; 申琴; 倪斌


    The polymorphism distributions of 15 STR loci (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818 and FGA) were investigated in a Hunan Han population using AmpFlSTR indentifiler kit, GeneAmp PCR system 9700 and ABI 310 genetic analyzer. Gene frequency, heterozygosity (H), polymorphism information content (PIC), power of discrimination (DP) and probability of paternity exclusion (PE) were calculated, and all loci were tested for Hardy-Weinberg equilibrium. Results indicate that the gene frequency of these 15 STR loci is in Hardy-Weinberg equilibrium. The H is at 0.593~0.900, PIC is at 0.54~0.85, DP is at 0.780~ 0.963, PE is at 0.282~0.785. Cumulative DP of the 15 STR is (1~1.6×10~(-17)) > 0.999 999 99, and the cumulative PE is 0.999 999 5. Therefore, the 15 STR loci used in this study are highly polymorphic in Hunan Han population and can be applied to population study, individual identification and paternity testing in forensic science.%应用美国AmpFISTR Indentifiler荧光标记复合扩增试剂盒,结合PE9700型PCR仪和美国ABI公司310型遗传分析仪,对湖南汉族人群D8S1179、D21S11、D7S820、CSF1PO、D3S1358TH01、D13S317、D16S539、D2S1338、D19S433、vWA、11POX、D18S51、D5S818和FGA共15个STR基因座进行多态性调查分析.结果显示15个SIR基因座的基因型分布符合Hardy-Weinberg平衡,其杂合度(H)介于0.593~0.900,多态信息含量(PIC)介于0.54~0.85,个体识别力(DP)介于0.780~0.963,非父排除率(PE)介于0.282~0.785,累计个体识别力为(1~1.6×10~(-17))>0.999 999 99,累计非父排除率为0.999 999 5.证明15个STR基因座在湖南省汉族人群中具有较高的多态性,可应用于该地区群体学研究、法医学个体识别和亲权鉴定等.

  1. Casework testing of the multiplex kits AmpFlSTR SEfiler Plus PCR amplification kit (AB), PowerPlex S5 System (Promega) and AmpFlSTR MiniFiler PCR amplification kit (AB). (United States)

    Müller, Kathrin; Sommerer, Thomas; Miltner, Erich; Schneider, Harald; Wiegand, Peter


    The short tandem repeat (STR) kits SEfiler Plus (D3S1358, FGA, D8S1179, D18S51, D21S11, TH01, VWA, SE33, D2S1338, D16S539, D19S433 and Amelogenin), PowerPlex S5 System (D18S51, D8S1179, TH01, FGA and Amelogenin) and MiniFiler (D13S317, D7S820, Amelogenin, D2S1338, D21S11, D16S539, D18S51, CSF1PO and FGA) were comparatively tested for their robustness and sensitivity. About 50 stains with highly degraded DNA and little DNA quantity served as examination material (e.g., hair with a telogen root, bones, degraded saliva stains on drinking vessels and skin cell mixtures). The PowerPlex S5 with five German DNA database (DAD) systems and the MiniFiler kit with four topical DAD systems and further STR markers show reduced amplicon lengths. The SEfiler Plus kit represents no MiniSTR multiplex, but contains the nine current DAD systems and further three systems D2S1338, D16S539 and D19S433, which are the potential expansion markers for the German DNA database. We have found on the basis of our comparative stain investigations, that the SEfiler Plus kit was less sensitive than the PowerPlex S5 and the MiniFiler kits. The MiniFiler and the PowerPlex S5 kit showed comparatively high sensitivity. Especially in analysing skin cell mixtures, the MiniFiler kit showed larger differences with regard to the performance of the fluorescent dyes/primer concentration co-ordination than the PowerPlex S5. The SEfiler Plus kit generated - just as both MiniSTR kits - relative robust typing results, but there appeared an increased sensitivity for 'allelic drop-outs' and 'imbalances'. Since the SEfiler Plus kit was not planned as MiniSTR concept, 'allelic drop-outs' were observed, as expected, more frequent in typing stains with degraded DNA and little DNA quantity, especially in the long polymerase chain reaction (PCR) products (e.g., D18S51).

  2. Tyrosine hydroxylase TH01 9.3 allele in the occurrence of sudden infant death syndrome in Swiss Caucasians. (United States)

    Studer, Jacqueline; Bartsch, Christine; Haas, Cordula


    Catecholamines, especially noradrenalin, are essential in the control of respiration and arousal. Thus, an impaired production of these neurotransmitters may contribute to the occurrence of sudden infant death syndrome (SIDS). The first step of the noradrenergic synthesis pathway is catalyzed by the enzyme tyrosine hydroxylase (TH). The TH-encoding gene contains a tetrameric short tandem repeat in intron 1 (TH01), with allele 9.3 reported to be associated with SIDS in German infants. We investigated the allelic frequency of the TH01 marker in 171 Swiss SIDS infants and 500 healthy and gender-matched Caucasian adults. In our study population, the allelic frequency of the 9.3 allele is similarly distributed in SIDS cases and controls (27.2% vs. 25.6%; p-value = 0.562). Nevertheless, the TH-encoding gene is only one of several genes involved in the noradrenergic biosynthesis pathway. Therefore, further genetic investigations are required with focus on the whole noradrenergic signaling system.

  3. Genetic variability and forensic efficiency of 39 microsatellite loci in the Li ethnic group from Hainan Island in the South China Sea. (United States)

    Chen, Jing; Xie, Bingbing; Yang, Yaran; Yang, Meng; Liu, Chao; Lv, Yuexin; Chen, Chuguang; Liu, Xu; Fang, Xiangdong; Wu, Huijuan; Yan, Jiangwei


    Investigation of allele and genotype frequencies of microsatellite loci in various populations is an essential pre-requisite in forensic application. The present study obtained population genetic data and forensic parameters of 39 autosomal Short Tandem Repeats (STRs) loci from a Chinese Li ethnic group and estimated the genetic relationships between Li and other reference populations. Thirty-nine STR loci, which include D19S433, D5S818, D21S11, D18S51, D6S1043, D3S1358, D13S317, D7S820, D16S539, CSF1PO, Penta D, D2S441, vWA, D8S1179, TPOX, Penta E, TH01, D12S391, D2S1338, FGA, D6S477, D18S535, D19S253, D15S659, D11S2368, D20S470, D1S1656, D22-GATA198B05, D8S1132, D4S2366, D21S1270, D13S325, D9S925, D3S3045, D14S608, D10S1435, D7S3048, D17S1290 and D5S2500, were amplified in two multiplex DNA-STR fluorescence detection systems for 189 unrelated healthy individuals of the Chinese Li ethnic group. The allele frequency distribution and several parameters commonly used in forensic science were statistically analysed. A total of 378 alleles were observed with corresponding allelic frequencies ranging from 0.0026-0.5899. The power of discrimination and power of exclusion ranged from 0.7569-0.9672 and 0.2513-0.7355, respectively. The power of exclusion (PE) ranged from 0.2580-0.7943 for trio paternity cases and 0.1693-0.5940 for duo paternity cases. The polymorphism information content (PIC) ranged from 0.5001-0.8611. The cumulative match probability across these 39 loci was 2.4242 × 10(-38). The results indicate that 39 STR loci are polymorphic among the Li ethnic group in Hainan Island in the South China Sea. This set of polymorphic STR loci provide highly polymorphic information and forensic efficiency for forensic individual identification and paternity testing, as well as basic population data for population genetics and anthropological research.

  4. STR-based genetic structure of the Berber population of Bejaia (Northern Algeria) and its relationships to various ethnic groups. (United States)

    Amir, Nadir; Sahnoune, Mohamed; Chikhi, Lounes; Atmani, Djebbar


    Patterns of genetic variation in human populations have been described for decades. However, North Africa has received little attention and Algeria, in particular, is poorly studied, Here we genotyped a Berber-speaking population from Algeria using 15 short tandem repeat (STR) loci D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818 and FGA from the commercially available AmpF/STR Identifiler kit. Altogether 150 unrelated North Algerian individuals were sampled across 10 administrative regions or towns from the Bejaia Wilaya (administrative district). We found that all of the STR loci met Hardy-Weinberg equilibrium expectations, after Bonferroni correction and that the Berber-speaking population of Bejaia presented a high level of observed heterozygosity for the 15 STR system (>0.7). Genetic parameters of forensic interest such as combined power of discrimination (PD) and combined probability of exclusion (PE) showed values higher than 0.999, suggesting that this set of STRs can be used for forensic studies. Our results were also compared to those published for 42 other human populations analyzed with the same set. We found that the Bejaia sample clustered with several North African populations but that some geographically close populations, including the Berber-speaking Mozabite from Algeria were closer to Near-Eastern populations. While we were able to detect some genetic structure among samples, we found that it was not correlated to language (Berber-speaking versus Arab-speaking) or to geography (east versus west). In other words, no significant genetic differences were found between the Berber-speaking and the Arab-speaking populations of North Africa. The genetic closeness of European, North African and Near-Eastern populations suggest that North Africa should be integrated in models aiming at reconstructing the demographic history of Europe. Similarly, the genetic proximity with sub-Saharan Africa is

  5. Second-generation sequencing of forensic STRs using the Ion Torrent™ HID STR 10-plex and the Ion PGM™. (United States)

    Fordyce, Sarah L; Mogensen, Helle Smidt; Børsting, Claus; Lagacé, Robert E; Chang, Chien-Wei; Rajagopalan, Narasimhan; Morling, Niels


    Second-generation sequencing (SGS) using Roche/454 and Illumina platforms has proved capable of sequencing the majority of the key forensic genetic STR systems. Given that Roche has announced that the 454 platforms will no longer be supported from 2015, focus should now be shifted to competing SGS platforms, such as the MiSeq (Illumina) and the Ion Personal Genome Machine (Ion PGM™; Thermo Fisher). There are currently several challenges faced with amplicon-based SGS STR typing in forensic genetics, including current lengths of amplicons for CE-typing and lack of uniform data analysis between laboratories. Thermo Fisher has designed a human identification (HID) short tandem repeat (STR) 10-plex panel including amelogenin, CSF1PO, D16S539, D3S1358, D5S818, D7S820, D8S1179, TH01, TPOX and vWA, where the primers have been designed specifically for the purpose of SGS and the data analysis is supported by Ion Torrent™ software. Hence, the combination of the STR 10-plex and the Ion PGM™ represents the first fully integrated SGS STR typing solution from PCR to data analysis. In this study, four experiments were performed to evaluate the alpha-version of the STR 10-plex: (1) typing of control samples; (2) analysis of sensitivity; (3) typing of mixtures; and (4) typing of biological crime case samples. Full profiles and concordant results between replicate SGS runs and CE-typing were observed for all control samples. Full profiles were seen with DNA input down to 50 pg, with the exception of a single locus drop-out in one of the 100 pg dilutions. Mixtures were easily deconvoluted down to 20:1, although alleles from the minor contributor had to be identified manually as some signals were not called by the Ion Torrent™ software. Interestingly, full profiles were obtained for all biological samples from real crime and identification cases, in which only partial profiles were obtained with PCR-CE assays. In conclusion, the Ion Torrent™ HID STR 10-plex panel offers an

  6. Towards simultaneous individual and tissue identification: A proof-of-principle study on parallel sequencing of STRs, amelogenin, and mRNAs with the Ion Torrent PGM. (United States)

    Zubakov, D; Kokmeijer, I; Ralf, A; Rajagopalan, N; Calandro, L; Wootton, S; Langit, R; Chang, C; Lagace, R; Kayser, M


    DNA-based individual identification and RNA-based tissue identification represent two commonly-used tools in forensic investigation, aiming to identify crime scene sample donors and helping to provide links between DNA-identified sample donors and criminal acts. Currently however, both analyses are typically performed separately. In this proof-of-principle study, we developed an approach for the simultaneous analysis of forensic STRs, amelogenin, and forensic mRNAs based on parallel targeted DNA/RNA sequencing using the Ion Torrent Personal Genome Machine(®) (PGM™) System coupled with the AmpliSeq™ targeted amplification. We demonstrated that 9 autosomal STRs commonly used for individual identification (CSF1PO, D16S539, D3S1358, D5S818, D7S820, D8S1179, TH01, TPOX, and vWA), the AMELX/AMELY system widely applied for sex identification, and 12 mRNA markers previously established for forensic tissue identification (ALAS2 and SPTB for peripheral blood, MMP10 and MMP11 for menstrual blood, HTN3 and STATH for saliva, PRM1 and TGM4 for semen, CYP2B7P1 and MUC4 for vaginal secretion, CCL27 and LCE1C for skin) together with two candidate reference mRNA markers (HPRT1 and SDHA) can all be successfully combined. Unambiguous mRNA-based tissue identification was achieved in all samples from all forensically relevant tissues tested, and STR sequencing analysis of the tissue sample donors was 100% concordant with conventional STR profiling using a commercial kit. Successful STR analysis was obtained from 1ng of genomic DNA and mRNA analysis from 10ng total RNA; however, sensitivity limits were not investigated in this proof-of-principle study and are expected to be much lower. Since dried materials with noticeable RNA degradation and small DNA/RNA amplicons with high-coverage sequencing were used, the achieved correct individual and tissue identification demonstrates the suitability of this approach for analyzing degraded materials in future forensic applications. Overall

  7. Genetic characterization of indigenous peoples from Oaxaca, Mexico, and its relation to linguistic and geographic isolation. (United States)

    Quinto-Cortés, Consuelo D; Arriola, Luis A; García-Hughes, Gianella; García-López, Rodrigo; Molina, Diana P; Flores, Margarita; Palacios, Rafael; Piñero, Daniel


    We used 15 short tandem repeat (STR) loci (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, VWA, TPOX, D18S51, D5S818, and FGA) to genetically characterize 361 individuals from 11 indigenous populations (Amuzgo, Chinanteco, Chontal, Huave, Mazateco, Mixe, Mixteco, Triqui, Zapoteco del Istmo, Zapoteco del Valle, and Zoque) from Oaxaca, Mexico. We also used previously published data from other Mexican peoples (Maya, Chol, Tepehua, Otomí, and Mestizos from northern and central Mexico) to delineate genetic relations, for a total of 541 individuals. Average heterozygosity (H) was lower in most populations from Oaxaca (range 0.687 in Zoque to 0.756 in Chontal) than values observed in Mestizo populations from Mexico (0.758 and 0.793 in central and northern Mestizo, respectively) but higher than values observed in other Amerindian populations from South America; the same relation was true for the number of alleles (n(a) ). We tested (using the software Structure) whether major geographic or linguistic barriers to gene flow existed among the populations of Oaxaca and found that the populations appeared to constitute one or two genetic groups, suggesting that neither geographic location nor linguistics had an effect on the genetic structure of these culturally and linguistically highly diverse indigenous peoples. Moreover, we found a low but statistically significant between-population differentiation. In addition, the genetic structure of Oaxacan populations did not fit an isolation-by-distance model. Finally, using AMOVA and a Bayesian clustering approach, we did not detect significant geographic or linguistic barriers to gene flow within Oaxaca. These results suggest that the indigenous communities of Oaxaca, although culturally isolated, can be genetically defined as a large, nearly panmictic population in which migration could be a more important population mechanism than genetic drift. Finally, compared with outgroups in Mexico (both

  8. Comparison of STR polymorphism among a Kirgiz ethnic group from Sinkiang and other groups

    Institute of Scientific and Technical Information of China (English)


    STR(Short tandem repeats)loci consist ofsi mple repeated sequences with2-6bp in length.The range of STR polymorphis m fragments is ap-proxi mately from100bp to350bp.STR appears tobe abundant in human genome and occurs every20kb on average[1-2].In present study,the frequencydistributions for nine STRloci were analyzed usingAmpFLSTR(ProfilerTMPCR Amplification Kit(Perkin-El mer).These STRs are D3S1358,VWA,CSF1PO,FGA,THO1,TPOX,D5S818,D13S317and D7S820.All these loci were analyzedby genescan.Establishment of a ...

  9. Genetic diversity at two pentanucleotide STR and thirteen tetranucleotide STR loci by multiplex PCR in four predominant population groups of central India. (United States)

    Sarkar, N; Kashyap, V K


    Genetic diversity study at STR loci in 208 individuals belonging to two backward groups, one caste and one tribal community of Central India called "Chhattisgarh" has been carried out to evaluate significance of Powerplex System loci in human identification and population diversity. Populations are Agharia (72), Satmani (50), Dheria Gond (36) and Teli (50). Fifteen loci (Powerplex 16 Kit) studied are Penta E, D18S51, D21S11, THO1, D3S1358, FGA, TPOX, D8S1179, vWA, Amelogenin, Penta D, CSF1PO, D16S539, D7S820, D13S317 and D5S818. The studied penta nucleotide STR (two) and 13 tetranucleotide (CODIS ) STR are found to be highly polymorphic genetic markers in all studied populations. Most common allele for the four studied population has been found to be same at THO1 (allele 9), D8S1179 (allele 14), CSF1PO (allele 12), Penta E (allele 11) and D16S539 (allele 11). Penta E is found to be most polymorphic (PD=0.89373) among studied 15 STR loci in four populations of Central India.

