Human Genome Epidemiology : A scientific foundation for using genetic information to improve health and prevent disease

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Stefania Boccia

2005-03-01

Full Text Available

Human health is determined by the interplay of genetic factors and the environment. In this context the recent advances in human genomics are expected to play a central role in medicine and public health by providing genetic information for disease prediction and prevention.

After the completion of the human genome sequencing, a fundamental step will be represented by the translation of these discoveries into meaningful actions to improve health and prevent diseases, and the field of epidemiology plays a central role in this effort. These are some of the issues addressed by Human Genome Epidemiology –A scientific foundation for using genetic information to improve health and prevent disease, a volume edited by Prof. M. Khoury, Prof. J. Little, Prof.W. Burke and published by Oxford university Press 2004.

This book describes the important role that epidemiological methods play in the continuum from gene discovery to the development and application of genetic tests. The Authors calls this continuum human genome epidemiology (HuGE to denote an evolving field of inquiry that uses systematic applications of epidemiological methods to assess the impact of human genetic variation on health and disease.

The book is divided into four sections and it is structured to allow readers to proceed systematically from the fundamentals of genome technology and discovery, to the epidemiological approaches, to gene characterisation, to the evaluation of genetic tests and their use in health services and public health.

Genetic epidemiology of Down syndrome in Iran

OpenAIRE

Manoochehr Shariati

2005-01-01

Down syndrome is the most common autosomal abnormality and occurs in approximately 1 per 700 live births. Down syndrome accounts for about one third of all moderate and sever mental handicaps in school-aged children. To reveal genetic epidemiology of Down syndrome, 545 karyotypes of referred cases to the author were evaluated. The frequencies of three cytogenetic variants of Down syndrome were trisomy 21 (77.5%), mosaicism (18%) and chromosomal translocation (4.5%). Male to female ratio was 1...

Participants' perceptions of research benefits in an African genetic epidemiology study.

Science.gov (United States)

Appiah-Poku, John; Newton, Sam; Kass, Nancy

2011-12-01

  Both the Council for International Organization of Medical Sciences and the Helsinki Declaration emphasize that the potential benefits of research should outweigh potential harms; consequently, some work has been conducted on participants' perception of benefits in therapeutic research. However, there appears to be very little work conducted with participants who have joined non-therapeutic research. This work was done to evaluate participants' perception of benefits in a genetic epidemiological study by examining their perception of the potential benefits of enrollment.   In-depth interviews lasting between 45 and 60 minutes were conducted with a convenient sample of 25 ill patients and 25 healthy accompanying relatives enrolled in a genetic epidemiological study of tuberculosis. Recorded interviews were transcribed and analyzed using content analysis.   Participants perceived that research was beneficial and some of the benefits included the generation of new knowledge, finding the cause of diseases, as well as the control, eradication and prevention of disease. Some thought that research was risky whilst others thought that the benefits outweighed the risks.   Participants perceived research to be beneficial and most of them thought that, though it was risky, the benefits outweighed the risks. It is our view that researchers need to give serious consideration to participant's perception of benefits in designing their consent forms, to see to the fulfillment of achievable goals. © 2011 Blackwell Publishing Ltd.

Epidemiologic and genetic characteristics of mumps viruses isolated in China from 1995 to 2010.

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Cui, Aili; Zhu, Zhen; Chen, Meng; Zheng, Huanying; Liu, Leng; Wang, Yan; Ma, Yan; Wang, Changyin; Fang, Xueqiang; Li, Ping; Guan, Ronghui; Wang, Shuang; Zhou, Jianhui; Zheng, Lei; Gao, Hui; Ding, Zhengrong; Li, Liqun; Bo, Fang; Sun, Zhaodan; Zhang, Zhenying; Feng, Daxing; He, Jilan; Chen, Hui; Jin, Li; Rota, Paul A; Xu, Wenbo

2014-01-01

The epidemiologic and genetic characteristics of mumps viruses detected in China from 1995 to 2010 were analyzed in this study. Mumps remains endemic in China with a high overall incidence rate. The incidence of mumps in Western China was higher than that in other regions of the country. Each year, most of mumps cases occurred between April and July, but a small peak also occurred in November and December. Mumps cases primarily affected the under 15 year old age group. Virologic data demonstrated that genotype F was the predominant circulating genotype throughout China for at least 15 years and no other genotype was detected between 1995 and 2010. Analysis of sequence data from the small hydrophobic (SH) gene indicated that multiple transmission chains of genotype F were found in various provinces of China, with no apparent chronologic and geographic restriction. This is the first report describing the epidemiology of mumps and genetic characterization of mumps viruses at the national level in China. Copyright © 2013 Elsevier B.V. All rights reserved.

Epidemiology of Brucellosis and Genetic Diversity of Brucella abortus in Kazakhstan.

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Shevtsova, Elena; Shevtsov, Alexandr; Mukanov, Kasim; Filipenko, Maxim; Kamalova, Dinara; Sytnik, Igor; Syzdykov, Marat; Kuznetsov, Andrey; Akhmetova, Assel; Zharova, Mira; Karibaev, Talgat; Tarlykov, Pavel; Ramanculov, Erlan

2016-01-01

Brucellosis is a major zoonotic infection in Kazakhstan. However, there is limited data on its incidence in humans and animals, and the genetic diversity of prevalent strains is virtually unstudied. Additionally, there is no detailed overview of Kazakhstan brucellosis control and eradication programs. Here, we analyzed brucellosis epidemiological data, and assessed the effectiveness of eradication strategies employed over the past 70 years to counteract this infection. We also conducted multiple loci variable-number tandem repeat analysis (MLVA) of Brucella abortus strains found in Kazakhstan. We analyzed official data on the incidence of animal brucellosis in Kazakhstan. The records span more than 70 years of anti-brucellosis campaigns, and contain a brief description of the applied control strategies, their effectiveness, and their impact on the incidence in humans. The MLVA-16 method was used to type 94 strains of B. abortus and serial passages of B. abortus 82, a strain used in vaccines. MLVA-8 and MLVA-11 analyses clustered strains into a total of four and seven genotypes, respectively; it is the first time that four of these genotypes have been described. MLVA-16 analysis divided strains into 28 distinct genotypes having genetic similarity coefficient that varies from 60 to100% and a Hunter & Gaston diversity index of 0.871. MST analysis reconstruction revealed clustering into "Kazakhstani-Chinese (Central Asian)", "European" and "American" lines. Detection of multiple genotypes in a single outbreak confirms that poorly controlled trade of livestock plays a crucial role in the spread of infection. Notably, the MLVA-16 profile of the B. abortus 82 strain was unique and did not change during 33 serial passages. MLVA genotyping may thus be useful for epidemiological monitoring of brucellosis, and for tracking the source(s) of infection. We suggest that countrywide application of MLVA genotyping would improve the control of brucellosis in Kazakhstan.

Local literature bias in genetic epidemiology: an empirical evaluation of the Chinese literature.

Directory of Open Access Journals (Sweden)

Zhenglun Pan

2005-12-01

Full Text Available BACKGROUND: Postulated epidemiological associations are subject to several biases. We evaluated whether the Chinese literature on human genome epidemiology may offer insights on the operation of selective reporting and language biases. METHODS AND FINDINGS: We targeted 13 gene-disease associations, each already assessed by meta-analyses, including at least 15 non-Chinese studies. We searched the Chinese Journal Full-Text Database for additional Chinese studies on the same topics. We identified 161 Chinese studies on 12 of these gene-disease associations; only 20 were PubMed-indexed (seven English full-text. Many studies (14-35 per topic were available for six topics, covering diseases common in China. With one exception, the first Chinese study appeared with a time lag (2-21 y after the first non-Chinese study on the topic. Chinese studies showed significantly more prominent genetic effects than non-Chinese studies, and 48% were statistically significant per se, despite their smaller sample size (median sample size 146 versus 268, p < 0.001. The largest genetic effects were often seen in PubMed-indexed Chinese studies (65% statistically significant per se. Non-Chinese studies of Asian-descent populations (27% significant per se also tended to show somewhat more prominent genetic effects than studies of non-Asian descent (17% significant per se. CONCLUSION: Our data provide evidence for the interplay of selective reporting and language biases in human genome epidemiology. These biases may not be limited to the Chinese literature and point to the need for a global, transparent, comprehensive outlook in molecular population genetics and epidemiologic studies in general.

A complex scenario of tuberculosis transmission is revealed through genetic and epidemiological surveys in Porto.

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Rito, Teresa; Matos, Carlos; Carvalho, Carlos; Machado, Henrique; Rodrigues, Gabriela; Oliveira, Olena; Ferreira, Eduarda; Gonçalves, Jorge; Maio, Lurdes; Morais, Clara; Ramos, Helena; Guimarães, João Tiago; Santos, Catarina L; Duarte, Raquel; Correia-Neves, Margarida

2018-01-25

Tuberculosis (TB) incidence is decreasing worldwide and eradication is becoming plausible. In low-incidence countries, intervention on migrant populations is considered one of the most important strategies for elimination. However, such measures are inappropriate in European areas where TB is largely endemic, such as Porto in Portugal. We aim to understand transmission chains in Porto through a genetic characterization of Mycobacterium tuberculosis strains and through a detailed epidemiological evaluation of cases. We genotyped the M. tuberculosis strains using the MIRU-VNTR system. We performed an evolutionary reconstruction of the genotypes with median networks, used in this context for the first time. TB cases from a period of two years were evaluated combining genetic, epidemiological and georeferencing information. The data reveal a unique complex scenario in Porto where the autochthonous population acts as a genetic reservoir of M. tuberculosis diversity with discreet episodes of transmission, mostly undetected using classical epidemiology alone. Although control policies have been successful in decreasing incidence in Porto, the discerned complexity suggests that, for elimination to be a realistic goal, strategies need to be adjusted and coupled with a continuous genetic characterization of strains and detailed epidemiological evaluation, in order to successfully identify and interrupt transmission chains.

Classification of rare missense substitutions, using risk surfaces, with genetic- and molecular-epidemiology applications.

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Tavtigian, Sean V; Byrnes, Graham B; Goldgar, David E; Thomas, Alun

2008-11-01

Many individually rare missense substitutions are encountered during deep resequencing of candidate susceptibility genes and clinical mutation screening of known susceptibility genes. BRCA1 and BRCA2 are among the most resequenced of all genes, and clinical mutation screening of these genes provides an extensive data set for analysis of rare missense substitutions. Align-GVGD is a mathematically simple missense substitution analysis algorithm, based on the Grantham difference, which has already contributed to classification of missense substitutions in BRCA1, BRCA2, and CHEK2. However, the distribution of genetic risk as a function of Align-GVGD's output variables Grantham variation (GV) and Grantham deviation (GD) has not been well characterized. Here, we used data from the Myriad Genetic Laboratories database of nearly 70,000 full-sequence tests plus two risk estimates, one approximating the odds ratio and the other reflecting strength of selection, to display the distribution of risk in the GV-GD plane as a series of surfaces. We abstracted contours from the surfaces and used the contours to define a sequence of missense substitution grades ordered from greatest risk to least risk. The grades were validated internally using a third, personal and family history-based, measure of risk. The Align-GVGD grades defined here are applicable to both the genetic epidemiology problem of classifying rare missense substitutions observed in known susceptibility genes and the molecular epidemiology problem of analyzing rare missense substitutions observed during case-control mutation screening studies of candidate susceptibility genes. (c) 2008 Wiley-Liss, Inc.

Cryptic relatedness in epidemiologic collections accessed for genetic association studies: experiences from the Epidemiologic Architecture for Genes Linked to Environment (EAGLE) study and the National Health and Nutrition Examination Surveys (NHANES).

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Malinowski, Jennifer; Goodloe, Robert; Brown-Gentry, Kristin; Crawford, Dana C

2015-01-01

Epidemiologic collections have been a major resource for genotype-phenotype studies of complex disease given their large sample size, racial/ethnic diversity, and breadth and depth of phenotypes, traits, and exposures. A major disadvantage of these collections is they often survey households and communities without collecting extensive pedigree data. Failure to account for substantial relatedness can lead to inflated estimates and spurious associations. To examine the extent of cryptic relatedness in an epidemiologic collection, we as the Epidemiologic Architecture for Genes Linked to Environment (EAGLE) study accessed the National Health and Nutrition Examination Surveys (NHANES) linked to DNA samples ("Genetic NHANES") from NHANES III and NHANES 1999-2002. NHANES are population-based cross-sectional surveys conducted by the National Center for Health Statistics at the Centers for Disease Control and Prevention. Genome-wide genetic data is not yet available in NHANES, and current data use agreements prohibit the generation of GWAS-level data in NHANES samples due issues in maintaining confidentiality among other ethical concerns. To date, only hundreds of single nucleotide polymorphisms (SNPs) genotyped in a variety of candidate genes are available for analysis in NHANES. We performed identity-by-descent (IBD) estimates in three self-identified subpopulations of Genetic NHANES (non-Hispanic white, non- Hispanic black, and Mexican American) using PLINK software to identify potential familial relationships from presumed unrelated subjects. We then compared the PLINKidentified relationships to those identified by an alternative method implemented in Kinship-based INference for Genome-wide association studies (KING). Overall, both methods identified familial relationships in NHANES III and NHANES 1999-2002 for all three subpopulations, but little concordance was observed between the two methods due in major part to the limited SNP data available in Genetic NHANES

A genetic analysis of Trichuris trichiura and Trichuris suis from Ecuador

DEFF Research Database (Denmark)

Meekums, Hayley; Hawash, Mohamed B F; Sparks, Alexandra M

2015-01-01

BACKGROUND: Since the nematodes Trichuris trichiura and T. suis are morphologically indistinguishable, genetic analysis is required to assess epidemiological cross-over between people and pigs. This study aimed to clarify the transmission biology of trichuriasis in Ecuador. FINDINGS: Adult...... Trichuris worms were collected during a parasitological survey of 132 people and 46 pigs in Esmeraldas Province, Ecuador. Morphometric analysis of 49 pig worms and 64 human worms revealed significant variation. In discriminant analysis morphometric characteristics correctly classified male worms according...... to genetically analyse Trichuris parasites. Although T. trichiura does not appear to be zoonotic in Ecuador, there is evidence of genetic exchange between T. trichiura and T. suis warranting more detailed genetic sampling....

Significance of epidemiological studies for estimating the genetic radiation hazards of man

International Nuclear Information System (INIS)

Stephan, G.

1982-01-01

Following a brief presentation of the fundamentals of epidemiological studies, the problems associated with such studies are discussed. Epidemiological investigations on survivors of the atomic bomb explosions in Hiroshima and Nagasaki and also on the population of Kerala, a state in south west India with a high natural radiation load, are then discussed. Consideration was given to the question whether the Down-Syndrom is a valid indicator for proving a causal relationship between radiation dose and genetic effects. (MG) [de

Unravelling the Molecular Epidemiology and Genetic Diversity among Burkholderia pseudomallei Isolates from South India Using Multi-Locus Sequence Typing.

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Tellapragada, Chaitanya; Kamthan, Aayushi; Shaw, Tushar; Ke, Vandana; Kumar, Subodh; Bhat, Vinod; Mukhopadhyay, Chiranjay

2016-01-01

There is a slow but steady rise in the case detection rates of melioidosis from various parts of the Indian sub-continent in the past two decades. However, the epidemiology of the disease in India and the surrounding South Asian countries remains far from well elucidated. Multi-locus sequence typing (MLST) is a useful epidemiological tool to study the genetic relatedness of bacterial isolates both with-in and across the countries. With this background, we studied the molecular epidemiology of 32 Burkholderia pseudomallei isolates (31 clinical and 1 soil isolate) obtained during 2006-2015 from various parts of south India using multi-locus sequencing typing and analysis. Of the 32 isolates included in the analysis, 30 (93.7%) had novel allelic profiles that were not reported previously. Sequence type (ST) 1368 (n = 15, 46.8%) with allelic profile (1, 4, 6, 4, 1, 1, 3) was the most common genotype observed. We did not observe a genotypic association of STs with geographical location, type of infection and year of isolation in the present study. Measure of genetic differentiation (FST) between Indian and the rest of world isolates was 0.14413. Occurrence of the same ST across three adjacent states of south India suggest the dispersion of B.pseudomallei across the south western coastal part of India with limited geographical clustering. However, majority of the STs reported from the present study remained as "outliers" on the eBURST "Population snapshot", suggesting the genetic diversity of Indian isolates from the Australasian and Southeast Asian isolates.

Unravelling the Molecular Epidemiology and Genetic Diversity among Burkholderia pseudomallei Isolates from South India Using Multi-Locus Sequence Typing.

Directory of Open Access Journals (Sweden)

Chaitanya Tellapragada

Full Text Available There is a slow but steady rise in the case detection rates of melioidosis from various parts of the Indian sub-continent in the past two decades. However, the epidemiology of the disease in India and the surrounding South Asian countries remains far from well elucidated. Multi-locus sequence typing (MLST is a useful epidemiological tool to study the genetic relatedness of bacterial isolates both with-in and across the countries. With this background, we studied the molecular epidemiology of 32 Burkholderia pseudomallei isolates (31 clinical and 1 soil isolate obtained during 2006-2015 from various parts of south India using multi-locus sequencing typing and analysis. Of the 32 isolates included in the analysis, 30 (93.7% had novel allelic profiles that were not reported previously. Sequence type (ST 1368 (n = 15, 46.8% with allelic profile (1, 4, 6, 4, 1, 1, 3 was the most common genotype observed. We did not observe a genotypic association of STs with geographical location, type of infection and year of isolation in the present study. Measure of genetic differentiation (FST between Indian and the rest of world isolates was 0.14413. Occurrence of the same ST across three adjacent states of south India suggest the dispersion of B.pseudomallei across the south western coastal part of India with limited geographical clustering. However, majority of the STs reported from the present study remained as "outliers" on the eBURST "Population snapshot", suggesting the genetic diversity of Indian isolates from the Australasian and Southeast Asian isolates.

Establishing a Twin Register : An Invaluable Resource for (Behavior) Genetic, Epidemiological, Biomarker, and 'Omics' Studies

NARCIS (Netherlands)

Odintsova, Veronika V; Willemsen, Gonneke; Dolan, Conor V; Hottenga, Jouke-Jan; Martin, Nicholas G; Slagboom, P Eline; Ordoñana, Juan R; Boomsma, Dorret I

2018-01-01

Twin registers are wonderful research resources for research applications in medical and behavioral genetics, epidemiology, psychology, molecular genetics, and other areas of research. New registers continue to be launched all over the world as researchers from different disciplines recognize the

Genetic epidemiology of hypertension: an update on the African diaspora.

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Daniel, Harold I; Rotimi, Charles N

2003-01-01

Hypertension is a serious global public health problem, affecting approximately 600 million people worldwide. The lifetime risk of developing the condition exceeds 50% in most populations. Despite considerable success in the pharmacological treatment of hypertension in all-human populations, the health-care community still lacks understanding of how and why individuals develop chronically elevated blood pressure. This gap in knowledge, and the high prevalence of hypertension and associated complications in some populations of African descent, have led some to conclude that hypertension is a "different disease" in people of African descent. Despite considerable evidence from epidemiologic studies showing that blood pressure distribution in populations of the African diaspora spans the known spectrum for all human populations, theories in support of unique "defects" among populations of African descent continue to gain wide acceptance. To date, no known environmental factors or genetic variants relevant to the pathophysiology of human hypertension have been found to be unique to Black populations. However, available genetic epidemiologic data demonstrate differential distributions of risk factors that are consistent with current environmental and geographic origins. This review summarizes the available evidence and demonstrates that as the exposure to known risk factors for hypertension (eg, excess consumption of salt and calories, stress, sedentary lifestyle, and degree of urbanization) increases among genetically susceptible individuals, the prevalence of hypertension and associated complications also increases across populations of the African diaspora. This observation is true for all human populations.

Characterizing Race/Ethnicity and Genetic Ancestry for 100,000 Subjects in the Genetic Epidemiology Research on Adult Health and Aging (GERA) Cohort.

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Banda, Yambazi; Kvale, Mark N; Hoffmann, Thomas J; Hesselson, Stephanie E; Ranatunga, Dilrini; Tang, Hua; Sabatti, Chiara; Croen, Lisa A; Dispensa, Brad P; Henderson, Mary; Iribarren, Carlos; Jorgenson, Eric; Kushi, Lawrence H; Ludwig, Dana; Olberg, Diane; Quesenberry, Charles P; Rowell, Sarah; Sadler, Marianne; Sakoda, Lori C; Sciortino, Stanley; Shen, Ling; Smethurst, David; Somkin, Carol P; Van Den Eeden, Stephen K; Walter, Lawrence; Whitmer, Rachel A; Kwok, Pui-Yan; Schaefer, Catherine; Risch, Neil

2015-08-01

Using genome-wide genotypes, we characterized the genetic structure of 103,006 participants in the Kaiser Permanente Northern California multi-ethnic Genetic Epidemiology Research on Adult Health and Aging Cohort and analyzed the relationship to self-reported race/ethnicity. Participants endorsed any of 23 race/ethnicity/nationality categories, which were collapsed into seven major race/ethnicity groups. By self-report the cohort is 80.8% white and 19.2% minority; 93.8% endorsed a single race/ethnicity group, while 6.2% endorsed two or more. Principal component (PC) and admixture analyses were generally consistent with prior studies. Approximately 17% of subjects had genetic ancestry from more than one continent, and 12% were genetically admixed, considering only nonadjacent geographical origins. Self-reported whites were spread on a continuum along the first two PCs, indicating extensive mixing among European nationalities. Self-identified East Asian nationalities correlated with genetic clustering, consistent with extensive endogamy. Individuals of mixed East Asian-European genetic ancestry were easily identified; we also observed a modest amount of European genetic ancestry in individuals self-identified as Filipinos. Self-reported African Americans and Latinos showed extensive European and African genetic ancestry, and Native American genetic ancestry for the latter. Among 3741 genetically identified parent-child pairs, 93% were concordant for self-reported race/ethnicity; among 2018 genetically identified full-sib pairs, 96% were concordant; the lower rate for parent-child pairs was largely due to intermarriage. The parent-child pairs revealed a trend toward increasing exogamy over time; the presence in the cohort of individuals endorsing multiple race/ethnicity categories creates interesting challenges and future opportunities for genetic epidemiologic studies. Copyright © 2015 by the Genetics Society of America.

Characterizing Race/Ethnicity and Genetic Ancestry for 100,000 Subjects in the Genetic Epidemiology Research on Adult Health and Aging (GERA) Cohort

Science.gov (United States)

Banda, Yambazi; Kvale, Mark N.; Hoffmann, Thomas J.; Hesselson, Stephanie E.; Ranatunga, Dilrini; Tang, Hua; Sabatti, Chiara; Croen, Lisa A.; Dispensa, Brad P.; Henderson, Mary; Iribarren, Carlos; Jorgenson, Eric; Kushi, Lawrence H.; Ludwig, Dana; Olberg, Diane; Quesenberry, Charles P.; Rowell, Sarah; Sadler, Marianne; Sakoda, Lori C.; Sciortino, Stanley; Shen, Ling; Smethurst, David; Somkin, Carol P.; Van Den Eeden, Stephen K.; Walter, Lawrence; Whitmer, Rachel A.; Kwok, Pui-Yan; Schaefer, Catherine; Risch, Neil

2015-01-01

Using genome-wide genotypes, we characterized the genetic structure of 103,006 participants in the Kaiser Permanente Northern California multi-ethnic Genetic Epidemiology Research on Adult Health and Aging Cohort and analyzed the relationship to self-reported race/ethnicity. Participants endorsed any of 23 race/ethnicity/nationality categories, which were collapsed into seven major race/ethnicity groups. By self-report the cohort is 80.8% white and 19.2% minority; 93.8% endorsed a single race/ethnicity group, while 6.2% endorsed two or more. Principal component (PC) and admixture analyses were generally consistent with prior studies. Approximately 17% of subjects had genetic ancestry from more than one continent, and 12% were genetically admixed, considering only nonadjacent geographical origins. Self-reported whites were spread on a continuum along the first two PCs, indicating extensive mixing among European nationalities. Self-identified East Asian nationalities correlated with genetic clustering, consistent with extensive endogamy. Individuals of mixed East Asian–European genetic ancestry were easily identified; we also observed a modest amount of European genetic ancestry in individuals self-identified as Filipinos. Self-reported African Americans and Latinos showed extensive European and African genetic ancestry, and Native American genetic ancestry for the latter. Among 3741 genetically identified parent–child pairs, 93% were concordant for self-reported race/ethnicity; among 2018 genetically identified full-sib pairs, 96% were concordant; the lower rate for parent–child pairs was largely due to intermarriage. The parent–child pairs revealed a trend toward increasing exogamy over time; the presence in the cohort of individuals endorsing multiple race/ethnicity categories creates interesting challenges and future opportunities for genetic epidemiologic studies. PMID:26092716

Molecular and genetic epidemiology of cancer in low- and medium-income countries.

Science.gov (United States)

Malhotra, Jyoti

2014-01-01

Genetic and molecular factors can play an important role in an individual's cancer susceptibility and response to carcinogen exposure. Cancer susceptibility and response to carcinogen exposure can be either through inheritance of high penetrance but rare germline mutations that constitute heritable cancer syndromes, or it can be inherited as common genetic variations or polymorphisms that are associated with low to moderate risk for development of cancer. These polymorphisms can interact with environmental exposures and can influence an individual's cancer risk through multiple pathways, including affecting the rate of metabolism of carcinogens or the immune response to these toxins. Thus, these genetic polymorphisms can account for some of the geographical differences seen in cancer prevalence between different populations. This review explores the role of molecular epidemiology in the field of cancer prevention and control in low- and medium-income countries. Using data from Human Genome Project and HapMap Project, genome-wide association studies have been able to identify multiple susceptibility loci for different cancers. The field of genetic and molecular epidemiology has been further revolutionized by the discovery of newer, faster, and more efficient DNA-sequencing technologies including next-generation sequencing. The new DNA-sequencing technologies can play an important role in planning and implementation of cancer prevention and screening strategies. More research is needed in this area, especially in investigating new biomarkers and measuring gene-environment interactions. Copyright © 2014 Icahn School of Medicine at Mount Sinai. Published by Elsevier Inc. All rights reserved.

Shared genetics underlying epidemiological association between endometriosis and ovarian cancer

DEFF Research Database (Denmark)

Lu, Yi; Cuellar-Partida, Gabriel; Painter, Jodie N

2015-01-01

Epidemiological studies have demonstrated associations between endometriosis and certain histotypes of ovarian cancer, including clear cell, low-grade serous and endometrioid carcinomas. We aimed to determine whether the observed associations might be due to shared genetic aetiology. To address...... this, we used two endometriosis datasets genotyped on common arrays with full-genome coverage (3194 cases and 7060 controls) and a large ovarian cancer dataset genotyped on the customized Illumina Infinium iSelect (iCOGS) arrays (10 065 cases and 21 663 controls). Previous work has suggested...... that a large number of genetic variants contribute to endometriosis and ovarian cancer (all histotypes combined) susceptibility. Here, using the iCOGS data, we confirmed polygenic architecture for most histotypes of ovarian cancer. This led us to evaluate if the polygenic effects are shared across diseases. We...

Genetic diversity and epidemiology of infectious hematopoietic necrosis virus in Alaska

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Emmenegger, E.G; Meyers, T.R.; Burton, T.O.; Kurath, G.

2000-01-01

Forty-two infectious hematopoietic necrosis virus (IHNV) isolates from Alaska were analyzed using the ribonuclease protection assay (RPA) and nucleotide sequencing. RPA analyses, utilizing 4 probes, N5, N3 (N gene), GF (G gene), and NV (NV gene), determined that the haplotypes of all 3 genes demonstrated a consistent spatial pattern. Virus isolates belonging to the most common haplotype groups were distributed throughout Alaska, whereas isolates in small haplotype groups were obtained from only 1 site (hatchery, lake, etc.). The temporal pattern of the GF haplotypes suggested a 'genetic acclimation' of the G gene, possibly due to positive selection on the glycoprotein. A pairwise comparison of the sequence data determined that the maximum nucleotide diversity of the isolates was 2.75% (10 mismatches) for the NV gene, and 1.99% (6 mismatches) for a 301 base pair region of the G gene, indicating that the genetic diversity of IHNV within Alaska is notably lower than in the more southern portions of the IHNV North American range. Phylogenetic analysis of representative Alaskan sequences and sequences of 12 previously characterized IHNV strains from Washington, Oregon, Idaho, California (USA) and British Columbia (Canada) distinguished the isolates into clusters that correlated with geographic origin and indicated that the Alaskan and British Columbia isolates may have a common viral ancestral lineage. Comparisons of multiple isolates from the same site provided epidemiological insights into viral transmission patterns and indicated that viral evolution, viral introduction, and genetic stasis were the mechanisms involved with IHN virus population dynamics in Alaska. The examples of genetic stasis and the overall low sequence heterogeneity of the Alaskan isolates suggested that they are evolutionarily constrained. This study establishes a baseline of genetic fingerprint patterns and sequence groups representing the genetic diversity of Alaskan IHNV isolates. This

Cannabis Beyond Good and Evil. How genetic and epidemiological factors shape the relationship between cannabis and psychosis

NARCIS (Netherlands)

Schubart, C.D.

2013-01-01

The studies presented in this thesis aimed to identify genetic and non-genetic (epidemiological) factors that shape the association between cannabis use and psychosis. We showed that the age of first use of cannabis is a determinant for the strength of the association between cannabis use and

Epidemiology, major risk factors and genetic predisposition for breast cancer in the Pakistani population.

Science.gov (United States)

Shaukat, Uzma; Ismail, Muhammad; Mehmood, Nasir

2013-01-01

Occurrence of breast cancer is related to genetic as well as cultural, environmental and life-style factors. Variations in diversity of these factors among different ethnic groups and geographical areas emphasize the immense need for studies in all racial-ethnic populations. The incidence of breast cancer in Pakistan is highest in Asians after Jews in Israel and 2.5 times higher than that in neighboring countries like Iran and India, accounting for 34.6% of female cancers. The Pakistani population is deficient in information regarding breast cancer etiology and epidemiology, but efforts done so far had suggested consanguinity as a major risk factor for frequent mutations leading to breast cancer and has also shed light on genetic origins in different ethnic groups within Pakistan. World-wide research efforts on different ethnicities have enhanced our understanding of genetic predisposition to breast cancer but despite these discoveries, 75% of the familial risk of breast cancer remains unexplained, highlighting the fact that the majority of breast cancer susceptibility genes remain unidentified. For this purpose Pakistani population provides a strong genetic pool to elucidate the genetic etiology of breast cancer because of cousin marriages. In this review, we describe the known breast cancer predisposition factors found in the local Pakistani population and the epidemiological research work done to emphasize the importance of exploring factors/variants contributing to breast cance, in order to prevent, cure and decrease its incidence in our country.

Variable-number-of-tandem-repeats analysis of genetic diversity in Pasteuria ramosa.

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Mouton, L; Ebert, D

2008-05-01

Variable-number-of-tandem-repeats (VNTR) markers are increasingly being used in population genetic studies of bacteria. They were recently developed for Pasteuria ramosa, an endobacterium that infects Daphnia species. In the present study, we genotyped P. ramosa in 18 infected hosts from the United Kingdom, Belgium, and two lakes in the United States using seven VNTR markers. Two Daphnia species were collected: D. magna and D. dentifera. Six loci showed length polymorphism, with as many as five alleles identified for a single locus. Similarity coefficient calculations showed that the extent of genetic variation between pairs of isolates within populations differed according to the population, but it was always less than the genetic distances among populations. Analysis of the genetic distances performed using principal component analysis revealed strong clustering by location of origin, but not by host Daphnia species. Our study demonstrated that the VNTR markers available for P. ramosa are informative in revealing genetic differences within and among populations and may therefore become an important tool for providing detailed analysis of population genetics and epidemiology.

Melanocortin-1 receptor, skin cancer and phenotypic characteristics (M-SKIP project: study design and methods for pooling results of genetic epidemiological studies

Directory of Open Access Journals (Sweden)

Raimondi Sara

2012-08-01

Full Text Available Abstract Background For complex diseases like cancer, pooled-analysis of individual data represents a powerful tool to investigate the joint contribution of genetic, phenotypic and environmental factors to the development of a disease. Pooled-analysis of epidemiological studies has many advantages over meta-analysis, and preliminary results may be obtained faster and with lower costs than with prospective consortia. Design and methods Based on our experience with the study design of the Melanocortin-1 receptor (MC1R gene, SKin cancer and Phenotypic characteristics (M-SKIP project, we describe the most important steps in planning and conducting a pooled-analysis of genetic epidemiological studies. We then present the statistical analysis plan that we are going to apply, giving particular attention to methods of analysis recently proposed to account for between-study heterogeneity and to explore the joint contribution of genetic, phenotypic and environmental factors in the development of a disease. Within the M-SKIP project, data on 10,959 skin cancer cases and 14,785 controls from 31 international investigators were checked for quality and recoded for standardization. We first proposed to fit the aggregated data with random-effects logistic regression models. However, for the M-SKIP project, a two-stage analysis will be preferred to overcome the problem regarding the availability of different study covariates. The joint contribution of MC1R variants and phenotypic characteristics to skin cancer development will be studied via logic regression modeling. Discussion Methodological guidelines to correctly design and conduct pooled-analyses are needed to facilitate application of such methods, thus providing a better summary of the actual findings on specific fields.

Melanocortin-1 receptor, skin cancer and phenotypic characteristics (M-SKIP) project: study design and methods for pooling results of genetic epidemiological studies

Science.gov (United States)

2012-01-01

Background For complex diseases like cancer, pooled-analysis of individual data represents a powerful tool to investigate the joint contribution of genetic, phenotypic and environmental factors to the development of a disease. Pooled-analysis of epidemiological studies has many advantages over meta-analysis, and preliminary results may be obtained faster and with lower costs than with prospective consortia. Design and methods Based on our experience with the study design of the Melanocortin-1 receptor (MC1R) gene, SKin cancer and Phenotypic characteristics (M-SKIP) project, we describe the most important steps in planning and conducting a pooled-analysis of genetic epidemiological studies. We then present the statistical analysis plan that we are going to apply, giving particular attention to methods of analysis recently proposed to account for between-study heterogeneity and to explore the joint contribution of genetic, phenotypic and environmental factors in the development of a disease. Within the M-SKIP project, data on 10,959 skin cancer cases and 14,785 controls from 31 international investigators were checked for quality and recoded for standardization. We first proposed to fit the aggregated data with random-effects logistic regression models. However, for the M-SKIP project, a two-stage analysis will be preferred to overcome the problem regarding the availability of different study covariates. The joint contribution of MC1R variants and phenotypic characteristics to skin cancer development will be studied via logic regression modeling. Discussion Methodological guidelines to correctly design and conduct pooled-analyses are needed to facilitate application of such methods, thus providing a better summary of the actual findings on specific fields. PMID:22862891

Investigation of genetic diversity and epidemiological characteristics of Pasteurella multocida isolates from poultry in southwest China by population structure, multi-locus sequence typing and virulence-associated gene profile analysis.

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Li, Zhangcheng; Cheng, Fangjun; Lan, Shimei; Guo, Jianhua; Liu, Wei; Li, Xiaoyan; Luo, Zeli; Zhang, Manli; Wu, Juan; Shi, Yang

2018-04-25

Fowl cholera caused by Pasteurella multocida has always been a disease of global importance for poultry production. The aim of this study was to obtain more information about the epidemiology of avian P. multocida infection in southwest China and the genetic characteristics of clinical isolates. P. multocida isolates were characterized by biochemical and molecular-biological methods. The distributions of the capsular serogroups, the phenotypic antimicrobial resistance profiles, lipopolysaccharide (LPS) genotyping and the presence of 19 virulence genes were investigated in 45 isolates of P. multocida that were associated with clinical disease in poultry. The genetic diversity of P. multocida strains was performed by 16S rRNA and rpoB gene sequence analysis as well as multilocus sequence typing (MLST). The results showed that most (80.0%) of the P. multocida isolates in this study represented special P. multocida subspecies, and 71.1% of the isolates showed multiple-drug resistance. 45 isolates belonged to capsular types: A (100%) and two LPS genotypes: L1 (95.6%) and L3 (4.4%). MLST revealed two new alleles (pmi77 and gdh57) and one new sequence type (ST342). ST129 types dominated in 45 P. multocida isolates. Isolates belonging to ST129 were with the genes ompH+plpB+ptfA+tonB, whereas ST342 included isolates with fur+hgbA+tonB genes. Population genetic analysis and the MLST results revealed that at least one new ST genotype was present in the avian P. multocida in China. These findings provide novel insights into the epidemiological characteristics of avian P. multocida isolates in southwest China.

Population genetic analysis of Enterocytozoon bieneusi in humans.

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Li, Wei; Cama, Vitaliano; Feng, Yaoyu; Gilman, Robert H; Bern, Caryn; Zhang, Xichen; Xiao, Lihua

2012-01-01

Genotyping based on sequence analysis of the ribosomal internal transcribed spacer has revealed significant genetic diversity in Enterocytozoonbieneusi. Thus far, the population genetics of E. bieneusi and its significance in the epidemiology of microsporidiosis have not been examined. In this study, a multilocus sequence typing of E. bieneusi in AIDS patients in Lima, Peru was conducted, using 72 specimens previously genotyped as A, D, IV, EbpC, WL11, Peru7, Peru8, Peru10 and Peru11 at the internal transcribed spacer locus. Altogether, 39 multilocus genotypes were identified among the 72 specimens. The observation of strong intragenic linkage disequilibria and limited genetic recombination among markers were indicative of an overall clonal population structure of E. bieneusi. Measures of pair-wise intergenic linkage disequilibria and a standardised index of association (IAS) based on allelic profile data further supported this conclusion. Both sequence-based and allelic profile-based phylogenetic analyses showed the presence of two genetically isolated groups in the study population, one (group 1) containing isolates of the anthroponotic internal transcribed spacer genotype A, and the other (group 2) containing isolates of multiple internal transcribed spacer genotypes (mainly genotypes D and IV) with zoonotic potential. The measurement of linkage disequilibria and recombination indicated group 2 had a clonal population structure, whereas group 1 had an epidemic population structure. The formation of the two sub-populations was confirmed by STRUCTURE and Wright's fixation index (FST) analyses. The data highlight the power of MLST in understanding the epidemiology of E. bieneusi. Published by Elsevier Ltd.

Integrating the landscape epidemiology and genetics of RNA viruses: rabies in domestic dogs as a model.

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Brunker, K; Hampson, K; Horton, D L; Biek, R

2012-12-01

Landscape epidemiology and landscape genetics combine advances in molecular techniques, spatial analyses and epidemiological models to generate a more real-world understanding of infectious disease dynamics and provide powerful new tools for the study of RNA viruses. Using dog rabies as a model we have identified how key questions regarding viral spread and persistence can be addressed using a combination of these techniques. In contrast to wildlife rabies, investigations into the landscape epidemiology of domestic dog rabies requires more detailed assessment of the role of humans in disease spread, including the incorporation of anthropogenic landscape features, human movements and socio-cultural factors into spatial models. In particular, identifying and quantifying the influence of anthropogenic features on pathogen spread and measuring the permeability of dispersal barriers are important considerations for planning control strategies, and may differ according to cultural, social and geographical variation across countries or continents. Challenges for dog rabies research include the development of metapopulation models and transmission networks using genetic information to uncover potential source/sink dynamics and identify the main routes of viral dissemination. Information generated from a landscape genetics approach will facilitate spatially strategic control programmes that accommodate for heterogeneities in the landscape and therefore utilise resources in the most cost-effective way. This can include the efficient placement of vaccine barriers, surveillance points and adaptive management for large-scale control programmes.

SimHap GUI: an intuitive graphical user interface for genetic association analysis.

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Carter, Kim W; McCaskie, Pamela A; Palmer, Lyle J

2008-12-25

Researchers wishing to conduct genetic association analysis involving single nucleotide polymorphisms (SNPs) or haplotypes are often confronted with the lack of user-friendly graphical analysis tools, requiring sophisticated statistical and informatics expertise to perform relatively straightforward tasks. Tools, such as the SimHap package for the R statistics language, provide the necessary statistical operations to conduct sophisticated genetic analysis, but lacks a graphical user interface that allows anyone but a professional statistician to effectively utilise the tool. We have developed SimHap GUI, a cross-platform integrated graphical analysis tool for conducting epidemiological, single SNP and haplotype-based association analysis. SimHap GUI features a novel workflow interface that guides the user through each logical step of the analysis process, making it accessible to both novice and advanced users. This tool provides a seamless interface to the SimHap R package, while providing enhanced functionality such as sophisticated data checking, automated data conversion, and real-time estimations of haplotype simulation progress. SimHap GUI provides a novel, easy-to-use, cross-platform solution for conducting a range of genetic and non-genetic association analyses. This provides a free alternative to commercial statistics packages that is specifically designed for genetic association analysis.

Genetic relationships and epidemiological links between wild type 1 poliovirus isolates in Pakistan and Afghanistan.

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Angez, Mehar; Shaukat, Shahzad; Alam, Muhammad M; Sharif, Salmaan; Khurshid, Adnan; Zaidi, Syed Sohail Zahoor

2012-02-22

Efforts have been made to eliminate wild poliovirus transmission since 1988 when the World Health Organization began its global eradication campaign. Since then, the incidence of polio has decreased significantly. However, serotype 1 and serotype 3 still circulate endemically in Pakistan and Afghanistan. Both countries constitute a single epidemiologic block representing one of the three remaining major global reservoirs of poliovirus transmission. In this study we used genetic sequence data to investigate transmission links among viruses from diverse locations during 2005-2007. In order to find the origins and routes of wild type 1 poliovirus circulation, polioviruses were isolated from faecal samples of Acute Flaccid Paralysis (AFP) patients. We used viral cultures, two intratypic differentiation methods PCR, ELISA to characterize as vaccine or wild type 1 and nucleic acid sequencing of entire VP1 region of poliovirus genome to determine the genetic relatedness. One hundred eleven wild type 1 poliovirus isolates were subjected to nucleotide sequencing for genetic variation study. Considering the 15% divergence of the sequences from Sabin 1, Phylogenetic analysis by MEGA software revealed that active inter and intra country transmission of many genetically distinct strains of wild poliovirus type 1 belonged to genotype SOAS which is indigenous in this region. By grouping wild type 1 polioviruses according to nucleotide sequence homology, three distinct clusters A, B and C were obtained with multiple chains of transmission together with some silent circulations represented by orphan lineages. Our results emphasize that there was a persistent transmission of wild type 1 polioviruses in Pakistan and Afghanistan during 2005-2007. The epidemiologic information provided by the sequence data can contribute to the formulation of better strategies for poliomyelitis control to those critical areas, associated with high risk population groups which include migrants

Genetic relationships and epidemiological links between wild type 1 poliovirus isolates in Pakistan and Afghanistan

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Angez Mehar

2012-02-01

Full Text Available Abstract Background/Aim Efforts have been made to eliminate wild poliovirus transmission since 1988 when the World Health Organization began its global eradication campaign. Since then, the incidence of polio has decreased significantly. However, serotype 1 and serotype 3 still circulate endemically in Pakistan and Afghanistan. Both countries constitute a single epidemiologic block representing one of the three remaining major global reservoirs of poliovirus transmission. In this study we used genetic sequence data to investigate transmission links among viruses from diverse locations during 2005-2007. Methods In order to find the origins and routes of wild type 1 poliovirus circulation, polioviruses were isolated from faecal samples of Acute Flaccid Paralysis (AFP patients. We used viral cultures, two intratypic differentiation methods PCR, ELISA to characterize as vaccine or wild type 1 and nucleic acid sequencing of entire VP1 region of poliovirus genome to determine the genetic relatedness. Results One hundred eleven wild type 1 poliovirus isolates were subjected to nucleotide sequencing for genetic variation study. Considering the 15% divergence of the sequences from Sabin 1, Phylogenetic analysis by MEGA software revealed that active inter and intra country transmission of many genetically distinct strains of wild poliovirus type 1 belonged to genotype SOAS which is indigenous in this region. By grouping wild type 1 polioviruses according to nucleotide sequence homology, three distinct clusters A, B and C were obtained with multiple chains of transmission together with some silent circulations represented by orphan lineages. Conclusion Our results emphasize that there was a persistent transmission of wild type1 polioviruses in Pakistan and Afghanistan during 2005-2007. The epidemiologic information provided by the sequence data can contribute to the formulation of better strategies for poliomyelitis control to those critical areas

Landscape genetics highlights the role of bank vole metapopulation dynamics in the epidemiology of Puumala hantavirus.

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Guivier, E; Galan, M; Chaval, Y; Xuéreb, A; Ribas Salvador, A; Poulle, M-L; Voutilainen, L; Henttonen, H; Charbonnel, N; Cosson, J F

2011-09-01

Rodent host dynamics and dispersal are thought to be critical for hantavirus epidemiology as they determine pathogen persistence and transmission within and between host populations. We used landscape genetics to investigate how the population dynamics of the bank vole Myodes glareolus, the host of Puumala hantavirus (PUUV), vary with forest fragmentation and influence PUUV epidemiology. We sampled vole populations within the Ardennes, a French PUUV endemic area. We inferred demographic features such as population size, isolation and migration with regard to landscape configuration. We next analysed the influence of M. glareolus population dynamics on PUUV spatial distribution. Our results revealed that the global metapopulation dynamics of bank voles were strongly shaped by landscape features, including suitable patch size and connectivity. Large effective size in forest might therefore contribute to the higher observed levels of PUUV prevalence. By contrast, populations from hedge networks highly suffered from genetic drift and appeared strongly isolated from all other populations. This might result in high probabilities of local extinction for both M. glareolus and PUUV. Besides, we detected signatures of asymmetric bank vole migration from forests to hedges. These movements were likely to sustain PUUV in fragmented landscapes. In conclusion, our study provided arguments in favour of source-sink dynamics shaping PUUV persistence and spread in heterogeneous, Western European temperate landscapes. It illustrated the potential contribution of landscape genetics to the understanding of the epidemiological processes occurring at this local scale. © 2011 Blackwell Publishing Ltd.

A genetic analysis of Trichuris trichiura and Trichuris suis from Ecuador.

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Meekums, Hayley; Hawash, Mohamed B F; Sparks, Alexandra M; Oviedo, Yisela; Sandoval, Carlos; Chico, Martha E; Stothard, J Russell; Cooper, Philip J; Nejsum, Peter; Betson, Martha

2015-03-19

Since the nematodes Trichuris trichiura and T. suis are morphologically indistinguishable, genetic analysis is required to assess epidemiological cross-over between people and pigs. This study aimed to clarify the transmission biology of trichuriasis in Ecuador. Adult Trichuris worms were collected during a parasitological survey of 132 people and 46 pigs in Esmeraldas Province, Ecuador. Morphometric analysis of 49 pig worms and 64 human worms revealed significant variation. In discriminant analysis morphometric characteristics correctly classified male worms according to host species. In PCR-RFLP analysis of the ribosomal Internal Transcribed Spacer (ITS-2) and 18S DNA (59 pig worms and 82 human worms), nearly all Trichuris exhibited expected restriction patterns. However, two pig-derived worms showed a "heterozygous-type" ITS-2 pattern, with one also having a "heterozygous-type" 18S pattern. Phylogenetic analysis of the mitochondrial large ribosomal subunit partitioned worms by host species. Notably, some Ecuadorian T. suis clustered with porcine Trichuris from USA and Denmark and some with Chinese T. suis. This is the first study in Latin America to genetically analyse Trichuris parasites. Although T. trichiura does not appear to be zoonotic in Ecuador, there is evidence of genetic exchange between T. trichiura and T. suis warranting more detailed genetic sampling.

Genetic characterization, molecular epidemiology, and phylogenetic relationships of insect-specific viruses in the taxon Negevirus.

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Nunes, Marcio R T; Contreras-Gutierrez, María Angélica; Guzman, Hilda; Martins, Livia C; Barbirato, Mayla Feitoza; Savit, Chelsea; Balta, Victoria; Uribe, Sandra; Vivero, Rafael; Suaza, Juan David; Oliveira, Hamilton; Nunes Neto, Joaquin P; Carvalho, Valeria L; da Silva, Sandro Patroca; Cardoso, Jedson F; de Oliveira, Rodrigo Santo; da Silva Lemos, Poliana; Wood, Thomas G; Widen, Steven G; Vasconcelos, Pedro F C; Fish, Durland; Vasilakis, Nikos; Tesh, Robert B

2017-04-01

The recently described taxon Negevirus is comprised of a diverse group of insect-specific viruses isolated from mosquitoes and phlebotomine sandflies. In this study, a comprehensive genetic characterization, molecular, epidemiological and evolutionary analyses were conducted on nearly full-length sequences of 91 new negevirus isolates obtained in Brazil, Colombia, Peru, Panama, USA and Nepal. We demonstrated that these arthropod restricted viruses are clustered in two major phylogenetic groups with origins related to three plant virus genera (Cilevirus, Higrevirus and Blunevirus). Molecular analyses demonstrated that specific host correlations are not present with most negeviruses; instead, high genetic variability, wide host-range, and cross-species transmission were noted. The data presented here also revealed the existence of five novel insect-specific viruses falling into two arthropod-restrictive virus taxa, previously proposed as distinct genera, designated Nelorpivirus and Sandewavirus. Our results provide a better understanding of the molecular epidemiology, evolution, taxonomy and stability of this group of insect-restricted viruses. Copyright © 2017 Elsevier Inc. All rights reserved.

Spatial evolutionary epidemiology of spreading epidemics.

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Lion, S; Gandon, S

2016-10-26

Most spatial models of host-parasite interactions either neglect the possibility of pathogen evolution or consider that this process is slow enough for epidemiological dynamics to reach an equilibrium on a fast timescale. Here, we propose a novel approach to jointly model the epidemiological and evolutionary dynamics of spatially structured host and pathogen populations. Starting from a multi-strain epidemiological model, we use a combination of spatial moment equations and quantitative genetics to analyse the dynamics of mean transmission and virulence in the population. A key insight of our approach is that, even in the absence of long-term evolutionary consequences, spatial structure can affect the short-term evolution of pathogens because of the build-up of spatial differentiation in mean virulence. We show that spatial differentiation is driven by a balance between epidemiological and genetic effects, and this quantity is related to the effect of kin competition discussed in previous studies of parasite evolution in spatially structured host populations. Our analysis can be used to understand and predict the transient evolutionary dynamics of pathogens and the emergence of spatial patterns of phenotypic variation. © 2016 The Author(s).

Genetic and Molecular Epidemiological Characterization of a Novel Adenovirus in Antarctic Penguins Collected between 2008 and 2013.

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Sook-Young Lee

Full Text Available Antarctica is considered a relatively uncontaminated region with regard to the infectious diseases because of its extreme environment, and isolated geography. For the genetic characterization and molecular epidemiology of the newly found penguin adenovirus in Antarctica, entire genome sequencing and annual survey of penguin adenovirus were conducted. The entire genome sequences of penguin adenoviruses were completed for two Chinstrap penguins (Pygoscelis antarctica and two Gentoo penguins (Pygoscelis papua. The whole genome lengths and G+C content of penguin adenoviruses were found to be 24,630-24,662 bp and 35.5-35.6%, respectively. Notably, the presence of putative sialidase gene was not identified in penguin adenoviruses by Rapid Amplification of cDNA Ends (RACE-PCR as well as consensus specific PCR. The penguin adenoviruses were demonstrated to be a new species within the genus Siadenovirus, with a distance of 29.9-39.3% (amino acid, 32.1-47.9% in DNA polymerase gene, and showed the closest relationship with turkey adenovirus 3 (TAdV-3 in phylogenetic analysis. During the 2008-2013 study period, the penguin adenoviruses were annually detected in 22 of 78 penguins (28.2%, and the molecular epidemiological study of the penguin adenovirus indicates a predominant infection in Chinstrap penguin population (12/30, 40%. Interestingly, the genome of penguin adenovirus could be detected in several internal samples, except the lymph node and brain. In conclusion, an analysis of the entire adenoviral genomes from Antarctic penguins was conducted, and the penguin adenoviruses, containing unique genetic character, were identified as a new species within the genus Siadenovirus. Moreover, it was annually detected in Antarctic penguins, suggesting its circulation within the penguin population.

Genetic Epidemiology of Type 2 Diabetes in Mexican Mestizos

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Eiralí Guadalupe García-Chapa

2017-01-01

Full Text Available There are currently about 415 million people with diabetes worldwide, a figure likely to increase to 642 million by 2040. In 2015, Mexico was the second Latin American country and sixth in the world in prevalence of this disorder with nearly 11.5 million of patients. Type 2 diabetes (T2D is the main kind of diabetes and its etiology is complex with environmental and genetic factors involved. Indeed, polymorphisms in several genes have been associated with this disease worldwide. To estimate the genetic epidemiology of T2D in Mexican mestizos a systematic bibliographic search of published articles through PubMed, Scopus, Google Scholar, and Web of Science was conducted. Just case-control studies of candidate genes about T2D in Mexican mestizo inhabitants were included. Nineteen studies that met the inclusion criteria were found. In total, 68 polymorphisms of 41 genes were assessed; 26 of them were associated with T2D risk, which were located in ABCA1, ADRB3, CAPN10, CDC123/CAMK1D, CDKAL1, CDKN2A/2B, CRP, ELMO1, FTO, HHEX, IGF2BP2, IRS1, JAZF1, KCNQ1, LOC387761, LTA, NXPH1, SIRT1, SLC30A8, TCF7L2, and TNF-α genes. Overall, 21 of the 41 analyzed genes were associated with T2D in Mexican mestizos. Such a genetic heterogeneity compares with findings in other ethnic groups.

Comparative review of human and canine osteosarcoma: morphology, epidemiology, prognosis, treatment and genetics.

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Simpson, Siobhan; Dunning, Mark David; de Brot, Simone; Grau-Roma, Llorenç; Mongan, Nigel Patrick; Rutland, Catrin Sian

2017-10-24

Osteosarcoma (OSA) is a rare cancer in people. However OSA incidence rates in dogs are 27 times higher than in people. Prognosis in both species is relatively poor, with 5 year OSA survival rates in people not having improved in decades. For dogs, 1 year survival rates are only around ~ 45%. Improved and novel treatment regimens are urgently required to improve survival in both humans and dogs with OSA. Utilising information from genetic studies could assist in this in both species, with the higher incidence rates in dogs contributing to the dog population being a good model of human disease. This review compares the clinical characteristics, gross morphology and histopathology, aetiology, epidemiology, and genetics of canine and human OSA. Finally, the current position of canine OSA genetic research is discussed and areas for additional work within the canine population are identified.

[Genetic, epidemiologic and clinical study of familial prostate cancer].

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Valéri, Antoine

2002-01-01

Prostate cancer (CaP) is the most frequent cancer among men over 50 and its frequency increases with age. It has become a significant public health problem due to the ageing population. Epidemiologists report familial aggregation in 15 to 25% of cases and inherited susceptibility with autosomal dominant or X-linked model in 5 to 10% of cases. Clinical and biological features of familial CaP remain controversial. To perform: (1) Genetic study of familial Cap (mapping of susceptibility genes), (2) epidemiologic study (prevalence, associated cancers in the genealogy, model of transmission), and clinical study of familial CaP. (I) conducting a nationwide family collection (ProGène study) with 2+ CaP we have performed a genomewide linkage analysis and identified a predisposing locus on 1q42.2-43 named PCaP (Predisposing to Cancer of the Prostate); (II) conducting a systematic genealogic analysis of 691 CaP followed up in 3 University departments of urology (Hospitals of Brest, Paris St Louis and Nancy) we have observed: (1) 14.2% of familial and 3.6% of hereditary CaP, (2) a higher risk of breast cancer in first degree relatives of probands (CaP+) in familial CaP than in sporadic CaP and in early onset CaP (< 55 years) when compared with late onset CaP ([dG]75 years), (3) an autosomal dominant model with brother-brother dependance), (4) the lack of specific clinical or biological feature (except for early onset) in hereditary CaP when compared with sporadic CaP. (1) The mapping of a susceptibility locus will permit the cloning of a predisposing gene on 1q42.2-43, offer the possibility of genetic screening in families at risk and permit genotype/phenotype correlation studies; (2) the transmission model will improve parameteric linkage studies; (3) the lack of distinct specific clinical patterns suggest diagnostic and follow up modalities for familial and hereditary CaP similar to sporadic cancer while encouraging early screening of families at risk, given the earlier

Meta-analysis in epidemiology | Yach | South African Medical Journal

African Journals Online (AJOL)

Meta-analysis is the structured and systematic qualitative and quantitative integration of the results of several independent studies (Le. the epidemiology of results). As in any epidemiological study, a meta-analysis needs to start with clearly stated aims and objectives. Attention needs to be paid to selection bias in selecting ...

Gene Set Analyses of Genome-Wide Association Studies on 49 Quantitative Traits Measured in a Single Genetic Epidemiology Dataset

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Jihye Kim

2013-09-01

Full Text Available Gene set analysis is a powerful tool for interpreting a genome-wide association study result and is gaining popularity these days. Comparison of the gene sets obtained for a variety of traits measured from a single genetic epidemiology dataset may give insights into the biological mechanisms underlying these traits. Based on the previously published single nucleotide polymorphism (SNP genotype data on 8,842 individuals enrolled in the Korea Association Resource project, we performed a series of systematic genome-wide association analyses for 49 quantitative traits of basic epidemiological, anthropometric, or blood chemistry parameters. Each analysis result was subjected to subsequent gene set analyses based on Gene Ontology (GO terms using gene set analysis software, GSA-SNP, identifying a set of GO terms significantly associated to each trait (pcorr < 0.05. Pairwise comparison of the traits in terms of the semantic similarity in their GO sets revealed surprising cases where phenotypically uncorrelated traits showed high similarity in terms of biological pathways. For example, the pH level was related to 7 other traits that showed low phenotypic correlations with it. A literature survey implies that these traits may be regulated partly by common pathways that involve neuronal or nerve systems.

Chapter 2. Fasciola, lymnaeids and human fascioliasis, with a global overview on disease transmission, epidemiology, evolutionary genetics, molecular epidemiology and control.

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Mas-Coma, Santiago; Valero, María Adela; Bargues, María Dolores

2009-01-01

Fascioliasis, caused by liver fluke species of the genus Fasciola, has always been well recognized because of its high veterinary impact but it has been among the most neglected diseases for decades with regard to human infection. However, the increasing importance of human fascioliasis worldwide has re-launched interest in fascioliasis. From the 1990s, many new concepts have been developed regarding human fascioliasis and these have furnished a new baseline for the human disease that is very different to a simple extrapolation from fascioliasis in livestock. Studies have shown that human fascioliasis presents marked heterogeneity, including different epidemiological situations and transmission patterns in different endemic areas. This heterogeneity, added to the present emergence/re-emergence of the disease both in humans and animals in many regions, confirms a worrying global scenario. The huge negative impact of fascioliasis on human communities demands rapid action. When analyzing how better to define control measures for endemic areas differing at such a level, it would be useful to have genetic markers that could distinguish each type of transmission pattern and epidemiological situation. Accordingly, this chapter covers aspects of aetiology, geographical distribution, epidemiology, transmission and control in order to obtain a solid baseline for the interpretation of future results. The origins and geographical spread of F. hepatica and F. gigantica in both the ruminant pre-domestication times and the livestock post-domestication period are analyzed. Paleontological, archaeological and historical records, as well as genetic data on recent dispersal of livestock species, are taken into account to establish an evolutionary framework for the two fasciolids across all continents. Emphasis is given to the distributional overlap of both species and the roles of transportation, transhumance and trade in the different overlap situations. Areas with only one Fasciola

Familial clustering and genetic risk for dementia in a genetically isolated Dutch population.

NARCIS (Netherlands)

K. Sleegers (Kristel); F. Forey; J. Theuns (Jessie); Y.S. Aulchenko (Yurii); S. Rademakers (Suzanne); M. Cruts (Marc); W.A. van Gool (Willem); P. Heutink (Peter); B.A. Oostra (Ben); J.C. van Swieten (John); C.M. van Duijn (Cornelia); C. van Broeckhoven (Christine)

2004-01-01

textabstractDespite advances in elucidating the genetic epidemiology of Alzheimer's disease and frontotemporal dementia, the aetiology for most patients with dementia remains unclear. We examined the genetic epidemiology of dementia in a recent genetically isolated Dutch population founded around

Familial clustering and genetic risk for dementia in a genetically isolated Dutch population

NARCIS (Netherlands)

Sleegers, K.; Roks, G.; Theuns, J.; Aulchenko, Y. S.; Rademakers, R.; Cruts, M.; van Gool, W. A.; van Broeckhoven, C.; Heutink, P.; Oostra, B. A.; van Swieten, J. C.; van Duijn, C. M.

2004-01-01

Despite advances in elucidating the genetic epidemiology of Alzheimer's disease and frontotemporal dementia, the aetiology for most patients with dementia remains unclear. We examined the genetic epidemiology of dementia in a recent genetically isolated Dutch population founded around 1750. The

[Causal analysis approaches in epidemiology].

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Dumas, O; Siroux, V; Le Moual, N; Varraso, R

2014-02-01

Epidemiological research is mostly based on observational studies. Whether such studies can provide evidence of causation remains discussed. Several causal analysis methods have been developed in epidemiology. This paper aims at presenting an overview of these methods: graphical models, path analysis and its extensions, and models based on the counterfactual approach, with a special emphasis on marginal structural models. Graphical approaches have been developed to allow synthetic representations of supposed causal relationships in a given problem. They serve as qualitative support in the study of causal relationships. The sufficient-component cause model has been developed to deal with the issue of multicausality raised by the emergence of chronic multifactorial diseases. Directed acyclic graphs are mostly used as a visual tool to identify possible confounding sources in a study. Structural equations models, the main extension of path analysis, combine a system of equations and a path diagram, representing a set of possible causal relationships. They allow quantifying direct and indirect effects in a general model in which several relationships can be tested simultaneously. Dynamic path analysis further takes into account the role of time. The counterfactual approach defines causality by comparing the observed event and the counterfactual event (the event that would have been observed if, contrary to the fact, the subject had received a different exposure than the one he actually received). This theoretical approach has shown limits of traditional methods to address some causality questions. In particular, in longitudinal studies, when there is time-varying confounding, classical methods (regressions) may be biased. Marginal structural models have been developed to address this issue. In conclusion, "causal models", though they were developed partly independently, are based on equivalent logical foundations. A crucial step in the application of these models is the

eCOMPAGT – efficient Combination and Management of Phenotypes and Genotypes for Genetic Epidemiology

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Specht Günther

2009-05-01

Full Text Available Abstract Background High-throughput genotyping and phenotyping projects of large epidemiological study populations require sophisticated laboratory information management systems. Most epidemiological studies include subject-related personal information, which needs to be handled with care by following data privacy protection guidelines. In addition, genotyping core facilities handling cooperative projects require a straightforward solution to monitor the status and financial resources of the different projects. Description We developed a database system for an efficient combination and management of phenotypes and genotypes (eCOMPAGT deriving from genetic epidemiological studies. eCOMPAGT securely stores and manages genotype and phenotype data and enables different user modes with different rights. Special attention was drawn on the import of data deriving from TaqMan and SNPlex genotyping assays. However, the database solution is adjustable to other genotyping systems by programming additional interfaces. Further important features are the scalability of the database and an export interface to statistical software. Conclusion eCOMPAGT can store, administer and connect phenotype data with all kinds of genotype data and is available as a downloadable version at http://dbis-informatik.uibk.ac.at/ecompagt.

The systematics and population genetics of Opisthorchis viverrini sensu lato: implications in parasite epidemiology and bile duct cancer.

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Sithithaworn, Paiboon; Andrews, Ross H; Petney, Trevor N; Saijuntha, Weerachai; Laoprom, Nonglak

2012-03-01

Together with host and environmental factors, the systematics and population genetic variation of Opisthorchis viverrini may contribute to recorded local and regional differences in epidemiology and host morbidity in opisthorchiasis and cholangiocarcinoma (CCA). In this review, we address recent findings that O. viverrini comprises a species complex with varying degrees of population genetic variation which are associated with specific river wetland systems within Thailand as well as the Lao PDR. Having an accurate understanding of systematics is a prerequisite for a meaningful assessment of the population structure of each species within the O. viverrini complex in nature, as well as a better understanding of the magnitude of genetic variation that occurs within different species of hosts in its life cycle. Whether specific genotypes are related to habitat type(s) and/or specific intermediate host species are discussed based on current available data. Most importantly, we focus on whether there is a correlation between incidence of CCA and genotype(s) of O. viverrini. This will provide a solid basis for further comprehensive investigations of the role of genetic variation within each species of O. viverrini sensu lato in human epidemiology and genotype related morbidity as well as co-evolution of parasites with primary and secondary intermediate species of host. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Molecular surveillance of norovirus, 2005-16 : an epidemiological analysis of data collected from the NoroNet network

NARCIS (Netherlands)

van Beek, Janko; de Graaf, Miranda; Al-Hello, Haider; Allen, David J; Ambert-Balay, Katia; Botteldoorn, Nadine; Brytting, Mia; Buesa, Javier; Cabrerizo, Maria; Chan, Martin; Cloak, Fiona; Di Bartolo, Ilaria; Guix, Susana; Hewitt, Joanne; Iritani, Nobuhiro; Jin, Miao; Johne, Reimar; Lederer, Ingeborg; Mans, Janet; Martella, Vito; Maunula, Leena; McAllister, Georgina; Niendorf, Sandra; Niesters, Hubert G; Podkolzin, Alexander T; Poljsak-Prijatelj, Mateja; Rasmussen, Lasse Dam; Reuter, Gábor; Tuite, Gráinne; Kroneman, Annelies; Vennema, Harry; Koopmans, Marion P G

BACKGROUND: The development of a vaccine for norovirus requires a detailed understanding of global genetic diversity of noroviruses. We analysed their epidemiology and diversity using surveillance data from the NoroNet network. METHODS: We included genetic sequences of norovirus specimens obtained

Genetic Characterization and Comparative Genome Analysis of Brucella melitensis Isolates from India

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Sarwar Azam

2016-01-01

Full Text Available Brucellosis is the most frequent zoonotic disease worldwide, with over 500,000 new human infections every year. Brucella melitensis, the most virulent species in humans, primarily affects goats and the zoonotic transmission occurs by ingestion of unpasteurized milk products or through direct contact with fetal tissues. Brucellosis is endemic in India but no information is available on population structure and genetic diversity of Brucella spp. in India. We performed multilocus sequence typing of four B. melitensis strains isolated from naturally infected goats from India. For more detailed genetic characterization, we carried out whole genome sequencing and comparative genome analysis of one of the B. melitensis isolates, Bm IND1. Genome analysis identified 141 unique SNPs, 78 VNTRs, 51 Indels, and 2 putative prophage integrations in the Bm IND1 genome. Our data may help to develop improved epidemiological typing tools and efficient preventive strategies to control brucellosis.