  10. 云南汉族人群20个常染色体STR 基因座遗传多态性%Genetic Polymorphism of 20 Autosomal STR Loci in Yunnan Han Popolation

    Institute of Scientific and Technical Information of China (English)

    胡利平; 杜雷; 张秀峰; 钟树荣; 聂爱婷; 李佳珏; 聂胜洁


    目的:研究云南汉族群体20个常染色体基因座的遗传多态性.方法采用PowerPlexR21 System试剂盒,对1085例云南汉族无关个体20个常染色体基因座(D3S1358、D1S1656、D6S1043、D13S317、Penta E、D16S539、D18S51、D2S1338、CSF1PO、Penta D、TH01、vWA、D21S11、D7S820、D5S818、TPOX、D8S1179、D12S391、D19S433、FGA)进行复合扩增,用AB 3130自动遗传分析仪进行扩增产物的电泳分离,用Genemapper ID v3.2软件进行STR基因分型分析,用Modified-Powerstates软件进行法医学遗传学参数统计分析以及H ardy-W einberg 平衡检验.结果在1085例云南汉族人群中,除T H 01和T PO X 基因座,其余ST R 基因座的均具有高度遗传多态性,杂合度( H)分布在0.6130~0.8743之间,随机匹配率( PM)分布在0.0179~0.2030之间,个体识别力(DP)在0.7970~0.9821之间,非父排除率(PE)在0.3067~0.7432之间,父权指数(PI)在1.2919-3.9766之间,多态性息含量( PIC)在0.5598~0.8958之间.基因型分布均符合 H ardy-W einberg 平衡定律.结论这20个常染色体基因座在云南汉族人群中具有较高的多态性和较好的个体识别能力,能满足法医学个体识别和亲权鉴定的需要.%Objective To study the genetic polymorphism of 20 autosomal short tandem repeats(STR)loci in Yunnan Han population. Methods The 20 STR loci(D3S1358,D1S1656,D6S1043,D13S317,Penta E,D16S539,D18S51,D2S1338,CSF1PO,Penta D,TH01,vWA,D21S11,D7S820,D5S818,TPOX, D8S1179,D12S391,D19S433 and FGA)which were included in the PowerPlexR21 System kit were genotyped in 1085 unrelated Han individuals living in Yunnan province using multiplex amplication. PCR products were separated and analyzed by the AB 3130 automatic genetic analyzer and GeneMapper ID v3.2 software. Forensic parameters of each locus were calculated by Modified-Powerstates software. Results All the studied loci except for TH01 and TPOX were highly

  11. Polymorphism analysis of 15 STR loci in a large sample of Guangdong (Southern China) Han population. (United States)

    Chen, Ling; Lu, Huijie; Qiu, Pingming; Yang, Xingyi; Liu, Chao


    AmpFℓSTR Sinofiler PCR Amplification Kit is specially developed for Chinese forensic laboratories, but there are little population-genetic data about this kit for Southern China. This kit contains 15 STR loci: D8S1179, D21S11, D7S820, CSF1PO, D3S1358, D13S317, D16S539, D2S1338, D19S433, vWA, D18S51, D6S1043, D12S391, D5S818 and FGA. We have conducted genotyping experiments on the 15 STR loci in 5234 unrelated individuals from Guangdong (Southern China). We observed a total of 243 alleles in the group with the allelic frequency values ranging from less than 0.0001 to 0.3686. Our statistic analysis indicates that the 15 STR loci conform to the Hardy-Weinberg's equilibrium (p>0.05). The highest polymorphism was found at D6S1043 locus and the lowest was found at D3S1358. The combined power of discrimination reached 0.99999999999999999977431 and the combined probability of paternity exclusion reached 0.999999721 for 15 STR loci. Guangdong Han population had significant differences compared with Shaanxi, Shandong and Henan province of Northern China. A Neighbor-joining tree indicates that the Guangdong Han has a close genetic relationship with the Yunnan population. Significant differences were found between Guangdong Han population and other reported populations (Japanese, Philippine, African American, Caucasian, Hispanic and Western Romanian) at 2-11 STR loci. The results may provide useful information for forensic sciences and population genetics studies. The present findings indicate that all the 15 STR loci are highly genetically polymorphic in the Han population of Guangdong.

  12. 四川省夹江县人群18个STR位点的遗传多态性%Genetic Polymorphism of 18 Short Tandem Repeat Loci in Jiajiang County of Sichuan Province

    Institute of Scientific and Technical Information of China (English)

    王乐; 赵兴春; 张建; 陈婷; 王邦义; 白雪; 叶健


    目的:利用DNATyperTM19试剂盒研究18个短串联重复序列(Short Tandem Repeat,STR)位点(D5S818、D21S11、D7S820、CSF1PO、D2S1338、D3S1358、vWA、D8S1179、D16S539、Pent E、TPOX、TH01、D19S433、D18S51、FGA、D6S1043、D13S317、D12S391)在四川省夹江县人群中的基因频率分布和群体遗传学参数,并计算DNATyperTM19试剂盒的相关技术参数.方法:利用血卡直接作为模板,采用PCR扩增和毛细管电泳检测技术对226名个体的18个STR基因座进行分析,并使用PowerStatsV12软件统计分析.结果:共检出202种等位基因,基因频率分布在0.002~0.527之间.18个STR基因型分布均符合Hardy-Weinberg平衡(P>0.05),杂合度均不低于0.633,随机匹配概率均不低于0.018,个人识别能力均不小于0.790,多态信息含量均不小于0.56,非父排除概率均不小于0.332,典型父权指数均不小于1.36.结论:本文研究了四川省夹江县人群18个STR位点的遗传多态性,为人类群体遗传学及法医学后续研究提供详实可靠的基础数据.DNATyperTM19试剂盒的累积随机匹配概率达到3.477× 10-22,累积非父排除概率为0.999999974.%Objective:The aim of this study was to determine the allele frequencies and population genetic parameters of 18 STR (short tandem repeat) loci (D5S818,D21S11,D7S820,CSF1PO,D2S1338,D3S1358,vWA,D8S1179,D16S539,Penta E,TPOX,TH01,D19S433,D18S51,FGA,D6S1043,D13S317,and D12S391) in Jiajiang county of Sichuan province and to calculate the technical parameters of the DNATyperTm19 kit.Methods:PCR amplification using blood as template directly and capillary electrophoresis technologies were employed to determine the genotypes of 18 STR loci for 226 individuals.PowerStatsV12 software was used for analysis and statistics.Results:202 alleles were recognized,with frequencies ranging from 0.002 to 0.527.No departures from Hardy-Weinberg expectations were detected for all 18 loci studied (P>0.05).The statistical analysis of 18 STR

  13. 浙江汉族人群中19个STR基因座遗传多态性检测结果分析及应用%Detection and application of 19 STR gene loci polymorphism in Han ethnic population of Zhejiang

    Institute of Scientific and Technical Information of China (English)

    陈芳; 付颖; 黄琼; 陈俭


    目的 应用Goldeneye DNA身份鉴定系统20A荧光标记复合扩增系统,检测其包含的19个CODIS系统短片段重复序列基因座在浙江汉族人群的遗传多态性,为其法医学应用提供基础数据.方法 通过对浙江省汉族人群中598名无关个体进行19个STR(D19S433、D5S818、D21S11、D18S51、D6S1043、D3S1358、D13S317、D7S820、D16S539、CSF1 PO、Penta D、vWA、D8S1179、TPOX、Penta E、TH01、D12S391、D2S1338、FGA)和Amelogenin基因座的复合扩增,PCR产物经ABI3130型全自动遗传分析仪检测,统计其STR基因座的群体遗传学参数并进行数据分析.结果 在19个STR基因座的等位基因中,分别检出14、9、17、17、18、8、8、8、7、9、11、11、10、7、24、8、11、13、19个等位基因,19个STR基因座杂合度(H)为0.588 6(TPOX)~0.916 4(Penta E),个人识别能力(DP)范围为0.787 6(TPOX) ~0.986 5(Penta E),联合应用19个STR基因座累计DP值达(1 ~2)×10-23,非父排除率(PE)范围从0.277 5(TPOX) ~0.829 0(PentaE),联合应用19个STR基因座累计PE达0.999 999 991,多态信息总量(PIC)范围为0.545 0(TPOX) ~0.913 4(Penta E).结论 联合应用19个STR基因座具有较强个体识别能力,可用于法庭科学中的亲权鉴定与个体识别.在实际工作中,采用该类遗传标记系统,可降低鉴定风险,提高工作效率,控制检测成本.%Objective To identify the genetic polymorphism of short tandem repeat (STR) loci of Han population form Zhejiang,and to evaluate their forensic application.Methods Nineteen allele loci,including D19S433,D5S818,D21S11,D18S51,D6S1043,D3S1358,D13S317,D7S820,D16S539,CSF1PO,Penta D,vWA,D8S1179,TPOX,Penta E,TH01,D12S391,D2S1338,FGA and Amelogenin loci were amplified by using GoldeneyeTM 20 A PCR amplification Kit,and the result were analyzed by using ABI 3130 genetic analyzer.A total of 598 unrelated individuals of Han population from Zhejiang were investigated to determine the distributions of allele frequencies

  14. Genetic polymorphisms of 17 STR loci in Han population in Nantong area%南通汉族群体17个常染色体STR基因座遗传多态性

    Institute of Scientific and Technical Information of China (English)

    张玉红; 韩海军; 贾东涛; 张越


    目的:研究南通汉族群体17个常染色体STR基因座遗传多态性。方法:利用AGCU 17+1荧光检测试剂盒,对467例南通汉族无关个体的17个常染色体 STR 基因座( CSF1PO、D13S317、D16S539、D18S51、D19S433、D21S11、D2S1338、D3S1358、D5S818、D6S1043、D7S820、D8S1179、FGA、Penta E、TH01、TPOX、vWA)进行扩增,用ABI 3100xl遗传分析仪和Gene-Mapper ID v3.2软件进行STR分型分析,用Cervus 3.0软件进行等位基因频率和遗传学参数统计分析,并检验Hardy-Wein-berg。结果:南通汉族群体中,17个STR基因座基因频率(GF)在0.0011~0.5096之间,杂合度(H)在0.6360~0.9336之间,期望杂合度(He)在0.6268~0.9219,个体识别能力(DP)在0.7974~0.9865之间,非父排除率(PE)在0.3363~0.8645之间,多态性息含量(PIC)在0.5635~0.9154之间,结果经χ2检验均符合Hardy-Weinberg平衡定律(P>0.05)。结论:南通汉族群体17个STR基因座具有较高多态性,能够满足南通汉族人群个体识别和亲权鉴定的需要,也可在群体遗传学等相关研究和实践中有较高的价值。%Objective:To investigate the genetic polymorphism of 17 short tandem repeat( STR) loci in autosomes of Han population living in Nantong are-a.Methods:AGCU17 +1 kit was used to amplify the 17 STR loci(CSF1PO,D13S317,D16S539,D18S51,D19S433,D21S11,D2S1338,D3S1358, D5S818,D6S1043,D7S820,D8S1179,FGA,Penta E,TH01,TPOX,vWA) from 467 unrelated individuals of Han population in Nantong area,and ABI 310xl analyzer and software GeneMapper ID v3.2 were used for STR genotyping.The allele frequencies and genetic parameters were calculated with soft-ware Cervus 3.0 and tested by Hardy-Weinberg equilibrium.Results:The genetic frequencies in 17 STR loci in Han population of Nantong area ranged from 0.001 1 to 0.509 6,and the heterozygosities (H)were from 0.6360 to 0.9336,the expected heterozygosity (He

  15. 新疆喀什地区维吾尔族18个STR基因座的遗传多态性%Genetic Polymorphisms of 18 STR Loci in Uygur Population of Kashi Prefecture of Xinjiang

    Institute of Scientific and Technical Information of China (English)

    张晓红; 李平; 翁玮霞; 刘长晖; 刘宏; 唐建新; 刘超


    目的 调查新疆喀什地区维吾尔族无关个体18个STR基因座(D18S51、D21S11、D3S1358、FGA、D8S1179、vWA、CSF1PO、D16S539、D7S820、D13S317、D5S818、D2S1338、D19S433、D12S391、TPOx、TH01、Penta E和D6S1043)的遗传多态性并研究其法医学应用价值.方法 采用DNA TyperTM 15 Plus试剂盒对1381名维吾尔族无关个体血样进行复合扩增,3130XL遗传分析仪对扩增产物检测,GeneMapper ID v3.2软件进行基因分型.计算群体遗传学参数,并与其他人群进行比较,计算Reynold's遗传距离,绘制系统发生树.结果 在1381名维吾尔族无关个体中,共发现231种等位基因,单个等位基因频率分布在0.0004~0.5304,H在0.644~0.923,PIC在0.587~0.918,DP在0.817~0.988,CPE大于0.9999999.与广州汉族人群遗传距离最大(0.088 3),与希腊人群遗传距离最小(0.0503).结论 这18个STR基因座在新疆喀什地区具有高度多态性,可满足该群体个体识别和亲权鉴定,其遗传多态性更接近欧洲.%Objective To investigate the genetic polymorphisms of 18 STR loci {D18S51, D21S11, D3S1358, FGA, D8S1179, vWA, CSF1PO, D16S539, D7S820, D13S317, D5S818, D2S1338, D19S433, D12S391, TPOX, TH01, Penta E and D6S1043) in unrelated Uygur individuals in Kashi prefecture of Xinjiang and to explore the application value in forensic practice. Methods Blood samples from 1 381 unrelated Uygur individuals were amplified by using DNA Typer?15 Plus kit. The amplified products were detected by using 3130XL Genetic Analyzer and the genotyping was done by using GeneMapper ID v3.2. Population genetics parameters were calculated and compared with that of the other population. The genetic distance of Reynold's was calculated and phylogenetic tree was constructed at last. Results Of the 1 381 unrelated Uygur individuals, 231 alleles were detected, with an allele frequency of 0.000 4-0.530 4. The H values were 0.644-0.923, PIC values were 0.587-0.918, and DP values were 0

  16. Allele frequency data of 21 autosomal short tandem repeat loci in Mesan and Basra provinces in South Iraq

    Directory of Open Access Journals (Sweden)

    Imad Hadi Hameed


    Full Text Available We focused on a sample of 100 unrelated persons from the provinces of southern Iraq. This is an analysis of the allele frequency and genotyping of those STR loci in an Iraqi population and this is the first study of its kind in Iraq. As such the data available could be utilized in the Iraqi database for the STR polymorphic markers. Chelex® kit was utilized to extract DNA then Power Plex21® kit (D3S1358, D13S317, PentaE, D16S539, D18S51, D2S1338, CSF1PO, Penta D, THO1, vWA, D21S11, D7S820, TPOX, D8S1179, FGA, D2S1338, D5S818, D6S1043, D12S391, D19S433 was used to amplify the isolated DNA. The mean PIC values and heterozygosity observed across 21 loci were 0.713 and 0.696, respectively. This shows high gene diversity. Those loci can be safely used to establish a DNA-based database for the Iraqi population because the power of discrimination values for all tested loci was from 71% to 97%.

  17. Genetic polymorphism at 15 STR loci among three important subpopulation of Bihar, India. (United States)

    Ashma, R; Kashyap, V K


    Genotype polymorphism studies at 15 highly polymorphic short tandem repeat (STR) loci were carried out in three genetically important minor caste groups (Yadav, Kurmi and Baniya) of Bihar, a eastern state of India to evaluate their significance in human identification and population genetics study. The selected communities practice endogamy. Despite of same geographical area, the physical features of Yadavs and Baniyas resemble North Indian Indo-Caucasoids whereas Kurmis resemble more to Indo-Austroloids. Among the chosen 15 loci, two are penta-nucleotide repeat: Penta-D and Penta-E, and 13 are tetra-nucleotide repeat: vWA D8S1179, TPOX, FGA, D5S818, D13S317, D7S820, D16S539, D3S1358, THO1, CSF1PO, D21S11, D18S51 and are validated for other population of India and world for forensic testing and human population study. Thirteen of these STR loci are present in the combined DNA index system (CODIS) [J. Forensic Sci. 44 (1999) 1277] and world-wide data is available.

  18. Genetic study of 15 STRs loci of Identifiler system in Angola population. (United States)

    Melo, Miguel Manuel; Carvalho, Mónica; Lopes, Virgínia; Anjos, Maria João; Serra, Armando; Vieira, Duarte Nuno; Sequeiros, Jorge; Corte-Real, Francisco


    Angola is located in the African continent, in the area of southern Africa and has a population of approximately 14 million inhabitants. The Angola population has origin from Occidental and Southern Bantu people that came from the great lakes region, creating the most ever known African migration of our days. Allele frequencies for the 15 STRs loci in the AmpFlSTR Identifiler kit (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, HUMTH01, D13S317, D16S539, D2S1338, D19S433, HUMVWA, TPOX, D18S51, D5S818, HUMFIBRA/FGA and including the segment of the X-Y homologous gene amelogenin) were studied for Angola population. The genotype frequency of the 15 STR loci showed no significant deviations from Hardy-Weinberg equilibrium expectations and great values for the combined power of discrimination and combined power of a priori exclusion validate the application of these markers in forensic genetics. Comparative analyses between Angola population data and other relevant population database from Africa, Europe and American are presented.

  19. Microsatellite diversity delineates genetic relationships of Shia and Sunni Muslim populations of Uttar Pradesh, India. (United States)

    Eaaswarkhanth, Muthukrishnan; Dubey, Bhawna; Ramakodi Meganathan, Poorlin; Noor, Sabahat; Haque, Ikramul


    In this study we characterize the genetic diversity and relationships between the Shia and Sunni Muslim populations of North India and geographically targeted neighboring and global populations. We examined a number of parameters of population genetic and forensic interest based on the allele frequencies from 15 autosomal STR loci (D8S1179, D21S11, D7S820, CSF1PO, D19S433, VWA, TPOX, D18S51, D3S1358, THO1, D13S317, D16S539, D2S1338, D5S818, and FGA). All the studied loci were consistent with Hardy-Weinberg equilibrium, except loci D18S51 and FGA for both Muslim populations, even after applying the Bonferroni correction. The combined power of exclusion and combined power of discrimination values for all 15 STR loci were 0.9999 and >0.99999, respectively, in both Muslim populations. Gene diversity values ranged from 0.6784 (TPOX) to 0.9027 (FGA) for Shia Muslims and from 0.7152 (CSF1PO) to 0.9120 (D18S51) for Sunni Muslims. The observed heterozygosity (H(o)) ranged from 0.5833 (D18S51) to 0.8595 (VWA) in Shia Muslims and from 0.6818 (CSF1PO) to 0.8333 (D21S11) in Sunni Muslims and was lower than the expected heterozygosity (H(e)) for 11 out of the 15 STRs typed. We analyzed the genetic affinities of the Shia and Sunni Muslim populations with their geographically closest neighboring North Indian, Middle Eastern, East Asian, and European populations using distance-based methods, including neighbor-joining trees and multidimensional scaling. In addition, we estimated the genetic contribution of the putative parental populations included in the analysis to the Shia and Sunni Muslim gene pool using admixture analysis. Although we observed a certain degree of genetic contribution from Iran to both Muslim populations, the results of the phylogenetic analyses based on autosomal STRs suggest genetic relatedness with some of the geographically closest neighboring Hindu religious populations.