High-resolution minisatellite-based typing as a portable approach to global analysis of Mycobacterium tuberculosis molecular epidemiology

Science.gov (United States)

Mazars, Edith; Lesjean, Sarah; Banuls, Anne-Laure; Gilbert, Michèle; Vincent, Véronique; Gicquel, Brigitte; Tibayrenc, Michel; Locht, Camille; Supply, Philip

2001-01-01

The worldwide threat of tuberculosis to human health emphasizes the need to develop novel approaches to a global epidemiological surveillance. The current standard for Mycobacterium tuberculosis typing based on IS6110 restriction fragment length polymorphism (RFLP) suffers from the difficulty of comparing data between independent laboratories. Here, we propose a high-resolution typing method based on variable number tandem repeats (VNTRs) of genetic elements named mycobacterial interspersed repetitive units (MIRUs) in 12 human minisatellite-like regions of the M. tuberculosis genome. MIRU-VNTR profiles of 72 different M. tuberculosis isolates were established by PCR analysis of all 12 loci. From 2 to 8 MIRU-VNTR alleles were identified in the 12 regions in these strains, which corresponds to a potential of over 16 million different combinations, yielding a resolution power close to that of IS6110-RFLP. All epidemiologically related isolates tested were perfectly clustered by MIRU-VNTR typing, indicating that the stability of these MIRU-VNTRs is adequate to track outbreak episodes. The correlation between genetic relationships inferred from MIRU-VNTR and IS6110-RFLP typing was highly significant. Compared with IS6110-RFLP, high-resolution MIRU-VNTR typing has the considerable advantages of being fast, appropriate for all M. tuberculosis isolates, including strains that have a few IS6110 copies, and permitting easy and rapid comparison of results from independent laboratories. This typing method opens the way to the construction of digital global databases for molecular epidemiology studies of M. tuberculosis. PMID:11172048

Epidemiology and genetics of intracranial aneurysms

International Nuclear Information System (INIS)

Caranci, F.; Briganti, F.; Cirillo, L.; Leonardi, M.; Muto, M.

2013-01-01

Intracranial aneurysms are acquired lesions (5–10% of the population), a fraction of which rupture leading to subarachnoid hemorrhage with devastating consequences. Until now, the exact etiology of intracranial aneurysms formation remains unclear. The low incidence of subarachnoid hemorrhage in comparison with the prevalence of unruptured IAs suggests that the vast majority of intracranial aneurysms do not rupture and that identifying those at highest risk is important in defining the optimal management. The most important factors predicting rupture are aneurysm size and site. In addition to ambiental factors (smoking, excessive alcohol consumption and hypertension), epidemiological studies have demonstrated a familiar influence contributing to the pathogenesis of intracranial aneurysms, with increased frequency in first- and second-degree relatives of people with subarachnoid hemorrhage. In comparison to sporadic aneurysms, familial aneurysms tend to be larger, more often located at the middle cerebral artery, and more likely to be multiple. Other than familiar occurrence, there are several heritable conditions associated with intracranial aneurysm formation, including autosomal dominant polycystic kidney disease, neurofibromatosis type I, Marfan syndrome, multiple endocrine neoplasia type I, pseudoxanthoma elasticum, hereditary hemorrhagic telangiectasia, and Ehlers-Danlos syndrome type II and IV. The familial occurrence and the association with heritable conditions indicate that genetic factors may play a role in the development of intracranial aneurysms. Genome-wide linkage studies in families and sib pairs with intracranial aneurysms have identified several loci on chromosomes showing suggestive evidence of linkage, particularly on chromosomes 1p34.3–p36.13, 7q11, 19q13.3, and Xp22. For the loci on 1p34.3–p36.13 and 7q11, a moderate positive association with positional candidate genes has been demonstrated (perlecan gene, elastin gene, collagen type 1 A2

Epidemiology and genetics of intracranial aneurysms

Energy Technology Data Exchange (ETDEWEB)

Caranci, F., E-mail: ferdinandocaranci@libero.it [Unit of Neuroradiology, Department of Diagnostic Radiology and Radiotherapy, Federico II University, Naples (Italy); Briganti, F., E-mail: frabriga@unina.it [Unit of Neuroradiology, Department of Diagnostic Radiology and Radiotherapy, Federico II University, Naples (Italy); Cirillo, L.; Leonardi, M. [Neuroradiology service, Bellaria Hospital, Bologna (Italy); Muto, M., E-mail: mutomar@tiscali.it [Neuroradiology Service Cardarelli Hospital Naples (Italy)

2013-10-01

Intracranial aneurysms are acquired lesions (5–10% of the population), a fraction of which rupture leading to subarachnoid hemorrhage with devastating consequences. Until now, the exact etiology of intracranial aneurysms formation remains unclear. The low incidence of subarachnoid hemorrhage in comparison with the prevalence of unruptured IAs suggests that the vast majority of intracranial aneurysms do not rupture and that identifying those at highest risk is important in defining the optimal management. The most important factors predicting rupture are aneurysm size and site. In addition to ambiental factors (smoking, excessive alcohol consumption and hypertension), epidemiological studies have demonstrated a familiar influence contributing to the pathogenesis of intracranial aneurysms, with increased frequency in first- and second-degree relatives of people with subarachnoid hemorrhage. In comparison to sporadic aneurysms, familial aneurysms tend to be larger, more often located at the middle cerebral artery, and more likely to be multiple. Other than familiar occurrence, there are several heritable conditions associated with intracranial aneurysm formation, including autosomal dominant polycystic kidney disease, neurofibromatosis type I, Marfan syndrome, multiple endocrine neoplasia type I, pseudoxanthoma elasticum, hereditary hemorrhagic telangiectasia, and Ehlers-Danlos syndrome type II and IV. The familial occurrence and the association with heritable conditions indicate that genetic factors may play a role in the development of intracranial aneurysms. Genome-wide linkage studies in families and sib pairs with intracranial aneurysms have identified several loci on chromosomes showing suggestive evidence of linkage, particularly on chromosomes 1p34.3–p36.13, 7q11, 19q13.3, and Xp22. For the loci on 1p34.3–p36.13 and 7q11, a moderate positive association with positional candidate genes has been demonstrated (perlecan gene, elastin gene, collagen type 1 A2

Microsatellite analysis of chloroquine resistance associated alleles and neutral loci reveal genetic structure of Indian Plasmodium falciparum.

Science.gov (United States)

Mallick, Prashant K; Sutton, Patrick L; Singh, Ruchi; Singh, Om P; Dash, Aditya P; Singh, Ashok K; Carlton, Jane M; Bhasin, Virendra K

2013-10-01

Efforts to control malignant malaria caused by Plasmodium falciparum are hampered by the parasite's acquisition of resistance to antimalarial drugs, e.g., chloroquine. This necessitates evaluating the spread of chloroquine resistance in any malaria-endemic area. India displays highly variable malaria epidemiology and also shares porous international borders with malaria-endemic Southeast Asian countries having multi-drug resistant malaria. Malaria epidemiology in India is believed to be affected by two major factors: high genetic diversity and evolving drug resistance in P. falciparum. How transmission intensity of malaria can influence the genetic structure of chloroquine-resistant P. falciparum population in India is unknown. Here, genetic diversity within and among P. falciparum populations is analyzed with respect to their prevalence and chloroquine resistance observed in 13 different locations in India. Microsatellites developed for P. falciparum, including three putatively neutral and seven microsatellites thought to be under a hitchhiking effect due to chloroquine selection were used. Genetic hitchhiking is observed in five of seven microsatellites flanking the gene responsible for chloroquine resistance. Genetic admixture analysis and F-statistics detected genetically distinct groups in accordance with transmission intensity of different locations and the probable use of chloroquine. A large genetic break between the chloroquine-resistant parasite of the Northeast-East-Island group and Southwest group (FST=0.253, Pstructure for Indian P. falciparum population. Overall, the study suggests that transmission intensity can be an efficient driver for genetic differentiation at both neutral and adaptive loci across India. Copyright © 2013 Elsevier B.V. All rights reserved.

Genetic epidemiology, hematological and clinical features of hemoglobinopathies in Iran.

Science.gov (United States)

Rahimi, Zohreh

2013-01-01

There is large variation in the molecular genetics and clinical features of hemoglobinopathies in Iran. Studying structural variants of hemoglobin demonstrated that the β-chain variants of hemoglobin S and D-Punjab are more prevalent in the Fars (southwestern Iran) and Kermanshah (western Iran) provinces, respectively. Also, α-chain variants of Hb Q-Iran and Hb Setif are prevalent in western Iran. The molecular basis and clinical severity of thalassemias are extremely heterogenous among Iranians due to the presence of multiethnic groups in the country. β-Thalassemia is more prevalent in northern and southern Iran. Among 52 different β-thalassemia mutations that have been identified among Iranian populations, IVSII-1 G:A is the most frequent mutation in most parts of the country. The presence of IVS I-5 G:C mutation with high frequency in southeastern Iran might reflect gene flow from neighboring countries. A wide spectrum of α-thalassemia alleles has been detected among Iranians with -α(3.7 kb) as the most prevalent α-thalassemia mutation. The prevention program of thalassemia birth in Iran has reduced the birth rate of homozygous β-thalassemia since the implementation of the program in 1997. In this review genetic epidemiology, clinical and hematological aspects of hemoglobinopathies, and the prevention programs of β-thalassemia in Iran will be discussed.

Genetic Epidemiology, Hematological and Clinical Features of Hemoglobinopathies in Iran

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Zohreh Rahimi

2013-01-01

Full Text Available There is large variation in the molecular genetics and clinical features of hemoglobinopathies in Iran. Studying structural variants of hemoglobin demonstrated that the β-chain variants of hemoglobin S and D-Punjab are more prevalent in the Fars (southwestern Iran and Kermanshah (western Iran provinces, respectively. Also, α-chain variants of Hb Q-Iran and Hb Setif are prevalent in western Iran. The molecular basis and clinical severity of thalassemias are extremely heterogenous among Iranians due to the presence of multiethnic groups in the country. β-Thalassemia is more prevalent in northern and southern Iran. Among 52 different β-thalassemia mutations that have been identified among Iranian populations, IVSII-1 G:A is the most frequent mutation in most parts of the country. The presence of IVS I-5 G:C mutation with high frequency in southeastern Iran might reflect gene flow from neighboring countries. A wide spectrum of α-thalassemia alleles has been detected among Iranians with as the most prevalent α-thalassemia mutation. The prevention program of thalassemia birth in Iran has reduced the birth rate of homozygous β-thalassemia since the implementation of the program in 1997. In this review genetic epidemiology, clinical and hematological aspects of hemoglobinopathies, and the prevention programs of β-thalassemia in Iran will be discussed.

Reporting of Human Genome Epidemiology (HuGE association studies: An empirical assessment

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Gwinn Marta

2008-05-01

Full Text Available Abstract Background Several thousand human genome epidemiology association studies are published every year investigating the relationship between common genetic variants and diverse phenotypes. Transparent reporting of study methods and results allows readers to better assess the validity of study findings. Here, we document reporting practices of human genome epidemiology studies. Methods Articles were randomly selected from a continuously updated database of human genome epidemiology association studies to be representative of genetic epidemiology literature. The main analysis evaluated 315 articles published in 2001–2003. For a comparative update, we evaluated 28 more recent articles published in 2006, focusing on issues that were poorly reported in 2001–2003. Results During both time periods, most studies comprised relatively small study populations and examined one or more genetic variants within a single gene. Articles were inconsistent in reporting the data needed to assess selection bias and the methods used to minimize misclassification (of the genotype, outcome, and environmental exposure or to identify population stratification. Statistical power, the use of unrelated study participants, and the use of replicate samples were reported more often in articles published during 2006 when compared with the earlier sample. Conclusion We conclude that many items needed to assess error and bias in human genome epidemiology association studies are not consistently reported. Although some improvements were seen over time, reporting guidelines and online supplemental material may help enhance the transparency of this literature.

Causal models in epidemiology: past inheritance and genetic future

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Kriebel David

2006-07-01

Full Text Available Abstract The eruption of genetic research presents a tremendous opportunity to epidemiologists to improve our ability to identify causes of ill health. Epidemiologists have enthusiastically embraced the new tools of genomics and proteomics to investigate gene-environment interactions. We argue that neither the full import nor limitations of such studies can be appreciated without clarifying underlying theoretical models of interaction, etiologic fraction, and the fundamental concept of causality. We therefore explore different models of causality in the epidemiology of disease arising out of genes, environments, and the interplay between environments and genes. We begin from Rothman's "pie" model of necessary and sufficient causes, and then discuss newer approaches, which provide additional insights into multifactorial causal processes. These include directed acyclic graphs and structural equation models. Caution is urged in the application of two essential and closely related concepts found in many studies: interaction (effect modification and the etiologic or attributable fraction. We review these concepts and present four important limitations. 1. Interaction is a fundamental characteristic of any causal process involving a series of probabilistic steps, and not a second-order phenomenon identified after first accounting for "main effects". 2. Standard methods of assessing interaction do not adequately consider the life course, and the temporal dynamics through which an individual's sufficient cause is completed. Different individuals may be at different stages of development along the path to disease, but this is not usually measurable. Thus, for example, acquired susceptibility in children can be an important source of variation. 3. A distinction must be made between individual-based and population-level models. Most epidemiologic discussions of causality fail to make this distinction. 4. At the population level, there is additional

Emergence of hepatitis C virus genotype 4: phylogenetic analysis reveals three distinct epidemiological profiles

NARCIS (Netherlands)

de Bruijne, Joep; Schinkel, Janke; Prins, Maria; Koekkoek, Sylvie M.; Aronson, Sem J.; van Ballegooijen, Marijn W.; Reesink, Hendrik W.; Molenkamp, Richard; van de Laar, Thijs J. W.

2009-01-01

Hepatitis C virus (HCV) genotype 4 (HCV-4) infection is considered to be difficult to treat and has become increasingly prevalent in European countries, including The Netherlands. Using a molecular epidemiological approach, the present study investigates the genetic diversity and evolutionary origin

Combining epidemiological and genetic networks signifies the importance of early treatment in HIV-1 transmission.

Science.gov (United States)

Zarrabi, Narges; Prosperi, Mattia; Belleman, Robert G; Colafigli, Manuela; De Luca, Andrea; Sloot, Peter M A

2012-01-01

Inferring disease transmission networks is important in epidemiology in order to understand and prevent the spread of infectious diseases. Reconstruction of the infection transmission networks requires insight into viral genome data as well as social interactions. For the HIV-1 epidemic, current research either uses genetic information of patients' virus to infer the past infection events or uses statistics of sexual interactions to model the network structure of viral spreading. Methods for a reliable reconstruction of HIV-1 transmission dynamics, taking into account both molecular and societal data are still lacking. The aim of this study is to combine information from both genetic and epidemiological scales to characterize and analyse a transmission network of the HIV-1 epidemic in central Italy.We introduce a novel filter-reduction method to build a network of HIV infected patients based on their social and treatment information. The network is then combined with a genetic network, to infer a hypothetical infection transmission network. We apply this method to a cohort study of HIV-1 infected patients in central Italy and find that patients who are highly connected in the network have longer untreated infection periods. We also find that the network structures for homosexual males and heterosexual populations are heterogeneous, consisting of a majority of 'peripheral nodes' that have only a few sexual interactions and a minority of 'hub nodes' that have many sexual interactions. Inferring HIV-1 transmission networks using this novel combined approach reveals remarkable correlations between high out-degree individuals and longer untreated infection periods. These findings signify the importance of early treatment and support the potential benefit of wide population screening, management of early diagnoses and anticipated antiretroviral treatment to prevent viral transmission and spread. The approach presented here for reconstructing HIV-1 transmission networks

Secondary Analysis and Integration of Existing Data to Elucidate the Genetic Architecture of Cancer Risk and Related Outcomes, R21 | Informatics Technology for Cancer Research (ITCR)

Science.gov (United States)

This funding opportunity announcement (FOA) encourages applications that propose to conduct secondary data analysis and integration of existing datasets and database resources, with the ultimate aim to elucidate the genetic architecture of cancer risk and related outcomes. The goal of this initiative is to address key scientific questions relevant to cancer epidemiology by supporting the analysis of existing genetic or genomic datasets, possibly in combination with environmental, outcomes, behavioral, lifestyle, and molecular profiles data.

Secondary Analysis and Integration of Existing Data to Elucidate the Genetic Architecture of Cancer Risk and Related Outcomes, R01 | Informatics Technology for Cancer Research (ITCR)

Science.gov (United States)

This funding opportunity announcement (FOA) encourages applications that propose to conduct secondary data analysis and integration of existing datasets and database resources, with the ultimate aim to elucidate the genetic architecture of cancer risk and related outcomes. The goal of this initiative is to address key scientific questions relevant to cancer epidemiology by supporting the analysis of existing genetic or genomic datasets, possibly in combination with environmental, outcomes, behavioral, lifestyle, and molecular profiles data.

Genetic epidemiology of motor neuron disease-associated variants in the Scottish population.

Science.gov (United States)

Black, Holly A; Leighton, Danielle J; Cleary, Elaine M; Rose, Elaine; Stephenson, Laura; Colville, Shuna; Ross, David; Warner, Jon; Porteous, Mary; Gorrie, George H; Swingler, Robert; Goldstein, David; Harms, Matthew B; Connick, Peter; Pal, Suvankar; Aitman, Timothy J; Chandran, Siddharthan

2017-03-01

Genetic understanding of motor neuron disease (MND) has evolved greatly in the past 10 years, including the recent identification of association between MND and variants in TBK1 and NEK1. Our aim was to determine the frequency of pathogenic variants in known MND genes and to assess whether variants in TBK1 and NEK1 contribute to the burden of MND in the Scottish population. SOD1, TARDBP, OPTN, TBK1, and NEK1 were sequenced in 441 cases and 400 controls. In addition to 44 cases known to carry a C9orf72 hexanucleotide repeat expansion, we identified 31 cases and 2 controls that carried a loss-of-function or pathogenic variant. Loss-of-function variants were found in TBK1 in 3 cases and no controls and, separately, in NEK1 in 3 cases and no controls. This study provides an accurate description of the genetic epidemiology of MND in Scotland and provides support for the contribution of both TBK1 and NEK1 to MND susceptibility in the Scottish population. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Molecular epidemiology of Epizootic haematopoietic necrosis virus (EHNV).

Science.gov (United States)

Hick, Paul M; Subramaniam, Kuttichantran; Thompson, Patrick M; Waltzek, Thomas B; Becker, Joy A; Whittington, Richard J

2017-11-01

Low genetic diversity of Epizootic haematopoietic necrosis virus (EHNV) was determined for the complete genome of 16 isolates spanning the natural range of hosts, geography and time since the first outbreaks of disease. Genomes ranged from 125,591-127,487 nucleotides with 97.47% pairwise identity and 106-109 genes. All isolates shared 101 core genes with 121 potential genes predicted within the pan-genome of this collection. There was high conservation within 90,181 nucleotides of the core genes with isolates separated by average genetic distance of 3.43 × 10 -4 substitutions per site. Evolutionary analysis of the core genome strongly supported historical epidemiological evidence of iatrogenic spread of EHNV to naïve hosts and establishment of endemic status in discrete ecological niches. There was no evidence of structural genome reorganization, however, the complement of non-core genes and variation in repeat elements enabled fine scale molecular epidemiological investigation of this unpredictable pathogen of fish. Copyright © 2017 Elsevier Inc. All rights reserved.

Microsatellite analysis of chloroquine resistance associated alleles and neutral loci reveal genetic structure of Indian Plasmodium falciparum

Science.gov (United States)

Mallick, Prashant K.; Sutton, Patrick L.; Singh, Ruchi; Singh, Om P.; Dash, Aditya P.; Singh, Ashok K.; Carlton, Jane M.; Bhasin, Virendra K.

2013-01-01

Efforts to control malignant malaria caused by Plasmodium falciparum are hampered by the parasite’s acquisition of resistance to antimalarial drugs, e.g., chloroquine. This necessitates evaluating the spread of chloroquine resistance in any malaria-endemic area. India displays highly variable malaria epidemiology and also shares porous international borders with malaria-endemic Southeast Asian countries having multi-drug resistant malaria. Malaria epidemiology in India is believed to be affected by two major factors: high genetic diversity and evolving drug resistance in P. falciparum. How transmission intensity of malaria can influence the genetic structure of chloroquine-resistant P. falciparum population in India is unknown. Here, genetic diversity within and among P. falciparum populations is analyzed with respect to their prevalence and chloroquine resistance observed in 13 different locations in India. Microsatellites developed for P. falciparum, including three putatively neutral and seven microsatellites thought to be under a hitchhiking effect due to chloroquine selection were used. Genetic hitchhiking is observed in five of seven microsatellites flanking the gene responsible for chloroquine resistance. Genetic admixture analysis and F-statistics detected genetically distinct groups in accordance with transmission intensity of different locations and the probable use of chloroquine. A large genetic break between the chloroquine-resistant parasite of the Northeast-East-Island group and Southwest group (FST = 0.253, P<0.001) suggests a long period of isolation or a possibility of different origin between them. A pattern of significant isolation by distance was observed in low transmission areas (r = 0.49, P=0.003, N = 83, Mantel test). An unanticipated pattern of spread of hitchhiking suggests genetic structure for Indian P. falciparum population. Overall, the study suggests that transmission intensity can be an efficient driver for genetic differentiation

Development and application of Human Genome Epidemiology

Science.gov (United States)

Xu, Jingwen

2017-12-01

Epidemiology is a science that studies distribution of diseases and health in population and its influencing factors, it also studies how to prevent and cure disease and promote health strategies and measures. Epidemiology has developed rapidly in recent years and it is an intercross subject with various other disciplines to form a series of branch disciplines such as Genetic epidemiology, molecular epidemiology, drug epidemiology and tumor epidemiology. With the implementation and completion of Human Genome Project (HGP), Human Genome Epidemiology (HuGE) has emerged at this historic moment. In this review, the development of Human Genome Epidemiology, research content, the construction and structure of relevant network, research standards, as well as the existing results and problems are briefly outlined.

Molecular Epidemiology and Genetic Variation of Pathogenic Vibrio parahaemolyticus in Peru

Science.gov (United States)

Gavilan, Ronnie G.; Zamudio, Maria L.; Martinez-Urtaza, Jaime

2013-01-01

Vibrio parahaemolyticus is a foodborne pathogen that has become a public health concern at the global scale. The epidemiological significance of V. parahaemolyticus infections in Latin America received little attention until the winter of 1997 when cases related to the pandemic clone were detected in the region, changing the epidemic dynamics of this pathogen in Peru. With the aim to assess the impact of the arrival of the pandemic clone on local populations of pathogenic V. parahaemolyticus in Peru, we investigated the population genetics and genomic variation in a complete collection of non-pandemic strains recovered from clinical sources in Peru during the pre- and post-emergence periods of the pandemic clone. A total of 56 clinical strains isolated in Peru during the period 1994 to 2007, 13 strains from Chile and 20 strains from Asia were characterized by Multilocus Sequence Typing (MLST) and checked for the presence of Variable Genomic Regions (VGRs). The emergence of O3:K6 cases in Peru implied a drastic disruption of the seasonal dynamics of infections and a shift in the serotype dominance of pathogenic V. parahaemolyticus. After the arrival of the pandemic clone, a great diversity of serovars not previously reported was detected in the country, which supports the introduction of additional populations cohabitating with the pandemic group. Moreover, the presence of genomic regions characteristic of the pandemic clone in other non-pandemic strains may represent early evidence of genetic transfer from the introduced population to the local communities. Finally, the results of this study stress the importance of population admixture, horizontal genetic transfer and homologous recombination as major events shaping the structure and diversity of pathogenic V. parahaemolyticus. PMID:23696906

The Complex Epidemiology of Carbapenem-Resistant Enterobacter Infections: A Multicenter Descriptive Analysis.

Science.gov (United States)

Lazarovitch, Tsilia; Amity, Keren; Coyle, Joseph R; Ackerman, Benjamin; Tal-Jasper, Ruthy; Ofer-Friedman, Hadas; Hayakawa, Kayoko; Bogan, Christopher; Lephart, Paul R; Kaplansky, Tamir; Maskit, Moran; Azouri, Tal; Zaidenstein, Ronit; Perez, Federico; Bonomo, Robert A; Kaye, Keith S; Marchaim, Dror

2015-11-01

The pandemic of carbapenem-resistant Enterobacteriaceae (CRE) was primarily due to clonal spread of bla KPC producing Klebsiella pneumoniae. Thus, thoroughly studied CRE cohorts have consisted mostly of K. pneumoniae. To conduct an extensive epidemiologic analysis of carbapenem-resistant Enterobacter spp. (CREn) from 2 endemic and geographically distinct centers. CREn were investigated at an Israeli center (Assaf Harofeh Medical Center, January 2007 to July 2012) and at a US center (Detroit Medical Center, September 2008 to September 2009). bla KPC genes were queried by polymerase chain reaction. Repetitive extragenic palindromic polymerase chain reaction and pulsed-field gel electrophoresis were used to determine genetic relatedness. In this analysis, 68 unique patients with CREn were enrolled. Sixteen isolates (24%) were from wounds, and 33 (48%) represented colonization only. All isolates exhibited a positive Modified Hodge Test, but only 93% (27 of 29) contained bla KPC. Forty-three isolates (63%) were from elderly adults, and 5 (7.4%) were from neonates. Twenty-seven patients died in hospital (40.3% of infected patients). Enterobacter strains consisted of 4 separate clones from Assaf Harofeh Medical Center and of 4 distinct clones from Detroit Medical Center. In this study conducted at 2 distinct CRE endemic regions, there were unique epidemiologic features to CREn: (i) polyclonality, (ii) neonates accounting for more than 7% of cohort, and (iii) high rate of colonization (almost one-half of all cases represented colonization). Since false-positive Modified Hodge Tests in Enterobacter spp. are common, close monitoring of carbapenem resistance mechanisms (particularly carbapenemase production) among Enterobacter spp. is important.

[About twins: Epidemiological, genetic, and obstetrical aspects, specific risks, and outcome].

Science.gov (United States)

Tauzin, M; Felix, A; Michot, C; Dedieu, C; Aoust, L; Fortas, F; Guillier, C; Ngo, J; Wachter, P-Y; Petermann, L; Kermorvant-Duchemin, E

2017-12-01

The incidence of twin pregnancies has increased steadily for the last 40 years due to assisted reproductive technology and increased maternal childbearing age. Multiple pregnancies, especially monochorionic twin pregnancies, carry a high risk for the mother and the fetuses and require close follow-up. Twins are exposed to a higher risk of perinatal anoxia, in utero fetal demise, preterm birth, congenital malformations, fetal growth restriction, and vascular complications. Compared to singletons, twins are at higher risk of perinatal mortality and impaired neurodevelopmental outcome, justifying a thorough follow-up by pediatricians, including assessment and management of familial and psychosocial impact. This paper discusses the epidemiological, obstetrical, and genetic issues raised by twin pregnancies and reviews the data on the perinatal and neurological long-term outcomes of twins, as well as the psychosocial impact of multiple births on twins and their families. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

Molecular surveillance of norovirus, 2005-16: an epidemiological analysis of data collected from the NoroNet network.

NARCIS (Netherlands)

van Beek, Janko; de Graaf, Miranda; Al-Hello, Haider; Allen, David J; Ambert-Balay, Katia; Botteldoorn, Nadine; Brytting, Mia; Buesa, Javier; Cabrerizo, Maria; Chan, Martin; Cloak, Fiona; Di Bartolo, Ilaria; Guix, Susana; Hewitt, Joanne; Iritani, Nobuhiro; Jin, Miao; Johne, Reimar; Lederer, Ingeborg; Mans, Janet; Martella, Vito; Maunula, Leena; McAllister, Georgina; Niendorf, Sandra; Niesters, Hubert G; Podkolzin, Alexander T; Poljsak-Prijatelj, Mateja; Rasmussen, Lasse Dam; Reuter, Gábor; Tuite, Gráinne; Kroneman, Annelies; Vennema, Harry; Koopmans, Marion P G

2018-01-01

The development of a vaccine for norovirus requires a detailed understanding of global genetic diversity of noroviruses. We analysed their epidemiology and diversity using surveillance data from the NoroNet network.

Molecular epidemiological analysis of Saffold cardiovirus genotype 3 from upper respiratory infection patients in Taiwan.

Science.gov (United States)

Lin, Tsuey-Li; Lin, Ting-Han; Chiu, Shu-Chun; Huang, Yuan-Pin; Ho, Cheng-Mao; Lee, Chia-Chi; Wu, Ho-Sheng; Lin, Jih-Hui

2015-09-01

Saffold cardiovirus (SAFV) belongs to the Cardiovirus genus of Picornaviridae family, and may be a relevant new human pathogen; Thus far, eleven genotypes have been identified. The SAFV type 3 (SAFV-3) is thought to be the major genotype and is detected relatively frequently in children with acute gastroenteritis and respiratory illness. The epidemiology and pathogenicity of SAFV-3 remain unclear. To investigate the genomic and epidemiologic profiles of SAFV-3 infection in Taiwan. Virus was detected in respiratory samples from children suffering for URI. SAFV-3 isolates were detected by isolation on cell culture and IF assay. The molecular typing was performed by RT-PCR and was sequenced to compare with reference strains available in the NCBI GeneBank. Serum samples were collected from 2005 to 2013 in Taiwan for seroprevalence investigation. A total of 226 specimens collected from children with URIs, 22 (9.73%) were positive for SAFV-3. The majority of SAFV-3 infections were found in children less than 6 years of age (14 of 22, 63.6%). Genetic analysis of VP1 coding region of Taiwanese isolates shown an 83.2-97.7% difference from other available SAFV-3 sequences in NCBI GenBank. Phylogenetic analysis revealed there is three genetic groups of SAFV-3 co-circulated in Taiwan during the study period. In addition, seroprevalence investigation results indicated that SAFV-3 infection occurs early in life and 43.7-77.8% of children aged between 6 months to 9 years old, had neutralizing antibodies against SAFV-3. SAFV-3 may have circulated in Taiwan for some time and it appears to be one of the etiological agents responsible for URIs in children. Copyright © 2015 Elsevier B.V. All rights reserved.

Web tools for molecular epidemiology of tuberculosis.

Science.gov (United States)

Shabbeer, Amina; Ozcaglar, Cagri; Yener, Bülent; Bennett, Kristin P

2012-06-01

In this study we explore publicly available web tools designed to use molecular epidemiological data to extract information that can be employed for the effective tracking and control of tuberculosis (TB). The application of molecular methods for the epidemiology of TB complement traditional approaches used in public health. DNA fingerprinting methods are now routinely employed in TB surveillance programs and are primarily used to detect recent transmissions and in outbreak investigations. Here we present web tools that facilitate systematic analysis of Mycobacterium tuberculosis complex (MTBC) genotype information and provide a view of the genetic diversity in the MTBC population. These tools help answer questions about the characteristics of MTBC strains, such as their pathogenicity, virulence, immunogenicity, transmissibility, drug-resistance profiles and host-pathogen associativity. They provide an integrated platform for researchers to use molecular epidemiological data to address current challenges in the understanding of TB dynamics and the characteristics of MTBC. Copyright © 2011. Published by Elsevier B.V.

[Genetic subtype and epidemiological feature of HIV-1 circulating strains among recently infected patients in Fujian province].

Science.gov (United States)

Deng, Yongyue; Zhang, Chunyang; Yan, Yansheng; Yan, Pingping; Wu, Shouli

2014-06-01

In order to evaluate the distribution of genetic subtypes and epidemiological feature of HIV-1 circulating strains in Fujian province. Blood samples and epidemiological data were collected from 104 newly infected patients who were distinguished by BED-CEIA methodology, during 2011-2012. Viral sequences(n = 81) of HIV-1 gag, env, and pol segments were amplified by nested PCR. Subtypes B and four Circulating Recombinant Forms, (CRF01_AE, CRF07_BC, CRF08_BC and CRF55_01B) were found in the samples, CRF01_AE(45.68%)and CRF07_BC(35.80%) were the two main HIV-1 strains in Fujian province. Compared with previous data, the proportion of CRF07_BC rose significantly while it gradually decreased in CRF01_AE. Heterosexual contact was still the principal transmission route in Fujian province, but the number of infection among men-who-have-sex-with- men grew rapidly. Results from this study suggested that different subtypes of HIV-1 strain existed in Fujian province. The distribution of subtypes and the mode of transmission were changing with the progress of epidemic. Dynamic monitoring of the molecular epidemiology trends of HIV-1 infection should be enhanced.

Genetic relatedness and recombination analysis of Allorhizobium vitis strains associated with grapevine crown gall outbreaks in Europe.

Science.gov (United States)

Kuzmanović, N; Biondi, E; Bertaccini, A; Obradović, A

2015-09-01

To analyse genetic diversity and epidemiological relationships among 54 strains of Allorhizobium vitis isolated in Europe during an 8-year period and to assess the relative contribution of mutation and recombination in shaping their diversity. By using random amplified polymorphic DNA (RAPD) PCR, strains studied were distributed into 12 genetic groups. Sequence analysis of dnaK, gyrB and recA housekeeping genes was employed to characterize a representative subcollection of 28 strains. A total of 15 different haplotypes were found. Nucleotide sequence analysis suggested the presence of recombination events in A. vitis, particularly affecting dnaK locus. Although prevalence of mutation over recombination was found, impact of recombination was about two times greater than mutation in the evolution of the housekeeping genes analysed. The RAPD analysis indicated high degree of genetic diversity among the strains. However, the most abundant RAPD group was composed of 35 strains, which could lead to the conclusion that they share a common origin and were distributed by the movement of infected grapevine planting material as a most common way of crossing long distances. Furthermore, it seems that recombination is acting as an important driving force in the evolution of A. vitis. As no substantial evidence of recombination was detected within recA gene fragment, this phylogenetic marker could be reliable to characterize phylogenetic relationships among A. vitis strains. We demonstrated clear epidemiological relationship between majority of strains studied, suggesting a need for more stringent phytosanitary measures in international trade. Moreover, this is the first study to report recombination in A. vitis. © 2015 The Society for Applied Microbiology.