  20. CODIS STR loci data from 41 sample populations. (United States)

    Budowle, B; Shea, B; Niezgoda, S; Chakraborty, R


    Allele distributions for 12 or 13 CODIS core tetrameric short tandem repeat (STR) loci CSFIPO, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D21S11, FGA, TH01, TPOX, and vWA were determined in 41 population data sets. The major population groups comprise African Americans, U.S. Caucasians, Hispanics, Far East Asians, and Native Americans. There was little evidence for departures from Hardy-Weinberg expectations (HWE) in any of the populations. The FST estimates over all thirteen STR loci are 0.0006 for African Americans, -0.0005 for Caucasians, 0.0021 for Hispanics, 0.0039 for Asians, and 0.0282 for Native Americans.

  1. Concordance study between the ParaDNA® Intelligence Test, a rapid DNA profiling assay, and a conventional STR typing kit (AmpFlSTR® SGM Plus®). (United States)

    Ball, G; Dawnay, N; Stafford-Allen, B; Panasiuk, M; Rendell, P; Blackman, S; Duxbury, N; Wells, S


    The ParaDNA® Intelligence Test enables STR profiling directly from human biological samples and evidence items collected from crime scene in 75min. Designed for non-expert use this system allows DNA information to be available to investigators before it would typically be available from a laboratory. The ParaDNA Intelligence Test system amplifies D3S1358, D8S119, D16S539, D18S1358 and TH01 STR loci and the gender typing locus amelogenin and detects the alleles present with HyBeacon® probes. Individual DNA samples from 381 UK Caucasian individuals were analysed using AmpFlSTR® SGM Plus® and the ParaDNA Intelligence Test with the derived STR profiles compared. Here we describe the high level of concordance demonstrated between the two systems and discuss this with reference to allele frequencies and the discriminatory power offered by the ParaDNA Intelligence Test.

  2. Population genetic data for 15 autosomal STR markers in Turkish Cypriots from Cyprus. (United States)

    Gurkan, Cemal; Demirdov, Damla Kanliada; Yamaci, Rezan Fahrioglu; Sevay, Huseyin


    Fifteen autosomal short tandem repeat (STR) markers [D8S1179, D21S11, D7S820, CSF1PO, D3S1358, THO1, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818 and FGA] were analyzed in 501 unrelated, randomly selected Turkish Cypriot individuals from the island of Cyprus. While no locus duplications or null alleles were detected in these samples, eight allelic variants were observed in total, 75% of which were intermediate allelic variants that were absent in the system allelic ladder. Allelic frequencies and statistical parameters of forensic interest were calculated at each locus. For the 15 STR loci tested, combined matching probability (pM) was 2.15717 × 10(-18) and combined power of exclusion (PE) was 0.9999995213. No deviations from the Hardy-Weinberg equilibrium were observed, except for the vWA locus, which became insignificant after the Bonferroni correction for multiple testing. Locus-by-locus comparisons of the Turkish Cypriot allelic frequencies with those published for the neighboring and/or historically related populations with similar loci coverage (Turkish, Greek, Greek Cypriot, Italian and Lebanese) revealed some statistically significant differences at one to five loci. In general, an increase in the number of such significant differences between the Turkish Cypriot data and those for other populations correlated closely with an increase in the geographic distance and/or a decrease in the amount of historical contact. The Turkish Cypriot autosomal STR population study will find immediate use in the Committee on Missing Persons in Cyprus Project on the "Exhumation, Identification and Return of Remains of Missing Persons" and it will also be available for criminal, parentage and other missing person investigations.

  3. Validation of the DNATyper™15 PCR Genotyping System for Forensic Application

    Directory of Open Access Journals (Sweden)

    Jian Ye


    Full Text Available We describe the optimization and validation of the DNATyper™15 multiplex polymerase chain reaction (PCR genotyping system for autosomal short tandem repeat (STR amplification at 14 autosomal loci (D6S1043, D21S11, D7S820, CSF1PO, D2S1338, D3S1358, D13S317, D8S1179, D16S539, Penta E, D5S818, vWA, D18S51, and FGA and  amelogenin, a sex-determining locus. Several DNATyper™15 assay variables were optimized, including hot start Taq polymerase concentration, Taq polymerase activation time, magnesium concentration, primer concentration, annealing temperature, reaction volume, and cycle number. The performance of the assay was validated with respect to species specificity, sensitivity to template concentration, stability, accuracy, influence of the DNA extraction methods, and the ability to genotype the mixture samples. The performance of the DNATyper™15 system on casework samples was compared with that of two widely used STR amplification kits, Identifiler™ (Applied Biosystems, Carlsbad, CA, USA and PowerPlex 16 ® (Promega, Madison, WI, USA. The conditions for PCR-based DNATyper™15 genotyping were optimized. Contamination from forensically relevant nonhuman DNA was not found to impact genotyping results, and full profiles were generated for all the reactions containing ≥ 0.125 ng of DNA template. No significant difference in performance was observed even after the DNATyper™15 assay components were subjected to 20 freeze-thaw cycles. The performances of DNATyper™15, Identifiler™, and PowerPlex 16 ® were comparable in terms of sensitivity and the ability to genotype the mixed samples and case-type samples, with the assays giving the same genotyping results for all the shared loci. The DNA extraction methods did not affect the performance of any of the systems. Our results demonstrate that the DNATyper™15 system is suitable for genotyping in both forensic DNA database work and case-type samples.

  4. The next generation of DNA profiling--STR typing by multiplexed PCR--ion-pair RP LC-ESI time-of-flight MS. (United States)

    Pitterl, Florian; Niederstätter, Harald; Huber, Gabriela; Zimmermann, Bettina; Oberacher, Herbert; Parson, Walther


    For the first time a multiplexed PCR approach suitable for mass spectrometric STR allele identification is presented. Thirteen forensically important STR markers (vWA, D21S11, D3S1358, D16S539, D8S1179, D7S820, D13S317, D5S818, TPOX, CSF1PO, D2S441, D10S1248, and D22S1045) and the gender typing locus amelogenin were simultaneously amplified. Ion-pair reversed-phase high-performance liquid chromatography electrospray-ionization time-of-flight mass spectrometry (ICEMS) was applied for genotyping, and allowed for highly efficient characterization of multiple PCR amplicons. Compared with electrophoretic sizing ICEMS enabled for the simultaneous detection of length and nucleotide variations. Thus, the obtained amount of biological information present within STR profiles was significantly increased even though the compatibility of typing results with electrophoretically generated data(bases) was maintained. Other advantages of the ICEMS platform included the abandonment of internal size standards, allelic ladders, and any kind of spectral calibration. The 14-plex PCR was tailor-made for ICEMS analysis by designing primer pairs that bind close to the repeat region, by using a proof reading polymerase for amplification, and by implementing molecular mass modifiers for prevention of molecular mass overlaps. In a series of experiments, the performance of the multiplexed PCR-ICEMS assay was evaluated. The ICEMS-based DNA profiling assay was found to be competitive regarding detection sensitivity and analyzability of degraded and casework samples with commercially available electrophoretic typing approaches, which suggests that multiplexed PCR-ICEMS assays could represent a valuable tool for (forensic) genetics.

  5. Observation and analysis of mutation on 546 parentage testing cases%546例亲子鉴定案件中基因突变的观察和分析

    Institute of Scientific and Technical Information of China (English)

    张晓嘉; 张更谦; 刘晋玎


    目的::在亲权鉴定案件中经常可以观察到突变,突变会直接影响到亲权指数( PI)的计算。这里我们观察分析15个STR基因座在山西汉族人群亲子鉴定案件中的突变特点和规律。方法:546例确认亲子关系案件来自于山西汉族人群,包括父-母-子三联体案件383例,二联体案件163例。用含15个STR基因座的PowerPlex ®16 System kit试剂盒对上述案例进行分析。结果:在546例亲子鉴定案件中共有22例出现突变,Penta E,D5S818,D7S820,vWA,D21S115个位点均出现3例突变,突变率最高为0.32%;FGA,D8S11792个位点突变均为2例,突变率为0.22%;CSF1PO,D3S1358,D18S513个位点突变均为1例,突变率为0.11%;未观察到其余基因座的基因突变。22例突变全部为一步突变,其中来自父亲的突变10例,来自母亲7例,5例无法确定突变来源。22例突变中增加1个基序的10例,减少1个基序的10例,增加减少不明确的2例。结论:山西汉族人群常染色体STR的突变率在0%~0.32%之间,该数据为计算突变情况下的亲权指数提供了数据支持。%Objective:Mutation is often observed and the mutation rate is important for the paternity index ( PI) calculation. Here we summarized the mutations of 15 STR loci in Chinese Han population from Shanxi Province,China. Methods:A total of 546 par-entage confirmed paternity cases from Shanxi Han population,including 383 triplets and 163 duos,were typed with PowerPlex ® 16 System kit. The mutation data were collected and analyzed. Results:Twenty two mutation events were observed. Among 15 STR loci, PentaE,D5S818,D7S820,vWA,D21S11 had the highest mutation rate of 0. 32%. The second place went to FGA,D8S1179 loci,in which 0. 22% mutation were found. One mutation event occurred in CSF1PO, D3S1358 and D18S51, respectively with the rate of 0. 11%. No mutation was observed in the rest of STRs. All the observed mutation events were single-step mutation. Ten of them

  6. A new sensitive short pentaplex (ShoP) PCR for typing of degraded DNA. (United States)

    Meissner, C; Bruse, P; Mueller, E; Oehmichen, M


    Analysis of short tandem repeat makers has become the most powerful tool for DNA typing in forensic casework analysis. Unfortunately, typing of DNA extracted from telogen shed hairs, bones buried in the soil or from paraffin-embedded, formalin-fixed tissue often reveals no results due to the degradation of DNA. The reduction in size of the target fragments by development of new primers and their combination in multiplex approaches open a new field of DNA analysis. Here we present a new sensitive short pentaplex PCR including the loci amelogenin, TH01, VWA, D3S1358 and D8S1179. Validation tests of our new method included sensitivity, mixtures, human specificity, artificial degradation of DNA by DNase I and case work analysis on a panel of different forensic samples. The detection limit was 12.5 pg of human DNA, and mixtures of 50 pg in a total of 1000 pg were clearly detectable and revealed complete profiles. Only DNA extracts of human primates displayed a few signals, whereas other animal, fungal or bacterial DNA showed no signals. Our method proved extremely valuable in the analysis of artificially degraded DNA and in forensic cases, where only poorly preserved DNA was available. This approach and other similar methods can aid in the analysis of samples where allelic drop out of larger fragments is observed. It is highly recommended to develop more of these multiplexes to improve poor quality DNA typing.

  7. Newborn genetic identification: a protocol using microsatellite DNA as an alternative to footprinting. (United States)

    de Pancorbo, M M; Rodríguez-Alarcón, J; Castro, A; Fernández-Fernández, I; Melchor, J C; Linares, A; García-Orad, A; Fernández-Llebrez del Rey, L; Aranguren, G; Santillana, L


    Newborn identification by foot- or finger-printing presents serious drawbacks. This study proposes an alternative method based on DNA analysis of blood-spots taken from the newborn child. CSF1PO, TPOX and TH01 microsatellite loci were chosen to develop a fast and reliable protocol to be applied in cases where it is suspected that newborn children have been exchanged. The advantage of these loci is that one can simultaneously amplify them by PCR multiplex reaction and determine their alleles, thereby reducing the time needed for identification tests. Moreover, the amplification products of these loci are very small (< 350 bp) and so can be analyzed in samples with degraded DNA. We have been able to prove that it is possible to obtain results in blood-spots taken from newborns up to 13 years before and kept at room temperature. Thus the protocol proposed here can be applied in long-term post-natal identification cases.

  8. A forensic laboratory tests the Berkeley microfabricated capillary array electrophoresis device. (United States)

    Greenspoon, Susan A; Yeung, Stephanie H I; Johnson, Kelly R; Chu, Wai K; Rhee, Han N; McGuckian, Amy B; Crouse, Cecelia A; Chiesl, Thomas N; Barron, Annelise E; Scherer, James R; Ban, Jeffrey D; Mathies, Richard A


    Miniaturization of capillary electrophoresis onto a microchip for forensic short tandem repeat analysis is the initial step in the process of producing a fully integrated and automated analysis system. A prototype of the Berkeley microfabricated capillary array electrophoresis device was installed at the Virginia Department of Forensic Science for testing. Instrument performance was verified by PowerPlex 16 System profiling of single source, sensitivity series, mixture, and casework samples. Mock sexual assault samples were successfully analyzed using the PowerPlex Y System. Resolution was assessed using the TH01, CSF1PO, TPOX, and Amelogenin loci and demonstrated to be comparable with commercial systems along with the instrument precision. Successful replacement of the Hjerten capillary coating method with a dynamic coating polymer was performed. The accurate and rapid typing of forensic samples demonstrates the successful technology transfer of this device into a practitioner laboratory and its potential for advancing high-throughput forensic typing.

  9. Recombination analysis of autosomal short tandem repeats in Chinese Han families. (United States)

    Liu, Qiu-Ling; Luo, Hong; Zhao, Hu; Huang, Xiao-Ling; Cheng, Jian-Ding; Lu, De-Jian


    Recombination fractions between forensic STRs can be extrapolated from the International HapMap Project, but the concordance between recombination fractions predicated from genetic maps and derived from observation of STR transmissions in families is still ambiguous for autosomal STRs because of limited family studies. Therefore, the main goal of this study is to compare recombination fractions estimated by pedigree analysis with those derived from HapMap phase SNP data. Genotypes of nine autosomal STR pairs (TPOX-D2S1772, D5S818-CSF1PO, D7S3048-D7S820, D8S1132-D8S1179, TH01-D11S2368, vWA-D12S391, D13S325-D13S317, D18S51-D18S1364, and D21S11-PentaD) from 207 two-generation families with two to five children (the number of families with five, four, three, and two children was 2, 3, 20, and 182, respectively) were used to analyze the recombination. The linkage analysis showed that significant linkage was observed at six STR pairs (D5S818-CSF1PO, D8S1132-D8S1179, TH01-D11S2368, vWA-D12S391, D13S325-D13S317, and D18S51-D18S1364) with genetic distances HapMap. Their recombination fractions calculated from family data were very close to those derived from HapMap. However, three STR pairs of TPOX-D2S1772, D7S3048-D7S820, and D21S11-PentaD showed no significant linkage with genetic distances from 43.38 to 91.49 cM. Our results indicate that recombination fractions extrapolated from HapMap can provide a substitute if empirical data are unavailable for the linkage STR pair with a genetic distance spanned <36.22 cM.

  10. Genetic polymorphism and forensic parameters of nine short tandem repeat loci in Ngöbé and Emberá Amerindians of Panama. (United States)

    Castro, Edgardo A; Trejos, Diomedes E; Berovides-Alvarez, Vicente; Arias, Tomás D; Ramos, Carlos W


    Nine STR loci (CSF1PO, TPOX, TH01, F13A01, FESFPS, VWA, D16S539, D7S820, and D13S317) were analyzed in unrelated Ngöbé and Emberá Amerindians of Panama. The chi-square test demonstrated statistically significant differences (P linguistic stock [Chibchan (Ngöbé) and Chocoan (Emberá)], both retain strong similarities in their allele-frequency distributions. Three loci (TPOX, VWA, and F13A01) in the Ngöbé and two loci (TH01 and TPOX) in the Emberá departed from Hardy-Weinberg equilibrium. The analysis of the STR markers demonstrates that, despite their low levels of genetic polymorphisms, most of them could be informative for forensic purposes, showing a combined power of discrimination of 0.9999 for both Amerindian populations. However, powers of exclusion in the Ngöbé were very low, particularly at the TH01 (0.04) and FESFPS (0.08) loci. The combined powers of exclusion were 0.9338 and 0.9890 for the Ngöbé and the Emberá, respectively. Furthermore, the combined typical paternity index in the Ngöbé was considerably low (2.58), and in the Emberá it was 40.44, which is also very low. The low genetic polymorphism levels suggest that theuse of additional loci supplementing the battery of the nine loci is recommended for paternity and forensic tests in both populations, particularly for the Ngöbé.

  11. Paternity analysis in special fatherless cases without direct testing of alleged father. (United States)

    Mixich, Francisc; Ioana, Mihai; Mixich, Vlad A


    The ability to establish the biological father, in which the father of a person is not available, named "reverse paternity determination", is based on the determination of STR alleles in mother and her child, other children and brothers of the alleged father, and deduction of genetic constitution of the father by the basis of genetic laws. Presented herein are two cases of reverse paternity determinations. Mother and parenthood DNA was isolated from 300 microl of fresh blood collected into tubes containing the EDTA, using Wizard Genomic DNA purification kit (Promega). DNA amplification was performed using GenePrint STR System (CTT, FFv, and Silver STR III multiplex) (Promega). Amplification results were read on 0.4 mm thick sequencing size polyacrilamide gel (4% for CTT and FFv, and 6% for Silver STR III). Gels were silver stained using Silver Sequence DNA Staining Reagents (Promega). Possible alleles of the alleged father for the loci CSF1PO, TPOX, TH01, F13A01, FESFPS, vWA, D16S539, D7S820, D13S317, LPL, F13B, and HPRTB were established by the selection from alleles determined in mother and parenthood, as to as obligate alleles with which the alleged father contributes to the genetic constitution of investigated child. Probability of paternity was calculated using population data on STR allele frequencies for Romanian population established by our laboratory. These are the first cases of litigious reverse paternity determinations in Romania.