Molecular epidemiology of measles virus in Italy during 2008

Directory of Open Access Journals (Sweden)

Fabio Magurano

2013-03-01

Full Text Available INTRODUCTION. In view of the goal of measles elimination, it is of great importance to assess the circulation of wild-type measles virus (MV. Genetic analysis is indispensable to understand the epidemiology of measles. A large measles outbreak occurred in Italy in 2008, with over 4000 cases reported to the enhanced measles surveillance system introduced in 2007, 37% of which were laboratory confirmed. METHODS. Urine and saliva samples were collected during 2008. A phylogenetic analysis of measles sequences was performed in order to understand the epidemiological situation of wild-type (MV circulation in that period. RESULT AND DISCUSSION. Data showed predominant circulation of the genotype D4. Genotypes A, D8, D9 and H1 were also detected in a small number of samples, probably representing imported cases.

[Eco-epidemiology: towards epidemiology of complexity].

Science.gov (United States)

Bizouarn, Philippe

2016-05-01

In order to solve public health problems posed by the epidemiology of risk factors centered on the individual and neglecting the causal processes linking the risk factors with the health outcomes, Mervyn Susser proposed a multilevel epidemiology called eco-epidemiology, addressing the interdependence of individuals and their connection with molecular, individual, societal, environmental levels of organization participating in the causal disease processes. The aim of this epidemiology is to integrate more than a level of organization in design, analysis and interpretation of health problems. After presenting the main criticisms of risk-factor epidemiology focused on the individual, we will try to show how eco-epidemiology and its development could help to understand the need for a broader and integrative epidemiology, in which studies designed to identify risk factors would be balanced by studies designed to answer other questions equally vital to public health. © 2016 médecine/sciences – Inserm.

Attitudes towards genetic testing: analysis of contradictions

DEFF Research Database (Denmark)

Jallinoja, P; Hakonen, A; Aro, A R

1998-01-01

A survey study was conducted among 1169 people to evaluate attitudes towards genetic testing in Finland. Here we present an analysis of the contradictions detected in people's attitudes towards genetic testing. This analysis focuses on the approval of genetic testing as an individual choice and o...... studies on attitudes towards genetic testing as well as in the health care context, e.g. in genetic counselling.......A survey study was conducted among 1169 people to evaluate attitudes towards genetic testing in Finland. Here we present an analysis of the contradictions detected in people's attitudes towards genetic testing. This analysis focuses on the approval of genetic testing as an individual choice...... and on the confidence in control of the process of genetic testing and its implications. Our analysis indicated that some of the respondents have contradictory attitudes towards genetic testing. It is proposed that contradictory attitudes towards genetic testing should be given greater significance both in scientific...

Genetic epidemiology of Scheuermann's disease

DEFF Research Database (Denmark)

Damborg, Frank; Engell, Vilhelm; Nielsen, Jan

2011-01-01

The genetic/environmental etiology of Scheuermann's disease is unclear. We estimated the heritability of the disease using an etiological model adjusted for sex and time of diagnosis, and examined whether the prevalence of Scheuermann's disease was constant over time.......The genetic/environmental etiology of Scheuermann's disease is unclear. We estimated the heritability of the disease using an etiological model adjusted for sex and time of diagnosis, and examined whether the prevalence of Scheuermann's disease was constant over time....

A Bayesian Approach to the Overlap Analysis of Epidemiologically Linked Traits.

Science.gov (United States)

Asimit, Jennifer L; Panoutsopoulou, Kalliope; Wheeler, Eleanor; Berndt, Sonja I; Cordell, Heather J; Morris, Andrew P; Zeggini, Eleftheria; Barroso, Inês

2015-12-01

Diseases often cooccur in individuals more often than expected by chance, and may be explained by shared underlying genetic etiology. A common approach to genetic overlap analyses is to use summary genome-wide association study data to identify single-nucleotide polymorphisms (SNPs) that are associated with multiple traits at a selected P-value threshold. However, P-values do not account for differences in power, whereas Bayes' factors (BFs) do, and may be approximated using summary statistics. We use simulation studies to compare the power of frequentist and Bayesian approaches with overlap analyses, and to decide on appropriate thresholds for comparison between the two methods. It is empirically illustrated that BFs have the advantage over P-values of a decreasing type I error rate as study size increases for single-disease associations. Consequently, the overlap analysis of traits from different-sized studies encounters issues in fair P-value threshold selection, whereas BFs are adjusted automatically. Extensive simulations show that Bayesian overlap analyses tend to have higher power than those that assess association strength with P-values, particularly in low-power scenarios. Calibration tables between BFs and P-values are provided for a range of sample sizes, as well as an approximation approach for sample sizes that are not in the calibration table. Although P-values are sometimes thought more intuitive, these tables assist in removing the opaqueness of Bayesian thresholds and may also be used in the selection of a BF threshold to meet a certain type I error rate. An application of our methods is used to identify variants associated with both obesity and osteoarthritis. © 2015 The Authors. *Genetic Epidemiology published by Wiley Periodicals, Inc.

Review of epidemiological studies of human populations exposed to ionizing radiation

International Nuclear Information System (INIS)

Rao, B.S.

2002-01-01

Epidemiological studies undertaken in many radiation exposed cohorts have played an important role in the quantification of radiation risk. Follow up of nearly 100,000 A-bomb survivors by the Radiation Effects Research Foundation (RERF), constitutes the most comprehensive human epidemiological study. The study population covered both sexes, different age groups and dose ranges from a few mSv to 2-3 Sv. Among nearly 90,000 cohorts, as on 1990, 54% are alive. Among these, 35,000 are those exposed as children at the age<20 years. Nearly 20 % of the mortalities (8,040) were due to cancer. It was estimated from the analysis of these data that among the cancers observed in LSS cohorts, 425±45 cases (335 solid cancers+90 leukaemias) were attributable to radiation exposure. Assuming a value of two for DDREF, ICRP 60, 1991 estimated a cancer risk of 5% per Sv for low dose and low dose rate exposure conditions. There have been a number of efforts to study the human populations exposed to low level radiations. Epidemiological studies on nuclear workers from USA, UK and Canada constituting 95,673 workers spanning 2,124,526 person years was reported by Cardis et al. (1995). Total number of deaths were 15,825, of which 3,976 were cancer mortalities. The excess relative risk for all cancers excluding leukaemia is -0.07 per Sv (-0.4- +0.3) and for leukaemia (excluding CLL) is 2.18 (0.1-5.7). Epidemiological studies in high background radiation areas (HBRA) of Yangjiang, China and coastal Kerala showed no detectable increase in the incidence of cancers or of any genetic disorders. Epidemiological studies in human populations exposed to elevated background radiation for several generations did not show any increase in the genetic disorders. Recent information on the background incidence of monogenic disorders in human populations and the recoverability factor of induced genetic changes suggests a risk much lower than the earlier ICRP estimates. Many other epidemiological studies of

Analysis of cryopyrin-associated periodic syndromes (CAPS) in German children: epidemiological, clinical and genetic characteristics.

Science.gov (United States)

Lainka, E; Neudorf, U; Lohse, P; Timmann, C; Bielak, M; Stojanov, S; Huss, K; von Kries, R; Niehues, T

2010-11-01

Cryopyrin-associated periodic syndromes (CAPS) are rare disorders belonging to the group of hereditary periodic fever (HPF)syndromes. These auto-inflammatory diseases(AID) are characterized by recurrent episodes of inflammation with attacks of fever variably associated with serosal, synovial and / or cutaneous inflammation, usually in a self-limiting manner, and with a mostly monogenic origin. The aims were to determine the incidence of CAPS and the spectrum of mutations in the NLRP3 (formerly= CIAS1) gene and to describe the clinical manifestations. A prospective surveillance of children with CAPS was conducted in Germany during a time period of 3 years(2003-2006). Monthly inquiries were sent to 370 children's hospitals by the German Paediatric Surveillance Unit (Clinic-ESPED, n1) and to 2 laboratories (Laboratory-ESPED, n2). Inclusion criteria were children ≤ 16 years of age, disease-associated NLRP3 mutation, more than 3 self-limiting episodes of fever > 38.5 ° C, and increased inflammation markers. Clinical, epidemiological and genetic data were evaluated via questionnaires. 6 out of 14 patients were identified in Clinic-ESPED (n1) and 13 / 14 in Laboratory-ESPED(n2). Clinical and laboratory surveys overlapped in 5 of 14 cases. The incidence of CAPS in German children was estimated to be 3.43 per 10⁷ person-years. The patients carried 11 different NLRP3 mutations and were classified as MWS(n = 6), CINCA (n = 4), FCAS (n = 1) and undefined CAPS (n = 3). The incidence of CAPS in Germany is very low and corresponds to 2-7 newly diagnosed patients ≤ 16 years per year. © Georg Thieme Verlag KG Stuttgart · New York.

Fertility and pregnancy: an epidemiologic perspective

National Research Council Canada - National Science Library

Wilcox, Allen J

2010-01-01

.... Weaving together history, biology, obstetrics, pediatrics, demography, infectious diseases, molecular genetics, and evolutionary biology, Allen Wilcox brings a fresh coherence to the epidemiologic...

Genomic Resources for Cancer Epidemiology

Science.gov (United States)

This page provides links to research resources, complied by the Epidemiology and Genomics Research Program, that may be of interest to genetic epidemiologists conducting cancer research, but is not exhaustive.

Protecting Privacy of Shared Epidemiologic Data without Compromising Analysis Potential

Directory of Open Access Journals (Sweden)

John Cologne

2012-01-01

Full Text Available Objective. Ensuring privacy of research subjects when epidemiologic data are shared with outside collaborators involves masking (modifying the data, but overmasking can compromise utility (analysis potential. Methods of statistical disclosure control for protecting privacy may be impractical for individual researchers involved in small-scale collaborations. Methods. We investigated a simple approach based on measures of disclosure risk and analytical utility that are straightforward for epidemiologic researchers to derive. The method is illustrated using data from the Japanese Atomic-bomb Survivor population. Results. Masking by modest rounding did not adequately enhance security but rounding to remove several digits of relative accuracy effectively reduced the risk of identification without substantially reducing utility. Grouping or adding random noise led to noticeable bias. Conclusions. When sharing epidemiologic data, it is recommended that masking be performed using rounding. Specific treatment should be determined separately in individual situations after consideration of the disclosure risks and analysis needs.

Protecting Privacy of Shared Epidemiologic Data without Compromising Analysis Potential

International Nuclear Information System (INIS)

Cologne, J.; Nakashima, E.; Funamoto, S.; Grant, E.J.; Chen, Y.; Hiroaki Katayama, H.

2012-01-01

Objective. Ensuring privacy of research subjects when epidemiologic data are shared with outside collaborators involves masking (modifying) the data, but over masking can compromise utility (analysis potential). Methods of statistical disclosure control for protecting privacy may be impractical for individual researchers involved in small-scale collaborations. Methods. We investigated a simple approach based on measures of disclosure risk and analytical utility that are straightforward for epidemiologic researchers to derive. The method is illustrated using data from the Japanese Atomic-bomb Survivor population. Results. Masking by modest rounding did not adequately enhance security but rounding to remove several digits of relative accuracy effectively reduced the risk of identification without substantially reducing utility. Grouping or adding random noise led to noticeable bias. Conclusions. When sharing epidemiologic data, it is recommended that masking be performed using rounding. Specific treatment should be determined separately in individual situations after consideration of the disclosure risks and analysis needs

Epidemiology of subtypes of depression

DEFF Research Database (Denmark)

Kessing, L V

2007-01-01

depression, dysthymia, and subsyndromal states; the association between stressful life events and depression appears to diminish with the number of depressive episodes. Finally, recent genetic findings are congruent with a model indicating that the majority of depressions develop in the interplay between...... genes and stressful experiences, whereas 'reactive' depressions and 'endogenous' depressions apparently exist at a lower prevalence. CONCLUSION: Further longitudinal, analytical, and genetic epidemiologic studies are needed to reveal which conditions are mild and transient, and which may be precursors......OBJECTIVE: There is a general clinical impression that depression differs qualitatively from non-depressive conditions, and that it can be identified as a categorical entity. In contrast, epidemiological studies support the view that depression is dynamic in nature and develops on a continuous...

Rabies in southeast Brazil: a change in the epidemiological pattern.

Science.gov (United States)

Queiroz, Luzia Helena; Favoretto, Silvana Regina; Cunha, Elenice Maria S; Campos, Angélica Cristine A; Lopes, Marissol Cardoso; de Carvalho, Cristiano; Iamamoto, Keila; Araújo, Danielle Bastos; Venditti, Leandro Lima R; Ribeiro, Erica S; Pedro, Wagner André; Durigon, Edison Luiz

2012-01-01

This epidemiological study was conducted using antigenic and genetic characterisation of rabies virus isolates obtained from different animal species in the southeast of Brazil from 1993 to 2007. An alteration in the epidemiological profile was observed. One hundred two samples were tested using a panel of eight monoclonal antibodies, and 94 were genetically characterised by sequencing the nucleoprotein gene. From 1993 to 1997, antigenic variant 2 (AgV-2), related to a rabies virus maintained in dog populations, was responsible for rabies cases in dogs, cats, cattle and horses. Antigenic variant 3 (AgV-3), associated with Desmodus rotundus, was detected in a few cattle samples from rural areas. From 1998 to 2007, rabies virus was detected in bats and urban pets, and four distinct variants were identified. A nucleotide similarity analysis resulted in two primary groups comprising the dog and bat antigenic variants and showing the distinct endemic cycles maintained in the different animal species in this region.

Pleiotropic Analysis of Lung Cancer and Blood Triglycerides

NARCIS (Netherlands)

Zuber, V.; Marconett, C.N.; Shi, J.; Hua, X.; Wheeler, W.; Yang, C.; Song, L; Dale, A.M.; Laplana, M.; Risch, A.; Witoelar, A.; Thompson, W.K.; Schork, A.J.; Bettella, F.; Wang, Y; Djurovic, S.; Zhou, B.; Borok, Z.; Heijden, H.F.M. van der; Graaf, J. de; Swinkels, D.W.; Aben, K.K.H.; McKay, J.; Hung, R.J.; Bikeboller, H.; Stevens, V.L.; Albanes, D.; Caporaso, N.E.; Han, Y.; Wei, Y.; Panadero, M.A.; Mayordomo, J.I.; Christiani, D.C.; Kiemeney, L.A.; Andreassen, O.A.; Houlston, R.; Amos, C.I.; Chatterjee, N.; Laird-Offringa, I.A.; Mills, I.G.; Landi, M.T.

2016-01-01

Epidemiologically related traits may share genetic risk factors, and pleiotropic analysis could identify individual loci associated with these traits. Because of their shared epidemiological associations, we conducted pleiotropic analysis of genome-wide association studies of lung cancer (12 160

Epidemiologic research topics in Germany: a keyword network analysis of 2014 DGEpi conference presentations.

Science.gov (United States)

Peter, Raphael Simon; Brehme, Torben; Völzke, Henry; Muche, Rainer; Rothenbacher, Dietrich; Büchele, Gisela

2016-06-01

Knowledge of epidemiologic research topics as well as trends is useful for scientific societies, researchers and funding agencies. In recent years researchers recognized the usefulness of keyword network analysis for visualizing and analyzing scientific research topics. Therefore, we applied keyword network analysis to present an overview of current epidemiologic research topics in Germany. Accepted submissions to the 9th annual congress of the German Society for Epidemiology (DGEpi) in 2014 were used as data source. Submitters had to choose one of 19 subject areas, and were ask to provide a title, structured abstract, names of authors along with their affiliations, and a list of freely selectable keywords. Keywords had been provided for 262 (82 %) submissions, 1030 keywords in total. Overall the most common keywords were: "migration" (18 times), "prevention" (15 times), followed by "children", "cohort study", "physical activity", and "secondary data analysis" (11 times each). Some keywords showed a certain concentration under one specific subject area, e.g. "migration" with 8 of 18 in social epidemiology or "breast cancer" with 4 of 7 in cancer epidemiology. While others like "physical activity" were equally distributed over multiple subject areas (cardiovascular & metabolic diseases, ageing, methods, paediatrics, prevention & health service research). This keyword network analysis demonstrated the high diversity of epidemiologic research topics with a large number of distinct keywords as presented at the annual conference of the DGEpi.

Biomarkers in Prostate Cancer Epidemiology

Directory of Open Access Journals (Sweden)

Mudit Verma

2011-09-01

Full Text Available Understanding the etiology of a disease such as prostate cancer may help in identifying populations at high risk, timely intervention of the disease, and proper treatment. Biomarkers, along with exposure history and clinical data, are useful tools to achieve these goals. Individual risk and population incidence of prostate cancer result from the intervention of genetic susceptibility and exposure. Biochemical, epigenetic, genetic, and imaging biomarkers are used to identify people at high risk for developing prostate cancer. In cancer epidemiology, epigenetic biomarkers offer advantages over other types of biomarkers because they are expressed against a person’s genetic background and environmental exposure, and because abnormal events occur early in cancer development, which includes several epigenetic alterations in cancer cells. This article describes different biomarkers that have potential use in studying the epidemiology of prostate cancer. We also discuss the characteristics of an ideal biomarker for prostate cancer, and technologies utilized for biomarker assays. Among epigenetic biomarkers, most reports indicate GSTP1 hypermethylation as the diagnostic marker for prostate cancer; however, NKX2-5, CLSTN1, SPOCK2, SLC16A12, DPYS, and NSE1 also have been reported to be regulated by methylation mechanisms in prostate cancer. Current challenges in utilization of biomarkers in prostate cancer diagnosis and epidemiologic studies and potential solutions also are discussed.

Hepatitis A virus infection: Epidemiology and genetic diversity

Directory of Open Access Journals (Sweden)

Báez Triana, Paula Andrea

2015-04-01

Full Text Available Hepatitis A virus infection is a global public health problem. The virus has a wide range of distribution and it is the main cause of acute hepatitis transmitted by the enteric route in Latin America. The viral particle is stable under environmental conditions and conserves its infectivity for several weeks, enabling its transmission by contaminated water and food. Worldwide, different epidemiological patterns have been identified, which may change over time by modification of social and economic variables in the population such as vaccination and the improvement of hygiene and primary health conditions. This leaves new populations susceptible to infection. In Latin America the circulation of genotype I and subgenotypes A and B has been described, but more research is needed to provide the knowledge needed to manage the prevention and control plans for the worldwide reduction of the prevalence of infection. For this paper, a literature review was performed on the SciELO, PubMed and ScienceDirect databases under the search terms "Hepatitis A", "Epidemiology," "Seroprevalence" and "Infection." From the results obtained, only papers published in English and Spanish to describe epidemiological and molecular studies of interest in Latin America were included.

Possible implication of the genetic composition of the Lutzomyia longipalpis (Diptera: Psychodidae) populations in the epidemiology of the visceral leishmaniasis.

Science.gov (United States)

Rocha, Leonardo de Souza; Falqueto, Aloisio; Dos Santos, Claudiney Biral; Grimaldi, Gabriel Júnior; Cupolillo, Elisa

2011-09-01

Lutzomyia longipalpis (Diptera: Psychodidae) is the principal vector of American visceral leishmaniasis. Several studies have indicated that the Lu. longipalpis population structure is complex. It has been suggested that genetic divergence caused by genetic drift, selection, or both may affect the vectorial capacity of Lu. longipalpis. However, it remains unclear whether genetic differences among Lu. longipalpis populations are directly implicated in the transmission features of visceral leishmaniasis. We evaluated the genetic composition and the patterns of genetic differentiation among Lu. longipalpis populations collected from regions with different patterns of transmission of visceral leishmaniasis by analyzing the sequence variation in the mitochondrial cytochrome b gene. Furthermore, we investigated the temporal distribution of haplotypes and compared our results with those obtained in a previous study. Our data indicate that there are differences in the haplotype composition and that there has been significant differentiation between the analyzed populations. Our results reveal that measures used to control visceral leishmaniasis might have influenced the genetic composition of the vector population. This finding raises important questions concerning the epidemiology of visceral leishmaniasis, because these differences in the genetic structures among populations of Lu. longipalpis may have implications with respect to their efficiency as vectors for visceral leishmaniasis.

Molecular epidemiology of Plum pox virus in Japan.

Science.gov (United States)

Maejima, Kensaku; Himeno, Misako; Komatsu, Ken; Takinami, Yusuke; Hashimoto, Masayoshi; Takahashi, Shuichiro; Yamaji, Yasuyuki; Oshima, Kenro; Namba, Shigetou

2011-05-01

For a molecular epidemiological study based on complete genome sequences, 37 Plum pox virus (PPV) isolates were collected from the Kanto region in Japan. Pair-wise analyses revealed that all 37 Japanese isolates belong to the PPV-D strain, with low genetic diversity (less than 0.8%). In phylogenetic analysis of the PPV-D strain based on complete nucleotide sequences, the relationships of the PPV-D strain were reconstructed with high resolution: at the global level, the American, Canadian, and Japanese isolates formed their own distinct monophyletic clusters, suggesting that the routes of viral entry into these countries were independent; at the local level, the actual transmission histories of PPV were precisely reconstructed with high bootstrap support. This is the first description of the molecular epidemiology of PPV based on complete genome sequences.

Genetic analysis

NARCIS (Netherlands)

Koornneef, M.; Alonso-Blanco, C.; Stam, P.

2006-01-01

The Mendelian analysis of genetic variation, available as induced mutants or as natural variation, requires a number of steps that are described in this chapter. These include the determination of the number of genes involved in the observed trait's variation, the determination of dominance

Spinocerebellar ataxias in Venezuela: genetic epidemiology and their most likely ethnic descent.

Science.gov (United States)

Paradisi, Irene; Ikonomu, Vassiliki; Arias, Sergio

2016-03-01

Dominantly inherited ataxias (spinocerebellar ataxias, SCAs) are a genetically heterogeneous group of neurologic diseases characterized by progressive cerebellar and spinal tract degeneration with ataxia and other signs, common to all known subtypes. Several types are relatively frequent worldwide, but in several countries, one specific SCA may show a higher prevalence owing to founder phenomena. In Venezuela, genetic epidemiological features of SCAs have been assessed during the last 30 years; mutations in ATXN1 (SCA1), ATXN2 (SCA2), ATXN3 (SCA3), CACNA1A (SCA6), ATXN7 (SCA7), ATXN8 (SCA8), ATXN10 (SCA10), TBP (SCA17) and ATN1 (dentatorubral pallidoluysian atrophy, DRPLA) loci were searched among 115 independent families. SCA7 was the most frequent subtype (26.6%), followed by SCA3 (25.0%), SCA2 (21.9%), SCA1 (17.2%), SCA10 (4.7%) and DRPLA (3.1%); in 43% of the families, the subtype remained unidentified. SCA7 mutations displayed strong geographic aggregation in two independent founder foci, and SCA1 showed a very remote founder effect for a subset of families. SCA10 families were scattered across the country, but all had an identical in-phase haplotype carried also by Mexican, Brazilian and Sioux patients, supporting a very old common Amerindian origin. Prevalence for dominant SCAs in Venezuela was estimated as 1:25 000 nuclear families, provenances of which are either Caucasoid, African or Amerindian.

Parkinson’s Disease in Sub-Saharan Africa: A Review of Epidemiology, Genetics and Access to Care

Science.gov (United States)

Bandmann, Oliver; Walker, Richard

2018-01-01

A low prevalence of Parkinson’s disease (PD) has been reported in the Sub-Saharan Africa (SSA) region. The genetic causes and clinical features of PD in this region have been poorly described. Very few reports have examined the availability and access to evidence-based quality care for people living with PD in this region. We reviewed all publications focusing on idiopathic PD from SSA published up to May 2016 and observed a prevalence of PD ranging from 7/100,000 in Ethiopia to 67/100,000 in Nigeria. The most recent community-based study reported a mean age at onset of 69.4 years. The infrequent occurrence of mutations in established PD genes was also observed in the region. Treatments were non-existent or at best irregular. Additionally, there is a lack of well-trained medical personnel and multidisciplinary teams in most countries in this region. Drugs for treating PD are either not available or unaffordable. Large-scale genetic and epidemiological studies are therefore needed in SSA to provide further insights into the roles of genetics and other etiological factors in the pathogenesis of PD. The quality of care also requires urgent improvement to meet the basic level of care required by PD patients. PMID:29860783

Integrated analysis of genetic data with R

Directory of Open Access Journals (Sweden)

Zhao Jing

2006-01-01

Full Text Available Abstract Genetic data are now widely available. There is, however, an apparent lack of concerted effort to produce software systems for statistical analysis of genetic data compared with other fields of statistics. It is often a tremendous task for end-users to tailor them for particular data, especially when genetic data are analysed in conjunction with a large number of covariates. Here, R http://www.r-project.org, a free, flexible and platform-independent environment for statistical modelling and graphics is explored as an integrated system for genetic data analysis. An overview of some packages currently available for analysis of genetic data is given. This is followed by examples of package development and practical applications. With clear advantages in data management, graphics, statistical analysis, programming, internet capability and use of available codes, it is a feasible, although challenging, task to develop it into an integrated platform for genetic analysis; this will require the joint efforts of many researchers.

The Changing Epidemiology of Autism Spectrum Disorders.

Science.gov (United States)

Lyall, Kristen; Croen, Lisa; Daniels, Julie; Fallin, M Daniele; Ladd-Acosta, Christine; Lee, Brian K; Park, Bo Y; Snyder, Nathaniel W; Schendel, Diana; Volk, Heather; Windham, Gayle C; Newschaffer, Craig

2017-03-20

Autism spectrum disorder (ASD) is a complex neurodevelopmental condition with lifelong impacts. Genetic and environmental factors contribute to ASD etiology, which remains incompletely understood. Research on ASD epidemiology has made significant advances in the past decade. Current prevalence is estimated to be at least 1.5% in developed countries, with recent increases primarily among those without comorbid intellectual disability. Genetic studies have identified a number of rare de novo mutations and gained footing in the areas of polygenic risk, epigenetics, and gene-by-environment interaction. Epidemiologic investigations focused on nongenetic factors have established advanced parental age and preterm birth as ASD risk factors, indicated that prenatal exposure to air pollution and short interpregnancy interval are potential risk factors, and suggested the need for further exploration of certain prenatal nutrients, metabolic conditions, and exposure to endocrine-disrupting chemicals. We discuss future challenges and goals for ASD epidemiology as well as public health implications.

Biomarkers in molecular epidemiology study of oral squamous cell carcinoma in the era of precision medicine

Directory of Open Access Journals (Sweden)

Qing-Hao Zhu

2017-01-01

Full Text Available Oral cancer, which occurs in the mouth, lips, and tongue, is a multifactorial disease whose etiology involves environment, genetic, and epigenetic factors. Tobacco use and alcohol consumption are regarded as the primary risk factors for oral squamous cell carcinoma (OSCC, and betel use, other chemicals, radiation, environmental, and genetics are reported as relevant risk factors for oral carcinogenesis. The human papillomavirus infection is an independent risk factor. Traditional epidemiology studies have revealed that environmental carcinogens are risk factors for OSCC. Molecular epidemiology studies have revealed that the susceptibility to OSCC is influenced by both environmental and genetic risk factors. However, the details and mechanisms of risk factors involved in OSCC are unclear. Advanced methods and techniques used in human genome studies provide great opportunities for researchers to explore and identify (a the details of such risk factors and (b genetic susceptibility involved in OSCC. Human genome epidemiology is a new branch of epidemiology, which leads the epidemiology study from the molecular epidemiology era into the era of genome-wide association study. In the era of precision medicine, molecular epidemiology studies should focus on biomarkers for cancer genomics and their potential utility in clinical practice. Here, we briefly reviewed several molecular epidemiology studies of OSCC, focusing on biomarkers as valuable utility in risk assessment, clinical screening, diagnosis, and prognosis prediction of OSCC in the era of precision medicine.

Arthritis Genetics Analysis Aids Drug Discovery

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... NIH Research Matters January 13, 2014 Arthritis Genetics Analysis Aids Drug Discovery An international research team identified 42 new ... Edition Distracted Driving Raises Crash Risk Arthritis Genetics Analysis Aids Drug Discovery Oxytocin Affects Facial Recognition Connect with Us ...

Developing genetic epidemiological models to predict risk for nasopharyngeal carcinoma in high-risk population of China.

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Hong-Lian Ruan

Full Text Available To date, the only established model for assessing risk for nasopharyngeal carcinoma (NPC relies on the sero-status of the Epstein-Barr virus (EBV. By contrast, the risk assessment models proposed here include environmental risk factors, family history of NPC, and information on genetic variants. The models were developed using epidemiological and genetic data from a large case-control study, which included 1,387 subjects with NPC and 1,459 controls of Cantonese origin. The predictive accuracy of the models were then assessed by calculating the area under the receiver-operating characteristic curves (AUC. To compare the discriminatory improvement of models with and without genetic information, we estimated the net reclassification improvement (NRI and integrated discrimination index (IDI. Well-established environmental risk factors for NPC include consumption of salted fish and preserved vegetables and cigarette smoking (in pack years. The environmental model alone shows modest discriminatory ability (AUC = 0.68; 95% CI: 0.66, 0.70, which is only slightly increased by the addition of data on family history of NPC (AUC = 0.70; 95% CI: 0.68, 0.72. With the addition of data on genetic variants, however, our model's discriminatory ability rises to 0.74 (95% CI: 0.72, 0.76. The improvements in NRI and IDI also suggest the potential usefulness of considering genetic variants when screening for NPC in endemic areas. If these findings are confirmed in larger cohort and population-based case-control studies, use of the new models to analyse data from NPC-endemic areas could well lead to earlier detection of NPC.

Genetic association of telomere length with hepatocellular carcinoma risk: A Mendelian randomization analysis.

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Cheng, Yue; Yu, Chengxiao; Huang, Mingtao; Du, Fangzhi; Song, Ci; Ma, Zijian; Zhai, Xiangjun; Yang, Yuan; Liu, Jibin; Bei, Jin-Xin; Jia, Weihua; Jin, Guangfu; Li, Shengping; Zhou, Weiping; Liu, Jianjun; Dai, Juncheng; Hu, Zhibin

2017-10-01

Observational studies show an association between telomere length and Hepatocellular carcinoma (HCC) risk, but the relationship is controversial. Particularly, it remains unclear whether the association is due to confounding or biases inherent in conventional epidemiological studies. Here, we applied Mendelian randomization approach to evaluate whether telomere length is causally associated with HCC risk. Individual-level data were from HBV-related HCC Genome-wide association studies (1,538 HBV positive HCC patients and 1,465 HBV positive controls). Genetic risk score, as proxy for actual measured telomere length, derived from nine telomere length-associated genetic variants was used to evaluate the effect of telomere length on HCC risk. We observed a significant risk signal between genetically increased telomere length and HBV-related HCC risk (OR=2.09, 95% CI 1.32-3.31, P=0.002). Furthermore, a U-shaped curve was fitted by the restricted cubic spline curve, which indicated that either short or long telomere length would increase HCC risk (P=0.0022 for non-linearity test). Subgroup analysis did not reveal significant heterogeneity between different age, gender, smoking status and drinking status groups. Our results indicated that a genetic background that favors longer or shorter telomere length may increase HBV-related HCC risk-a U-shaped association. Copyright © 2017 Elsevier Ltd. All rights reserved.

Intra-species diversity and epidemiology varies among coagulase-negative Staphylococcus species causing bovine intramammary infections.

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Piessens, V; De Vliegher, S; Verbist, B; Braem, G; Van Nuffel, A; De Vuyst, L; Heyndrickx, M; Van Coillie, E

2012-02-24

Although many studies report coagulase-negative staphylococci (CNS) as the predominant cause of subclinical bovine mastitis, their epidemiology is poorly understood. In the current study, the genetic diversity within four CNS species frequently associated with bovine intramammary infections, Staphylococcus haemolyticus, S. simulans, S. chromogenes, and S. epidermidis, was determined. For epidemiological purposes, CNS genotypes recovered from bovine milk collected on six Flemish dairy farms were compared with those from the farm environment, and their distribution within the farms was investigated. Genetic diversity was assessed by two molecular typing techniques, amplification fragment length polymorphism (AFLP) and random amplification of polymorphic DNA (RAPD) analysis. Subtyping revealed the highest genetic heterogeneity among S. haemolyticus isolates. A large variety of genotypes was found among environmental isolates, of which several could be linked with intramammary infection, indicating that the environment could act as a potential source for infection. For S. simulans, various genotypes were found in the environment, but a link with IMI was less obvious. For S. epidermidis and S. chromogenes, genetic heterogeneity was limited and the sporadic isolates from environment displayed largely the same genotypes as those from milk. The higher clonality of the S. epidermidis and S. chromogenes isolates from milk suggests that specific genotypes probably disseminate within herds and are more udder-adapted. Environmental sources and cow-to-cow transmission both seem to be involved in the epidemiology of CNS, although their relative importance might substantially vary between species. Copyright © 2011 Elsevier B.V. All rights reserved.

Molecular epidemiology and evolutionary genetics of Mycobacterium tuberculosis in Taipei.