  12. Genetic variation among four Mexican populations (Huichol, Purepecha, Tarahumara, and Mestizo) revealed by two VNTRs and four STRs. (United States)

    Rangel-Villalobos, H; Rivas, F; Sandoval, L; Ibarra, B; Garcìa-Carvajal, Z Y; Cantú, J M; Figuera, L E


    Allele distributions of two polymorphisms with variable number of tandem repeats (VNTR), D1S80 and APOB, and four polymorphisms with short tandem repeats (STR), VWA, TH01, CSF1PO, and HPRTB, were analyzed in three Mexican ethnic groups: Huichol, Purepecha, and Tarahumara. Genotype distribution was in agreement with Hardy-Weinberg expectations for each locus and ethnic group. Heterozygosity (H), power of discrimination, and probability of exclusion were estimated. The three groups presented some distinctive genetic features: (1) a diminished genetic diversity (H = 66.8% to 73.4%) and mean number of alleles by locus (5.8 to 6.3) in comparison with Mexican mestizos (H = 78.3%, 10.5 alleles/locus), and (2) uneven allele distributions as evidenced by "distinctive alleles" with high frequencies, especially in the Tarahumara and the Huichol. Genetic relatedness analysis included data from a previously typed mestizo population, the largest and most widely distributed population in Mexico. Allele distribution differentiation was observed among all four groups, except between mestizo and Purepecha (p > 0.05), which was interpreted as indicating a larger Spanish component in the Purepecha as a result of gene flow effects. Although intrapopulation inbreeding (FIS) was not significant, heterozygote deficiency in the total population (FIT) and divergence among populations (FST) were significant (p Purepechas, and Huichols in relation to Tarahumaras. Correlation between the observed genetic features and the geographic isolation level points to genetic drift as the main cause of differentiation among these Mexican populations.

  13. A model-based 'varimax' sampling strategy for a heterogeneous population. (United States)

    Akram, Nuzhat A; Farooqi, Shakeel R


    Sampling strategies are planned to enhance the homogeneity of a sample, hence to minimize confounding errors. A sampling strategy was developed to minimize the variation within population groups. Karachi, the largest urban agglomeration in Pakistan, was used as a model population. Blood groups ABO and Rh factor were determined for 3000 unrelated individuals selected through simple random sampling. Among them five population groups, namely Balochi, Muhajir, Pathan, Punjabi and Sindhi, based on paternal ethnicity were identified. An index was designed to measure the proportion of admixture at parental and grandparental levels. Population models based on index score were proposed. For validation, 175 individuals selected through stratified random sampling were genotyped for the three STR loci CSF1PO, TPOX and TH01. ANOVA showed significant differences across the population groups for blood groups and STR loci distribution. Gene diversity was higher across the sub-population model than in the agglomerated population. At parental level gene diversities are significantly higher across No admixture models than Admixture models. At grandparental level the difference was not significant. A sub-population model with no admixture at parental level was justified for sampling the heterogeneous population of Karachi.

  14. CODIS位点在排除亲权中的应用价值%Study on application of CODIS loci to excluding paternity

    Institute of Scientific and Technical Information of China (English)

    方建新; 刘锡杰; 程大霖


    目的对 CODIS位点 (FGA、 vWA、 CSF1PO、 TH01、 TPOX、 D3S1358 、 D5S818、 D7S820 、 D8S1179、 D13S317、 D16S539、 D18S51和 D21S11共 13个 STR位点 ) 在 100例排除亲权的亲子鉴定中的应用价值进行研究。方法采用 Profiler Plus及 Cofiler 荧光标记复合扩增系统,通过 310遗传分析仪对上述二个检测体系扩增产物的基因型进行分析。结果在排除亲权的母亲 -孩子 -假设父亲三联体组中,所有观察案例其出现的排除指标数都在 3个以上,平均排除指标数为 6.63 个;在假设父亲 -孩子二联体组中, 94.0%的观察案例其排除指标数均在 3个以上,平均排除指标数为 5.01个。结论 CODIS位点在排除亲权的二联体和三联体组合亲子鉴定中,都符合鉴定应用要求 ; 选择多态性较高的位点与增加排除指标存在直接的联系,以 DP、 H、 PE作为衡量 DNA位点应用价值的指标在具体鉴定实践中是可靠和可行的。

  15. Genetic analysis of allelic variants, single-step mutations, three allelic variants of the 15 STR loci in the population of Northeast Bosnia

    Directory of Open Access Journals (Sweden)

    Hadžiavdić Vesna


    Full Text Available Diversity of nuclear DNA microsatellite markers were analyzed in a reference sample of the population of northeast Bosnia. 437 samples taken from unrelated individuals were processed and three samples of paternity proof were shown. Detection effectiveness profile of the research, points to a valid choice of method of extraction, amplification and genotyping STR loci with PowerPlextm16. Genetic analysis of allelic variants of the 15 STR loci detected 17 samples determined as microvariants. Samples were divided into 15 different allelic variants at 7 different loci, and are: in locus D7S820, D16S539, D3S1358, D18S51, PENTA D, PENTA E and in locus vWA. Genetic analysis of mutations in cases of paternity determined three examples of single-step mutations in the loci FGA, Penta D and D3S1358. Genetic analysis of observed STR loci detected three allelic variant of genotype combination 7/10/11.3 in locus D7S820 Type II.

  16. A case study of SNPSTR efficiency in paternity testing with locus incompatibility. (United States)

    Ye, Yi; Luo, Haibo; Liao, Linchuan; Zhang, Ji; Wei, Wei; Wang, Zheng; Hou, Yiping


    Instead of testing the additional STR loci, SNPSTR was included in the paternity testing for an alleged father-son duo case, with one inconsistency at the CSF1PO locus. We have chosen CSF1PO STR and five closely linked SNPs rs10077461, rs2569076, rs2228422, rs3733673 and rs3829987 to establish the SNPSTR and examined its potential use in paternity testing. A total of 152 haplotypes from 76 unrelated individuals were obtained by the nested-AS-PCR and 60 SNPSTR haplotypes were observed. The discrimination power of the SNPSTR haplotype was greater than either the STR or SNP haplotype alone. Its SNP part could be used to distinguish fathers from uncles. When SNPSTR was introduced into the calculation of parentage statistics, the paternity probability increased to 99.998%. Based on our findings, we concluded that SNPSTR could be considered a useful tool in forensic science.

  17. Population data of nine STRs of Mexican-Mestizos from Mexico City. (United States)

    Luna-Vazquez, A; Vilchis-Dorantes, G; Paez-Riberos, L A; Muñoz-Valle, F; González-Martin, A; Rangel-Villalobos, H


    One hundred and thirteen individuals were PCR-typed for nine STR loci with the AmpFlSTR Profiler Plus PCR amplification kit, including the following autosomal STRs: D3S1358, vWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317 and D7S820. Allele frequencies for each STR were estimated, and they were compared to other populations. Genotype distribution by locus and by two-loci combination was in agreement with Hardy-Weinberg expectations for all nine STRs. For this region of Mexico, the combined probability of exclusion (PE) and power of discrimination (PD) were estimated: PE=99.964% and PD>99.999%.

  18. A study on ten short tandem repeat systems: African immigrant and Spanish population data. (United States)

    Gamero, J J; Romero, J L; Gonzalez, J L; Arufe, M I; Cuesta, M I; Corte-Real, F; Carvalho, M; Anjos, M J; Vieira, D N; Vide, M C


    This work presents the results obtained from a genetic-population study for the D1S1656 system in the population of Southwest Spain (Huelva, Cádiz and Sevilla), Spaniards of Caucasian origin from North Africa (Ceuta), as well as in the black Central West African and Moroccan immigrant populations in Spain. The results of a study of the autochtonous population of the Canary Islands (n=138), and immigrant Central West African populations in Spain (n=132), obtained for nine short tandem repeat (STR) loci (D3S1358, VWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, D7S820), as well as the amelogenin locus, all contained in Profiler Plus (Perkin-Elmer) PCR amplification kits, are also presented. Except for the FGA and VWA data on immigrant Central West African populations in Spain, no deviations from the Hardy-Weinberg equilibrium were detected.

  19. Diversity of nuclear short tandem repeat loci in representative sample of North-eastern Bosnian and Herzegovina population

    Directory of Open Access Journals (Sweden)

    Hadžiavdić Vesna


    Full Text Available Diversity of nuclear microsatellite markers were analyzed in a reference sample of the population of northeast Bosnia and Herzegovina. 437 samples taken from unrelated individuals were processed and three samples of paternity proof were shown. Detection effectiveness profile of the research, points to a valid choice of method of extraction, amplification and genotyping short tandem repeat (STR loci with PowerPlextm16 kit. Genetic analysis of allelic variants of the 15 STR loci PowerPlextm16 kit detected 17 samples determined as rare allelic variants or microvariants. Samples were divided into 15 different allelic variants at 7 different loci, and are: in locus D7S820, D16S539, D3S1358, D18S51, PENTA D, PENTA E and in locus vWA. Genetic analysis of mutations in cases of paternity determined three examples of single-step mutations in the loci FGA, Penta D and D3S1358. Genetic analysis of observed STR loci detected three allelic variant of genotype combination 7/10/11.3 in locus D7S820 Type II. Population genetic analysis of STR loci in a representative sample of the population of northeast Bosnia and Herzegovina included the application of the assessment tests of within-population genetic diversity and interpopulation diversity, as well as genetic differentiation between populations: North-eastern Bosnia and Herzegovina (BH and BH general reference, then the Croatian population, Macedonian, Serbian and Slovenian. Based on the result analysis of specific forensic parameters, it can be assumed that the most informative marker is PENTA E for population genetic analysis and forensic testing in the population of northeast Bosnia and Herzegovina. Research results fit regional STR database of this part of Europe.

  20. [Mono- and dizygotic twins in forensic paternity testing in practice at the Department of Forensic Medicine (Silesian Academy of Medicine, Katowice) in the years 1996-2003]. (United States)

    Raczek, Ewa


    Giving an opinion on disputable paternity, concerning monozygotic twins in practice at the Department of Forensic Medicine (Silesian Academy of Medicine, Katowice) demonstrated their ideal agreement according to examined genetic markers possible. Even the mutation, which was revealed using the RFLP-VNTR method was the same for both twin sisters. In the case of dizygotic twins a firm differentiation of paternity index and probability of paternity was proved. This was the consequence of independent features segregation in first, reductive meiotic division. While the rare, out-ladder allele 16 at the CSF1PO locus was transmitted to both twins: a daughter and a son by the putative father.

  1. Comparison of allele frequencies of eight STR loci from Argentinian Amerindian and European populations. (United States)

    Sala, A; Penacino, G; Corach, D


    Eight STR systems (THO1, FABP, VWA, FES/FPS, HPRTB, F13A1, CSF1PO, and D6S366) were investigated in different ethnic groups of Argentina. Allele and genotype frequencies, power of exclusion, and discriminative power were investigated. Hardy-Weinberg expectations were calculated from heterozygosity levels. FST and G tests demonstrated that significant differences exist among the investigated populations for some of the eight STRs markers. The Wichi Indians are clearly separated from the Mapuche and Tehuelche, who in turn are closer to the European population, suggesting non-Amerindian admixture.

  2. Polymorphisms of 15 short tandem repeat loci in Mongolian nationality of Gansu province%甘肃蒙古族人群15个短串联重复序列基因座遗传多态性

    Institute of Scientific and Technical Information of China (English)

    范瑾; 任甫


    目的:调查甘肃蒙古族人群无关个体的15个短串联重复序列(STR)基因座(D8S1179,D21S11,D7S820,CSF1P0,D3S1358,D5S818,D13S317,D16S539,D2S1338,D19S433,vWA,D12S391,D18S51,D6S1043,FGA)的遗传多态性.方法:采用AmpFeSTR Sinofiler荧光标记复合扩增系统对198名甘肃肃北地区蒙古族个体血样DNA进行15个STR基因座的复合扩增,用3130 xl遗传分析仪对扩增产物进行检测.结果:15个STR基因座均符合Hardy-Weinberg平衡,杂合度在0.707 1~0.873 7之间,累积个人识别概率和累积非父排除率分别为0.999 999 3和0.999 999 997.结论:上述15个STR基因座在甘肃蒙古族人群中等位基因分布较好,个体识别率高,适合法医个体识别和亲子鉴定.%Objective: To investigate the polymorphism of 15 short tandem repeat (STR) loci (D8S1179, D21S11, D7S820, CSF1P0, D3S1358, D5S818, D13S317, D16S539, D2S1338, D19S433, vWA, D12S391, D18S51, D6S1043, FGA) in Mongolian nationality of Gansu province. Methods: The genotypes of 15 STR loci in Mongolian population of Gansu province were generated by multiplexing PCR using the Sinofiler PCR system and genotyping using ABI 3130 xl Genetic Analyzer. Results: All loci met Hardy-Weinberg equilibrium expectations. The heterozygosity of the 15 STR loci was between 0. 707 1 and 0. 873 7, cumulate PE was 0. 999 999 3, and cumulate DP was 0. 999 999 997. Conclusion: The genetic polymorphisms of the 15 STR loci in Mongolian population of Gansu province are high. Present data suggest that the 15 loci of Sinofiler system can be applied as candidate markers of forensic individual identification and paternity testing.

  3. Genetic analysis of 3 tri-allelic variant cases in paternity identification.%STR基因座中检出三带型等位基因三例及遗传分析

    Institute of Scientific and Technical Information of China (English)

    韩莉莉; 潘棱; 沈晓丽; 林赛梅; 林立芳; 唐海燕; 胡洁


    目的 探讨亲子鉴定中三带型等位基因的特点.方法 对5000个个体利用Chelex法提取血液DNA,通过复合荧光扩增和毛细管电泳确定DNA-STR基因型,对于D21Sll三带型者进一步进行染色体核型分析.结果 4个个体STR基因座出现三带型等位基因现象,1个在D3S1358基因座,2个在D13S317基因座,1个在D21S11基因座,而D21S11三带型基因者经染色体核型分析被确诊为21三体综合征.结论 三带型等位基因在STR基因座中极少出现,应用不同试剂盒加以验证,如怀疑三体综合征还应做染色体核型分析.%Objective To investigate the genetic features of three-banded alleles and overview. Methods Chelex method was used to extract DNA from 5 000 individuals, we determined DNA-STR genotype by multiplex fluorescent amplication and capillary electrophoresis, and karyotype analysis were used to test trisomy syndrome. Results 4 individuals were confirmed to have three-banded alleles, I in D3S1358 locus,2 in D13S317 locus, and 1 in D21S 11 locus which was diagnosed to be Down syndrome by karyotype analysis. Conclusion It is seldom to detect three-banded allele.Different amplication kit should be used to confirm three-banded allele, and karyotype analysis is recommended to diagnose trisomy syndrome.

  4. New CODIS core loci allele frequencies for 96,400 Brazilian individuals. (United States)

    Aguiar, Vitor R C; de Castro, Amanda M; Almeida, Vanessa C O; Malta, Frederico S V; Ferreira, Alessandro C S; Louro, Iúri D


    We have reported the allele frequencies of 15 STR loci, including the original 13 CODIS core loci, in over 100,000 Brazilian individuals. A new CODIS core loci has been proposed, but the recently established Brazilian Integrated Network of DNA Databases made a decision in 2010 to postpone the implementation of this new set of loci due to the lack of allele frequency data for the Brazilian population. We aimed to report allele frequencies of 20 loci, estimated from 96,400 Brazilian individuals undergoing paternity testing during 2011-2013. The percentage of missing data was less than 0.6% for all loci, except for CSF1PO (3.15%) and D7S820 (2.5%). The dropout rates estimated by the MicroDrop software were 0.013 for CSF1PO, 0.000037 for D7S820 and less than 0.000001 for other loci. Small missing data percentages and dropout rates reflect the high quality of the data.

  5. Optimization of short tandem repeats (STR) typing method and allele frequency of 8 STR markers in referring to forensic medicine of Semnan Province. (United States)

    Eskandarion, M; Najafi, M; Akbari Eidgahi, M; Alipour Tabrizi, A; Golmohamadi, T


    Background and Objective: Short Tandem Repeats (STR) show considerable differences among individuals in the population from which they used for identification. There are various methods for analysis of these STR loci, and capillary electrophoresis method already used as an international standard. Due to the high costs of this process, this study aimed to set up a Multiplex PCR method in some standard STR loci so that we can use its PCR product in STR analysis with different methods of HPLC, GC-Mass, and Capillary Electrophoresis. Materials and Methods: 8 typical STR loci in the identification selected according to their size in the two groups of four (CSF1PO, VWA, D18S51, PentaD and TPOX, Amelogenin, FGA, SE33) from NIST (National Institute of Standards and Technology). The above SSR primers prepared from Genbank and Monoplex PCR was designed based on their size. Then, with the changes in temperature conditions, magnesium ion, primers concentration, and setting-up, Hot Start Multiplex PCR of four markers was carried out. PCR product investigated on the agarose gel electrophoresis (3%) and the results of genotyping analyzed by Genetic Analyzer. Results: The Results showed that all STR loci under study are detectable as Monoplex PCR at a temperature of 62°-66° and 1.5 mM magnesium ion. Moreover, Multiplex PCR results showed that when the concentration of primer and temperature measured by the fixed concentration of magnesium, CSF1PO, and D18S51 loci bands are weaker than desired. Using a standard buffer and set Magnesium conditions against changes in the primer concentration and temperature, when Taq polymerase enzyme is added to test tubes at a temperature of 94°, Multiplex PCR bands are visible desirably. Capillary electrophoresis genotyping results obtained in all eight loci and the Locus FGA had the most allelic diversity and the loci TPOX and CSF1PO had the lowest allelic diversity. TPOX and CSF1PO loci had the lowest allelic frequencies, and FGA locus had

  6. Polymorphism Profile of Nine Short Tandem Repeat Loci in the Han Chinese

    Institute of Scientific and Technical Information of China (English)

    Shuangding Li; Chunxia Yan; Yajun Deng; Ruilin Wang; Jian Wang; Huanming Yang; Shengbin Li


    Nine short tandem repeat (STR) markers (D3S1358, VWA, FGA, THO1, TPOX,CSFIPO, D5S818, D13S317, and D7S820) and a sex-identification marker (Amel-ogenin locus) were amplified with multiplex PCR and were genotyped with afour-color fluorescence method in samples from 174 unrelated Han individuals inNorth China. The allele frequencies, genotype frequencies, heterozygosity, prob-ability of discrimination powers, probability of paternity exclusion and Hardy-Weinberg equilibrium expectations were determined. The results demonstratedthat the genotypes at all these STR loci in Han population conform to Hardy-Weinberg equilibrium expectations. The combined discrimination power (DP) was1.05 × 10-10 within nine STR loci analyzed and the probability of paternity exclusion(EPP) was 0.9998. The results indicate that these nine STR loci and the Amelo-genin locus are useful markers for human identification, paternity and maternitytesting and sex determination in forensic sciences.