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Dou, Horng-Yunn; Tseng, Fan-Chen; Lin, Chih-Wei; Chang, Jia-Ru; Sun, Jun-Ren; Tsai, Wen-Shing; Lee, Shi-Yi; Su, Ih-Jen; Lu, Jang-Jih

2008-12-22

The control of tuberculosis in densely populated cities is complicated by close human-to-human contacts and potential transmission of pathogens from multiple sources. We conducted a molecular epidemiologic analysis of 356 Mycobacterium tuberculosis (MTB) isolates from patients presenting pulmonary tuberculosis in metropolitan Taipei. Classical antibiogram studies and genetic characterization, using mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) typing and spoligotyping, were applied after culture. A total of 356 isolates were genotyped by standard spoligotyping and the strains were compared with in the international spoligotyping database (SpolDB4). All isolates were also categorized using the 15 loci MIRU-VNTR typing method and combin with NTF locus and RD deletion analyses. Of 356 isolates spoligotyped, 290 (81.4%) displayed known spoligotypes and 66 were not identified in the database. Major spoligotypes found were Beijing lineages (52.5%), followed by Haarlem lineages (13.5%) and EAI plus EAI-like lineages (11%). When MIRU-VNTR was employed, 140 patterns were identified, including 36 clusters by 252 isolates and 104 unique patterns, and the largest cluster comprised 95 isolates from the Beijing family. The combination of spoligotyping and MIRU-VNTR revealed that 236 (67%) of the 356 isolates were clustered in 43 genotypes. Strains of the Beijing family was more likely to be of modern strain and a higher percentage of multiple drug resistance than other families combined (P = 0.08). Patients infected with Beijing strains were younger than those with other strains (mean 58.7 vs. 64.2, p = 0.02). Moreover, 85.3% of infected persons younger than 25 years had Beijing modern strain, suggesting a possible recent spread in the young population by this family of TB strain in Taipei. Our data on MTB genotype in Taipei suggest that MTB infection has not been optimally controlled. Control efforts should be reinforced in view of the

DNA methylation analysis from saliva samples for epidemiological studies.

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Nishitani, Shota; Parets, Sasha E; Haas, Brian W; Smith, Alicia K

2018-06-18

Saliva is a non-invasive, easily accessible tissue, which is regularly collected in large epidemiological studies to examine genetic questions. Recently, it is becoming more common to use saliva to assess DNA methylation. However, DNA extracted from saliva is a mixture of both bacterial and human DNA derived from epithelial and immune cells in the mouth. Thus, there are unique challenges to using salivary DNA in methylation studies that can influence data quality. This study assesses: (1) quantification of human DNA after extraction; (2) delineation of human and bacterial DNA; (3) bisulfite conversion (BSC); (4) quantification of BSC DNA; (5) PCR amplification of BSC DNA from saliva and; (6) quantitation of DNA methylation with a targeted assay. The framework proposed will allow saliva samples to be more widely used in targeted epigenetic studies.

Molecular and epidemiological characterization of HIV-1 subtypes among Libyan patients.

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Daw, Mohamed A; El-Bouzedi, Abdallah; Ahmed, Mohamed O; Dau, Aghnyia A

2017-04-28

The epidemiological and clinical aspects of human immunodeficiency virus subtypes are of great interest worldwide. These subtypes are rarely studied in North African countries. Libya is a large country with the longest coast on the Mediterranean Sea, facing the Southern European countries. Studies on the characterization of HIV-1 subtypes are limited in Libya. This study aimed to determine the magnitude of the HIV problem among the Libyan population and to better understand the genetic diversity and the epidemiologic dynamics of HIV 1, as well as to correlate that with the risk factors involved. A total of 159 HIV-1 strains were collected from 814 HIV positive patients from the four Libyan regions during a 16-year period (1995-2010). To determine the HIV-1 subtypes, genetic analysis and molecular sequencing were carried out using provirus polygene. Epidemiologic and demographic information was obtained from each participant and correlated with HIV-1 subtypes using logistic regression. The overall prevalence of HIV among Libyans ranged from 5 to 10 per 100,000 during the study period. It was higher among intravenous drug users (IVDUs) (53.9%), blood recipients (25.9%) and heterosexuals (17.6%) than by vertical transmission (2.6%). Prevalence was higher among males aged 20-40 years (M:F 1:6, P > 0.001). Among the 159 strains of HIV-1 available for typing, 117 strains (73.6%) were subtype B, 29 (18.2%) were CRF02_AG, and 13 (8.2%) were subtype A. HIV-1 subtype B was the most prevalent all over the country, and it was more prevalent in the Northern region, particularly among IVDUs (P HIV-1 infection is emerging in Libya with a shifting prevalence of subtypes associated with the changing epidemiology of HIV-1 among risk groups. A genetic analysis of HIV-1 strains demonstrated low subtype heterogeneity with the evolution of subtype B, and CRF_20 AG, as well as HIV-1 subtype A. Our study highlights the importance of expanded surveillance programs to control HIV

Complete genome sequence of hypervirulent and outbreak-associated Acinetobacter baumannii strain LAC-4: epidemiology, resistance genetic determinants and potential virulence factors

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Ou, Hong-Yu; Kuang, Shan N.; He, Xinyi; Molgora, Brenda M.; Ewing, Peter J.; Deng, Zixin; Osby, Melanie; Chen, Wangxue; Xu, H. Howard

2015-01-01

Acinetobacter baumannii is an important human pathogen due to its multi-drug resistance. In this study, the genome of an ST10 outbreak A. baumannii isolate LAC-4 was completely sequenced to better understand its epidemiology, antibiotic resistance genetic determinants and potential virulence factors. Compared with 20 other complete genomes of A. baumannii, LAC-4 genome harbors at least 12 copies of five distinct insertion sequences. It contains 12 and 14 copies of two novel IS elements, ISAba25 and ISAba26, respectively. Additionally, three novel composite transposons were identified: Tn6250, Tn6251 and Tn6252, two of which contain resistance genes. The antibiotic resistance genetic determinants on the LAC-4 genome correlate well with observed antimicrobial susceptibility patterns. Moreover, twelve genomic islands (GI) were identified in LAC-4 genome. Among them, the 33.4-kb GI12 contains a large number of genes which constitute the K (capsule) locus. LAC-4 harbors several unique putative virulence factor loci. Furthermore, LAC-4 and all 19 other outbreak isolates were found to harbor a heme oxygenase gene (hemO)-containing gene cluster. The sequencing of the first complete genome of an ST10 A. baumannii clinical strain should accelerate our understanding of the epidemiology, mechanisms of resistance and virulence of A. baumannii. PMID:25728466

Molecular Epidemiology of Yellow Fever in Bolivia from 1999 to 2008

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Baronti, Cécile; Goitia, Norma Janeth Velasquez; Cook, Shelley; Roca, Yelin; Revollo, Jimmy; Flores, Jorge Vargas

2011-01-01

Abstract Yellow fever (YF) is a serious public health problem in Bolivia since at least the 19th century. Surprisingly, very limited information has been made available to date regarding the genetic characterisation and epidemiology of Bolivian YF virus (YFV) strains. Here, we conducted the genetic characterization of 12 human isolates of YFV collected in Bolivia between 1999 and 2008, by sequencing and analysis of two regions of the viral genome: a fragment encoding structural proteins “PrM” (premembrane and envelope) and a distal region “EMF,” spanning the end of the virus genome. Our study reveals a high genetic diversity of YFV strains circulating in Bolivia during the last decade: we identified not only “Peruvian-like” genotype II viruses (related to previously characterized Bolivian strains), but also, for the fist time, “Brazilian-like” genotype I viruses. During the complete period of the study, only cases of “jungle” YF were detected (i.e., circulation of YFV via a sylvatic cycle) with no cluster of urban cases. However, the very significant spread of the Aedes aegypti mosquito across Bolivian cities threatens the country with the reappearance of an urban YFV transmission cycle and thus is required a sustained epidemiological surveillance. PMID:20925524

Microsatellite data analysis for population genetics

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Theories and analytical tools of population genetics have been widely applied for addressing various questions in the fields of ecological genetics, conservation biology, and any context where the role of dispersal or gene flow is important. Underlying much of population genetics is the analysis of ...

The Analysis of Polyploid Genetic Data

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Meirmans, P.G.; Liu, S.; van Tienderen, P.H.

2018-01-01

Though polyploidy is an important aspect of the evolutionary genetics of both plants and animals, the development of population genetic theory of polyploids has seriously lagged behind that of diploids. This is unfortunate since the analysis of polyploid genetic data—and the interpretation of the

Effects of smoking on the genetic risk of obesity: the population architecture using genomics and epidemiology study

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Fesinmeyer Megan D

2013-01-01

Full Text Available Abstract Background Although smoking behavior is known to affect body mass index (BMI, the potential for smoking to influence genetic associations with BMI is largely unexplored. Methods As part of the ‘Population Architecture using Genomics and Epidemiology (PAGE’ Consortium, we investigated interaction between genetic risk factors associated with BMI and smoking for 10 single nucleotide polymorphisms (SNPs previously identified in genome-wide association studies. We included 6 studies with a total of 56,466 subjects (16,750 African Americans (AA and 39,716 European Americans (EA. We assessed effect modification by testing an interaction term for each SNP and smoking (current vs. former/never in the linear regression and by stratified analyses. Results We did not observe strong evidence for interactions and only observed two interactions with p-values TMEM18, the risk allele (C was associated with BMI only among AA females who were former/never smokers (β = 0.018, p = 0.002, vs. current smokers (β = 0.001, p = 0.95, pinteraction = 0.10. For rs9939609/FTO, the A allele was more strongly associated with BMI among current smoker EA females (β = 0.017, p = 3.5x10-5, vs. former/never smokers (β = 0.006, p = 0.05, pinteraction = 0.08. Conclusions These analyses provide limited evidence that smoking status may modify genetic effects of previously identified genetic risk factors for BMI. Larger studies are needed to follow up our results. Clinical Trial Registration NCT00000611

Clinical and Molecular Epidemiology of Human Parainfluenza Viruses 1-4 in Children from Viet Nam.

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Linster, Martin; Do, Lien Anh Ha; Minh, Ngo Ngoc Quang; Chen, Yihui; Zhe, Zhu; Tuan, Tran Anh; Tuan, Ha Manh; Su, Yvonne C F; van Doorn, H Rogier; Moorthy, Mahesh; Smith, Gavin J D

2018-05-01

HPIVs are serologically and genetically grouped into four species that account for up to 10% of all hospitalizations due to acute respiratory infection in children under the age of five. Genetic and epidemiological data for the four HPIVs derived from two pediatric cohorts in Viet Nam are presented. Respiratory samples were screened for HPIV1-4 by real-time PCR. Demographic and clinical data of patients infected with different HPIV were compared. We used a hemi-nested PCR approach to generate viral genome sequences from HPIV-positive samples and conducted a comprehensive phylogenetic analysis. In total, 170 samples tested positive for HPIV. HPIV3 was most commonly detected in our cohort and 80 co-detections of HPIV with other respiratory viruses were found. Phylogenetic analyses suggest local endemic circulation as well as punctuated introductions of new HPIV lineages. Viral gene flow analysis revealed that Viet Nam is a net importer of viral genetic diversity. Epidemiological analyses imply similar disease severity for all HPIV species. HPIV sequences from Viet Nam formed local clusters and were interspersed with sequences from diverse geographic regions. Combined, this new knowledge will help to investigate global HPIV circulation patterns in more detail and ultimately define more suitable vaccine strains.

Australasian disasters of national significance: an epidemiological analysis, 1900-2012.

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Bradt, David A; Bartley, Bruce; Hibble, Belinda A; Varshney, Kavita

2015-04-01

A regional epidemiological analysis of Australasian disasters in the 20th century to present was undertaken to examine trends in disaster epidemiology; to characterise the impacts on civil society through disaster policy, practice and legislation; and to consider future potential limitations in national disaster resilience. A surveillance definition of disaster was developed conforming to the Centre for Research on the Epidemiology of Disasters (CRED) criteria (≥10 deaths, ≥100 affected, or declaration of state emergency or appeal for international assistance). The authors then applied economic and legislative inclusion criteria to identify additional disasters of national significance. The surveillance definition yielded 165 disasters in the period, from which 65 emerged as disasters of national significance. There were 38 natural disasters, 22 technological disasters, three offshore terrorist attacks and two domestic mass shootings. Geographic analysis revealed that states with major population centres experienced the vast majority of disasters of national significance. Timeline analysis revealed an increasing incidence of disasters since the 1980s, which peaked in the period 2005-2009. Recent seasonal bushfires and floods have incurred the highest death toll and economic losses in Australasian history. Reactive hazard-specific legislation emerged after all terrorist acts and after most disasters of national significance. Timeline analysis reveals an increasing incidence in natural disasters over the past 15 years, with the most lethal and costly disasters occurring in the past 3 years. Vulnerability to disaster in Australasia appears to be increasing. Reactive legislation is a recurrent feature of Australasian disaster response that suggests legislative shortsightedness and a need for comprehensive all-hazards model legislation in the future. © 2015 Australasian College for Emergency Medicine and Australasian Society for Emergency Medicine.

Molecular epidemiology, and possible real-world applications in breast cancer.

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Ito, Hidemi; Matsuo, Keitaro

2016-01-01

Gene-environment interaction, a key idea in molecular epidemiology, has enabled the development of personalized medicine. This concept includes personalized prevention. While genome-wide association studies have identified a number of genetic susceptibility loci in breast cancer risk, however, the application of this knowledge to practical prevention is still underway. Here, we briefly review the history of molecular epidemiology and its progress in breast cancer epidemiology. We then introduce our experience with the trial combination of GWAS-identified loci and well-established lifestyle and reproductive risk factors in the risk prediction of breast cancer. Finally, we report our exploration of the cumulative risk of breast cancer based on this risk prediction model as a potential tool for individual risk communication, including genetic risk factors and gene-environment interaction with obesity.

An analysis of the genetic diversity and genetic structure of ...

African Journals Online (AJOL)

Scientific approaches to conservation of threatened species depend on a good understanding of the genetic information of wild and artificial population. The genetic diversity and structure analysis of 10 Eucommia ulmoides population was analyzed using inter-simple sequence repeat (ISSR) markers in this paper.

Molecular markers in the epidemiology and diagnosis of coccidioidomycosis.

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Duarte-Escalante, Esperanza; Frías-De-León, María Guadalupe; Zúñiga, Gerardo; Martínez-Herrera, Erick; Acosta-Altamirano, Gustavo; Reyes-Montes, María Del Rocío

2014-01-01

The prevalence of coccidioidomycosis in endemic areas has been observed to increase daily. To understand the causes of the spread of the disease and design strategies for fungal detection in clinical and environmental samples, scientists have resorted to molecular tools that allow fungal detection in a natural environment, reliable identification in clinical cases and the study of biological characteristics, such as reproductive and genetic structure, demographic history and diversification. We conducted a review of the most important molecular markers in the epidemiology of Coccidioides spp. and the diagnosis of coccidioidomycosis. A literature search was performed for scientific publications concerning the application of molecular tools for the epidemiology and diagnosis of coccidioidomycosis. The use of molecular markers in the epidemiological study and diagnosis of coccidioidomycosis has allowed for the typing of Coccidioides spp. isolates, improved understanding of their mode of reproduction, genetic variation and speciation and resulted in the development specific, rapid and sensitive strategies for detecting the fungus in environmental and clinical samples. Molecular markers have revealed genetic variability in Coccidioides spp. This finding influences changes in the epidemiology of coccidioidomycosis, such as the emergence of more virulent or antifungal resistant genotypes. Furthermore, the molecular markers currently used to identify Coccidioides immitis and Coccidioides posadasii are specific and sensitive. However, they must be validated to determine their application in diagnosis. This manuscript is part of the series of works presented at the "V International Workshop: Molecular genetic approaches to the study of human pathogenic fungi" (Oaxaca, Mexico, 2012). Copyright © 2013 Revista Iberoamericana de Micología. Published by Elsevier Espana. All rights reserved.

Molecular Epidemiological Analysis of Dengue Fever in Bolivia from 1998 to 2008

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Roca, Yelin; Baronti, Cécile; Revollo, Roberto Jimmy; Cook, Shelley; Loayza, Roxana; Ninove, Laetitia; Fernandez, Roberto Torrez; Flores, Jorge Vargas; Herve, Jean-Pierre; de Lamballerie, Xavier

2012-01-01

Dengue fever was first recognized in Bolivia in 1931. However, very limited information was available to date regarding the genetic characterization and epidemiology of Bolivian dengue virus strains. Here, we performed genetic characterization of the full-length envelope gene of 64 Bolivian isolates from 1998 to 2008 and investigated their origin and evolution to determine whether strains circulated simultaneously or alternatively, and whether or not multiple introductions of distinct viral variants had occurred during the period studied. We determined that, during the last decade, closely related viruses circulated during several consecutive years (5, 6, and 6 years for DENV-1, DENV-2, and DENV-3, respectively) and the co-circulation of two or even three serotypes was observed. Emergence of new variants (distinct from those identified during the previous episodes) was identified in the case of DENV-1 (2007 outbreak) and DENV-2 (2001 outbreak). In all cases, it is likely that the viruses originated from neighboring countries. PMID:19505253

The Analysis of Polyploid Genetic Data.

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Meirmans, Patrick G; Liu, Shenglin; van Tienderen, Peter H

2018-03-16

Though polyploidy is an important aspect of the evolutionary genetics of both plants and animals, the development of population genetic theory of polyploids has seriously lagged behind that of diploids. This is unfortunate since the analysis of polyploid genetic data-and the interpretation of the results-requires even more scrutiny than with diploid data. This is because of several polyploidy-specific complications in segregation and genotyping such as tetrasomy, double reduction, and missing dosage information. Here, we review the theoretical and statistical aspects of the population genetics of polyploids. We discuss several widely used types of inferences, including genetic diversity, Hardy-Weinberg equilibrium, population differentiation, genetic distance, and detecting population structure. For each, we point out how the statistical approach, expected result, and interpretation differ between different ploidy levels. We also discuss for each type of inference what biases may arise from the polyploid-specific complications and how these biases can be overcome. From our overview, it is clear that the statistical toolbox that is available for the analysis of genetic data is flexible and still expanding. Modern sequencing techniques will soon be able to overcome some of the current limitations to the analysis of polyploid data, though the techniques are lagging behind those available for diploids. Furthermore, the availability of more data may aggravate the biases that can arise, and increase the risk of false inferences. Therefore, simulations such as we used throughout this review are an important tool to verify the results of analyses of polyploid genetic data.

Mutation scanning analysis of genetic variation within and among Echinococcus species: implications and future prospects.

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Jabbar, Abdul; Gasser, Robin B

2013-07-01

Adult tapeworms of the genus Echinococcus (family Taeniidae) occur in the small intestines of carnivorous definitive hosts and are transmitted to particular intermediate mammalian hosts, in which they develop as fluid-filled larvae (cysts) in internal organs (usually lung and liver), causing the disease echinococcosis. Echinococcus species are of major medical importance and also cause losses to the meat and livestock industries, mainly due to the condemnation of infected offal. Decisions regarding the treatment and control of echinococcosis rely on the accurate identification of species and population variants (strains). Conventional, phenetic methods for specific identification have some significant limitations. Despite advances in the development of molecular tools, there has been limited application of mutation scanning methods to species of Echinococcus. Here, we briefly review key genetic markers used for the identification of Echinococcus species and techniques for the analysis of genetic variation within and among populations, and the diagnosis of echinococcosis. We also discuss the benefits of utilizing mutation scanning approaches to elucidate the population genetics and epidemiology of Echinococcus species. These benefits are likely to become more evident following the complete characterization of the genomes of E. granulosus and E. multilocularis.

Genetic characterization of canine parvovirus from dogs in Pakistan.

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Shabbir, M Z; Sohail, M U; Chaudhary, U N; Yaqub, W; Rashid, I; Saleem, M H; Munir, M

Canine parvoviruses (CPV) exist as antigenic variants with varying frequencies and genetic variabilities across the globe. Given the endemicity and high prevalence in Pakistan, we characterized the CPVs originating from dogs-population to elucidate viral diversity and evolution. Fecal samples from clinically diseased pups (n = 17) of different breeds and age (2-6 months) were processed for hemagglutination assay (HA), and later for partial amplification of VP2 gene sequence and amino acid analysis. A total of 11 samples (64.71%) were found positive both in hemagglutination and PCR assays. Phylogenetic and evolutionary analysis demonstrated higher genetic heterogeneity in studied strains and constituted seven clusters within the CPV-2a group, however, they shared high level of identity with Chinese strains. Further studies are necessary to elucidate genetic analysis and epidemiology of CPV variants across a wide geographical area of the country.

COMPUTER METHODS OF GENETIC ANALYSIS.

Directory of Open Access Journals (Sweden)

A. L. Osipov

2017-02-01

Full Text Available The basic statistical methods used in conducting the genetic analysis of human traits. We studied by segregation analysis, linkage analysis and allelic associations. Developed software for the implementation of these methods support.

The effect of ethnicity and genetic ancestry on the epidemiology, clinical features and outcome of systemic lupus erythematosus.

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Lewis, Myles J; Jawad, Ali S

2017-04-01

In this in-depth review, we examine the worldwide epidemiology of SLE and summarize current knowledge on the influence of race/ethnicity on clinical manifestations, disease activity, damage accumulation and outcome in SLE. Susceptibility to SLE has a strong genetic component, and trans-ancestral genetic studies have revealed a substantial commonality of shared genetic risk variants across different genetic ancestries that predispose to the development of SLE. The highest increased risk of developing SLE is observed in black individuals (incidence 5- to 9-fold increased, prevalence 2- to 3-fold increased), with an increased risk also observed in South Asians, East Asians and other non-white groups, compared with white individuals. Black, East Asian, South Asian and Hispanic individuals with SLE tend to develop more severe disease with a greater number of manifestations and accumulate damage from lupus more rapidly. Increased genetic risk burden in these populations, associated with increased autoantibody reactivity in non-white individuals with SLE, may explain the more severe lupus phenotype. Even after taking into account socio-economic factors, race/ethnicity remains a key determinant of poor outcome, such as end-stage renal failure and mortality, in SLE. Community measures to expedite diagnosis through increased awareness in at-risk racial/ethnic populations and ethnically personalized treatment algorithms may help in future to improve long-term outcomes in SLE. © The Author 2016. Published by Oxford University Press on behalf of the British Society for Rheumatology. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Genetic analysis in Bartter syndrome from India.

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Sharma, Pradeep Kumar; Saikia, Bhaskar; Sharma, Rachna; Ankur, Kumar; Khilnani, Praveen; Aggarwal, Vinay Kumar; Cheong, Hae

2014-10-01

Bartter syndrome is a group of inherited, salt-losing tubulopathies presenting as hypokalemic metabolic alkalosis with normotensive hyperreninemia and hyperaldosteronism. Around 150 cases have been reported in literature till now. Mutations leading to salt losing tubulopathies are not routinely tested in Indian population. The authors have done the genetic analysis for the first time in the Bartter syndrome on two cases from India. First case was antenatal Bartter syndrome presenting with massive polyuria and hyperkalemia. Mutational analysis revealed compound heterozygous mutations in KCNJ1(ROMK) gene [p(Leu220Phe), p(Thr191Pro)]. Second case had a phenotypic presentation of classical Bartter syndrome however, genetic analysis revealed only heterozygous novel mutation in SLC12A gene p(Ala232Thr). Bartter syndrome is a clinical diagnosis and genetic analysis is recommended for prognostication and genetic counseling.

Panel 1: Epidemiology and Diagnosis.

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Homøe, Preben; Kværner, Kari; Casey, Janet R; Damoiseaux, Roger A M J; van Dongen, Thijs M A; Gunasekera, Hasantha; Jensen, Ramon G; Kvestad, Ellen; Morris, Peter S; Weinreich, Heather M

2017-04-01

Objective To create a literature review between 2011 and June 1, 2015, on advances in otitis media (OM) epidemiology and diagnosis (including relevant audiology studies). Data Sources Electronic search engines (PubMed, EMBASE, and Cochrane Library) with a predefined search strategy. Review Methods Articles with appropriate epidemiologic methodology for OM, including acute mastoiditis and eustachian tube dysfunction. Items included OM worldwide and in high-risk populations, OM-related hearing loss, news in OM diagnostics, prenatal risk factors and comorbidities, postnatal risk factors, genetics, microbiological epidemiology, guidelines, and quality of life. Conclusions Diagnostic evidence and genetic studies are increasing; guidelines are introduced worldwide; and there is evidence of benefit of pneumococcal conjugate vaccines. New risk factors and comordities are identified in the study period, and quality of life is affected in children and their families. Implications for Practice Chronic suppurative OM occurs worldwide and contributes to lifelong hearing loss. Uniform definitions are still lacking and should be provided. An association between HIV and chronic suppurative OM has been found. Tympanometry is recommended for diagnosis, with or without pneumatic otoscopy. Video otoscopy, algorithms, and validated questionnaires may assist clinicians. Childhood obesity is associated with OM. Heritability accounts for 20% to 50% of OM diagnoses. OM-prone children seem to produce weaker immunologic responses to pneumococcal conjugate vaccines. Clinicians tend to individualize treatment without adhering to guidelines.

Alzheimer’s disease is not “brain aging”: neuropathological, genetic, and epidemiological human studies

Science.gov (United States)

Head, Elizabeth; Schmitt, Frederick A.; Davis, Paulina R.; Neltner, Janna H.; Jicha, Gregory A.; Abner, Erin L.; Smith, Charles D.; Van Eldik, Linda J.; Kryscio, Richard J.; Scheff, Stephen W.

2011-01-01

Human studies are reviewed concerning whether “aging”-related mechanisms contribute to Alzheimer’s disease (AD) pathogenesis. AD is defined by specific neuropathology: neuritic amyloid plaques and neocortical neurofibrillary tangles. AD pathology is driven by genetic factors related not to aging per se, but instead to the amyloid precursor protein (APP). In contrast to genes involved in APP-related mechanisms, there is no firm connection between genes implicated in human “accelerated aging” diseases (progerias) and AD. The epidemiology of AD in advanced age is highly relevant but deceptively challenging to address given the low autopsy rates in most countries. In extreme old age, brain diseases other than AD approximate AD prevalence while the impact of AD pathology appears to peak by age 95 and decline thereafter. Many distinct brain diseases other than AD afflict older human brains and contribute to cognitive impairment. Additional prevalent pathologies include cerebrovascular disease and hippocampal sclerosis, both high-morbidity brain diseases that appear to peak in incidence later than AD chronologically. Because of these common brain diseases of extreme old age, the epidemiology differs between clinical “dementia” and the subset of dementia cases with AD pathology. Additional aging-associated mechanisms for cognitive decline such as diabetes and synapse loss have been linked to AD and these hypotheses are discussed. Criteria are proposed to define an “aging-linked” disease, and AD fails all of these criteria. In conclusion, it may be most fruitful to focus attention on specific pathways involved in AD rather than attributing it to an inevitable consequence of aging. PMID:21516511

Impact of HFE genetic testing on clinical presentation of hereditary hemochromatosis: new epidemiological data

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Ka Chandran

2005-06-01

Full Text Available Abstract Background Hereditary hemochromatosis (HH is a common inherited disorder of iron metabolism in Northern European populations. The discovery of a candidate gene in 1996 (HFE, and of its main mutation (C282Y, has radically altered the way to diagnose this disease. The aim of this study was to assess the impact of the HFE gene discovery on the clinical presentation and epidemiology of HH. Methods We studied our cohort of 415 patients homozygous for the C282Y allele and included in a phlebotomy program in a blood centre in western Brittany, France. Results In this cohort, 56.9% of the patients were male and 21.9% began their phlebotomy program before the implementation of the genetic test. A significant decrease in the sex ratio was noticed following implementation of this DNA test, from 3.79 to 1.03 (p -5, meaning that the proportion of diagnosed females relatives to males greatly increased. The profile of HH patients at diagnosis changed after the DNA test became available. Serum ferritin and iron values were lower and there was a reduced frequency of clinical signs displayed at diagnosis, particularly skin pigmentation (20.1 vs. 40.4%, OR = 0.37, p Conclusion This study highlights the importance of the HFE gene discovery, which has simplified the diagnosis of HH and modified its clinical presentation and epidemiology. This study precisely measures these changes. Enhanced diagnosis of HFE-related HH at an early stage and implementation of phlebotomy treatment are anticipated to maintain normal life expectancy for these patients.

Mycobacterium bovis in Burkina Faso: epidemiologic and genetic links between human and cattle isolates.

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Sanou, Adama; Tarnagda, Zekiba; Kanyala, Estelle; Zingué, Dezemon; Nouctara, Moumini; Ganamé, Zakaria; Combary, Adjima; Hien, Hervé; Dembele, Mathurin; Kabore, Antoinette; Meda, Nicolas; Van de Perre, Philippe; Neveu, Dorine; Bañuls, Anne Laure; Godreuil, Sylvain

2014-10-01

In sub-Saharan Africa, bovine tuberculosis (bTB) is a potential hazard for animals and humans health. The goal of this study was to improve our understanding of bTB epidemiology in Burkina Faso and especially Mycobacterium bovis transmission within and between the bovine and human populations. Twenty six M. bovis strains were isolated from 101 cattle carcasses with suspected bTB lesions during routine meat inspections at the Bobo Dioulasso and Ouagadougou slaughterhouses. In addition, 7 M. bovis strains were isolated from 576 patients with pulmonary tuberculosis. Spoligotyping, RDAf1 deletion and MIRU-VNTR typing were used for strains genotyping. The isolation of M. bovis strains was confirmed by spoligotyping and 12 spoligotype signatures were detected. Together, the spoligotyping and MIRU-VNTR data allowed grouping the 33 M. bovis isolates in seven clusters including isolates exclusively from cattle (5) or humans (1) or from both (1). Moreover, these data (genetic analyses and phenetic tree) showed that the M. bovis isolates belonged to the African 1 (Af1) clonal complex (81.8%) and the putative African 5 (Af5) clonal complex (18.2%), in agreement with the results of RDAf1 deletion typing. This is the first detailed molecular characterization of M. bovis strains from humans and cattle in Burkina Faso. The distribution of the two Af1 and putative Af5 clonal complexes is comparable to what has been reported in neighbouring countries. Furthermore, the strain genetic profiles suggest that M. bovis circulates across the borders and that the Burkina Faso strains originate from different countries, but have a country-specific evolution. The genetic characterization suggests that, currently, M. bovis transmission occurs mainly between cattle, occasionally between cattle and humans and potentially between humans. This study emphasizes the bTB risk in cattle but also in humans and the difficulty to set up proper disease control strategies in Burkina Faso.

Spatio-temporal Analysis of the Genetic Diversity of Arctic Rabies Viruses and Their Reservoir Hosts in Greenland.

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Dennis Hanke

2016-07-01

Full Text Available There has been limited knowledge on spatio-temporal epidemiology of zoonotic arctic fox rabies among countries bordering the Arctic, in particular Greenland. Previous molecular epidemiological studies have suggested the occurrence of one particular arctic rabies virus (RABV lineage (arctic-3, but have been limited by a low number of available samples preventing in-depth high resolution phylogenetic analysis of RABVs at that time. However, an improved knowledge of the evolution, at a molecular level, of the circulating RABVs and a better understanding of the historical perspective of the disease in Greenland is necessary for better direct control measures on the island. These issues have been addressed by investigating the spatio-temporal genetic diversity of arctic RABVs and their reservoir host, the arctic fox, in Greenland using both full and partial genome sequences. Using a unique set of 79 arctic RABV full genome sequences from Greenland, Canada, USA (Alaska and Russia obtained between 1977 and 2014, a description of the historic context in relation to the genetic diversity of currently circulating RABV in Greenland and neighboring Canadian Northern territories has been provided. The phylogenetic analysis confirmed delineation into four major arctic RABV lineages (arctic 1-4 with viruses from Greenland exclusively grouping into the circumpolar arctic-3 lineage. High resolution analysis enabled distinction of seven geographically distinct subclades (3.I - 3.VII with two subclades containing viruses from both Greenland and Canada. By combining analysis of full length RABV genome sequences and host derived sequences encoding mitochondrial proteins obtained simultaneously from brain tissues of 49 arctic foxes, the interaction of viruses and their hosts was explored in detail. Such an approach can serve as a blueprint for analysis of infectious disease dynamics and virus-host interdependencies. The results showed a fine-scale spatial population

A review for detecting gene-gene interactions using machine learning methods in genetic epidemiology.

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Koo, Ching Lee; Liew, Mei Jing; Mohamad, Mohd Saberi; Salleh, Abdul Hakim Mohamed

2013-01-01

Recently, the greatest statistical computational challenge in genetic epidemiology is to identify and characterize the genes that interact with other genes and environment factors that bring the effect on complex multifactorial disease. These gene-gene interactions are also denoted as epitasis in which this phenomenon cannot be solved by traditional statistical method due to the high dimensionality of the data and the occurrence of multiple polymorphism. Hence, there are several machine learning methods to solve such problems by identifying such susceptibility gene which are neural networks (NNs), support vector machine (SVM), and random forests (RFs) in such common and multifactorial disease. This paper gives an overview on machine learning methods, describing the methodology of each machine learning methods and its application in detecting gene-gene and gene-environment interactions. Lastly, this paper discussed each machine learning method and presents the strengths and weaknesses of each machine learning method in detecting gene-gene interactions in complex human disease.