  7. Validation of nine non-CODIS STR loci for forensic use in a population from Central Poland. (United States)

    Kuzniar, Piotr; Jastrzebska, Emilia; Ploski, Rafal


    The D7S1517, D3S1744, D12S391, D2S1360, D6S474, D8S1132, D5S2500, D10S2325 and D4S236613 are STR loci potentially useful for forensic purposes whose analysis has recently become facilitated by availability of a commercial kit. The purpose of the study was to evaluate the usefulness of these loci for forensic identification in a population of Central Poland. The distribution of alleles of the nine STRs was determined in sample of 353 unrelated individuals born in Central Poland and indices of forensic informativeness were calculated. The studied loci were highly informative and did not show departures from Hardy-Weinberg equilibrium. For the loci located on the same chromosomes (D2S1360, D3S1744 D4S2366, D5S2500, D7S1517, D8S1132, D12S391) as other loci commonly used for identification purposes (TPOX, D2S1338, D3S1358, FGA, D5S818, D7S820, D8S1179 and D12S391) appropriate pairwise analysis of linkage disequilibrium was performed. In all cases no statistically significant deviation from independence was found. We conclude that the studied STRs are informative and, when necessary, can be used to extend the results obtained with other STRs commonly analyzed for identification purposes, in particular the CODIS set.

  8. Analysis of the CODIS autosomal STR loci in four main Colombian regions. (United States)

    Paredes, Manuel; Galindo, Aida; Bernal, Margarita; Avila, Sandra; Andrade, Diana; Vergara, Carlos; Rincón, Magner; Romero, Rosa Elena; Navarrete, Mayda; Cárdenas, Martha; Ortega, Janeth; Suarez, Dayana; Cifuentes, Adriana; Salas, Antonio; Carracedo, Angel


    Genotype polymorphism studies at the 13 loci STRs included in the combined DNA index system [CODIS and PCR-based short tandem repeat loci, in: Proceedings of the Second European Symposium on Human Identification, Promega Corporation, Madison, WI, 1998, pp. 73-88; J. Forensic Sci. 46 (2001) 453] (CODIS: D3S1358, HUMvWA31, HUMFGA, D8S1179 D21S11, D18S51, D5S818, D13S317, D7S820, HUMTH01, HUMTPOX, HUMCSF1PO and D16S539) were carried out in a sample of 1429 unrelated Colombian individuals belonging to 25 different departments. As many other countries in Latino-America, Colombia shows an important admixture component, basically integrated by Amerindians, European-descendants and African-descendants. Due to the fact that only partial population analyses have been carried out in the country, the main aim of the present analysis is to establish a database of forensic interest based on the widely used CODIS systems covering the main Colombian regions.

  9. Identification and characterization of variant alleles at CODIS STR loci. (United States)

    Allor, Catherine; Einum, David D; Scarpetta, Marco


    Short tandem repeat (STR) profiles from 32,671 individuals generated by the ABI Profiler Plus and Cofiler systems were screened for variant alleles not represented within manufacturer-provided allelic ladders. A total of 85 distinct variants were identified at 12 of the 13 CODIS loci, most of which involve a truncated tetranucleotide repeat unit. Twelve novel alleles, identified at D3S1358, FGA, D18S51, D5S818, D7S820 and TPOX, were confirmed by nucleotide sequence analysis and include both insertions and deletions involving the repeat units themselves as well as DNA flanking the repeat regions. Population genetic data were collected for all variants and frequencies range from 0.0003 (many single observations) to 0.0042 (D7S820 '10.3' in North American Hispanics). In total, the variant alleles identified in this study are carried by 1.6% of the estimated 1 million individuals tested annually in the U.S. for the purposes of parentage resolution. A paternity case involving a recombination event of paternal origin is presented and demonstrates how variant alleles can significantly strengthen the genetic evidence in troublesome cases. In such instances, increased costs and turnaround time associated with additional testing may be eliminated.

  10. 多重置换扩增在含抑制物检材中的应用%Application of Multiple Displacement Amplification in Samples with Inhibitors

    Institute of Scientific and Technical Information of China (English)

    丁东雪; 丁梅


    目的:研究多重置换扩增(multiple displacement amplification,MDA)在含抑制物检材中的抗抑制能力,与磁珠法纯化检材相比较,证明其在法医学中的应用及意义。方法将不同浓度血红素和腐殖酸与样本DNA进行混合,分为MDA处理组、磁珠法处理组和空白对照组,PCR-STR单基因座D3S1358扩增联合聚丙烯酰胺凝胶电泳检测,并应用AmpFℓSTR®IdentifilerTM Plus试剂盒联合毛细管电泳检测。结果血红素质量浓度大于1 ng/μL或腐殖酸质量浓度大于0.1 ng/μL时,空白对照组经单基因座STR检测不能得到扩增产物;磁珠法处理组血红素质量浓度大于100 ng/μL或腐殖酸浓度大于1 ng/μL时,不能够得到扩增产物;MDA处理组各浓度抑制物均能成功扩增,完全不受抑制物影响。结论 MDA技术可消除血红素及腐殖酸的抑制作用,其抗抑制能力优于磁珠法纯化DNA,具有一定的法医学应用意义。%ObjectiveTo explore the ability of inhibition resistibility of multiple displacement amplification (MDA)in samples with inhibitors. To explain the application and value of MDA in forensic medicine by comparing with using magnetic beads methods(MBM)to purify sample.MethodsDifferent concentra-tions of hemoglobin and humid acid(HA)mixed with DNA samples and then divided the samples into MDA group, MBM group and control group.D3S1358locus was amplified and detected by polyacry-lamide gel electrophoresis detection system and AmpFℓSTR® IdentifilerTM Plus Kit-capillary electrophore-sis detection system.ResultsWhen hemoglobin concentrations exceed 1 ng/μL or HA concentrations ex-ceed 0.1 ng/μL, amplification products could not be obtained by single-locus system in control group. When hemoglobin concentration exceeds 100 ng/μL or HA concentrations exceed 1 ng/μL, the samples could not be amplified by MBM. Inhibitors in different concentrations were amplified successfully in MDA group without

  11. Genetic polymorphism of 15 STR loci in Qingdao Hah population%青岛地区汉族群体15个STR基因座的遗传多态性研究

    Institute of Scientific and Technical Information of China (English)

    张红岩; 万加华; 高自华; 戚其玮; 赵晶; 徐俐; 王雪倩


    Objective; To know the population genetic data of 15 short tandem repeat (STR) loci in Chinese Han population in the Qingdao aren Methods; 200 cases of ACD-blood specimens were collected form the unrelated individuals in Qingdao, The DNA samples were extracted with Chelex methed and amplified by multiplex PCR technique, The PCR produces and afterward genetyped were analyzed by an automatic genetic analyzer of ABI, Statistical analysis was carried out Matrix Laboratory Results; This study of IS loci of parameter on genetic polymorphisms were obtained. Conclusion; All of the IS loci have higher combined discrimination power and the exclusion probability, it can meet the needs of the parentage testing and personal identification in forensic medicine.%目的 了解15个短串联重复STR基因座在青岛地区汉族群体的遗传学数据.方法 对来自青岛地区汉族的200个无关个体的血样,Chelex法提取DNA,PCR复合扩增,采用ABI的全自动遗传分析仪进行基因分型,用Matlab编程进行统计学处理.结果 获得了D21S11,D7S820,D13S317,D19S433,D3S1358,D8S1179,CSF1P0,THO1,D16SS39,D2S1338,VWA,TPOX,D18S51,D5S818,FGA十五个STR基因座的遗传多态性参数.结论 15个STR基因座的累计个人识别率和非父排除率较高,适用于法医学亲子鉴定和个体识别

  12. A New Multiplex Assay of 17 Autosomal STRs and Amelogenin for Forensic Application (United States)

    Zhang, Suhua; Tian, Huaizhou; Wu, Jun; Zhao, Shumin; Li, Chengtao


    This paper describes a newly devised autosomal short tandem repeat (STR) multiplex polymerase chain reaction (PCR) systems for 17 autosomal loci (D1S1656, D2S441, D3S1358, D3S3045, D6S477, D7S3048, D8S1132, D10S1435, D10S1248, D11S2368, D13S325, D14S608, D15S659, D17S1290, D18S535, D19S253 and D22-GATA198B05) and Amelogenin. Primers for the loci were designed and optimized so that all of the amplicons were distributed from 50 base pairs (bp) to less than 500 bp within a five-dye chemistry design with the fifth dye reserved for the sizing standard. Strategies were developed to overcome challenges that encountered in creating the final assay. The limits of the multiplex were tested, resulting in the successful amplification of genomic DNA range from 0.25–4 ng with 30 PCR cycles. A total of 681 individuals from the Chinese Han population were studied and forensic genetic data were present. No significant deviations from Hardy–Weinberg equilibrium were observed. A total of 180 alleles were detected for the 17 autosomal STRs. The cumulative mean exclusion chance in duos (CMECD) was 0.999967, and cumulative mean exclusion chance in trios (CMECT) was 0.99999995. We conclude that the present 17plex autosomal STRs assay provides an additional powerful tool for forensic applications. PMID:23451235

  13. Genetic structure of the Azores Islands: a study using 15 autosomal short tandem repeat loci. (United States)

    Santos, Cristina; Alvarez, Luis; Aluja, Maria Pilar; Bruges-Armas, Jacome; Lima, Manuela


    The Azores archipelago (Portugal), located in the Atlantic Ocean, 1,500 km from the European mainland, is formed by nine islands of volcanic origin. The relative position of these islands allows the definition of three geographical groups: Eastern, Central and Western. Previous studies of the Azores using Short Tandem Repeats (STRs) have highlighted differences in the frequencies of several loci, when compared to Mainland Portugal or Madleira Island. Furthermore, linkage disequilibrium (LD), described for Azorean samples has been tentatively explained as reflecting the presence of genetic sub-structuring in the archipelago. To provide information concerning the genetic profile of the Azores Islands and to evaluate the presence of substructuring we have determined the allelic frequencies of 15 autosomal STR loci, using the AmpFlSTR Identifiler Kit, in representative samples from the Azorean Islands. Either considering the Azores as a whole, or analysing by island all the loci were in conformity with Hardy-Weinberg equilibrium. Average gene diversity ranged from 0.7669 in Corvo to 0.7972 in Terceira Island. Allelic independence between loci, tested for the global sample, detected significant LD (after correction for multiple tests) for pairs D21S11/D7S820 and D3S1358/D5S818. The exact test of population differentiation, combining the information of the 15 markers analysed, revealed significant differences between the three groups of islands, and between islands. Inter-island analysis reinforces the previous data that suggested the existence of sub-structuring in the Azores archipelago. Moreover, the data generated by this study can be used in a future forensic genetic database of the Azores after the appropriate enlacement of sample size by island, preventing, in that way, misinterpretations caused by population substructuring and small sample sizes.

  14. A new multiplex assay of 17 autosomal STRs and Amelogenin for forensic application.

    Directory of Open Access Journals (Sweden)

    Suhua Zhang

    Full Text Available This paper describes a newly devised autosomal short tandem repeat (STR multiplex polymerase chain reaction (PCR systems for 17 autosomal loci (D1S1656, D2S441, D3S1358, D3S3045, D6S477, D7S3048, D8S1132, D10S1435, D10S1248, D11S2368, D13S325, D14S608, D15S659, D17S1290, D18S535, D19S253 and D22-GATA198B05 and Amelogenin. Primers for the loci were designed and optimized so that all of the amplicons were distributed from 50 base pairs (bp to less than 500 bp within a five-dye chemistry design with the fifth dye reserved for the sizing standard. Strategies were developed to overcome challenges that encountered in creating the final assay. The limits of the multiplex were tested, resulting in the successful amplification of genomic DNA range from 0.25-4 ng with 30 PCR cycles. A total of 681 individuals from the Chinese Han population were studied and forensic genetic data were present. No significant deviations from Hardy-Weinberg equilibrium were observed. A total of 180 alleles were detected for the 17 autosomal STRs. The cumulative mean exclusion chance in duos (CMECD was 0.999967, and cumulative mean exclusion chance in trios (CMECT was 0.99999995. We conclude that the present 17plex autosomal STRs assay provides an additional powerful tool for forensic applications.

  15. 孕妇外周血浆胎儿DNA的STR检测

    Institute of Scientific and Technical Information of China (English)

    魏建波; 秦斐; 王伟; 俞禾涛


    目的探讨利用孕妇血浆中游离胎儿DNA进行遗传病产前基因诊断的可行性。方法用QIAamp DNA Kit抽提孕妇血浆DNA,应用AmpFl STR profiler试剂盒扩增9个(D3S1358,VWA,FGA,D5S818,D13S317,D7S820,D8S1179,D21S11,D18S51)具有高度多态性的短串联重复序列(short tandem repeat,STR)位点,以多重荧光PCR方法对不同孕期的36份孕妇血浆标本中DNA进行STR等位基因扩增,同时扩增孕妇丈夫外周血DNA。PCR产物经ABI Prism377序列分析仪电泳后,用基因扫描软件进行分析,以胎儿父源性STR等位基因在孕妇血浆中DNA的检出确认胎儿DNA存在。结果孕早期4份(4/6)、孕中期19份(19/20)、孕晚期9份(9/10)检出胎儿父源性等位基因,即胎儿DNA。4份样本未检到胎儿DNA。结论应用多重荧光PCR方法对孕妇血浆中DNA进行STR多态位点的复合扩增,可获得男性和女性胎儿DNA信息,可用于无创伤性产前诊断。

  16. Retrospective genetic study of germinative mutations in Str loci of individuals potentially exposed to ionizing radiation;Estudo genetico retrospectivo de mutacoes germinativas em Loci Str de individuos potencialmente expostos a radiacao ionizante

    Energy Technology Data Exchange (ETDEWEB)

    Costa, Emilia Oliveira Alves


    The Brazilian radiological accident that occurred in 1987, in Goiania, it was a terrible radiation episode. As a consequence, hundreds of people were contaminated due to the Cesium-137 radiation. Recently, many studies had shown that genome instabilities, such as, mutations, chromosomal aberrations, micronuclei formation and micro satellite instability and a delay on cellular death are usually reported on mammal cells exposed to ionizing radiation, being considered as a manly risk to humans. Mutations can be spontaneous, and the occurrence is dependent on the organism, or, induced, being associated to mutagenic exposition. Ionizing radiations are an example of physical and mutagenic agents that could harm the cell repair and could cause the development of many types of cancer. The evaluation of the biological effects of the ionizing radiation, in somatic and germ line cells, with a consequent determination of the radio-induced mutations, it is extremely important to estimate the genetic risks, manly in population exposed to radiation. The analyses of repetitive DNA sequences have been demonstrated that such sequences are prone to high rates of spontaneous mutations. The minisatellites and microsatellites have been used to demonstrate the induction of germ line mutation rates on mouse, humans, among others organisms. The aim of the present study was to analyze the frequency of microsatellite alterations to determine the mutation rates occurred in germ cells of the parents exposed to the ionizing radiation of the Cesium-137. The studied group was constitute of 10 families of individuals accidentally exposed to Cesium-137 and by the control group constituted by 645 healthy individuals who carried out paternity tests on 2009. We found only one mutation of paternal origin in the D8S1179 locus on the exposed group, being the mutation rate of 0.002. In the control group, we found 01 mutation on D16S539 loei and on D3S1358; 02 mutations on Penta E loeus; 04 mutations on D

  17. 13个STR基因座在亲子鉴定案例中的基因突变观察%Mutations observed at 13 CODIS STR loci in cases of paternity testing

    Institute of Scientific and Technical Information of China (English)

    邓志辉; 吴国光; 程良红; 魏天莉; 苏宇清; 郝桂琴


    目的 观察美国CODIS系统的13个STR基因座在532例认定亲子关系的亲子鉴定案中的基因突变情况,探讨STR基因座突变率及突变类型。方法 经“Profilg Plus"及“Cofilex”试剂盒检测的587例亲子鉴定案,对其中有1~2个STR基因座不符合遗传规律者,增加HLA等血型基因和“PowerPlex16~(TM)”试剂盒检测。必要时,还增加Y-STR基因座检测和HLA等位基因测序。结果 认定亲子关系的532例,观察1052次减数分裂,发现17例亲子鉴定中的18次基因突变事件,其中16例1个STR基因座的基因发生突变,1例2个STR基因座的基因发生突变;突变的基因座包括D5S818、D3S1358、D16S539、CSFIPO、D21S11、D13917、D7S820、vWA、D18S51和FGA,其中以FGA和D18S51基因座的突变率最高(0.29%);18次突变事件,其中来自父亲11次,来自母亲5次,无法确定2次。结论 用美国CODIS系统的STR基因座进行亲子鉴定,在有1~2个基因座不符合遗传规律时,要综合分析,并增加其它的遗传标记进行检测。