A Review for Detecting Gene-Gene Interactions Using Machine Learning Methods in Genetic Epidemiology

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Ching Lee Koo

2013-01-01

Full Text Available Recently, the greatest statistical computational challenge in genetic epidemiology is to identify and characterize the genes that interact with other genes and environment factors that bring the effect on complex multifactorial disease. These gene-gene interactions are also denoted as epitasis in which this phenomenon cannot be solved by traditional statistical method due to the high dimensionality of the data and the occurrence of multiple polymorphism. Hence, there are several machine learning methods to solve such problems by identifying such susceptibility gene which are neural networks (NNs, support vector machine (SVM, and random forests (RFs in such common and multifactorial disease. This paper gives an overview on machine learning methods, describing the methodology of each machine learning methods and its application in detecting gene-gene and gene-environment interactions. Lastly, this paper discussed each machine learning method and presents the strengths and weaknesses of each machine learning method in detecting gene-gene interactions in complex human disease.

Strategies to work with HLA data in human populations for histocompatibility, clinical transplantation, epidemiology and population genetics: HLA-NET methodological recommendations.

Science.gov (United States)

Sanchez-Mazas, A; Vidan-Jeras, B; Nunes, J M; Fischer, G; Little, A-M; Bekmane, U; Buhler, S; Buus, S; Claas, F H J; Dormoy, A; Dubois, V; Eglite, E; Eliaou, J F; Gonzalez-Galarza, F; Grubic, Z; Ivanova, M; Lie, B; Ligeiro, D; Lokki, M L; da Silva, B Martins; Martorell, J; Mendonça, D; Middleton, D; Voniatis, D Papioannou; Papasteriades, C; Poli, F; Riccio, M E; Vlachou, M Spyropoulou; Sulcebe, G; Tonks, S; Nevessignsky, M Toungouz; Vangenot, C; van Walraven, A-M; Tiercy, J-M

2012-12-01

HLA-NET (a European COST Action) aims at networking researchers working in bone marrow transplantation, epidemiology and population genetics to improve the molecular characterization of the HLA genetic diversity of human populations, with an expected strong impact on both public health and fundamental research. Such improvements involve finding consensual strategies to characterize human populations and samples and report HLA molecular typings and ambiguities; proposing user-friendly access to databases and computer tools and defining minimal requirements related to ethical aspects. The overall outcome is the provision of population genetic characterizations and comparisons in a standard way by all interested laboratories. This article reports the recommendations of four working groups (WG1-4) of the HLA-NET network at the mid-term of its activities. WG1 (Population definitions and sampling strategies for population genetics' analyses) recommends avoiding outdated racial classifications and population names (e.g. 'Caucasian') and using instead geographic and/or cultural (e.g. linguistic) criteria to describe human populations (e.g. 'pan-European'). A standard 'HLA-NET POPULATION DATA QUESTIONNAIRE' has been finalized and is available for the whole HLA community. WG2 (HLA typing standards for population genetics analyses) recommends retaining maximal information when reporting HLA typing results. Rather than using the National Marrow Donor Program coding system, all ambiguities should be provided by listing all allele pairs required to explain each genotype, according to the formats proposed in 'HLA-NET GUIDELINES FOR REPORTING HLA TYPINGS'. The group also suggests taking into account a preliminary list of alleles defined by polymorphisms outside the peptide-binding sites that may affect population genetic statistics because of significant frequencies. WG3 (Bioinformatic strategies for HLA population data storage and analysis) recommends the use of programs capable

Genetic Diversity and Geographic Population Structure of Bovine Neospora caninum Determined by Microsatellite Genotyping Analysis

Science.gov (United States)

Regidor-Cerrillo, Javier; Díez-Fuertes, Francisco; García-Culebras, Alicia; Moore, Dadín P.; González-Warleta, Marta; Cuevas, Carmen; Schares, Gereon; Katzer, Frank; Pedraza-Díaz, Susana; Mezo, Mercedes; Ortega-Mora, Luis M.

2013-01-01

The cyst-forming protozoan parasite Neospora caninum is one of the main causes of bovine abortion worldwide and is of great economic importance in the cattle industry. Recent studies have revealed extensive genetic variation among N . caninum isolates based on microsatellite sequences (MSs). MSs may be suitable molecular markers for inferring the diversity of parasite populations, molecular epidemiology and the basis for phenotypic variations in N . caninum , which have been poorly defined. In this study, we evaluated nine MS markers using a panel of 11 N . caninum -derived reference isolates from around the world and 96 N . caninum bovine clinical samples and one ovine clinical sample collected from four countries on two continents, including Spain, Argentina, Germany and Scotland, over a 10-year period. These markers were used as molecular tools to investigate the genetic diversity, geographic distribution and population structure of N . caninum . Multilocus microsatellite genotyping based on 7 loci demonstrated high levels of genetic diversity in the samples from all of the different countries, with 96 microsatellite multilocus genotypes (MLGs) identified from 108 N . caninum samples. Geographic sub-structuring was present in the country populations according to pairwise F ST. Principal component analysis (PCA) and Neighbor Joining tree topologies also suggested MLG segregation partially associated with geographical origin. An analysis of the MLG relationships, using eBURST, confirmed that the close genetic relationship observed between the Spanish and Argentinean populations may be the result of parasite migration (i.e., the introduction of novel MLGs from Spain to South America) due to cattle movement. The eBURST relationships also revealed genetically different clusters associated with the abortion. The presence of linkage disequilibrium, the co-existence of specific MLGs to individual farms and eBURST MLG relationships suggest a predominant clonal

Uses of the Twins UK genetic database.

Science.gov (United States)

Spector, Tim D

2007-11-01

Tim Spector is a Professor of Genetic Epidemiology at King's College London and Director of the Twin Research and Genetic Epidemiology Unit at St Thomas' Hospital, London. Professor Spector graduated from St Bartholomew's Hospital Medical School, London, in 1982. After working in General Medicine, he completed a MSc in Epidemiology, and his MD degree at the University of London in 1989. He founded the UK Twins Registry of 10,000 twins in 1993, which is one of the largest collections of genotype and phenotype information on twins worldwide, whose breadth of research has expanded to cover a wide range of common complex traits many of which were previously thought to be mainly due to aging and the environment. He has published over 350 research articles on common diseases. He has written several original articles on the genetics of a wide range of diseases and traits including back pain, acne, inflammation, obesity, memory, musical ability and sexuality. He is the principal investigator of the EU Euroclot and Treat OA study, and a partner in five others. He has written several books, focusing on osteoporosis and genetics and, in 2003, he published a popular book on genetics: Your Genes Unzipped.

Prune-belly syndrome: case series and review of the literature regarding early prenatal diagnosis, epidemiology, genetic factors, treatment, and prognosis.

Science.gov (United States)

Tonni, Gabriele; Ida, Vito; Alessandro, Ventura; Bonasoni, Maria Paola

2013-02-01

Prune-belly syndrome (PBS) is a rare congenital syndrome characterized by deficient abdominal muscles, urinary tract malformation, and in males, cryptorchidism and has an estimated incidence of 1 in 35,000 to 1 in 50,000 live births. The syndrome might be due to severe bladder outlet obstruction or to abdominal muscle deficiency secondary to a migrational defect of the lateral mesoblast between weeks 6 and 7 of pregnancy. The current review of the medical record reports a special focus on epidemiology, genetic factors, early prenatal diagnosis clusters, treatment, and prognosis of PBS.

Global foot-and-mouth disease research update and gap analysis: 2 - epidemiology, wildlife and economics

Science.gov (United States)

In 2014, the Global Foot-and-mouth disease Research ings in the fields of (i) epidemiology, (ii) wildlife and (iii) Alliance (GFRA) conducted a gap analysis of foot-and- economics. Although the three sections, epidemiology, wildlife and economics are presented as separate entities, the fields are ...

Epidemiología y genética: ¿alianza estratégica en el nuevo milenio? Epidemiology and genetics: a strategic alliance in the new millennium?

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Gustavo Bergonzoli

2005-01-01

Full Text Available Although the information derived from biological markers could conceivably be used to overcome some of the problems intrinsic to virtually all epidemiologic study designs-case definition, true exposure level, host susceptibility and resistance to factors of interest, the misclassification of study subjects (false positive and false negative test results, etc.-, we are still unable to resolve all such problems with the tools available at present. Biological markers seem more promising as potential indicators of the degree of susceptibility than as indicators of disease occurrence, an application requiring further technical refinement. Currently biological markers are employed in public health mainly to screen for particular diseases. Unfortunately, these markers have their limitations. For one thing, it is unlikely that they will completely eliminate the problem of false positive and false negative results, since DNA from solid tumors undergoes slight degradation due to necrosis and since genetic markers are susceptible to the effects of exposure to medication, diet, sex, ethnicity, and even the circadian cycle. And even if false positives and negatives were ultimately eliminated, it would be impossible to use many of the analytical tools based on two by two tables, such as the chi squared test, logistic regression, the Poisson regression, Cox' proportional hazards ratio, etc., since such tools rely on comparisons of the number of false positives and negatives in the exposed and non-exposed groups. Finally, albeit no less important, certain ethical issues must be carefully considered before allowing the massive use of human genetic markers, which could lead to violations of the rights of individuals, families, and communities if carried out in an indiscriminate, unregulated fashion. Epidemiology is rapidly broadening its scope, a trend that will continue into the future; new analytical tools will be developed, and the working hypotheses to which

Primer Part 1-The building blocks of epilepsy genetics.

Science.gov (United States)

Helbig, Ingo; Heinzen, Erin L; Mefford, Heather C

2016-06-01

This is the first of a two-part primer on the genetics of the epilepsies within the Genetic Literacy Series of the Genetics Commission of the International League Against Epilepsy. In Part 1, we cover the foundations of epilepsy genetics including genetic epidemiology and the range of genetic variants that can affect the risk for developing epilepsy. We discuss various epidemiologic study designs that have been applied to the genetics of the epilepsies including population studies, which provide compelling evidence for a strong genetic contribution in many epilepsies. We discuss genetic risk factors varying in size, frequency, inheritance pattern, effect size, and phenotypic specificity, and provide examples of how genetic risk factors within the various categories increase the risk for epilepsy. We end by highlighting trends in epilepsy genetics including the increasing use of massive parallel sequencing technologies. Wiley Periodicals, Inc. © 2016 International League Against Epilepsy.

Epidemiology of idiopathic pulmonary fibrosis

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Ley B

2013-11-01

Full Text Available Brett Ley, Harold R Collard Department of Medicine, Division of Pulmonary and Critical Care Medicine, University of California San Francisco, San Francisco, California, USA Abstract: Idiopathic pulmonary fibrosis is a chronic fibrotic lung disease of unknown cause that occurs in adults and has a poor prognosis. Its epidemiology has been difficult to study because of its rarity and evolution in diagnostic and coding practices. Though uncommon, it is likely underappreciated both in terms of its occurrence (ie, incidence, prevalence and public health impact (ie, health care costs and resource utilization. Incidence and mortality appear to be on the rise, and prevalence is expected to increase with the aging population. Potential risk factors include occupational and environmental exposures, tobacco smoking, gastroesophageal reflux, and genetic factors. An accurate understanding of its epidemiology is important, especially as novel therapies are emerging. Keywords: idiopathic pulmonary fibrosis, epidemiology, incidence, prevalence, mortality, risk factors

VNTR analysis reveals unexpected genetic diversity within Mycoplasma agalactiae, the main causative agent of contagious agalactia

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Ayling Roger D

2008-11-01

Full Text Available Abstract Background Mycoplasma agalactiae is the main cause of contagious agalactia, a serious disease of sheep and goats, which has major clinical and economic impacts. Previous studies of M. agalactiae have shown it to be unusually homogeneous and there are currently no available epidemiological techniques which enable a high degree of strain differentiation. Results We have developed variable number tandem repeat (VNTR analysis using the sequenced genome of the M. agalactiae type strain PG2. The PG2 genome was found to be replete with tandem repeat sequences and 4 were chosen for further analysis. VNTR 5 was located within the hypothetical protein MAG6170 a predicted lipoprotein. VNTR 14 was intergenic between the hypothetical protein MAG3350 and the hypothetical protein MAG3340. VNTR 17 was intergenic between the hypothetical protein MAG4060 and the hypothetical protein MAG4070 and VNTR 19 spanned the 5' end of the pseudogene for a lipoprotein MAG4310 and the 3' end of the hypothetical lipoprotein MAG4320. We have investigated the genetic diversity of 88 M. agalactiae isolates of wide geographic origin using VNTR analysis and compared it with pulsed field gel electrophoresis (PFGE and random amplified polymorphic DNA (RAPD analysis. Simpson's index of diversity was calculated to be 0.324 for PFGE and 0.574 for VNTR analysis. VNTR analysis revealed unexpected diversity within M. agalactiae with 9 different VNTR types discovered. Some correlation was found between geographical origin and the VNTR type of the isolates. Conclusion VNTR analysis represents a useful, rapid first-line test for use in molecular epidemiological analysis of M. agalactiae for outbreak tracing and control.

Journal of Genetics | Indian Academy of Sciences

Indian Academy of Sciences (India)

population stratification; ancestry informative markers (AIMs); race; ethnicity; genetic epidemiology; forensic genetics; Hispanics. ... Department of Microbiology, Mount Sinai School of Medicine, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, NY 10029 ...

Introducing medical genetics services in Ethiopia using the MiGene Family History App.

Science.gov (United States)

Quinonez, Shane C; Yeshidinber, Abate; Lourie, Michael A; Bekele, Delayehu; Mekonnen, Yemisrach; Nigatu, Balkachew; Metaferia, Gesit; Jebessa, Solomie

2018-06-11

Almost all low-income countries and many middle-income countries lack the capacity to deliver medical genetics services. We developed the MiGene Family History App (MFHA), which assists doctors with family history collection and population-level epidemiologic analysis. The MFHA was studied at St. Paul's Hospital in Addis Ababa, Ethiopia. A needs assessment was used to assess Ethiopian physicians' experience with genetics services. The MFHA then collected patient data over a 6-month period. The majority of doctors provide genetics services, with only 16% reporting their genetics knowledge is sufficient. A total of 1699 patients from the pediatric ward (n = 367), neonatal intensive care unit (NICU) (n = 477), and antenatal clinic (n = 855) were collected using the MFHA with a 4% incidence of a MFHA-screened condition present. The incidence was 11.7% in the pediatric ward, 3% in the NICU, and 0.5% in the antenatal clinic. Heart malformations (5.5% of patients) and trisomy 21 (4.4% of patients) were the most common conditions in the pediatric ward. Medical genetics services are needed in Ethiopia. As other countries increase their genetics capacity, the MFHA can provide fundamental genetics services and collect necessary epidemiologic data.

Rapid Genetic Analysis in Congenital Hyperinsulinism

DEFF Research Database (Denmark)

Christesen, Henrik Thybo; Brusgaard, Klaus; Alm, Jan

2007-01-01

BACKGROUND: In severe, medically unresponsive congenital hyperinsulinism (CHI), the histological differentiation of focal versus diffuse disease is vital, since the surgical management is completely different. Genetic analysis may help in the differential diagnosis, as focal CHI is associated...... with a paternal germline ABCC8 or KCNJ11 mutation and a focal loss of maternal chromosome 11p15, whereas a maternal mutation, or homozygous/compound heterozygous ABCC8 and KCNJ11 mutations predict diffuse-type disease. However, genotyping usually takes too long to be helpful in the absence of a founder mutation....... METHODS: In 4 patients, a rapid genetic analysis of the ABBC8 and KCNJ11 genes was performed within 2 weeks on request prior to the decision of pancreatic surgery. RESULTS: Two patients had no mutations, rendering the genetic analysis non-informative. Peroperative multiple biopsies showed diffuse disease...

[Bibliometric analysis of scientific articles on epidemiological study of burns in China].

Science.gov (United States)

Cheng, W F; Shen, Z A; Zhao, D X; Li, D W; Shang, Y R

2017-04-20

Objective: To analyze the current status of epidemiological study of burns in China, and to explore the related strategies. Methods: Retrospective or cross-sectional scientific articles in Chinese or English on epidemiological study of burns in China published from January 2005 to December 2015 were systemically retrieved from 4 databases. The databases include PubMed, Embase, China Biology Medicine disc, and Chinese Journals Full - text Database . From the results retrieved, data with regard to publication year, journal distribution, number of institutions participated in the study, affiliation of the first author and its location, and admission time span and age of patients in all the scientific articles were collected. Furthermore, the definition of age range and the grouping method of age of pediatric patients in English articles on epidemiological study of pediatric burns of China were recorded. Data were processed with descriptive statistical analysis. Results: A total of 256 scientific articles conforming to the study criteria were retrieved, among which 214 (83.59%) articles were in Chinese, and 42 (16.41%) articles were in English; 242 (94.53%) articles were retrospective studies, and 14 (5.47%) articles were cross-sectional studies. During the 11 years, the number of the relevant articles was fluctuant on the whole. The scientific articles were published in 130 journals, with 42 English articles in source journals for SCIENCE CITATION INDEX EXPANDED - JOURNAL LIST, accounting for 16.41%, and 116 Chinese articles in Source Journal for Chinese Scientific and Technical Papers, accounting for 45.31%. Totally 215 (83.98%) articles were single-center studies, and 29 (11.33%) articles were multicenter studies which were conducted by three or more centers. The number of affiliations of the first author of articles was 161 in total. The top 10 institutions regarding the article publishing number published 58 articles, accounting for 22.66%. Scientific articles on

Selection bias in genetic-epidemiological studies of cleft lip and palate

Energy Technology Data Exchange (ETDEWEB)

Christensen, K.; Holm, N.V.; Kock, K. (Odense Univ. (Denmark)); Olsen, J. (Aarhus Univ. (Denmark)); Fogh-Anderson, P.

1992-09-01

The possible impact of selection bias in genetic and epidemiological studies of cleft lip and palate was studied, using three nationwide ascertainment sources and an autopsy study in a 10% sample of the Danish population. A total of 670 cases were identified. Two national record systems, when used together, were found suitable for ascertaining facial cleft in live births. More than 95% ascertainment was obtained by means of surgical files for cleft lip (with or without cleft palate) without associated malformations/syndromes. However, surgical files could be a poor source for studying isolated cleft palate (CP) (only a 60% and biased ascertainment), and they cannot be used to study the prevalence of associated malformations or syndromes in facial cleft cases. The male:female ratio was 0.88 in surgically treated cases of CP and was 1.5 in nonoperated CP cases, making the overall sex ratio for CP 1.1 (95% confidence limits 0.86-1.4) The sex ratio for CP without associated malformation was 1.1 (95% confidence limits 0.84-1.6). One of the major test criteria in CP multifactorial threshold models (higher CP liability among male CP relatives) must be reconsidered, if other investigations confirm that a CP sex-ratio reversal to male predominance occurs when high ascertainment is achieved. 24 refs., 1 fig., 4 tabs.

Dynamic Path Analysis in Life-Course Epidemiology

DEFF Research Database (Denmark)

Gamborg, Michael Orland; Boje Jensen, Gorm; Sørensen, Thorkild I.A.

2011-01-01

it works through other risk factors. In this paper, the dynamic path analysis model is presented as a tool to analyze these dynamic mechanisms in life-course epidemiology. A key feature of dynamic path analysis is its ability to decompose the total effect of a risk factor into a direct effect (not mediated...... by other variables) and indirect effects (mediated through other variables). This is illustrated by examining the associations between repeated measurements of body mass index (BMI) and systolic blood pressure (SBP) and the risk of CHD in a sample of Danish men between 1976 and 2006. The effect of baseline...... BMI on the risk of CHD is decomposed into a direct effect and indirect effects going through later BMI, concurrent SBP, or later SBP. In conclusion, dynamic path analysis is a flexible tool that by the decomposition of effects can be used to increase the understanding of mechanisms that underlie...

Detection of Healthcare-Related Extended-Spectrum Beta-Lactamase-Producing Escherichia coli Transmission Events Using Combined Genetic and Phenotypic Epidemiology.

Directory of Open Access Journals (Sweden)

Anne F Voor In 't Holt

Full Text Available Since the year 2000 there has been a sharp increase in the prevalence of healthcare-related infections caused by extended-spectrum beta-lactamase (ESBL-producing Escherichia coli. However, the high community prevalence of ESBL-producing E. coli isolates means that many E. coli typing techniques may not be suitable for detecting E. coli transmission events. Therefore, we investigated if High-throughput MultiLocus Sequence Typing (HiMLST and/or Raman spectroscopy were suitable techniques for detecting recent E. coli transmission events.This study was conducted from January until December 2010 at Erasmus University Medical Center, Rotterdam, the Netherlands. Isolates were typed using HiMLST and Raman spectroscopy. A genetic cluster was defined as two or more patients carrying identical isolates. We used predefined definitions for epidemiological relatedness to assess healthcare-related transmission.We included 194 patients; strains of 112 patients were typed using HiMLST and strains of 194 patients were typed using Raman spectroscopy. Raman spectroscopy identified 16 clusters while HiMLST identified 10 clusters. However, no healthcare-related transmission events were detected. When combining data from both typing techniques, we identified eight clusters (n = 34 patients, as well as 78 patients with a non-cluster isolate. However, we could not detect any healthcare-related transmission in these 8 clusters.Although clusters were genetically detected using HiMLST and Raman spectroscopy, no definite epidemiological relationships could be demonstrated which makes the possibility of healthcare-related transmission events highly unlikely. Our results suggest that typing of ESBL-producing E. coli using HiMLST and/or Raman spectroscopy is not helpful in detecting E. coli healthcare-related transmission events.

An Integrative Analysis of Foot-and-Mouth Disease Virus Carriers in Vietnam Achieved Through Targeted Surveillance and Molecular Epidemiology.

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de Carvalho Ferreira, H C; Pauszek, S J; Ludi, A; Huston, C L; Pacheco, J M; Le, V T; Nguyen, P T; Bui, H H; Nguyen, T D; Nguyen, T; Nguyen, T T; Ngo, L T; Do, D H; Rodriguez, L; Arzt, J

2017-04-01

Foot-and-mouth disease (FMD) is a major constraint to transboundary trade in animal products, yet much of its natural ecology and epidemiology in endemic regions is still poorly understood. To address this gap, a multidisciplinary, molecular and conventional epidemiological approach was applied to an investigation of endemic FMD in Vietnam. Within the study space, it was found that 22.3% of sampled ruminants had previously been infected with FMD virus (FMDV), of which 10.8% were persistent, asymptomatic carriers (2.4% of the total population). Descriptive data collected from targeted surveillance and a farm questionnaire showed a significantly lower prevalence of FMDV infection for dairy farms. In contrast, farms of intermediate size and/or history of infection in 2010 were at increased risk of FMD exposure. At the individual animal level, buffalo had the highest exposure risk (over cattle), and there was spatial heterogeneity in exposure risk at the commune level. Conversely, carrier prevalence was higher for beef cattle, suggesting lower susceptibility of buffalo to persistent FMDV infection. To characterize virus strains currently circulating in Vietnam, partial FMDV genomic (VP1) sequences from carrier animals collected between 2012 and 2013 (N = 27) and from FMDV outbreaks between 2009 and 2013 (N = 79) were compared by phylogenetic analysis. Sequence analysis suggested that within the study period, there were two apparent novel introductions of serotype A viruses and that the dominant lineage of serotype O in Vietnam shifted from SEA/Mya-98 to ME-SA/PanAsia. FMDV strains shared close ancestors with FMDV from other South-East Asian countries indicating substantial transboundary movement of the predominant circulating strains. Close genetic relationships were observed between carrier and outbreak viruses, which may suggest that asymptomatic carriers of FMDV contribute to regional disease persistence. Multiple viral sequences obtained from carrier cattle

Global stability analysis of epidemiological models based on Volterra–Lyapunov stable matrices

International Nuclear Information System (INIS)

Liao Shu; Wang Jin

2012-01-01

Highlights: ► Global dynamics of high dimensional dynamical systems. ► A systematic approach for global stability analysis. ► Epidemiological models of environment-dependent diseases. - Abstract: In this paper, we study the global dynamics of a class of mathematical epidemiological models formulated by systems of differential equations. These models involve both human population and environmental component(s) and constitute high-dimensional nonlinear autonomous systems, for which the global asymptotic stability of the endemic equilibria has been a major challenge in analyzing the dynamics. By incorporating the theory of Volterra–Lyapunov stable matrices into the classical method of Lyapunov functions, we present an approach for global stability analysis and obtain new results on some three- and four-dimensional model systems. In addition, we conduct numerical simulation to verify the analytical results.

Molecular Epidemiology and Genomics of Group A Streptococcus

Science.gov (United States)

Bessen, Debra E.; McShan, W. Michael; Nguyen, Scott V.; Shetty, Amol; Agrawal, Sonia; Tettelin, Hervé

2014-01-01

Streptococcus pyogenes (group A streptococcus; GAS) is a strict human pathogen with a very high prevalence worldwide. This review highlights the genetic organization of the species and the important ecological considerations that impact its evolution. Recent advances are presented on the topics of molecular epidemiology, population biology, molecular basis for genetic change, genome structure and genetic flux, phylogenomics and closely related streptococcal species, and the long- and short-term evolution of GAS. The application of whole genome sequence data to addressing key biological questions is discussed. PMID:25460818

Genetic variation analysis and relationships among environmental strains of Scedosporium apiospermum sensu stricto in Bangkok, Thailand.

Directory of Open Access Journals (Sweden)

Thanwa Wongsuk

Full Text Available The Scedosporium apiospermum species complex is an emerging filamentous fungi that has been isolated from environment. It can cause a wide range of infections in both immunocompetent and immunocompromised individuals. We aimed to study the genetic variation and relationships between 48 strains of S. apiospermum sensu stricto isolated from soil in Bangkok, Thailand. For PCR, sequencing and phylogenetic analysis, we used the following genes: actin; calmodulin exons 3 and 4; the second largest subunit of the RNA polymerase II; ß-tubulin exon 2-4; manganese superoxide dismutase; internal transcribed spacer; transcription elongation factor 1α; and beta-tubulin exons 5 and 6. The present study is the first phylogenetic analysis of relationships among S. apiospermum sensu stricto in Thailand and South-east Asia. This result provides useful information for future epidemiological study and may be correlated to clinical manifestation.

Genetic diversity and phylogenetic analysis of Aleutian mink disease virus isolates in north-east China.

Science.gov (United States)

Leng, Xue; Liu, Dongxu; Li, Jianming; Shi, Kun; Zeng, Fanli; Zong, Ying; Liu, Yi; Sun, Zhibo; Zhang, Shanshan; Liu, Yadong; Du, Rui

2018-05-01

Aleutian mink disease is the most important disease in the mink-farming industry worldwide. So far, few large-scale molecular epidemiological studies of AMDV, based on the NS1 and VP2 genes, have been conducted in China. Here, eight new Chinese isolates of AMDV from three provinces in north-east China were analyzed to clarify the molecular epidemiology of AMDV. The seroprevalence of AMDV in north-east China was 41.8% according to counterimmuno-electrophoresis. Genetic variation analysis of the eight isolates showed significant non-synonymous substitutions in the NS1 and VP2 genes, especially in the NS1 gene. All eight isolates included the caspase-recognition sequence NS1:285 (DQTD↓S), but not the caspase recognition sequence NS1:227 (INTD↓S). The LN1 and LN2 strains had a new 10-amino-acid deletion in-between amino acids 28-37, while the JL3 strain had a one-amino-acid deletion at position 28 in the VP2 protein, compared with the AMDV-G strain. Phylogenetic analysis based on most of NS1 (1755 bp) and complete VP2 showed that the AMDV genotypes did not cluster according to their pathogenicity or geographic origin. Local and imported ADMV species are all prevalent in mink-farming populations in the north-east of China. This is the first study to report the molecular epidemiology of AMDV in north-east China based on most of NS1 and the complete VP2, and further provides information about polyG deletions and new variations in the amino acid sequences of NS1 and VP2 proteins. This report is a good foundation for further study of AMDV in China.

Rationale for an integrated approach to genetic epidemiology.

Science.gov (United States)

Laberge, Claude M; Knoppers, Bartha Maria

1992-10-01

Genetic knowledge is now in the public domain and its interpretation by the media and the citizens brings the issues into the public forum of discussion for the necessary ethical, legal and socio-cultural evaluation of its application. Science is being perceived by some as dangerous and as requiring international regulation. Others feel that genetic knowledge will be the breakthrough that will permit medical progress and individual autonomy with regards to personal health and lifestyle choices. The mapping of the human genome has already yielded valuable information on an increasing number of diseases and their variants. Prevailing popular and journalistic archetypes ("imaginaires") used in the media are perceived by the producers as slowing down the possible application of genetic knowledge. The answers to these dilemmas are not readily apparent nor are they prescribed by classical philosophy of medicine. Since genetic knowledge eventually resides with the individual who carries the genes of disease and/or susceptibility, a logical approach to integration of this knowledge at a societal level would seem to reside with individual education and decision-making. The politics of the ensuing social debate could transform the current social contract since an individual's interests need to be balanced against those of his or her immediate family in the sharing of information. The ethical foundations of such a contract requires the genetic education of "Everyone" as a matter of urgent priority. Genetic education should not serve ideological power struggles between the medical establishment and the ethical-legal alliance. Instead, it should ensure the transfer of knowledge to physicians, to patients, to users, to planners, to social science and humanities researchers and to politicians, so that they may make "informed" and free decisions....

Journal of Genetics | Indian Academy of Sciences

Indian Academy of Sciences (India)

Home; Journals; Journal of Genetics. Shanker Jayashree. Articles written in Journal of Genetics. Volume 94 Issue 3 September 2015 pp 539-549 Review Article. Genetic epidemiology of coronary artery disease: an Asian Indian perspective · Shanker Jayashree Maitra Arindam Kakkar V. Vijay · More Details Abstract Fulltext ...

Analysis of genetic diversity inpigeonpeagermplasm using ...

Indian Academy of Sciences (India)

Navya

2016-11-25

Nov 25, 2016 ... accessions from Orissa (105) and AP (15) do not group with any Indian accessions. ... In the present work, comparison between SSAP and REMAP revealed ... (sequence-specific amplified polymorphism) for genetic analysis of sweet potato. ... Sharma,V.and Nandinemi, M.R. 2014 Assessment of genetic ...

Clinico-epidemiologic features of oculocutaneous albinism in ...

African Journals Online (AJOL)

Background: Oculocutaneous albinism (OCA) is a genetically heterogeneous group of disorders characterized by the absence or reduced pigmentation of the skin, hair and eyes. To assess the clinico-epidemiologic features of different forms of OCA among Egyptian patients, we performed a retrospective study to determine ...

Participatory epidemiology: the contribution of participatory research to epidemiology

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Mario Bach

2017-02-01

Full Text Available Abstract Background Epidemiology has contributed in many ways to identifying various risk factors for disease and to promoting population health. However, there is a continuing debate about the ability of epidemiology not only to describe, but also to provide results which can be better translated into public health practice. It has been proposed that participatory research approaches be applied to epidemiology as a way to bridge this gap between description and action. A systematic account of what constitutes participatory epidemiology practice has, however, been lacking. Methods A scoping review was carried out focused on the question of what constitutes participatory approaches to epidemiology for the purpose of demonstrating their potential for advancing epidemiologic research. Relevant databases were searched, including both the published and non-published (grey literature. The 102 identified sources were analyzed in terms of comparing common epidemiologic approaches to participatory counterparts regarding central aspects of the research process. Exemplary studies applying participatory approaches were examined more closely. Results A highly diverse, interdisciplinary body of literature was synthesized, resulting in a framework comprised of seven aspects of the research process: research goal, research question, population, context, data synthesis, research management, and dissemination of findings. The framework specifies how participatory approaches not only differ from, but also how they can enhance common approaches in epidemiology. Finally, recommendations for the further development of participatory approaches are given. These include: enhancing data collection, data analysis, and data validation; advancing capacity building for research at the local level; and developing data synthesis. Conclusion The proposed framework provides a basis for systematically developing the emergent science of participatory epidemiology.

Advancing ecological understandings through technological transformations in noninvasive genetics.

Science.gov (United States)

Beja-Pereira, Albano; Oliveira, Rita; Alves, Paulo C; Schwartz, Michael K; Luikart, Gordon

2009-09-01

Noninvasive genetic approaches continue to improve studies in molecular ecology, conservation genetics and related disciplines such as forensics and epidemiology. Noninvasive sampling allows genetic studies without disturbing or even seeing the target individuals. Although noninvasive genetic sampling has been used for wildlife studies since the 1990s, technological advances continue to make noninvasive approaches among the most used and rapidly advancing areas in genetics. Here, we review recent advances in noninvasive genetics and how they allow us to address important research and management questions thanks to improved techniques for DNA extraction, preservation, amplification and data analysis. We show that many advances come from the fields of forensics, human health and domestic animal health science, and suggest that molecular ecologists explore literature from these fields. Finally, we discuss how the combination of advances in each step of a noninvasive genetics study, along with fruitful areas for future research, will continually increase the power and role of noninvasive genetics in molecular ecology and conservation genetics. © 2009 Blackwell Publishing Ltd.

Mycobacterium bovis in Burkina Faso: epidemiologic and genetic links between human and cattle isolates.