  18. Automated analysis of sequence polymorphism in STR alleles by PCR and direct electrospray ionization mass spectrometry. (United States)

    Planz, John V; Sannes-Lowery, Kristen A; Duncan, David D; Manalili, Sheri; Budowle, Bruce; Chakraborty, Ranajit; Hofstadler, Steven A; Hall, Thomas A


    Short tandem repeats (STRs) are the primary genetic markers used for the analysis of biological samples in forensic and human identity testing. The discrimination power of a combination of STRs is sufficient in many human identity testing comparisons unless the evidence is substantially compromised and/or there are insufficient relatives or a potential mutation may have arisen in kinship analyses. An automated STR assay system that is based on electrospray ionization mass spectrometry (ESI-MS) has been developed that can increase the discrimination power of some of the CODIS core STR loci and thus provide more information in typical and challenged samples and cases. Data from the ESI-MS STR system is fully backwards compatible with existing STR typing results generated by capillary electrophoresis. In contrast, however, the ESI-MS analytical system also reveals nucleotide polymorphisms residing within the STR alleles. The presence of these polymorphisms expands the number of alleles at a locus. Population studies were performed on the 13 core CODIS STR loci from African Americans, Caucasians and Hispanics capturing both the length of the allele, as well as nucleotide variations contained within repeat motifs or flanking regions. Such additional polymorphisms were identified in 11 of the 13 loci examined whereby several nominal length alleles were subdivided. A substantial increase in heterozygosity was observed, with close to or greater than 5% of samples analyzed being heterozygous with equal-length alleles in at least one of five of the core CODIS loci. This additional polymorphism increases discrimination power significantly, whereby the seven most polymorphic STR loci have a discrimination power equivalent to the 10 most discriminating of the CODIS core loci. An analysis of substructure among the three population groups revealed a higher θ than would be observed compared with using alleles designated by nominal length, i.e., repeats solely. Two loci, D3S1358

  19. Evaluation of incest cases of Turkey in terms of DNA profiling difficulties. (United States)

    Emre, Ramazan; Canturk, Kemal Murat; Komur, Ilhami; Dogan, Muhammed; Demirel, Husrev; Baspınar, Bunyamin


    We scanned suspicious 1200 paternity cases and 650 sexual abuse victims in Council of Forensic Medicine of Turkey between 2011 and 2014 and detected 50 incest cases and evaluated the forensic and genetic data of incest cases for source of DNA evidence, gender, age, SES (Socioeconomic status) and geographic location of victim, abusive person, extent of incest, pregnancy from incest and date of gestation termination and also aimed to discuss some DNA profiling difficulties. We detected incest from DNA evidences of curettage material (34%; Chorionic Villi (12%) and fetal tissue (22%)), alive baby after pregnancy (28%), sperm in vaginal swab (10%), sperm in anal swab (2%), sperm on clothing (24%) and in one case both sperm on clothing and in vaginal swab (2%). It was found that the most common incestuous relationship was elder-brother-sister incest (34%) and the second most common relationship was father-daughter incest (28%). The rarest incest was mother-son incest with only one reported case (2%). Forty-three victims (86%) were younger than 18 years old and 7 victims (14%) were older than 18 years old. Thirty-eight cases described full sexual intercourse and 31 of them culminated in pregnancy and 14 of them gave birth at the end of pregnancy. We had paternity rejection problem 3 (10%) of 31 incest cases between tested genetically related alleged fathers. Totally 20 STR loci did not discriminate the alleged fathers in two cases and we treated this problem increasing the number of STR loci and finally got the discrimination. In one case we detected same triallelic variant pattern at the same D3S1358 STR locus in both tested parents but child had not got STR variant; had only two alleles at this loci. We then evaluated the peak height values of STR variant alleles of tested persons and concluded a tetra-allelic baby without any STR incompatibility of 15 STR loci. Finally, forensic experts should aware of some DNA profiling difficulties while analyzing paternity incest

  20. Evaluation of reliability on STR typing at leukemic patients used for forensic purposes. (United States)

    Filoglu, G; Bulbul, O; Rayimoglu, G; Yediay, F E; Zorlu, T; Ongoren, S; Altuncul, H


    Over the past decades, main advances in the field of molecular biology, coupled with benefits in genomic technologies, have led to detailed molecular investigations in the genetic diversity generated by researchers. Short tandem repeat (STR) loci are polymorphic loci found throughout all eukaryotic genome. DNA profiling identification, parental testing and kinship analysis by analysis of STR loci have been widely used in forensic sciences since 1993. Malignant tissues may sometimes be the source of biological material for forensic analysis, including identification of individuals or paternity testing. There are a number of studies on microsatellite instability in different types of tumors by comparing the STR profiles of malignant and healthy tissues on the same individuals. Defects in DNA repair pathways (non-repair or mis-repair) and metabolism lead to an accumulation of microsatellite alterations in genomic DNA of various cancer types that result genomic instabilities on forensic analyses. Common forms of genomic instability are loss of heterozygosity (LOH) and microsatellite instability (MSI). In this study, the applicability of autosomal STR markers, which are routinely used in forensic analysis, were investigated in order to detect genotypes in blood samples collected from leukemic patients to estimate the reliability of the results when malignant tissues are used as a source of forensic individual identification. Specimens were collected from 90 acute and 10 chronic leukemia volunteers with oral swabs as well as their paired peripheral blood samples from the Oncology Centre of the Department of Hematology at Istanbul University, during the years 2010-2011. Specimens were tested and compared with 16 somatic STR loci (CSFIPO, THO1, TPOX, vWA, D2S1338, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D19S433, D21S11 and FGA) widely used in forensic identification and kinship. Only two STR instabilities were encountered among 100 specimens. An MSI in

  1. Distribution of polymorphisms IL4-590 C/T and IL4 RP2 in the human populations of Madeira, Azores, Portugal, Cape Verde and Guinea-Bissau. (United States)

    Berenguer, Anabela G; Câmara, Rita A; Brehm, António D; Oliveira, Susana; Fernandes, Ana T


    The IL4 gene is located on chromosome 5q23.3-31.2. Polymorphisms within this cytokine gene, like the derivative allele T of IL4-590, have been reported as being associated to elevated IgE serum levels and asthma. In the present work, the allelic and genotypic frequency of the IL4-590 and IL4 RP2 polymorphisms was carried out in 599 individuals from Madeira, Azores, Portugal mainland, Cape Verde and Guinea-Bissau and in a sample of 101 asthmatics from Madeira population. In all populations the polymorphisms were in LD and presented a significant dissimilar allelic and genotypic distribution (pMadeira when compared to Azores. Significant differences regarding both loci were found between Madeira population and the group of asthmatics. Genotype 183183TT frequency is higher for African populations while 253253CC prevails in Caucasian populations. The existence of a Hardy-Weinberg Disequilibrium in Guinea-Bissau population not observed in neutral markers leads to the hypothesis of natural selection occurring in these loci probably associated to a rapid population growth an hypothesis strengthened by neutral STRs D5S818 and CSF1PO gene diversity.

  2. A Simple, Inexpensive and Safe Method for DNA Extraction of Frigid and Clotted Blood Samples

    Directory of Open Access Journals (Sweden)

    Nasrin Mohammadi


    Full Text Available Background: Extraction of blood genomicDNAis one of the main approaches for clinical and molecular biology studies. Although several methods have been developed for extraction of blood genomic DNA, most of these methods consume long time and use expensive chemicals such as proteinase K and toxic organic solvent such as phenol and chloroform. The objective of this study was to developed easy and safe method forDNAextraction from clotted and frozen whole blood. This method has many advantages: time reducing, using inexpensive materials, without phenol and chloroform, achieving of high molecular weight and good quality genomicDNA.Materials and Methods: DNA extraction was performed by two methods (new and phenol-chloroform method. Then quantity and quality parameters were evaluated by 1% agarose gel electrophoresis, Nano drop analysis and efficiency of Polymerase Chain Reaction (PCR.Results: Extracted DNA from 500μL of blood samples were 457.7ng/μl and 212ng/μL and their purity (OD260/OD280 were 1.8 and 1.81 for new recommended and phenol–chloroform methods respectively. The PCR results indicated that D16S539 and CSF1PO loci were amplified.Conclusion: These results shown that this method is simple, fast, safe and most economical.

  3. Reference database of hypervariable genetic markers of Argentina: application for molecular anthropology and forensic casework. (United States)

    Sala, A; Penacino, G; Carnese, R; Corach, D


    The population of Argentina is mostly composed of people of European ancestry. Aboriginal communities are at present very reduced in number and restricted to small geographically isolated patches. Three aboriginal communities, the Mapuche, Tehuelche and Wichi, were selected for short tandem repeat (STR) investigation. The metropolitan population of the city of Buenos Aires was analyzed, with both micro- and minisatellites. The minisatellite loci D1S7, D2S44, D4S139, D5S110, D8S358, D10S28, and D17S26 were typed on HaeIII-digested DNA obtained from unrelated individuals. D1S80 was typed by polymerase chain reaction (PCR). The autosomal STRs THO1, FABP, D6S366, CSF1PO, TPOX, F13A1, FES/FPS, vWA, MBPA/B, D16S539, D7S820, D13S317, and RENA4 and the sex chromosome STRs HPRTB, DYS385, DYS3891, DYS38911, DYS19, DYS390, DYS391, DYS392, DYS393 and YCAII were also investigated. As a by-product of our investigations, a reference database was created that is routinely used in forensic casework and paternity testing. STR allele frequency distributions are characterized by significant differences within and also between different populations. In contrast, the minisatellite bin distribution of the metropolitan population is not significantly different from other Caucasian populations.

  4. Automation and integration of polymerase chain reaction with capillary electrophoresis for high throughput genotyping and disease diagnosis

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, N.


    Genotyping is to detect specific loci in the human genome. These loci provide important information for forensic testing, construction of genetic linkage maps, gene related disease diagnosis and pharmacogenetic research. Genotyping is becoming more and more popular after these loci can be easily amplified by polymerase chain reaction (PCR). Capillary electrophoresis has its unique advantages for DNA analysis due to its fast heat dissipation and ease of automation. Four projects are described in which genotyping is performed by capillary electrophoresis emphasizing different aspects. First, the author demonstrates a principle to determine the genotype based on capillary electrophoresis system. VNTR polymorphism in the human D1S80 locus was studied. Second, the separation of four short tandem repeat (STR) loci vWF, THO1, TPOX and CSF1PO (CTTv) by using poly(ethylene oxide) (PEO) was studied in achieving high resolution and preventing rehybridization of the DNA fragments. Separation under denaturing, non-denaturing conditions and at elevated temperature was discussed. Third, a 250 {micro}m i.d., 365 {micro}m o.d. fused silica capillary was used as the microreactor for PCR. Fourth, direct PCR from blood was studied to simplify the sample preparation for genotyping to minimum.

  5. Genetic characteristics of Sasang typology: a systematic review. (United States)

    Sohn, Kyungwoo; Jeong, Ansuk; Yoon, Miyoung; Lee, Sunkyung; Hwang, Sangmoon; Chae, Han


    A systematic review on studies related to the genetic characteristics of Sasang types was conducted with the goal of delineating genetic characteristics of Sasang typology. Six electronic databases of up to the March 2011 were examined with the key words of Sasang typology, constitution, and genetics in both Korean and English. Predefined review criteria were used, including demographic characteristics, type classification methods, genotyping methods, and genotypes. Fifty-nine potentially relevant studies were identified and 40 peer reviewed research articles that contained genetic data were included. Fourteen articles reported statistically significant differences among Sasang types, which are heritability, structural variation, genome-wide screening, and pathophysiological function. Although significant genotypes were reported with vWA, CSF1PO, Penta D, HLA-Cw*04, HLA-Cw*07, PPAR-γ, MDR1, IL-α, IL-β, and IL-6 receptor, results of the review indicate that there was no conclusive genotype related to the Sasang typology. Considering the features of Sasang typology, it is recommended that the macroscopic systems medical approach on genetics be employed, rather than the single genes association approach.

  6. Polymorphism and genetic relationship of 15 STR loci in Wa and Bulang populations in Shuangjiang County, Yunnan Province%云南双江佤族、布朗族15个STR基因座遗传多态性及遗传关系分析

    Institute of Scientific and Technical Information of China (English)

    刘建兴; 李利华; 景强; 胡利平; 聂胜洁; 姜良豹; 许冰莹


    Objective To investigate genetic polymorphisms in Wa and Bulang populations in Shuangjiang County,Yunnan Province, and to evaluate their forensic application values and genetic relationships among other populations.Methods Fifteen STR loci included in the Power PLex 16 system Kit were amplified. The PCR products were analyzed by ABI Prism 3100 Genetic Analyzer. Forensic parameters of the two minorities were obtained, and genetic distances between Wa, Bulang and other populations were calculated by STR loci included in the CODIS system. Results In Wa and Bulang populations, the 15 STR loci were polymorphic. In genetic distance analysis, the distance between Wa and Bulang was the nearest (0.011 0). The other distances were as follows: 0. 030 2, between Wa and Buryat;0.024 3, between Wa and Ewenke; 0. 034 3, between Bulang and Buryat; and 0.030 9, between Bulang and Ewenke.The genetic distances of Wa and Bulang with Hah populations were both near. The distance was 0.014 0 between Wa and Han populations in Zhengjiang Province, and 0.0124 between Bulang and Han populations in Anhui Province.Conclusions The 15 STR loci were polymorphic in Wa and Bulang, which could provide a powerful discrimination tool for forensic applications. The investigations of genetic distances between different populations are useful to study their origins ,migrations and genetic relationships.%目的 检测云南双江县佤族、布朗族15个STR基因座遗传多态性及与其他群体的遗传关系.方法 以Power PLex 16 system Kit复合扩增15个STR基因座(D3S1358、THO1、D21S11、D18S51、Penta E、D5S818、D13S317、D7S820、D16S539、CSF1PO、Penta D、VWA、D8S1179、TPOX、FGA),用ABI PRISM 310遗传分析仪检测扩增产物,计算群体等位基因频率等法医学参数,并结合文献发表的国内其他群体的遗传学资料,运用CODIS系统13个基因座计算群体间的遗传距离.结果 15个STR基因座在佤族、布朗族中均具有较高的遗传多态性,

  7. 3种国产化试剂盒与IdentifilerTM试剂盒检验结果比较%A comparative study on the typing difference between the IdentifilerTM kit and three domestic genotyping kits

    Institute of Scientific and Technical Information of China (English)

    吴微微; 郝宏蕾; 林锦锋; 应晓兰; 苏艳佳; 金敏贵


    目的 比较3种常用国产化PCR扩增试剂盒与IdentifilerTM试剂盒的检验结果.方法 对455份中国汉族无关个体血样,分别用IdentifilerTM、DNA TyperTM15、GoldenEye 16BT、AGCU 17+1 4种试剂盒进行检测,对其中共有的11个基因座位分型结果进行比较,并对有差异的样本进行测序分析.结果 3种国产化试剂盒在455份样本中,发现4例样本的分型结果有差异,差异率为0.88%.其中,DNA TyperTM15试剂盒CSF1PO基因座发现1例等位基因丢失,AGCU 17+1试剂盒D18S51基因座发现1例等位基因扩增不平衡,测序结果表明,2例均系点突变导致;GoldenEye16BT试剂盒D21S11基因座发现2例假3峰型,其中1例测序未发现碱基突变,分析3峰原因可能是stutter滑脱峰所致.结论 与IdentifilerTM试剂盒比较,3种国产化试剂盒均有分型差异现象,成因不同,在实践中应给予注意.%Objective To study the difference of DNA testing results between the IdentifilerTM kit and three domestic genotyping kits. Methods 455 unrelated individuals of Han population in China were typed using the ldentifilerTM, DNA TyperTM 15, GoldenEye 16BT and AGCU17 + 1 kits respectively. The genotypes were compared at 11 mutual loci among these four kits, and those samples with inconsistent genotypes were further analyzed by sequencing. Results Total 4 samples were observed to have inconsistent genotypes in all 455 individuals with three domestic genotyping kits, and the frequency was 0.88%. For these four samples, one allele dropout, one amplification imbalance, and two false tri-peak were observed at CSF1PO locus with the TyperTMl5 kit, D18S51 locus with the AGCU17 + 1 kit and D21S 11 locus with the 16BT kit correspondingly. The results of sequence analysis showed that all of these differences were caused by point mutation except a false tri-peak sample was caused by replication slippage. Conclusion Compared with the IdentifilerTM kit, occasional genotyping differences could

  8. Determination of suitable pollinizers for some selected local persimmon (Diospyros kaki L. types

    Directory of Open Access Journals (Sweden)

    Fatma Seren SAĞIR


    Full Text Available Selection of suitable pollinizers is very important for persimmon that have a widespread problem in fruit setting. This study aims to contribute for solving this problem. Study was carried out in 2010 vegetation period with 17 years old persimmon trees in Adana conditions. For this purpose, the suitability of Bruniquel and Ghora Gali pollinizer cultivars were searched for 9 local persimmon types (07TH05, 07TH06, 07TH13, 07TH14, 07TH17, 31TH01, 31TH02, 31TH03 and 33TH01. In laboratory tests of pollen viability, germination and quantity, it was determined that the potential of Ghora Gali and Bruniquel is satisfactory for a pollinizer. With controlled-pollination treatments, fruit drop was reduced compared with open pollination and non-pollination treatments. In terms of this, the best pollinator for 07TH14 and 33TH01 was Bruniquel and for 07TH06 and 07TH17 it was Ghora Gali. Both Bruniquel and Ghora Gali became suitable pollinators for 07TH05. In 07TH13, 31TH02 and 31TH03 genotypes, the best results were obtained from open pollination treatments. At the same time, 07TH14 and 33TH01 genotypes have high affinity to parthenocarpy because of their fruit set ability while there is not any pollinizer.