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Adama Sanou

2014-10-01

Full Text Available In sub-Saharan Africa, bovine tuberculosis (bTB is a potential hazard for animals and humans health. The goal of this study was to improve our understanding of bTB epidemiology in Burkina Faso and especially Mycobacterium bovis transmission within and between the bovine and human populations.Twenty six M. bovis strains were isolated from 101 cattle carcasses with suspected bTB lesions during routine meat inspections at the Bobo Dioulasso and Ouagadougou slaughterhouses. In addition, 7 M. bovis strains were isolated from 576 patients with pulmonary tuberculosis. Spoligotyping, RDAf1 deletion and MIRU-VNTR typing were used for strains genotyping. The isolation of M. bovis strains was confirmed by spoligotyping and 12 spoligotype signatures were detected. Together, the spoligotyping and MIRU-VNTR data allowed grouping the 33 M. bovis isolates in seven clusters including isolates exclusively from cattle (5 or humans (1 or from both (1. Moreover, these data (genetic analyses and phenetic tree showed that the M. bovis isolates belonged to the African 1 (Af1 clonal complex (81.8% and the putative African 5 (Af5 clonal complex (18.2%, in agreement with the results of RDAf1 deletion typing.This is the first detailed molecular characterization of M. bovis strains from humans and cattle in Burkina Faso. The distribution of the two Af1 and putative Af5 clonal complexes is comparable to what has been reported in neighbouring countries. Furthermore, the strain genetic profiles suggest that M. bovis circulates across the borders and that the Burkina Faso strains originate from different countries, but have a country-specific evolution. The genetic characterization suggests that, currently, M. bovis transmission occurs mainly between cattle, occasionally between cattle and humans and potentially between humans. This study emphasizes the bTB risk in cattle but also in humans and the difficulty to set up proper disease control strategies in Burkina Faso.

Translational Epidemiology in Psychiatry

Science.gov (United States)

Weissman, Myrna M.; Brown, Alan S.; Talati, Ardesheer

2012-01-01

Translational research generally refers to the application of knowledge generated by advances in basic sciences research translated into new approaches for diagnosis, prevention, and treatment of disease. This direction is called bench-to-bedside. Psychiatry has similarly emphasized the basic sciences as the starting point of translational research. This article introduces the term translational epidemiology for psychiatry research as a bidirectional concept in which the knowledge generated from the bedside or the population can also be translated to the benches of laboratory science. Epidemiologic studies are primarily observational but can generate representative samples, novel designs, and hypotheses that can be translated into more tractable experimental approaches in the clinical and basic sciences. This bedside-to-bench concept has not been explicated in psychiatry, although there are an increasing number of examples in the research literature. This article describes selected epidemiologic designs, providing examples and opportunities for translational research from community surveys and prospective, birth cohort, and family-based designs. Rapid developments in informatics, emphases on large sample collection for genetic and biomarker studies, and interest in personalized medicine—which requires information on relative and absolute risk factors—make this topic timely. The approach described has implications for providing fresh metaphors to communicate complex issues in interdisciplinary collaborations and for training in epidemiology and other sciences in psychiatry. PMID:21646577

Characterization of Microsatellites in Pseudogymnoascus destructans for White-nose Syndrome Genetic Analysis.

Science.gov (United States)

Drees, Kevin P; Parise, Katy L; Rivas, Stephanie M; Felton, Lindsey L; Puechmaille, Sébastien J; Keim, Paul; Foster, Jeffrey T

2017-10-01

Despite only emerging in the past decade, white-nose syndrome has become among the most devastating wildlife diseases known. The pathogenic fungus Pseudogymnoascus destructans infects hibernating bats and typically leads to high rates of mortality at hibernacula during winter in North America. We developed a set of genetic markers to better differentiate P. destructans isolates. We designed and successfully characterized these 23 microsatellite markers of P. destructans for use in disease ecology and epidemiology research. We validated these loci with DNA extracted from a collection of P. destructans isolates from the US and Canada, as well as from Europe (the likely introduction source based on currently available data). Genetic diversity calculated for each locus and for the multilocus panel as a whole indicates sufficient allelic diversity to differentiate among and between samples from both Europe and North America. Indices of genetic diversity indicate a loss of allelic diversity that is consistent with the recent introduction and rapid spread of an emerging pathogen.

An integrated system for genetic analysis

Directory of Open Access Journals (Sweden)

Duan Xiao

2006-04-01

Full Text Available Abstract Background Large-scale genetic mapping projects require data management systems that can handle complex phenotypes and detect and correct high-throughput genotyping errors, yet are easy to use. Description We have developed an Integrated Genotyping System (IGS to meet this need. IGS securely stores, edits and analyses genotype and phenotype data. It stores information about DNA samples, plates, primers, markers and genotypes generated by a genotyping laboratory. Data are structured so that statistical genetic analysis of both case-control and pedigree data is straightforward. Conclusion IGS can model complex phenotypes and contain genotypes from whole genome association studies. The database makes it possible to integrate genetic analysis with data curation. The IGS web site http://bioinformatics.well.ox.ac.uk/project-igs.shtml contains further information.

Genetic analysis of Asian measles virus strains--new endemic genotype in Nepal.

Science.gov (United States)

Truong, A T; Mulders, M N; Gautam, D C; Ammerlaan, W; de Swart, R L; King, C C; Osterhaus, A D; Muller, C P

2001-07-01

In many parts of Asia measles virus (MV) continues to be endemic. However, little is known about the genetic characteristics of viruses circulating on this continent. This study reports the molecular epidemiological analysis based on the entire nucleocapsid (N) and hemagglutinin (H) genes of the first isolates from Nepal and Taiwan, as well as of recent MV strains from India, Indonesia, and China. Four isolates collected in various regions in Nepal during 1999 belonged to a new genotype, tentatively called D8. Another Nepalese isolate and one from India belonged to genotype D4. The diversity of the Nepalese strains indicated that measles continues to be endemic in this country. The isolate from Taiwan grouped with D3 viruses and one Chinese strain isolated in The Netherlands was assigned to the previously described clade H, known to be endemic in Mainland China. Molecular characterization emerges as an important tool for monitoring virus endemicity and vaccination efforts.

Analysis of large brain MRI databases for investigating the relationships between brain, cognitive, and genetic polymorphisms

International Nuclear Information System (INIS)

Mazoyer, B.

2006-01-01

A major challenge for the years to come is the understanding of the brain-behaviour relationships, and in particular the investigation and quantification of the impact of genetic polymorphism on these relationships. In this framework, a promising experimental approach, which we will refer to as neuro-epidemiologic imaging, consists in acquiring multimodal (brain images, psychometric an d sociological data, genotypes) data in large (several hundreds or thousands ) cohorts of subjects. Processing of such large databases requires on first place the conception and implementation of automated 'pipelines', including image registration, spatial normalisation tissue segmentation, and multivariate statistical analysis. Given the number of images and data to be processed, such pipelines must be both fully automated and robust enough to be able to handle multi-center MRI data, e.g. having inhomogeneous characteristics in terms of resolution and contrast. This approach will be illustrated using two databases collected in aged healthy subjects, searching for the impact of genetic and environmental on two markers of brain aging, namely white matter hyper-signals, and grey matter atrophy. (author)

Assessment of intercentre reproducibility and epidemiological concordance of Legionella pneumophila serogroup 1 genotyping by amplified fragment length polymorphism analysis

DEFF Research Database (Denmark)

Fry, N K; Bangsborg, Jette Marie; Bernander, S

2000-01-01

The aims of this work were to assess (i) the intercentre reproducibility and epidemiological concordance of amplified fragment length polymorphism analysis for epidemiological typing of Legionella pneumophila serogroup 1, and (ii) the suitability of the method for standardisation and implementation...... by members of the European Working Group on Legionella Infections. Fifty coded isolates comprising two panels of well-characterised strains, a "reproducibility" panel (n=20) and an "epidemiologically related" panel (n=30), were sent to 13 centres in 12 European countries. Analysis was undertaken in each...... using gel analysis software yielded R=1.00 and E=1.00, with 12, 13 or 14 types. This method can be used as a simple, rapid screening tool for epidemiological typing of isolates of Legionella pneumophila serogroup 1. Results demonstrate that the method can be highly reproducible (R=1...

A brief summary of the epidemiology and genetic relatedness of avian influenza H9N2 virus in birds and mammals in the Middle East and North Africa.

Science.gov (United States)

Nagy, A; Mettenleiter, T C; Abdelwhab, E M

2017-12-01

H9N2 is the most widespread avian influenza virus subtype in poultry worldwide. It infects a broad spectrum of host species including birds and mammals. Infections in poultry and humans vary from silent to fatal. Importantly, all AIV, which are fatal in humans (e.g. H5N1, H7N9) acquired their 'internal' gene segments from H9N2 viruses. Although H9N2 is endemic in the Middle East (ME) and North Africa since the late 1990s, little is known about its epidemiology and genetics on a regional level. In this review, we summarised the epidemiological situation of H9N2 in poultry and mammals in Iran, Iraq, Kuwait, Qatar, United Arab Emirates, Oman, Bahrain, Yemen, Saudi Arabia, Jordan, Palestine, Israel, Syria, Lebanon, Turkey, Egypt, Sudan, Libya, Tunisia, Algeria and Morocco. The virus has been isolated from humans in Egypt and serosurveys indicated widespread infection particularly among poultry workers and pigs in some countries. Some isolates replicated well in experimentally inoculated dogs, mice, hamsters and ferrets. Insufficient protection of immunised poultry was frequently reported most likely due to concurrent viral or bacterial infections and antigenic drift of the field viruses from outdated vaccine strains. Genetic analysis indicated several distinct phylogroups including a panzootic genotype in the Asian and African parts of the ME, which may be useful for the development of vaccines. The extensive circulation of H9N2 for about 20 years in this region where the H5N1 virus is also endemic in some countries, poses a serious public health threat. Regional surveillance and control strategy are highly recommended.

A possible correlation between the host genetic background in the epidemiology of Hepatitis B virus in the Amazon region of Brazil

Directory of Open Access Journals (Sweden)

A. K. C. R. Santos

1995-08-01

Full Text Available The Amazon region of Brazil is an area of great interest because of the large distribution of hepatitis B virus in specific Western areas. Seven urban communities and 24 Indian groups were visited in a total of 4,244 persons. Each individual was interviewed in order to obtain demographic and familial information. Whole blood was collected for serology and genetic determinations. Eleven genetic markers and three HBV markers were tested. Among the most relevant results it was possible to show that (i there was a large variation of previous exposure to HBV in both urban and non-urban groups ranging from 0 to 59.2%; (ii there was a different pattern of epidemiological distribution of HBV that was present even among a same linguistic Indian group, with mixed patterns of correlation between HBsAg and anti-HBs and (iii the prevalence of HBV markers (HBsAg and anti-HBs were significantly higher (P=0.0001 among the Indian population (18.8% than the urban groups (12.5%. Its possible that the host genetic background could influence and modulate the replication of the virus in order to generate HB carrier state.

Advancing ecological understandings through technological transformations in noninvasive genetics

Science.gov (United States)

Albano Beja-Pereira; Rita Oliveira; Paulo C. Alves; Michael K. Schwartz; Gordon Luikart

2009-01-01

Noninvasive genetic approaches continue to improve studies in molecular ecology, conservation genetics and related disciplines such as forensics and epidemiology. Noninvasive sampling allows genetic studies without disturbing or even seeing the target individuals. Although noninvasive genetic sampling has been used for wildlife studies since the 1990s, technological...

Implications of host genetic variation on the risk and prevalence of infectious diseases transmitted through the environment.

Science.gov (United States)

Doeschl-Wilson, Andrea B; Davidson, R; Conington, J; Roughsedge, T; Hutchings, M R; Villanueva, B

2011-07-01

Previous studies have shown that host genetic heterogeneity in the response to infectious challenge can affect the emergence risk and the severity of diseases transmitted through direct contact between individuals. However, there is substantial uncertainty about the degree and direction of influence owing to different definitions of genetic variation, most of which are not in line with the current understanding of the genetic architecture of disease traits. Also, the relevance of previous results for diseases transmitted through environmental sources is unclear. In this article a compartmental genetic-epidemiological model was developed to quantify the impact of host genetic diversity on epidemiological characteristics of diseases transmitted through a contaminated environment. The model was parameterized for footrot in sheep. Genetic variation was defined through continuous distributions with varying shape and degree of dispersion for different disease traits. The model predicts a strong impact of genetic heterogeneity on the disease risk and its progression and severity, as well as on observable host phenotypes, when dispersion in key epidemiological parameters is high. The impact of host variation depends on the disease trait for which variation occurs and on environmental conditions affecting pathogen survival. In particular, compared to homogeneous populations with the same average susceptibility, disease risk and severity are substantially higher in populations containing a large proportion of highly susceptible individuals, and the differences are strongest when environmental contamination is low. The implications of our results for the recording and analysis of disease data and for predicting response to selection are discussed.

The Genetic and Environmental Factors for Keratoconus

Directory of Open Access Journals (Sweden)

Ariela Gordon-Shaag

2015-01-01

Full Text Available Keratoconus (KC is the most common cornea ectatic disorder. It is characterized by a cone-shaped thin cornea leading to myopia, irregular astigmatism, and vision impairment. It affects all ethnic groups and both genders. Both environmental and genetic factors may contribute to its pathogenesis. This review is to summarize the current research development in KC epidemiology and genetic etiology. Environmental factors include but are not limited to eye rubbing, atopy, sun exposure, and geography. Genetic discoveries have been reviewed with evidence from family-based linkage analysis and fine mapping in linkage region, genome-wide association studies, and candidate genes analyses. A number of genes have been discovered at a relatively rapid pace. The detailed molecular mechanism underlying KC pathogenesis will significantly advance our understanding of KC and promote the development of potential therapies.

Survey Definitions of Gout for Epidemiologic Studies: Comparison With Crystal Identification as the Gold Standard

NARCIS (Netherlands)

Dalbeth, N.; Schumacher, H.R.; Fransen, J.; Neogi, T.; Jansen, T.L; Brown, M.; Louthrenoo, W.; Vazquez-Mellado, J.; Eliseev, M.; McCarthy, G.; Stamp, L.K.; Perez-Ruiz, F.; Sivera, F.; Ea, H.K.; Gerritsen, M.; Scire, C.A.; Cavagna, L.; Lin, C.; Chou, Y.Y.; Tausche, A.K.; Rocha Castelar-Pinheiro, G. da; Janssen, M; Chen, J.H.; Cimmino, M.A.; Uhlig, T.; Taylor, W.J.

2016-01-01

OBJECTIVE: To identify the best-performing survey definition of gout from items commonly available in epidemiologic studies. METHODS: Survey definitions of gout were identified from 34 epidemiologic studies contributing to the Global Urate Genetics Consortium (GUGC) genome-wide association study.

The leukemias: Epidemiologic aspects

International Nuclear Information System (INIS)

Linet, M.S.

1984-01-01

Particularly geared to physicians and cancer researchers, this study of the epidemiology and etiology of leukemia analyzes the four major leukemia subtypes in terms of genetic and familial determinant factors and examines the incidence, distribution and frequency of reported leukemia clusters. Linet discusses the connection between other types of malignancies, their treatments, and the subsequent development of leukemia and evaluates the impact on leukemia onset of such environmental factors as radiation therapy, drugs, and occupational hazards

16 CFR 1000.26 - Directorate for Epidemiology.

Science.gov (United States)

2010-01-01

... 16 Commercial Practices 2 2010-01-01 2010-01-01 false Directorate for Epidemiology. 1000.26... AND FUNCTIONS § 1000.26 Directorate for Epidemiology. The Directorate for Epidemiology, managed by the Associate Executive Director for Epidemiology, is responsible for the collection and analysis of data on...

Gene set analysis for interpreting genetic studies

DEFF Research Database (Denmark)

Pers, Tune H

2016-01-01

Interpretation of genome-wide association study (GWAS) results is lacking behind the discovery of new genetic associations. Consequently, there is an urgent need for data-driven methods for interpreting genetic association studies. Gene set analysis (GSA) can identify aetiologic pathways...

HIV-1 Genetic Variability in Cuba and Implications for Transmission and Clinical Progression.

Science.gov (United States)

Blanco, Madeline; Machado, Liuber Y; Díaz, Héctor; Ruiz, Nancy; Romay, Dania; Silva, Eladio

2015-10-01

INTRODUCTION Serological and molecular HIV-1 studies in Cuba have shown very low prevalence of seropositivity, but an increasing genetic diversity attributable to introduction of many HIV-1 variants from different areas, exchange of such variants among HIV-positive people with several coinciding routes of infection and other epidemiologic risk factors in the seropositive population. The high HIV-1 genetic variability observed in Cuba has possible implications for transmission and clinical progression. OBJECTIVE Study genetic variability for the HIV-1 env, gag and pol structural genes in Cuba; determine the prevalence of B and non-B subtypes according to epidemiologic and behavioral variables and determine whether a relationship exists between genetic variability and transmissibility, and between genetic variability and clinical disease progression in people living with HIV/AIDS. METHODS Using two molecular assays (heteroduplex mobility assay and nucleic acid sequencing), structural genes were characterized in 590 people with HIV-1 (480 men and 110 women), accounting for 3.4% of seropositive individuals in Cuba as of December 31, 2013. Nonrandom sampling, proportional to HIV prevalence by province, was conducted. Relationships between molecular results and viral factors, host characteristics, and patients' clinical, epidemiologic and behavioral variables were studied for molecular epidemiology, transmission, and progression analyses. RESULTS Molecular analysis of the three HIV-1 structural genes classified 297 samples as subtype B (50.3%), 269 as non-B subtypes (45.6%) and 24 were not typeable. Subtype B prevailed overall and in men, mainly in those who have sex with men. Non-B subtypes were prevalent in women and heterosexual men, showing multiple circulating variants and recombinant forms. Sexual transmission was the predominant form of infection for all. B and non-B subtypes were encountered throughout Cuba. No association was found between subtypes and

Quantitative genetic analysis of total glucosinolate, oil and protein ...

African Journals Online (AJOL)

Quantitative genetic analysis of total glucosinolate, oil and protein contents in Ethiopian mustard ( Brassica carinata A. Braun) ... Seeds were analyzed using HPLC (glucosinolates), NMR (oil) and NIRS (protein). Analyses of variance, Hayman's method of diallel analysis and a mixed linear model of genetic analysis were ...

Clostridium difficile infection: Evolution, phylogeny and molecular epidemiology.

Science.gov (United States)

Elliott, Briony; Androga, Grace O; Knight, Daniel R; Riley, Thomas V

2017-04-01

Over the recent decades, Clostridium difficile infection (CDI) has emerged as a global public health threat. Despite growing attention, C. difficile remains a poorly understood pathogen, however, the exquisite sensitivity offered by next generation sequencing (NGS) technology has enabled analysis of the genome of C. difficile, giving us access to massive genomic data on factors such as virulence, evolution, and genetic relatedness within C. difficile groups. NGS has also demonstrated excellence in investigations of outbreaks and disease transmission, in both small and large-scale applications. This review summarizes the molecular epidemiology, evolution, and phylogeny of C. difficile, one of the most important pathogens worldwide in the current antibiotic resistance era. Copyright © 2016 Elsevier B.V. All rights reserved.

Molecular epidemiology: new rules for new tools?

Science.gov (United States)

Merlo, Domenico Franco; Sormani, Maria Pia; Bruzzi, Paolo

2006-08-30

Molecular epidemiology combines biological markers and epidemiological observations in the study of the environmental and genetic determinants of cancer and other diseases. The potential advantages associated with biomarkers are manifold and include: (a) increased sensitivity and specificity to carcinogenic exposures; (b) more precise evaluation of the interplay between genetic and environmental determinants of cancer; (c) earlier detection of carcinogenic effects of exposure; (d) characterization of disease subtypes-etiologies patterns; (e) evaluation of primary prevention measures. These, in turn, may translate into better tools for etiologic research, individual risk assessment, and, ultimately, primary and secondary prevention. An area that has not received sufficient attention concerns the validation of these biomarkers as surrogate endpoints for cancer risk. Validation of a candidate biomarker's surrogacy is the demonstration that it possesses the properties required for its use as a substitute for a true endpoint. The principles underlying the validation process underwent remarkable developments and discussion in therapeutic research. However, the challenges posed by the application of these principles to epidemiological research, where the basic tool for this validation (i.e., the randomized study) is seldom possible, have not been thoroughly explored. The validation process of surrogacy must be applied rigorously to intermediate biomarkers of cancer risk before using them as risk predictors at the individual as well as at the population level.

Epidemiology of brain tumors in childhood--a review

International Nuclear Information System (INIS)

Baldwin, Rachel Tobias; Preston-Martin, Susan

2004-01-01

Malignant brain tumors are the leading cause of cancer death among children and the second most common type of pediatric cancer. Despite several decades of epidemiologic investigation, the etiology of childhood brain tumors (CBT) is still largely unknown. A few genetic syndromes and ionizing radiation are established risk factors. Many environmental exposures and infectious agents have been suspected of playing a role in the development of CBT. This review, based on a search of the medical literature through August 2003, summarizes the epidemiologic evidence to date. The types of exposures discussed include ionizing radiation, N-nitroso compounds (NOC), pesticides, tobacco smoke, electromagnetic frequencies (EMF), infectious agents, medications, and parental occupational exposures. We have chosen to focus on perinatal exposures and review some of the recent evidence indicating that such exposures may play a significant role in the causation of CBT. The scientific community is rapidly learning more about the molecular mechanisms by which carcinogenesis occurs and how the brain develops. We believe that advances in genetic and molecular biologic technology, including improved histologic subtyping of tumors, will be of huge importance in the future of epidemiologic research and will lead to a more comprehensive understanding of CBT etiology. We discuss some of the early findings using these technologies

Genetic epidemiology of sporadic colorectal cancer

Czech Academy of Sciences Publication Activity Database

Vodička, Pavel; Pardini, Barbara; Souček, P.; Novotný, J.; Naccarati, Alessio; Vodičková, Ludmila; Hánová, Monika; Tulupová, Elena; Poláková, Veronika; Halamková, J.; Hemminki, K.

2006-01-01

Roč. 18, Supplement 1 (2006), S8-S8 ISSN 1107-3756. [The 11th World Congress on Advances in Oncology and 9th International Symposium on Molecular Medicine . 12.10.2006-14.10.2006, Hersonissos] R&D Projects: GA ČR GA310/05/2626; GA MZd NR8563 Institutional research plan: CEZ:AV0Z50390512 Keywords : DNA repair genes Subject RIV: EB - Genetics ; Molecular Biology

Developments in statistical analysis in quantitative genetics

DEFF Research Database (Denmark)

Sorensen, Daniel

2009-01-01

of genetic means and variances, models for the analysis of categorical and count data, the statistical genetics of a model postulating that environmental variance is partly under genetic control, and a short discussion of models that incorporate massive genetic marker information. We provide an overview......A remarkable research impetus has taken place in statistical genetics since the last World Conference. This has been stimulated by breakthroughs in molecular genetics, automated data-recording devices and computer-intensive statistical methods. The latter were revolutionized by the bootstrap...... and by Markov chain Monte Carlo (McMC). In this overview a number of specific areas are chosen to illustrate the enormous flexibility that McMC has provided for fitting models and exploring features of data that were previously inaccessible. The selected areas are inferences of the trajectories over time...

Atopic dermatitis in diverse racial and ethnic groups-Variations in epidemiology, genetics, clinical presentation and treatment.

Science.gov (United States)

Kaufman, Bridget P; Guttman-Yassky, Emma; Alexis, Andrew F

2018-04-01

Atopic dermatitis (AD) is a chronic inflammatory skin condition that affects diverse ethnic groups with varying prevalence. Despite a predominance of studies in individuals of European ancestry, AD has been found to occur more frequently in Asian and Black individuals than Whites. Therefore, an understanding of the unique clinical features of AD in diverse ethnic groups, as well as the differences in genetic polymorphisms that influence susceptibility to AD and response to current therapies, is paramount for management of an increasingly diverse patient population. In this article, we review key nuances in the epidemiology, pathophysiology, clinical presentation and treatment of AD in non-White ethnic groups, which are largely underappreciated in the literature. We highlight the need for studies evaluating the tissue molecular and cellular phenotypes of AD in non-White patients, as well as greater inclusion of minority groups in clinical trials, to develop targeted treatments for a multi-ethnic population. © 2018 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Risk factors for Alzheimer's disease : a genetic-epidemiologic study

NARCIS (Netherlands)

C.M. van Duijn (Cornelia)

1992-01-01

textabstractThe work presented in this thesis has been motivated by the Jack of knowledge of risk factors for Alzheimer's disease. It has been long recognised that genetic factors are implicated, in particular in early-onset Alzheimer's disease.4 But to what extent are genetic factors involved?

Implementation and reporting of causal mediation analysis in 2015: a systematic review in epidemiological studies.

Science.gov (United States)

Liu, Shao-Hsien; Ulbricht, Christine M; Chrysanthopoulou, Stavroula A; Lapane, Kate L

2016-07-20

Causal mediation analysis is often used to understand the impact of variables along the causal pathway of an occurrence relation. How well studies apply and report the elements of causal mediation analysis remains unknown. We systematically reviewed epidemiological studies published in 2015 that employed causal mediation analysis to estimate direct and indirect effects of observed associations between an exposure on an outcome. We identified potential epidemiological studies through conducting a citation search within Web of Science and a keyword search within PubMed. Two reviewers independently screened studies for eligibility. For eligible studies, one reviewer performed data extraction, and a senior epidemiologist confirmed the extracted information. Empirical application and methodological details of the technique were extracted and summarized. Thirteen studies were eligible for data extraction. While the majority of studies reported and identified the effects of measures, most studies lacked sufficient details on the extent to which identifiability assumptions were satisfied. Although most studies addressed issues of unmeasured confounders either from empirical approaches or sensitivity analyses, the majority did not examine the potential bias arising from the measurement error of the mediator. Some studies allowed for exposure-mediator interaction and only a few presented results from models both with and without interactions. Power calculations were scarce. Reporting of causal mediation analysis is varied and suboptimal. Given that the application of causal mediation analysis will likely continue to increase, developing standards of reporting of causal mediation analysis in epidemiological research would be prudent.

Evaluation of Genetic Pattern of Non-Tuberculosis Mycobacterium Using VNTR Method

Directory of Open Access Journals (Sweden)

Noorozi J

2011-06-01

Full Text Available Background and Objectives: Epidemiological studies of Non-tuberculosis Mycobacterium is important because of the drug resistance pattern and worldwide dissemination of these organisms. One of genetic fingerprinting methods for epidemiological studies is VNTR (Variable Number Tandem Repeat. In this study genetic pattern of atypical Mycobacterium was evaluated by VNTR method for epidemiologic studies. Methods: 48 pulmonary and non pulmonary specimens separated from patients with the symptoms of pulmonary tuberculosis (PTB and identified as Non-tuberculosis Mycobacteriumby phenotypic and PCR-RFLP methods were selected for this study. Clinical samples and their standard strains were evaluated according to VNTR pattern using the 7 genetic loci including ETR-B. ETR-F. ETR-C. MPTR-A. ETR-A. ETR-E. ETR-D.Results: The results of VNTR method showed that none of the 7 loci had any polymorphism in the standard strains of atypical mycobacterium. Some of these variable number tandem repeat in 42 clinical samples of non-tuberculosis Mycobacterium were polymorphic while the PCR product (for any loci was not found in the remaining 6 specimens. Conclusion: Although the used genetic loci of this study were suitable for epidemiological studies of Mycobacterium tuberculosis, these loci were not able to determine the diversity of genetics of non-tuberculosis Mycobacterium Therefore, it seems necessary that other loci be studied using VNTR method.

Molecular Epidemiology of Heart Failure

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J. Gustav Smith, MD, PhD

2017-12-01

Full Text Available Heart failure (HF is the end-stage of all heart disease and arguably constitutes the greatest unmet therapeutic need in cardiovascular medicine today. Classic epidemiological studies have established clinical risk factors for HF, but the cause remains poorly understood in many cases. Biochemical analyses of small case-control series and animal models have described a plethora of molecular characteristics of HF, but a single unifying pathogenic theory is lacking. Heart failure appears to result not only from cardiac overload or injury but also from a complex interplay among genetic, neurohormonal, metabolic, inflammatory, and other biochemical factors acting on the heart. Recent development of robust, high-throughput tools in molecular biology provides opportunity for deep molecular characterization of population-representative cohorts and HF cases (molecular epidemiology, including genome sequencing, profiling of myocardial gene expression and chromatin modifications, plasma composition of proteins and metabolites, and microbiomes. The integration of such detailed information holds promise for improving understanding of HF pathophysiology in humans, identification of therapeutic targets, and definition of disease subgroups beyond the current classification based on ejection fraction which may benefit from improved individual tailoring of therapy. Challenges include: 1 the need for large cohorts with deep, uniform phenotyping; 2 access to the relevant tissues, ideally with repeated sampling to capture dynamic processes; and 3 analytical issues related to integration and analysis of complex datasets. International research consortia have formed to address these challenges and combine datasets, and cohorts with up to 1 million participants are being collected. This paper describes the molecular epidemiology of HF and provides an overview of methods and tissue types and examples of published and ongoing efforts to systematically evaluate molecular

Genetic correlations between intraocular pressure, blood pressure and primary open-angle glaucoma: a multi-cohort analysis.

Science.gov (United States)

Aschard, Hugues; Kang, Jae H; Iglesias, Adriana I; Hysi, Pirro; Cooke Bailey, Jessica N; Khawaja, Anthony P; Allingham, R Rand; Ashley-Koch, Allison; Lee, Richard K; Moroi, Sayoko E; Brilliant, Murray H; Wollstein, Gadi; Schuman, Joel S; Fingert, John H; Budenz, Donald L; Realini, Tony; Gaasterland, Terry; Scott, William K; Singh, Kuldev; Sit, Arthur J; Igo, Robert P; Song, Yeunjoo E; Hark, Lisa; Ritch, Robert; Rhee, Douglas J; Gulati, Vikas; Haven, Shane; Vollrath, Douglas; Zack, Donald J; Medeiros, Felipe; Weinreb, Robert N; Cheng, Ching-Yu; Chasman, Daniel I; Christen, William G; Pericak-Vance, Margaret A; Liu, Yutao; Kraft, Peter; Richards, Julia E; Rosner, Bernard A; Hauser, Michael A; Klaver, Caroline C W; vanDuijn, Cornelia M; Haines, Jonathan; Wiggs, Janey L; Pasquale, Louis R

2017-11-01

Primary open-angle glaucoma (POAG) is the most common chronic optic neuropathy worldwide. Epidemiological studies show a robust positive relation between intraocular pressure (IOP) and POAG and modest positive association between IOP and blood pressure (BP), while the relation between BP and POAG is controversial. The International Glaucoma Genetics Consortium (n=27 558), the International Consortium on Blood Pressure (n=69 395), and the National Eye Institute Glaucoma Human Genetics Collaboration Heritable Overall Operational Database (n=37 333), represent genome-wide data sets for IOP, BP traits and POAG, respectively. We formed genome-wide significant variant panels for IOP and diastolic BP and found a strong relation with POAG (odds ratio and 95% confidence interval: 1.18 (1.14-1.21), P=1.8 × 10 -27 ) for the former trait but no association for the latter (P=0.93). Next, we used linkage disequilibrium (LD) score regression, to provide genome-wide estimates of correlation between traits without the need for additional phenotyping. We also compared our genome-wide estimate of heritability between IOP and BP to an estimate based solely on direct measures of these traits in the Erasmus Rucphen Family (ERF; n=2519) study using Sequential Oligogenic Linkage Analysis Routines (SOLAR). LD score regression revealed high genetic correlation between IOP and POAG (48.5%, P=2.1 × 10 -5 ); however, genetic correlation between IOP and diastolic BP (P=0.86) and between diastolic BP and POAG (P=0.42) were negligible. Using SOLAR in the ERF study, we confirmed the minimal heritability between IOP and diastolic BP (P=0.63). Overall, IOP shares genetic basis with POAG, whereas BP has limited shared genetic correlation with IOP or POAG.

Biostatistics and epidemiology a primer for health and biomedical professionals

CERN Document Server

Wassertheil-Smoller, Sylvia

2015-01-01

Since the publication of the first edition, Biostatistics and Epidemiology has attracted loyal readers from across specialty areas in the biomedical community. Not only does this textbook teach foundations of epidemiological design and statistical methods, but it also includes topics applicable to new areas of research. Areas covered in the fourth edition include a new chapter on risk prediction, risk reclassification and evaluation of biomarkers, new material on propensity analyses, and a vastly expanded chapter on genetic epidemiology, which  is particularly relevant to those who wish to understand the epidemiological and statistical aspects of scientific articles in this rapidly advancing field. Biostatistics and Epidemiology was written to be accessible for readers without backgrounds in mathematics. It provides clear explanations of underlying principles, as well as practical guidelines of "how to do it" and "how to interpret it."a philosophical explanation of the logic of science, subsections that ...

AFLP polymorphisms allow high resolution genetic analysis of American Tegumentary Leishmaniasis agents circulating in Panama and other members of the Leishmania genus.