  9. Identifikasi bite marks dengan ekstraksi DNA metode Chelex (Bite marks identification with Chelex methods in DNA extraction

    Directory of Open Access Journals (Sweden)

    Imelda Kristina Sutrisno


    Full Text Available Background: In the case of crime often encountered evidence in bite marks form that was found on the victim’s body. Generally, bitemarks identification use standard techniques that compare the interpretation picture with the tooth model of suspected person. However, sometimes the techniques do not obtain accurate results. Therefore another technique is needed to support the identification process,such as DNA analysis that use the remaining epithelium attached in saliva to identify the DNA of the suspected person. In this processes a limited DNA material could be met, not only less in quantity but also less in quality. Chelex known as one of an effective DNA extraction method in DNA forensic case is needed to overcome this problem. Purpose: The study was aimed to examine the use of Chelex as DNA extraction method on a bitemarks sample models. Methods: The blood and bitemarks of 5 persons with were taken. The DNA of each subject was exctracted with Chelex and quantified the quantity with UV Spechtrophotometer. The DNA results was amplified by PCR at locus vWA and TH01 then vizualised by electrophoresis. Results: The electrophoresis’s results showed band at locus vWA and TH01 for blood sample and bite marks with no significant differences. Conclusion: The study showed that Chelex method could be use to extract DNA from bitemarks.Latar belakang: Dalam kasus kejahatan sering dijumpai bukti dalam bentuk bekas gigitan (bitemarks yang ditemukan pada tubuh korban. Umumnya, untuk mengidentifikasi bite marks menggunakan teknik standar yaitu membandingkan foto interpretasi dengan model gigi dari orang yang dicurigai. Namun demikian teknik ini terkadang tidak mendapatkan hasil yang akurat, sehingga diperlukan teknik lain untuk menunjang keberhasilan proses identifikasi pelaku, yakni melalui analisis DNA bitemarks, yang diperoleh dari saliva yang mengandung sisa epitel tersangka pelaku. Sampel DNA yang berasal dari bitemarks umumnya terbatas, tidak hanya

  10. Detection and quantitative characterization of artificial extra peaks following polymerase chain reaction amplification of 14 short tandem repeat systems used in forensic investigations

    DEFF Research Database (Denmark)

    Meldgaard, Michael; Morling, N


    Detection on automated DNA sequencers of polymerase chain reaction (PCR) products of tetra- and penta-nucleotide short tandem repeat (STR) loci frequently reveals one or more extra peaks along with the true, major allele peak. The most frequent extra peak pattern is a single smaller peak which......, while Hum-TH01, HumCD4, and D12S391 were virtually unaffected by low-stringency conditions. Replacement of the Taq DNA polymerase with DNA polymerases with lower processivity resulted in higher levels of extra peaks. Our results support the hypothesis that extra peaks are produced due to slipped...

  11. A report of the 1995 and 1996 Paternity Testing Workshops of the English Speaking Working Group of the International Society for Forensic Haemogenetics

    DEFF Research Database (Denmark)

    Bjerre, A; Syndercombe-Court, Denise; Lincoln, P


    We report the results of the 1995 and 1996 Paternity Testing Workshops of the English Speaking Working Group of the International Society for Forensic Haemogenetics. In 1995, 18 laboratories participated and in 1996, 21 laboratories participated. Each year, blood samples from three persons (child...... for investigations in crime cases by the European DNA Profiling Group. In 1996, eight laboratories reported the results of PCR based typing of the short tandem repeat (STR) locus HumTH01, six laboratories reported results of HumVWA31A typing, and five laboratories reported the results of typing of the STR locus Hum...

  12. A new pentaplex PCR system for forensic casework analysis. (United States)

    Lederer, T; Seidl, S; Graham, B; Betz, P


    In 1998 the Federal Criminal Police Office of Germany (BKA) established a central genetic database of offenders and suspects to facilitate comparisons with biological samples from future criminal offences. The five obligatory short tandem repeat (STR) loci in this database (TH01, SE33, vWA, FGA and D21S11) were co-amplified in a new PCR pentaplex analysing system together with the sex-specific locus amelogenin. Due to overlapping fragment sizes, amplification products were fluorescent dye-labelled with different colours, separated by electrophoresis and detected directly using the ABI PRISM 310 Genetic Analyzer. Reproducible and reliable results were obtained from as low as 125 pg template DNA, indicating high specificity and sensitivity of the assay. Environmental studies and enzymatic digest with DNase I revealed an excellent stability of the pentaplex system with typeable results even in cases of partially degraded DNA. Complete and reproducible DNA typing was possible in blood-stain mixtures with the minor component as low as 10%. Mean stutter peak intensities were analysed for all loci and ranged from 2.7 +/- 0.8% (TH01) to 10.6 +/- 1.6% (vWA) of the main signal intensity. Allele frequencies were determined in a North Bavarian population sample (n = 121). The combination of five systems resulted in a mean exclusion chance of 99.86% and a power of discrimination of 99.999996%. No deviation from Hardy-Weinberg equilibrium could be found.

  13. Statistical modelling of Ion PGM HID STR 10-plex MPS Data

    DEFF Research Database (Denmark)

    Vilsen, Søren B; Tvedebrink, Torben; Mogensen, Helle Smidt


    We investigated the results of short tandem repeat (STR) markers of dilution series experiments and reference profiles generated using the Ion PGM massively parallel sequencing platform utilising the HID STR 10-plex panel. The STR markers were identified by the marker specific flanking regions...... of the STR region. We investigated the following: (1) the usage of quality measures for identifying substitution errors, (2) the heterozygote balance and compared it to that of capillary electrophoresis (CE), (3) the stability of the coverage and the consequence of IonExpress Barcode adapter (IBA) sampling...... of stutter ratio than the parental allele repeat length, when markers with compound and complex repeat patterns or markers which contained micro-variants were considered, such as marker TH01 showed R(2) of 0.02 and 0.78 for parent allele repeat length and LUS, respectively. The one-inflated negative binomial...

  14. Avaliação do transplante de medula óssea alogênico por meio do estudo de regiões de repetições seqüenciais no genoma humano (VNTRs e STRs Evaluation of allogeneic bone marrow transplantation by analysis of repeated sequences in the human genome (VNTRs and STRs

    Directory of Open Access Journals (Sweden)

    Rita K. Santana


    Full Text Available Os objetivos deste estudo foram estabelecer um protocolo para a análise de minissatélites ou VNTRs e microssatélites ou STRs em pacientes que se submeteram ao TMO alogênico; verificar a validade da metodologia e dos loci estudados e avaliar o tipo de recuperação do paciente. Foram analisados o DNA do paciente anterior e posterior ao transplante de 14 indivíduos e dos respectivos doadores. Amplificações por PCR de seis loci: D1S80, SE33, HumTH01, 33.6, HumARA e HumTPO foram realizadas. Os produtos amplificados foram separados por eletro­forese vertical em gel de poliacrilamida, e os fragmentos visualizados por coloração pela prata. Esse procedimento mostrou ser válido na verificação da recuperação alogênica, autóloga e provavelmente na quimérica. Da somatória dos loci estudados, 63,1% apresentaram resultados possíveis de serem avaliados e, desses, 19,0% mostraram resultado informativo, 13,1% parcialmente informativo e 31,0% não informativo. Os 36,9% restantes não foram possíveis de avaliação. Dos loci avaliados, o que demostrou maior índice de resultado informativo foi o SE33, parcialmente informativo o HumTPO e não informativo o HumTH01, sendo o locus 33.6 o que mais apresentou resultados não possíveis de serem avaliados. Por outro lado, determinou-se a recuperação do paciente posterior ao transplante em 71,4% dos indivíduos, sendo que, desses, 90% apresentaram recuperação alogênica e 10% recuperação autóloga.The purposes of this study were to establish a protocol for the analysis of minisatellites or VNTRs and microsatellites or STRs in patients who undergo allogeneic bone marrow transplantation; to verify the validity of the methodology and of the studied loci and to verify the type of recovery of the patient. The pre-transplant and post-transplant DNA of 14 recipients and their respective donors were analyzed. Six loci were amplified by PCR (D1S80, SE33, HumTH01, 33.6, HumARA and HumTPO. The amplified

  15. Efficacy of DNA typing as an accurate method in forensic medicine

    Directory of Open Access Journals (Sweden)

    Namazi H


    Full Text Available DNA typing is a new method with important applications in forensic medicine. In the present study, we evaluated application of DNA typing in Iran. Loci Hum LPL, Hum Tpox, Hum F13, Hum vw 31A, Hum TH01 and Hum FES/FPS of DNA short tandem repeats were studied. To determine sensitivity of the test, 85 mother-child couples (1020 chromosomes that were referred to DNA section of legal medicine organization of Iran were included and for determination of it's specificity 42 brother-sister couples (1200 chromosomes and 58 non-relative couples were examined. The results show lack of mutations in the studied loci and acceptable sensitivity of the test. Of 12 alleles of siblings, there were 2-6 differences, in contrast with 3-9 differences in non-relatives, so the test has 100% specificity in these loci. Considering polymorphism, power of exclusion of these 6 sites was 99%.

  16. Population genetic analysis of the GlobalFiler STR loci in 748 individuals from the Kazakh population of Xinjiang in northwest China. (United States)

    Zhang, Honghua; Yang, Shuping; Guo, Wei; Ren, Bo; Pu, Liwen; Ma, Teng; Xia, Mingying; Jin, Li; Li, Liming; Li, Shilin


    The six-dye GlobalFiler™ Express PCR amplification kit incorporates 21 commonly used autosomal short tandem repeat (STR) loci and three gender determination loci. In this study, we analyzed the GlobalFiler STR loci on 748 unrelated individuals from a Chinese Kazakh population of Xinjiang, China. No significant deviations from Hardy-Weinberg equilibrium and linkage disequilibrium were observed within and between 21 autosomal STR loci. SE33 showed the greatest power of discrimination in Kazakh population. The combined power of discrimination of Kazakh was 99.999999999999999999999996797 %. No significant differences of allele frequencies were observed between Kazakh and Uyghur at all 15 tested STR loci, as well as Mongolian. Significant differences were only observed between Kazakh and the other Chinese populations at TH01. Multiple STR loci showed significant differences between Kazakh and Arab, as well as South Portuguese. The multidimensional scaling plot (MDS) plot and neighbor-joining tree also showed Kazakh is genetically close to Uyghur.

  17. DNA typing from cigarette butts. (United States)

    Watanabe, Yoshihisa; Takayama, Tomohiro; Hirata, Keiji; Yamada, Sadao; Nagai, Atsushi; Nakamura, Isao; Bunai, Yasuo; Ohya, Isao


    We performed DNA typing for D1S80, HLADQA1, TH01 and PM using the butts of 100 cigarettes that were smoked by ten different individuals (ten cigarettes per individual). The results obtained from DNA typing for D1S80 agreed with the results obtained using bloodstains in 76 cigarette butt samples. Sixteen samples produced false results, showing the loss of the longer allelic hetero-band. When examined using agarose gel electrophoresis, high-molecular weight DNA was not observed in these samples. The same results were also observed for buccal swab samples and saliva stains obtained from the same individuals. In the remaining eight cigarette butt samples, PCR products were not detected. The results obtained from DNA typing for TH01, HLADQA1 and PM agreed with the results obtained using bloodstains in 90 samples. In the remaining ten samples of a specific kind of cigarette (Marlboro), the PCR products were not detected. The extracts from the ends of the Marlboro cigarettes were stained yellow. When the DNA extracted from Marlboro cigarette butts was treated with Microcon-100 (amicon) or SizeSep 400 Span Columns (Amersham Pharmacia Biotech), PCR products could be detected. When PCR amplification was performed after adding extracts from the ends of unsmoked Marlboro cigarettes to DNA extracted from bloodstains, PCR products could not be detected. The present data indicate that the degradation of high-molecular weight DNA and the inhibition of PCR by dyes of the cigarette end should be kept in mind when performing DNA typing using cigarette ends.

  18. Screening of different Trichoderma species against agriculturally important foliar plant pathogens. (United States)

    Prabhakaran, Narayanasamy; Prameeladevi, Thokala; Sathiyabama, Muthukrishnan; Kamil, Deeba


    Different isolates of Trichoderma were isolated from soil samples which were collected from different part of India. These isolates were grouped into four Trichoderma species viz., Trichoderma asperellum (Ta), T. harzianum (Th), T. pseudokoningii (Tp) and T. longibrachiatum (Tl) based on their morphological characters. Identification of the above isolates was also confirmed through ITS region analysis. These Trichoderma isolates were tested for in vitro biological control of Alternaria solani, Bipolaris oryzae, Pyricularia oryzae and Sclerotinia scierotiorum which cause serious diseases like early blight (target spot) of tomato and potato, brown leaf spot disease in rice, rice blast disease, and white mold disease in different plants. Under in vitro conditions, all the four species of Trichoderma (10 isolates) proved 100% potential inhibition against rice blast pathogen Pyracularia oryzae. T. harzianum (Th-01) and T. asperellum (Ta-10) were effective with 86.6% and 97.7%, growth inhibition of B. oryzae, respectively. Among others, T. pseudokoningii (Tp-08) and T. Iongibrachiatum (Tl-09) species were particularly efficient in inhibiting growth of S. sclerotiorum by 97.8% and 93.3%. T. Iongibrachiatum (TI-06 and TI-07) inhibited maximum mycelial growth of A. solani by 87.6% and 84.75. However, all the T. harzianum isolates showed significantly higher inhibition against S. sclerotiorum (CD value 9.430), causing white mold disease. This study led to the selection of potential Trichoderma isolates against rice blast, early blight, brown leaf spot in rice and white mold disease in different crops.

  19. Powerplex® ES versus Powerplex® S5--casework testing of the new screening kit. (United States)

    Poetsch, Micaela; Kamphausen, Thomas; Bajanowski, Thomas; Schwark, Thorsten; von Wurmb-Schwark, Nicole


    The new Powerplex® S5 Mini STR-System from Promega with the four provided STR loci D18S51, D8S1179, TH01 and FGA as well as the Amelogenin marker (PCR products ranging from 80 to 220 bp not considering the longer FGA fragments) is designed as a screening tool especially in difficult casework samples. To test its suitability we amplified highly degraded DNA from casework samples, which had shown no or only poor results in analyses with the Powerplex® ES kit, as well as artificially degraded DNA or DNA samples containing PCR inhibitors. Despite a tendency for allelic drop-ins in the amplification of highly degraded DNA the Powerplex® S5 kit was a reliable tool for the analysis of casework samples with degraded DNA which gave better results than the Powerplex® ES kit in 64% of analysed swabs. Furthermore, it was especially suitable for the investigation of formalin fixed tissue, tissue samples showing advanced putrefaction or telogen hair samples. However, there was no strict relation between positive Powerplex® S5 results and amplification success with the Powerplex® ES kit.

  20. An analysis of the alleged skeletal remains of Carin Goring.

    Directory of Open Access Journals (Sweden)

    Anna Kjellström

    Full Text Available In 1991, treasure hunters found skeletal remains in an area close to the destroyed country residence of former Nazi leader Hermann Göring in northeastern Berlin. The remains, which were believed to belong to Carin Göring, who was buried at the site, were examined to determine whether it was possible to make a positive identification. The anthropological analysis showed that the remains come from an adult woman. The DNA analysis of several bone elements showed female sex, and a reference sample from Carin's son revealed mtDNA sequences identical to the remains. The profile has one nucleotide difference from the Cambridge reference sequence (rCRS, the common variant 263G. A database search resulted in a frequency of this mtDNA sequence of about 10% out of more than 7,000 European haplotypes. The mtDNA sequence found in the ulna, the cranium and the reference sample is, thus, very common among Europeans. Therefore, nuclear DNA analysis was attempted. The remains as well as a sample from Carin's son were successfully analysed for the three nuclear markers TH01, D7S820 and D8S1179. The nuclear DNA analysis of the two samples revealed one shared allele for each of the three markers, supporting a mother and son relationship. This genetic information together with anthropological and historical files provides an additional piece of circumstantial evidence in our efforts to identify the remains of Carin Göring.

  1. Mutation rate analysis at 19 autosomal microsatellites. (United States)

    Qian, Xiao-Qin; Yin, Cai-Yong; Ji, Qiang; Li, Kai; Fan, Han-Ting; Yu, Yan-Fang; Bu, Fan-Li; Hu, Ling-Li; Wang, Jian-Wen; Mu, Hao-Fang; Haigh, Steven; Chen, Feng


    Previous studies have demonstrated that a large sample size is needed to reliably estimate population- and locus-specific microsatellite mutation rates. Therefore, we conducted a long-term collaboration study and performed a comprehensive analysis on the mutation characteristics of 19 autosomal short tandem repeat (STR) loci. The STR loci located on 15 of 22 autosomal chromosomes were analyzed in a total of 21,106 samples (11,468 parent-child meioses) in a Chinese population. This provided 217,892 allele transfers at 19 STR loci. An overall mutation rate of 1.20 × 10(-3) (95% CI, 1.06-1.36 × 10(-3) ) was observed in the populations across 18 of 19 STR loci, except for the TH01 locus with no mutation found. Most STR mutations (97.7%) were single-step mutations, and only a few mutations (2.30%) comprised two and multiple steps. Interestingly, approximately 93% of mutation events occur in the male germline. The mutation ratios increased with the paternal age at child birth (r = 0.99, ptesting, kinship analysis, and population genetics.

  2. "Paterniplex", a highly discriminative decaplex STR multiplex tailored for investigating special problems in paternity testing. (United States)

    Betz, Thomas; Immel, Uta-Dorothee; Kleiber, Manfred; Klintschar, Michael


    The goal of the study was to develop a STR multiplex ("Paterniplex") that is--as supplement to commercially available multiplex kits like the Identifiler kit (Applied Biosystems, Foster City, CA)--suitable for solving complex paternity cases such as deficiency cases or cases with mutations. The Paterniplex comprises the nine highly polymorphic STRs D8S1132, D7S1517, D10S2325, D12S391, Se33, D17S976, Penta E, Penta D and FGA in addition to Amelogenin as sex determination marker. The loci were selected because of their high degree of polymorphism (higher than that of the widely used TH01 marker). Only one locus, FGA, is shared with the Identifiler kit to avoid sample mix up. The study further gives details on the population genetics of the loci in a German Caucasian population (allelic distribution, Hardy-Weinberg Equilibrium and forensic efficiency markers such as the Discriminating Power) and three examples for cases that could not be solved using commercially available kits alone, but using the Paterniplex in addition to a commercial kit.

  3. Whole genome nucleosome sequencing identifies novel types of forensic markers in degraded DNA samples (United States)

    Dong, Chun-nan; Yang, Ya-dong; Li, Shu-jin; Yang, Ya-ran; Zhang, Xiao-jing; Fang, Xiang-dong; Yan, Jiang-wei; Cong, Bin


    In the case of mass disasters, missing persons and forensic caseworks, highly degraded biological samples are often encountered. It can be a challenge to analyze and interpret the DNA profiles from these samples. Here we provide a new strategy to solve the problem by taking advantage of the intrinsic structural properties of DNA. We have assessed the in vivo positions of more than 35 million putative nucleosome cores in human leukocytes using high-throughput whole genome sequencing, and identified 2,462 single nucleotide variations (SNVs), 128 insertion-deletion polymorphisms (indels). After comparing the sequence reads with 44 STR loci commonly used in forensics, five STRs (TH01, TPOX, D18S51, DYS391, and D10S1248)were matched. We compared these “nucleosome protected STRs” (NPSTRs) with five other non-NPSTRs using mini-STR primer design, real-time PCR, and capillary gel electrophoresis on artificially degraded DNA. Moreover, genotyping performance of the five NPSTRs and five non-NPSTRs was also tested with real casework samples. All results show that loci located in nucleosomes are more likely to be successfully genotyped in degraded samples. In conclusion, after further strict validation, these markers could be incorporated into future forensic and paleontology identification kits, resulting in higher discriminatory power for certain degraded sample types. PMID:27189082

  4. STR基因座多态性与强奸犯的关联研究%Association study between the genetic polymorphism of 15 STR loci and the crime of rape

    Institute of Scientific and Technical Information of China (English)

    杨春; 巴华杰; 高志勤; 林子清; 赵汉清; 刘冰泉; 马骏; 朱爱华


    Objective To investigate the relationship between rapists and related allele genes based on the analysis of 15 short tandem repeats (STRs) loci genetic polymorphism. Methods The method of Genome-wide scan was being used. Buccal swab samples of 129 rapists and 156 random populations were collected and PCR compound amplification was carried out with the aid of AmpFISTR Identifiler system. Then the products were subjected to electrophoresis and gene detection with AB13100 type gene analysis system so as to calculate and compare the alleles of 15 STRs gene frequency in the two groups. Results All the 15 STRs loci allele gene frequency in rapists and random population was found to coincide with Hardy-Weinberg law(P>0. 05). Allele 28 of D21S11 (rapists: 1.55% ,control group:5. 13%) ,allele22 of FGA(rapists:24.03% ,control group:16.99%),allele23 of FGA(rapists: 17.05% ,control group:26.28%) ,allele 10 of TH01(rapists:1.16% ,control group:4.17%) ,allele 8 of TPOX(rapists:55.77% ,control group:63.77%),allele 12 of TPOX(rapists:4.26% ,control group: 1.28%) were different between the two groups (P0.05). Conclusion Allele 28 of D21 S11,allele 22 and 23 of FGA, allele 10 of TH01, allele 8 and 12 of TPOX may be associated with the violent crime of rape. It is suggested that there are existing sensitive or resistance genes about the violent crime of rape in chromosome 2,4,11,21.%目的 通过对15个STR基因座多态性的分析,了解强奸犯与STR基因座相关等位基因的关联情况.方法 运用全基因组扫描的方法,对129名强奸犯与156名随机人群采用AmpFISTR Identifiler荧光标记复合扩增体系进行PCR复合扩增,然后应用ABI3100型基因分析系统对扩增产物进行电泳和基因检测.观察两个群体中15个STR基因座等位基因频率的分布差异.结果 15个STR基因座等位基因频率均符合Hardy-Weinberg平衡;D21S11-28(强奸犯组1.55%,对照组5.13%)、FGA-22(强奸犯24.03%,对照组16.99%)、FGA-23(强奸犯17

  5. Quantitative real-time PCR (qPCR) assay for human-dog-cat species identification and nuclear DNA quantification. (United States)

    Kanthaswamy, S; Premasuthan, A; Ng, J; Satkoski, J; Goyal, V


    In the United States, human forensic evidence collected from crime scenes is usually comingled with biomaterial of canine and feline origins. Knowledge of the concentration of nuclear DNA extracted from a crime scene biological sample and the species from which the sample originated is essential for DNA profiling. The ability to accurately detect and quantify target DNA in mixed-species samples is crucial when target DNA may be overwhelmed by non-target DNA. We have designed and evaluated a species-specific (human, dog and cat) nuclear DNA identification assay based on the TaqMan(®) quantitative real-time PCR (qPCR) technology that can simultaneously detect and measure minute quantities of DNA specific to either humans, dogs and/or cats. The fluorogenic triplex assay employs primers and hydrolysis probes that target the human TH01 locus as well as the dog and cat Melanocortin 1 Receptor (MC1R) sequences in a species-specific manner. We also demonstrate that the assay is a highly sensitive, reliable and robust method for identifying and quantifying mixed-species templates of human-dog-cat origin with as little as 0.4 pg of human and cat nuclear DNA, respectively, and 4.0 pg of dog nuclear DNA.

  6. Evaluation of the protective capabilities of nucleosome STRs obtained by large-scale sequencing. (United States)

    Dong, Chunnan; Yang, Yadong; Yan, Jiangwei; Fu, Lihong; Zhang, Xiaojing; Cong, Bin; Li, Shujin


    Partial DNA profiles are often obtained from degraded forensic samples and are hard to analyze and interpret. With in-depth studies on degraded DNA, an increasing number of forensic scientists have focused on the intrinsic structural properties of DNA. In theory, nucleosomes offer protection to the bound DNA by limiting access to enzymes. In our study, we performed large-scale DNA sequencing on nucleosome core DNA of human leucocytes. Five nucleosome short tandem repeats (STRs) were selected (including three forensic common STRs (i.e. TPOX, TH01, and D10S1248) and two unpublished STRs (i.e. AC012568.7 and AC007160.3)). We performed a population genetic investigation and forensic genetic statistical analysis of these two unpublished loci on 108 healthy unrelated individuals of the HeBei Han population in China. We estimated the protective capabilities of five selected nucleosome loci and MiniFiler™ loci with artificial degraded DNA and case samples. We also analyzed differences between sequencing results and software predicted results. Our findings showed that nucleosome STRs were more likely to be detected than MiniFiler™ loci. They were well protected from degradation by nucleosomes and could be candidates for further nucleosome multiplex construction, which would increase the chances of obtaining a better balanced profile with fewer allelic drop-outs.

  7. 西藏昌都藏族15个短串联重复序列基因座的遗传多样性%Polymorphism of fifteen short tandem repeat loci in Tibetan of Changdu area

    Institute of Scientific and Technical Information of China (English)

    康龙丽; 李月娅; 章晓风; 赵锋仓; 赵健民; 马利锋; 贺学; 李生斌


    i of Changdu Tibetan possess characteristics of high genetic diversity. They can be employed in minority genetics investigation, and individual and paternity test in forensic medicine.%的分布特点.用ARLEQUIN 3.0软件计算等位基因频率和各种多态性参数.结果 西藏昌都藏族群体中15个STR位点上观察到135个等位基因,等位基因频率分布在0.0065~0.5455之间;平均杂合度为0.7340,个体识别力除了TPOX(0.7927)和TH01(0.7919)外均大于0.8,累计个体识别力为0.9999998,累计非父排除率为0.99999997.结论 西藏昌都藏族15个STR位点均具有高度遗传多态性,是群体遗传学研究和法医学鉴定的可选位点.

  8. 中国牡丹江地区朝鲜族群体九个STR基因座的遗传多态性研究%Genetic polymorphism of 9 STR loci in Korean population of Mudanjiang

    Institute of Scientific and Technical Information of China (English)

    卜晓波; 宋洁; 韩彦龙; 张书捷; 傅松滨


    目的 调查中国牡丹江地区朝鲜族群体CSFIPO,TPOX,TH01,D16S539.D7S820,D13S317,F13A01,FESFPS,vWA 9个短串联重复序列(short tandem repeats,STR)基因座的基因多态性.方法 应用扩增片段长度多态性分型技术,获得等位基因频率分布.结果 X2检验表明9个基因座基因型分布均符合Hardy.Weinberg平衡.总偶合率为5.43595E-09,总个体识别率达0.999999995,三联体累计非父排除率为0.9982,二联体累计非父排除率为0.9711.结论 9个基因座在牡丹江地区朝鲜族群体有较高的非父排除率和个人识别机率,可应用于法医学亲子鉴定和个体识别.中国牡丹江地区和中国延吉地区朝鲜族人群6个基因频率相比较,CSFIPO、TPOX和TP01 3个基因座的基因频率分布差异有统计学意义,D7S820、D17S317和vWA 3个基因座的基因频率分布差异无统计学意义.%Objective To investigate the genetic polymorphism of 9 short tandem repeats(STR) gene loci,namely CSFLPO,TPOX,TH01,D16S539,D7S820,D13S317,F13A01,FESFPS and vwA in Chinese Korean pop.dabon in Mudanjiang area.Methods Amplified fragment length polymorphism(Amp-FLP)method wLq uscd to get the allele frequeney distribution.Results The genotype distributions of the 9 STR loci are conformed to Hardy-Weinberg equilibrium by x2 test analysis. The total accord frequency,the accumulated total discrimination power and the accumulative exeluding probability of paternity were calculated.Conclusion The results snggested that all the 9 gene loci have high power of excluding probability of patemity and individual identification.They can be used in paternity testing and individual identificmion for forensic medicine.The gene frequencies of CSnP0.TP0X and TP01 gene loci have signifieant differences between the Korean population in Mudanjiang area and those in Yanji area,but there is no difference in gene loci 0f D7S820.D17S317 and vWA.

  9. Characterisation of genetic structure of the Mayan population in Guatemala by autosomal STR analysis. (United States)

    Martinez-Gonzalez, L J; Alvarez-Cubero, M J; Saiz, M; Alvarez, J C; Martinez-Labarga, C; Lorente, J A


    Currently, the Guatemalan population comprises genetically isolated groups due to geographic, linguistic and cultural factors. For example, Mayan groups within the Guatemala population have preserved their own language, culture and religion. These practices have limited genetic admixture and have maintained the genetic identity of Mayan populations. This study is designed to define the genetic structure of the Mayan-Guatemalan groups Kaqchiquel, K'iche', Mam and Q'eqchi' through autosomal short tandem repeat (STR) polymorphisms and to analyse the genetic relationships between them and with other Mayan groups. Fifteen STR polymorphisms were analysed in 200 unrelated donors belonging to the Kaqchiquel (n = 50), K'iche' (n = 50), Mam (n = 50) and Q'eqchi' (n = 50) groups living in Guatemala. Genetic distance, non-metric MDS and AMOVA were used to analyse the genetic relationships between population groups. Within the Mayan population, the STRs D18S51 and FGA were the most informative markers and TH01 was the least informative. AMOVA and genetic distance analyses showed that the Guatemalan-Native American populations are highly similar to Mayan populations living in Mexico. The Mayan populations from Guatemala and other Native American groups display high genetic homogeneity. Genetic relationships between these groups are more affected by cultural and linguistic factors than geographical and local flow. This study represents one of the first steps in understanding Mayan-Guatemalan populations, the associations between their sub-populations and differences in gene diversity with other populations. This article also demonstrates that the Mestizo population shares most of its ancestral genetic components with the Guatemala Mayan populations.

  10. Genetic Variation of 25 Y-Chromosomal and 15 Autosomal STR Loci in the Han Chinese Population of Liaoning Province, Northeast China. (United States)

    Yao, Jun; Wang, Bao-Jie


    In the present study, we investigated the genetic characteristics of 25 Y-chromosomal and 15 autosomal short tandem repeat (STR) loci in 305 unrelated Han Chinese male individuals from Liaoning Province using AmpFISTR® Yfiler® Plus and IdentifilerTM PCR amplification kits. Population comparison was performed between Liaoning Han population and different ethnic groups to better understand the genetic background of the Liaoning Han population. For Y-STR loci, the overall haplotype diversity was 0.9997 and the discrimination capacity was 0.9607. Gene diversity values ranged from 0.4525 (DYS391) to 0.9617 (DYS385). Rst and two multi-dimensional scaling plots showed that minor differences were observed when the Liaoning Han population was compared to the Jilin Han Chinese, Beijing Han Chinese, Liaoning Manchu, Liaoning Mongolian, Liaoning Xibe, Shandong Han Chinese, Jiangsu Han Chinese, Anhui Han Chinese, Guizhou Han Chinese and Liaoning Hui populations; by contrast, major differences were observed when the Shanxi Han Chinese, Yunnan Bai, Jiangxi Han Chinese, Guangdong Han Chinese, Liaoning Korean, Hunan Tujia, Guangxi Zhuang, Gansu Tibetan, Xishuangbanna Dai, South Korean, Japanese and Hunan Miao populations. For autosomal STR loci, DP ranged from 0.9621 (D2S1338) to 0.8177 (TPOX), with PE distributing from 0.7521 (D18S51) to 0.2988 (TH01). A population comparison was performed and no statistically significant differences were detected at any STR loci between Liaoning Han, China Dong, and Shaanxi Han populations. The results showed that the 25 Y-STR and 15 autosomal STR loci in the Liaoning Han population were valuable for forensic applications and human genetics, and Liaoning Han was an independent endogenous ethnicity with a unique subpopulation structure.

  11. Statistical modelling of Ion PGM HID STR 10-plex MPS data. (United States)

    Vilsen, Søren B; Tvedebrink, Torben; Mogensen, Helle Smidt; Morling, Niels


    We investigated the results of short tandem repeat (STR) markers of dilution series experiments and reference profiles generated using the Ion PGM massively parallel sequencing platform utilising the HID STR 10-plex panel. The STR markers were identified by the marker specific flanking regions of the STR region. We investigated the following: (1) the usage of quality measures for identifying substitution errors, (2) the heterozygote balance and compared it to that of capillary electrophoresis (CE), (3) the stability of the coverage and the consequence of IonExpress Barcode adapter (IBA) sampling with decreasing amounts of template DNA, (4) the hypothesis that the parental longest uninterrupted stretch (LUS) is a better linear predictor of stutter ratio than the parent allele length, (5) the use of parental allele length as a predictor of shoulder ratio, and (6) the removal of non-systematic erroneous sequences using dynamic thresholds created by fitting the distribution of the non-systematic erroneous sequences. We found that, due to MID sampling, the average coverage on a marker could not be used as an apt predictor of the amount of template DNA. The parental LUS was shown to be better predictor of stutter ratio than the parental allele repeat length, when markers with compound and complex repeat patterns or markers which contained micro-variants were considered, such as marker TH01 showed R(2) of 0.02 and 0.78 for parent allele repeat length and LUS, respectively. The one-inflated negative binomial method (OINB) and geometric model that can be used to remove non-systematic noise left on average 1.8 and 1.2 systematic errors per STR system, respectively.

  12. A New Topological Degree Theory for Perturbations of Demicontinuous Operators and Applications to Nonlinear Equations with Nonmonotone Nonlinearities

    Directory of Open Access Journals (Sweden)

    Teffera M. Asfaw


    Full Text Available Let X be a real reflexive locally uniformly convex Banach space with locally uniformly convex dual space X⁎. Let T:X⊇DT→2X⁎ be maximal monotone of type Γdϕ (i.e., there exist d≥0 and a nondecreasing function ϕ:0,∞→0,∞ with ϕ(0=0 such that 〈v⁎,x-y〉≥-dx-ϕy for all x∈DT, v⁎∈Tx, and y∈X,L:X⊃D(L→X⁎ be linear, surjective, and closed such that L-1:X⁎→X is compact, and C:X→X⁎ be a bounded demicontinuous operator. A new degree theory is developed for operators of the type L+T+C. The surjectivity of L can be omitted provided that RL is closed, L is densely defined and self-adjoint, and X=H, a real Hilbert space. The theory improves the degree theory of Berkovits and Mustonen for L+C, where C is bounded demicontinuous pseudomonotone. New existence theorems are provided. In the case when L is monotone, a maximality result is included for L and L+T. The theory is applied to prove existence of weak solutions in X=L20,T;H01Ω of the nonlinear equation given by ∂u/∂t-∑i=1N(∂/∂xiAix,u,∇u+Hλx,u,∇u=fx,t,  x,t∈QT;  ux,t=0,  x,t∈∂QT; and ux,0=ux,T,  x∈Ω, where λ>0, QT=Ω×0,T, ∂QT=∂Ω×0,T, Aix,u,∇u=∂/∂xiρx,u,∇u+aix,u,∇u  (i=1,2,…,N, Hλx,u,∇u=-λΔu+gx,u,∇u, Ω is a nonempty, bounded, and open subset of RN with smooth boundary, and ρ,ai,g:Ω¯×R×RN→R satisfy suitable growth conditions. In addition, a new existence result is given concerning existence of weak solutions for nonlinear wave equation with nonmonotone nonlinearity.