Directory of Open Access Journals (Sweden)

Carlos M Restrepo

Full Text Available American Tegumentary Leishmaniasis is caused by parasites of the genus Leishmania, and causes significant health problems throughout the Americas. In Panama, Leishmania parasites are endemic, causing thousands of new cases every year, mostly of the cutaneous form. In the last years, the burden of the disease has increased, coincident with increasing disturbances in its natural sylvatic environments. The study of genetic variation in parasites is important for a better understanding of the biology, population genetics, and ultimately the evolution and epidemiology of these organisms. Very few attempts have been made to characterize genetic polymorphisms of parasites isolated from Panamanian patients of cutaneous leishmaniasis. Here we present data on the genetic variability of local isolates of Leishmania, as well as specimens from several other species, by means of Amplified Fragment Length Polymorphisms (AFLP, a technique seldom used to study genetic makeup of parasites. We demonstrate that this technique allows detection of very high levels of genetic variability in local isolates of Leishmania panamensis in a highly reproducible manner. The analysis of AFLP fingerprints generated by unique selective primer combinations in L. panamensis suggests a predominant clonal mode of reproduction. Using fluorescently labeled primers, many taxon-specific fragments were identified which may show potential as species diagnostic fragments. The AFLP permitted a high resolution genetic analysis of the Leishmania genus, clearly separating certain groups among L. panamensis specimens and highly related species such as L. panamensis and L. guyanensis. The phylogenetic networks reconstructed from our AFLP data are congruent with established taxonomy for the genus Leishmania, even when using single selective primer combinations. Results of this study demonstrate that AFLP polymorphisms can be informative for genetic characterization in Leishmania parasites, at

Epidemiology and genetics of ventricular fibrillation during acute myocardial infarction

DEFF Research Database (Denmark)

Glinge, Charlotte; Sattler, Stefan; Jabbari, Reza

2016-01-01

of a family member is a risk factor for SCD and VF during acute myocardial infarction (MI), independent of traditional risk factors including family history of MI, suggesting a genetic component in the susceptibility to VF. To prevent SCD and VF due to MI, we need a better understanding of the genetic...... and molecular mechanisms causing VF in this apparently healthy population. Even though new insights and technologies have become available, the genetic predisposition to VF during MI remains poorly understood. Findings from a variety of different genetic studies have failed to reach reproducibility, although...... several genetic variants, both common and rare variants, have been associated to either VF or SCD. For this review, we searched PubMed for potentially relevant articles, using the following MeSH-terms: "sudden cardiac death", "ventricular fibrillation", "out-of-hospital cardiac arrest", "myocardial...

[Molecular epidemiological analysis of HIV-1 variants circulating in Russia in 1987-2015].

Science.gov (United States)

Lapovok, I A; Lopatukhin, A E; Kireev, D E; Kazennova, E V; Lebedev, A V; Bobkova, M R; Kolomeets, A N; Turbina, G I; Shipulin, G A; Ladnaya, N N; Pokrovsky, V V

To simultaneously analyze HIV-1 samples from all Russian regions to characterize the epidemiology of HIV infection in the country as a whole. The most extensive study was conducted to examine nucleotide sequences of the pol gene of HIV-1 samples isolated from HIV-positive persons in different regions of Russia, with the diagnosis date being fixed during 1987-2015. The nucleotide sequences of the HIV-1 genome were analyzed using computer programs and on-line applications to identify a virus subtype and new recombinant forms. The nucleotide sequences of the pol gene were analyzed in 1697 HIV-1 samples and the findings were that the genetic variant subtype A1 (IDU-A) was dominant throughout the entire territory of Russia (in more than 80% of all infection cases). Other virus variants circulating in Russia were analyzed; the phenomenon of the higher distribution of the recombinant form CRF63/02A in Siberia, which had been previously described in the literature, was also confirmed. Four new recombinant forms generated by the virus subtype A1 (IDU-A) and B and two AG recombinant forms were found. There was a larger genetic distance between the viruses of IDU-A variant circulating among the injecting drug users and those infected through heterosexual contact, as well as a change in the viruses of subtype G that caused the outbreak in the south of the country over time in 1988-1989. The findings demonstrate continuous HIV-1 genetic variability and recombination over time in Russia, as well as increased genetic diversity with higher HIV infection rates in the population.

Examining the role of unmeasured confounding in mediation analysis with genetic and genomic applications.

Science.gov (United States)

Lutz, Sharon M; Thwing, Annie; Schmiege, Sarah; Kroehl, Miranda; Baker, Christopher D; Starling, Anne P; Hokanson, John E; Ghosh, Debashis

2017-07-19

In mediation analysis if unmeasured confounding is present, the estimates for the direct and mediated effects may be over or under estimated. Most methods for the sensitivity analysis of unmeasured confounding in mediation have focused on the mediator-outcome relationship. The Umediation R package enables the user to simulate unmeasured confounding of the exposure-mediator, exposure-outcome, and mediator-outcome relationships in order to see how the results of the mediation analysis would change in the presence of unmeasured confounding. We apply the Umediation package to the Genetic Epidemiology of Chronic Obstructive Pulmonary Disease (COPDGene) study to examine the role of unmeasured confounding due to population stratification on the effect of a single nucleotide polymorphism (SNP) in the CHRNA5/3/B4 locus on pulmonary function decline as mediated by cigarette smoking. Umediation is a flexible R package that examines the role of unmeasured confounding in mediation analysis allowing for normally distributed or Bernoulli distributed exposures, outcomes, mediators, measured confounders, and unmeasured confounders. Umediation also accommodates multiple measured confounders, multiple unmeasured confounders, and allows for a mediator-exposure interaction on the outcome. Umediation is available as an R package at https://github.com/SharonLutz/Umediation A tutorial on how to install and use the Umediation package is available in the Additional file 1.

Molecular Infectious Disease Epidemiology: Survival Analysis and Algorithms Linking Phylogenies to Transmission Trees

Science.gov (United States)

Kenah, Eben; Britton, Tom; Halloran, M. Elizabeth; Longini, Ira M.

2016-01-01

Recent work has attempted to use whole-genome sequence data from pathogens to reconstruct the transmission trees linking infectors and infectees in outbreaks. However, transmission trees from one outbreak do not generalize to future outbreaks. Reconstruction of transmission trees is most useful to public health if it leads to generalizable scientific insights about disease transmission. In a survival analysis framework, estimation of transmission parameters is based on sums or averages over the possible transmission trees. A phylogeny can increase the precision of these estimates by providing partial information about who infected whom. The leaves of the phylogeny represent sampled pathogens, which have known hosts. The interior nodes represent common ancestors of sampled pathogens, which have unknown hosts. Starting from assumptions about disease biology and epidemiologic study design, we prove that there is a one-to-one correspondence between the possible assignments of interior node hosts and the transmission trees simultaneously consistent with the phylogeny and the epidemiologic data on person, place, and time. We develop algorithms to enumerate these transmission trees and show these can be used to calculate likelihoods that incorporate both epidemiologic data and a phylogeny. A simulation study confirms that this leads to more efficient estimates of hazard ratios for infectiousness and baseline hazards of infectious contact, and we use these methods to analyze data from a foot-and-mouth disease virus outbreak in the United Kingdom in 2001. These results demonstrate the importance of data on individuals who escape infection, which is often overlooked. The combination of survival analysis and algorithms linking phylogenies to transmission trees is a rigorous but flexible statistical foundation for molecular infectious disease epidemiology. PMID:27070316

Colorectal Cancer in Iran: Molecular Epidemiology and Screening Strategies

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Roya Dolatkhah

2015-01-01

Full Text Available Purpose. The increasing incidence of colorectal cancer (CRC in the past three decades in Iran has made it a major public health burden. This study aimed to report its epidemiologic features, molecular genetic aspects, survival, heredity, and screening pattern in Iran. Methods. A comprehensive literature review was conducted to identify the relevant published articles. We used medical subject headings, including colorectal cancer, molecular genetics, KRAS and BRAF mutations, screening, survival, epidemiologic study, and Iran. Results. Age standardized incidence rate of Iranian CRCs was 11.6 and 10.5 for men and women, respectively. Overall five-year survival rate was 41%, and the proportion of CRC among the younger age group was higher than that of western countries. Depending on ethnicity, geographical region, dietary, and genetic predisposition, mutation genes were considerably diverse and distinct among CRCs across Iran. The high occurrence of CRC in records of relatives of CRC patients showed that family history of CRC was more common among young CRCs. Conclusion. Appropriate screening strategies for CRC which is amenable to early detection through screening, especially in relatives of CRCs, should be considered as the first step in CRC screening programs.

Colorectal Cancer in Iran: Molecular Epidemiology and Screening Strategies

International Nuclear Information System (INIS)

Dolatkhah, R.; Somi, M. H.; Dolatkhah, R.; Kermani, I. A.; Dastgiri, S.

2015-01-01

The increasing incidence of colorectal cancer (CRC) in the past three decades in Iran has made it a major public health burden. This study aimed to report its epidemiologic features, molecular genetic aspects, survival, heredity, and screening pattern in Iran. Methods. A comprehensive literature review was conducted to identify the relevant published articles. We used medical subject headings, including colorectal cancer, molecular genetics, KRAS and BRAF mutations, screening, survival, epidemiologic study, and Iran. Results. Age standardized incidence rate of Iranian CRCs was 11.6 and 10.5 for men and women, respectively. Overall five-year survival rate was 41%, and the proportion of CRC among the younger age group was higher than that of western countries. Depending on ethnicity, geographical region, dietary, and genetic predisposition, mutation genes were considerably diverse and distinct among CRCs across Iran. The high occurrence of CRC in records of relatives of CRC patients showed that family history of CRC was more common among young CRCs. Conclusion. Appropriate screening strategies for CRC which is amenable to early detection through screening, especially in relatives of CRCs, should be considered as the first step in CRC screening programs.

Triglyceride-Rich Lipoproteins and Atherosclerotic Cardiovascular Disease: New Insights From Epidemiology, Genetics, and Biology.

Science.gov (United States)

Nordestgaard, Børge G

2016-02-19

Scientific interest in triglyceride-rich lipoproteins has fluctuated over the past many years, ranging from beliefs that these lipoproteins cause atherosclerotic cardiovascular disease (ASCVD) to being innocent bystanders. Correspondingly, clinical recommendations have fluctuated from a need to reduce levels to no advice on treatment. New insight in epidemiology now suggests that these lipoproteins, marked by high triglycerides, are strong and independent predictors of ASCVD and all-cause mortality, and that their cholesterol content or remnant cholesterol likewise are strong predictors of ASCVD. Of all adults, 27% have triglycerides >2 mmol/L (176 mg/dL), and 21% have remnant cholesterol >1 mmol/L (39 mg/dL). For individuals in the general population with nonfasting triglycerides of 6.6 mmol/L (580 mg/dL) compared with individuals with levels of 0.8 mmol/L (70 mg/dL), the risks were 5.1-fold for myocardial infarction, 3.2-fold for ischemic heart disease, 3.2-fold for ischemic stroke, and 2.2-fold for all-cause mortality. Also, genetic studies using the Mendelian randomization design, an approach that minimizes problems with confounding and reverse causation, now demonstrate that triglyceride-rich lipoproteins are causally associated with ASCVD and all-cause mortality. Finally, genetic evidence also demonstrates that high concentrations of triglyceride-rich lipoproteins are causally associated with low-grade inflammation. This suggests that an important part of inflammation in atherosclerosis and ASCVD is because of triglyceride-rich lipoprotein degradation and uptake into macrophage foam cells in the arterial intima. Taken together, new insights now strongly suggest that elevated triglyceride-rich lipoproteins represent causal risk factors for low-grade inflammation, ASCVD, and all-cause mortality. © 2016 American Heart Association, Inc.

Genetic population structure of marine viral haemorrhagic septicaemia virus (VHSV)

DEFF Research Database (Denmark)

Snow, M.; Bain, N.; Black, J.

2004-01-01

The nucleotide sequences of a specific region of the nucleoprotein gene were compared in order to investigate the genetic population structure of marine viral haemorrhagic septicaemia virus (VHSV). Analysis of the sequence from 128 isolates of diverse geographic and host origin renders this the m......The nucleotide sequences of a specific region of the nucleoprotein gene were compared in order to investigate the genetic population structure of marine viral haemorrhagic septicaemia virus (VHSV). Analysis of the sequence from 128 isolates of diverse geographic and host origin renders...... this the most comprehensive molecular epidemiological study of marine VHSV conducted to date. Phylogenetic analysis of nucleoprotein gene sequences confirmed the existence of the 4 major genotypes previously identified based on N- and subsequent G-gene based analyses. The range of Genotype I included subgroups...... of isolates associated with rainbow trout aquaculture (Genotype la) and those from the Baltic marine environment (Genotype Ib) to emphasise the relatively close genetic relationship between these isolates. The existence of an additional genotype circulating within the Baltic Sea (Genotype II) was also...

Genetic structure and phylogeography of Aedes aegypti, the dengue and yellow-fever mosquito vector in Bolivia.

Science.gov (United States)

Paupy, Christophe; Le Goff, Gilbert; Brengues, Cécile; Guerra, Mabel; Revollo, Jimmy; Barja Simon, Zaïra; Hervé, Jean-Pierre; Fontenille, Didier

2012-08-01

Between the 16th and 18th centuries, Aedes aegypti (Diptera: Culicidae), a mosquito native to Africa, invaded the Americas, where it was successively responsible for the emergence of yellow fever (YF) and dengue (DEN). The species was eradicated from numerous American countries in the mid-20th century, but re-invaded them in the 1970s and 1980s. Little is known about the precise identities of Ae. aegypti populations which successively thrived in South America, or their relation with the epidemiological changes in patterns of YF and DEN. We examined these questions in Bolivia, where Ae. aegypti, eradicated in 1943, re-appeared in the 1980s. We assessed the genetic variability and population genetics of Ae. aegypti samples in order to deduce their genetic structure and likely geographic origin. Using a 21-population set covering Bolivia, we analyzed the polymorphism at nine microsatellite loci and in two mitochondrial DNA regions (COI and ND4). Microsatellite markers revealed a significant genetic structure among geographic populations (F(ST)=0.0627, PBolivia. Analysis of mtDNA sequences revealed the existence of two genetic lineages, one dominant lineage recovered throughout Bolivia, and the second restricted to rural localities in South Bolivia. Phylogenic analysis indicated that this minority lineage was related to West African Ae. aegypti specimens. In conclusion, our results suggested a temporal succession of Ae. aegypti populations in Bolivia, that potentially impacted the epidemiology of dengue and yellow fever. Copyright © 2012 Elsevier B.V. All rights reserved.

Analysis of genetic structure and relationship among nine ...

Indian Academy of Sciences (India)

These results indicated that the clustering analysis using the Structure program might provide an ..... of the current genetic relations among the breeds, and con- tribute to ... sis of the genetic structure of the Canary goat populations using.

Gene-environment interactions in cancer epidemiology: a National Cancer Institute Think Tank report.

Science.gov (United States)

Hutter, Carolyn M; Mechanic, Leah E; Chatterjee, Nilanjan; Kraft, Peter; Gillanders, Elizabeth M

2013-11-01

Cancer risk is determined by a complex interplay of genetic and environmental factors. Genome-wide association studies (GWAS) have identified hundreds of common (minor allele frequency [MAF] > 0.05) and less common (0.01 Think Tank" on January 10-11, 2012. The objective of the Think Tank was to facilitate discussions on (1) the state of the science, (2) the goals of G × E interaction studies in cancer epidemiology, and (3) opportunities for developing novel study designs and analysis tools. This report summarizes the Think Tank discussion, with a focus on contemporary approaches to the analysis of G × E interactions. Selecting the appropriate methods requires first identifying the relevant scientific question and rationale, with an important distinction made between analyses aiming to characterize the joint effects of putative or established genetic and environmental factors and analyses aiming to discover novel risk factors or novel interaction effects. Other discussion items include measurement error, statistical power, significance, and replication. Additional designs, exposure assessments, and analytical approaches need to be considered as we move from the current small number of success stories to a fuller understanding of the interplay of genetic and environmental factors. © 2013 WILEY PERIODICALS, INC.

Timing Analysis of Genetic Logic Circuits using D-VASim

DEFF Research Database (Denmark)

Baig, Hasan; Madsen, Jan

and propagation delay analysis of single as well as cascaded geneticlogic circuits can be performed. D-VASim allows user to change the circuit parameters during runtime simulation to observe its effectson circuit’s timing behavior. The results obtained from D-VASim can be used not only to characterize the timing...... delay analysis may play a very significant role in the designing of genetic logic circuits. In thisdemonstration, we present the capability of D-VASim (Dynamic Virtual Analyzer and Simulator) to perform the timing and propagationdelay analysis of genetic logic circuits. Using D-VASim, the timing...... behavior of geneticlogic circuits but also to analyze the timing constraints of cascaded genetic logic circuits....

Genetic analysis of Mexican Criollo cattle populations.

Science.gov (United States)

Ulloa-Arvizu, R; Gayosso-Vázquez, A; Ramos-Kuri, M; Estrada, F J; Montaño, M; Alonso, R A

2008-10-01

The objective of this study was to evaluate the genetic structure of Mexican Criollo cattle populations using microsatellite genetic markers. DNA samples were collected from 168 animals from four Mexican Criollo cattle populations, geographically isolated in remote areas of Sierra Madre Occidental (West Highlands). Also were included samples from two breeds with Iberian origin: the fighting bull (n = 24) and the milking central American Criollo (n = 24) and one Asiatic breed: Guzerat (n = 32). Genetic analysis consisted of the estimation of the genetic diversity in each population by the allele number and the average expected heterozygosity found in nine microsatellite loci. Furthermore, genetic relationships among the populations were defined by their genetic distances. Our data shows that Mexican cattle populations have a relatively high level of genetic diversity based either on the mean number of alleles (10.2-13.6) and on the expected heterozygosity (0.71-0.85). The degree of observed homozygosity within the Criollo populations was remarkable and probably caused by inbreeding (reduced effective population size) possibly due to reproductive structure within populations. Our data shows that considerable genetic differentiation has been occurred among the Criollo cattle populations in different regions of Mexico.

Assessment of genetic and nongenetic interactions for the prediction of depressive symptomatology: an analysis of the Wisconsin Longitudinal Study using machine learning algorithms.

Science.gov (United States)

Roetker, Nicholas S; Page, C David; Yonker, James A; Chang, Vicky; Roan, Carol L; Herd, Pamela; Hauser, Taissa S; Hauser, Robert M; Atwood, Craig S

2013-10-01

We examined depression within a multidimensional framework consisting of genetic, environmental, and sociobehavioral factors and, using machine learning algorithms, explored interactions among these factors that might better explain the etiology of depressive symptoms. We measured current depressive symptoms using the Center for Epidemiologic Studies Depression Scale (n = 6378 participants in the Wisconsin Longitudinal Study). Genetic factors were 78 single nucleotide polymorphisms (SNPs); environmental factors-13 stressful life events (SLEs), plus a composite proportion of SLEs index; and sociobehavioral factors-18 personality, intelligence, and other health or behavioral measures. We performed traditional SNP associations via logistic regression likelihood ratio testing and explored interactions with support vector machines and Bayesian networks. After correction for multiple testing, we found no significant single genotypic associations with depressive symptoms. Machine learning algorithms showed no evidence of interactions. Naïve Bayes produced the best models in both subsets and included only environmental and sociobehavioral factors. We found no single or interactive associations with genetic factors and depressive symptoms. Various environmental and sociobehavioral factors were more predictive of depressive symptoms, yet their impacts were independent of one another. A genome-wide analysis of genetic alterations using machine learning methodologies will provide a framework for identifying genetic-environmental-sociobehavioral interactions in depressive symptoms.

Genetic effects of radiation in atomic-bomb survivors and their children. Past, present and future

International Nuclear Information System (INIS)

Nakamura, Nori

2006-01-01

Genetic studies in the offspring of atomic bomb survivors have been conducted since 1948 at the Atomic Bomb Casualty Commission and its successor, the Radiation Effects Research Foundation, in Hiroshima and Nagasaki. Past studies include analysis of birth defects (untoward pregnancy outcome; namely, malformation, stillbirth, and perinatal death), chromosome aberrations, alterations of plasma and erythrocyte proteins as well as epidemiologic study on mortality (any cause) and cancer incidence (the latter study is still ongoing). There is, thus far, no indication of genetic effects in the offspring of survivors. Recently, the development of molecular biological techniques and human genome sequence databases made it possible to analyze DNA from parents and their offspring (trio-analysis). In addition, a clinical program is underway to establish the frequency of adult-onset multi-factorial diseases (diabetes mellitus, high blood pressure, and cardiovascular disease etc) in the offspring. The complementary kinds of data that will emerge from this three-pronged approach (clinical, epidemiologic, and molecular aspects) promise to shed light on health effects in the offspring of radiation-exposed people. (author)

Identification of dietary patterns using factor analysis in an epidemiological study in São Paulo

Directory of Open Access Journals (Sweden)

Dirce Maria Lobo Marchioni

Full Text Available CONTEXT AND OBJECTIVE: Diet and nutrition are environmental factors in health/disease relationships. From the epidemiological viewpoint, diet represents a complex set of highly correlated exposures. Our objective was to identify patterns of food intake in a group of individuals living in São Paulo, and to develop objective dietary measurements for epidemiological purposes. DESIGN AND LOCAL: Exploratory factor analysis of data in a case-control study in seven teaching hospitals in São Paulo. METHODS: The participants were 517 patients (260 oral cancer cases and 257 controls admitted to the study hospitals between November 1998 and March 2001. The weekly intake frequencies for dairy products, cereals, meat, processed meat, vegetables, pulses, fruits and sweets were assessed by means of a semi-quantitative food frequency questionnaire. Dietary patterns were identified by factor analysis, based on the intake of the eight food groups, using principal component analysis as an extraction method followed by varimax rotation. RESULTS: Factor analysis identified three patterns that accounted for 55% of the total variability within the sample. The first pattern ("prudent" was characterized by vegetable, fruit and meat intake; the second ("traditional" by cereals (mainly rice and pulses (mainly beans; and the third ("snacks" by dairy products and processed meat. CONCLUSION: This study identified food intake patterns through an a posteriori approach. Such analysis may be useful for nutritional intervention programs and, after computing scores for each individual according to the patterns identified, for establishing a relationship between diet and other epidemiological measurements of interest.

Molecular genetics

International Nuclear Information System (INIS)

Parkinson, D.R.; Krontiris, T.G.

1986-01-01

In this chapter the authors review new findings concerning the molecular genetics of malignant melanoma in the context of other information obtained from clinical, epidemiologic, and cytogenetic studies in this malignancy. These new molecular approaches promise to provide a more complete understanding of the mechanisms involved in the development of melanoma, thereby suggesting new methods for its treatment and prevention

Genetic disorders from an endogamous population

African Journals Online (AJOL)

Abdulbari Bener

b Dept. of Evidence for Population Health Unit, School of Epidemiology and Health Sciences, University of Manchester, Manchester, UK ... genetics counseling and screening for the hereditary diseases programme. Results: The ..... Elementary.

Multivariate Methods for Meta-Analysis of Genetic Association Studies.

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Dimou, Niki L; Pantavou, Katerina G; Braliou, Georgia G; Bagos, Pantelis G

2018-01-01

Multivariate meta-analysis of genetic association studies and genome-wide association studies has received a remarkable attention as it improves the precision of the analysis. Here, we review, summarize and present in a unified framework methods for multivariate meta-analysis of genetic association studies and genome-wide association studies. Starting with the statistical methods used for robust analysis and genetic model selection, we present in brief univariate methods for meta-analysis and we then scrutinize multivariate methodologies. Multivariate models of meta-analysis for a single gene-disease association studies, including models for haplotype association studies, multiple linked polymorphisms and multiple outcomes are discussed. The popular Mendelian randomization approach and special cases of meta-analysis addressing issues such as the assumption of the mode of inheritance, deviation from Hardy-Weinberg Equilibrium and gene-environment interactions are also presented. All available methods are enriched with practical applications and methodologies that could be developed in the future are discussed. Links for all available software implementing multivariate meta-analysis methods are also provided.

[EPIDEMIOLOGIC SITUATION BY NATURAL-FOCI INFECTIONS IN THE CRIMEA FEDERAL DISTRICT IN 2014-2015].

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Popova, A-Yu; Kulichenko, A N; Maletskaya, O V; Vasilenko, N F; Shaposhnikova, L I; Kotenev, E S; Dubyansky, V M; Volynkina, A S; Lisitskaya, Ya V; Samarina, I V; Penkovskaya, N A; Evstafiev, I L; Tovpinets, N N; Tsapko, N V; Belova, O A; Agapitov, D S; Samoded, T N; Nadolny, A A; Kovalenko, I S; Yakunin, S N; Shvarsalon, N K; Zinich, L S; Tikhonov, S N; Lyamkin, G I; Zharnikova, I V; Evchenko, Yu M

2016-01-01

Analysis of epidemic manifestations of natural-foci infections (NFI), clarification of spectrum of their causative agents, determination of epizootic activity of natural foci in the Crimea Federal District (KFD). Epizootologic examination of 10 administrative districts of KDF was carried out. 291 pools (2705 specimens) of ixodes ticks and 283 samples of organs of small mammals were studied by PCRmethod for the presence of DNA/RNA of causative agents of a number of NFI. Morbidity by NFI in KFD was registered by 6 nosologies: Lyme borreliosis, Marseilles fever, leptospirosis; tularemia, intestine yersiniosis and tick-borne viral encephalitis, wherein, transmissive infections made up 91.6%. Circulation of causative agents of Crimea hemorrhagic fever, Q fever, group of tick-borne spotted fever, Lyme borreliosis, human granulocytic anaplasmosis, human monocytic ehrlichiosis, hemorrhagic fever with renal syndrome, West Nile fever, tularemia and leptospirosis was established. Due to activity of natural foci of NFI further monitoring of epidemiologic and epizootologic manifestations of these infections in the Crimea, including using genetic methods of analysis, is necessary for ensuring sanitary-epidemiologic welfare of KFD population.

Genetic characterization and phylogenetic analysis of porcine circovirus type 2 (PCV2) in Serbia.

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Savic, Bozidar; Milicevic, Vesna; Jakic-Dimic, Dobrila; Bojkovski, Jovan; Prodanovic, Radisa; Kureljusic, Branislav; Potkonjak, Aleksandar; Savic, Borivoje

2012-01-01

Porcine circovirus type 2 (PCV2) is the main causative agent of postweaning multisystemic wasting syndrome (PMWS). To characterize and determine the genetic diversity of PCV2 in the porcine population of Serbia, nucleotide and deduced amino acid sequences of the open reading frame 2 (ORF2) of PCV2 collected from the tissues of pigs that either had died as a result of PMWS or did not exhibit disease symptoms were analyzed. Sequencing and phylogenetic analysis showed considerable diversity among PCV2 ORF2 sequences and the existence of two main PCV2 genotypes, PCV2b and PCV2a, with at least three clusters, 1A/B, 1C and 2D. In order to provide further proof that the 1C strain is circulating in the porcine population, the whole viral genome of one PCV2 isolate was sequenced. Genotyping and phylogenetic analysis using the entire viral genome sequences confirmed that there was a PMWS-associated 1C strain emerging in Serbia. Our analysis also showed that PCV2b is dominant in the porcine population, and that it is exclusively associated with PMWS occurrences in the country. These data constitute a useful basis for further epidemiological studies regarding the heterogeneity of PCV2 strains on the European continent.

[Coronary heart disease: epidemiologic-genetic aspects].

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Epstein, F H

1985-01-01

Coronary heart disease and the risk factors which predispose to it aggregate in families. How much of this clustering of disease is "explained" by the familial resemblance in predisposing factors? The published reports which bear on this question fall into six distinct study designs: prospective studies, persons at high or low risk or persons with and without a positive family history as points of departure, case-control studies, studies of patients who had a coronary angiogram and studies in different ethnic groups. The findings of the 16 investigations reviewed suggest that there are as yet unidentified factors - genetic, environmental or both - which are responsible for familial clustering of coronary heart disease, apart from the three main risk factors (serum lipids, blood pressure, smoking) and diabetes. Future research must put greater emphasis on studies of families rather than individuals and on closer collaboration between epidemiologists and geneticists, in order to fill these gaps in knowledge. It is likely that the individual predisposition to coronary heart disease is due in part to genetic influences which remain to be discovered in the course of such studies. They would help in identifying susceptible person in the population with greater precision than is now possible. The "high-risk strategy" of coronary heart disease prevention will become more efficient as more specific and sensitive tests of disease prediction are developed. In the meantime, preventive programmes must be put into action on the basis of what is already known, on the level of both the high-risk and the community-wide mass strategy.

The Current Status of the Disease Caused by Enterovirus 71 Infections: Epidemiology, Pathogenesis, Molecular Epidemiology, and Vaccine Development.

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Chang, Ping-Chin; Chen, Shou-Chien; Chen, Kow-Tong

2016-09-09

Enterovirus 71 (EV71) infections have a major public health impact in the Asia-Pacific region. We reviewed the epidemiology, pathogenesis, and molecular epidemiology of EV71 infection as well as EV71 vaccine development. Previous studies were found using the search terms "enterovirus 71" and "epidemiology" or "pathogenesis" or "molecular epidemiology" or "vaccine" in Medline and PubMed. Articles that were not published in the English language, manuscripts without an abstract, and opinion articles were excluded from the review. The reported epidemiology of cases caused by EV71 infection varied from country to country; seasonal variations in incidence were observed. Most cases of EV71 infection that resulted in hospitalization for complications occurred in children less than five years old. The brainstem was the most likely major target of EV71 infection. The emergence of the EV71 epidemic in the Asia-Pacific region has been associated with the circulation of different genetic lineages (genotypes B3, B4, C1, C2, and C4) that appear to be undergoing rapid evolutionary changes. The relationship between the gene structure of the EV71 virus and the factors that ensure its survival, circulation, and evasion of immunity is still unknown. EV71 infection has emerged as an important global public health problem. Vaccine development, including the development of inactivated whole-virus live attenuated, subviral particles, and DNA vaccines, has been progressing.

Psychopathology in 7-year-old children: Differences in maternal and paternal ratings and the genetic epidemiology.

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Wesseldijk, Laura W; Fedko, Iryna O; Bartels, Meike; Nivard, Michel G; van Beijsterveldt, Catharina E M; Boomsma, Dorret I; Middeldorp, Christel M

2017-04-01

The assessment of children's psychopathology is often based on parental report. Earlier studies have suggested that rater bias can affect the estimates of genetic, shared environmental and unique environmental influences on differences between children. The availability of a large dataset of maternal as well as paternal ratings of psychopathology in 7-year old children enabled (i) the analysis of informant effects on these assessments, and (ii) to obtain more reliable estimates of the genetic and non-genetic effects. DSM-oriented measures of affective, anxiety, somatic, attention-deficit/hyperactivity, oppositional-defiant, conduct, and obsessive-compulsive problems were rated for 12,310 twin pairs from the Netherlands Twin Register by mothers (N = 12,085) and fathers (N = 8,516). The effects of genetic and non-genetic effects were estimated on the common and rater-specific variance. For all scales, mean scores on maternal ratings exceeded paternal ratings. Parents largely agreed on the ranking of their child's problems (r 0.60-0.75). The heritability was estimated over 55% for maternal and paternal ratings for all scales, except for conduct problems (44-46%). Unbiased shared environmental influences, i.e., on the common variance, were significant for affective (13%), oppositional (13%), and conduct problems (37%). In clinical settings, different cutoffs for (sub)clinical scores could be applied to paternal and maternal ratings of their child's psychopathology. Only for conduct problems, shared environmental and genetic influences explain an equal amount in differences between children. For the other scales, genetic factors explain the majority of the variance, especially for the common part that is free of rater bias. © 2016 The Authors. American Journal of Medical Genetics Part B: Neuropsychiatric Genetics Published by Wiley Periodicals, Inc. © 2016 The Authors. American Journal of Medical Genetics Part B: Neuropsychiatric Genetics Published by Wiley

COELIAC DISEASE IN CENTRAL AND SOUTH AMERICA: time for a concerted approach to its epidemiology

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Affifa FARRUKH

2015-06-01

Full Text Available Central and South America offer an opportunity to resolve some of the current controversies that surround the epidemiology of celiac disease. Through a concerted action which brings together clinicians, researchers and patients there is an opportunity to establish robust data sets which will allow detailed analysis of environmental and genetic factors. In this review available data from the continent together with data from Spain and Italy are drawn together to give a current picture in the hope that it will stimulate further research.

Dengue 1 diversity and microevolution, French Polynesia 2001-2006: connection with epidemiology and clinics.

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Elodie Descloux

Full Text Available BACKGROUND: Dengue fever (DF is an emerging infectious disease in the tropics and subtropics. Determinants of DF epidemiology and factors involved in severe cases-dengue haemorrhagic fever (DHF and dengue shock syndrome (DSS-remain imperfectly characterized. Since 2000, serotype 1 (DENV-1 has predominated in the South Pacific. The aim of this study was (i to determine the origin and (ii to study the evolutionary relationships of DENV-1 viruses that have circulated in French Polynesia (FP from the severe 2001 outbreak to the recent 2006 epidemic, and (iii to analyse the viral intra-host genetic diversity according to clinical presentation. METHODOLOGY/PRINCIPAL FINDINGS: Sequences of 181 envelope gene and 12 complete polyproteins of DENV-1 viruses obtained from human sera in FP during the 2001-2006 period were generated. Phylogenetic analysis showed that all DENV-1 FP strains belonged to genotype IV-"South Pacific" and derived from a single introduction event from South-East Asia followed by a 6-year in situ evolution. Although the ratio of nonsynonymous/synonymous substitutions per site indicated strong negative selection, a mutation in the envelope glycoprotein (S222T appeared in 2002 and was subsequently fixed. It was noted that genetic diversification was very significant during the 2002-2005 period of endemic DENV-1 circulation. For nine DF sera and eight DHF/DSS sera, approximately 40 clones/serum of partial envelope gene were sequenced. Importantly, analysis revealed that the intra-host genetic diversity was significantly lower in severe cases than in classical DF. CONCLUSIONS/SIGNIFICANCE: First, this study showed that DENV-1 epidemiology in FP was different from that described in other South-Pacific islands, characterized by a long sustained viral circulation and the absence of new viral introduction over a 6-year period. Second, a significant part of DENV-1 evolution was observed during the endemic period characterized by the rapid

Snippets from the past: the evolution of Wade Hampton Frost's epidemiology as viewed from the American Journal of Hygiene/Epidemiology.

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Morabia, Alfredo

2013-10-01

Wade Hampton Frost, who was a Professor of Epidemiology at Johns Hopkins University from 1919 to 1938, spurred the development of epidemiologic methods. His 6 publications in the American Journal of Hygiene, which later became the American Journal of Epidemiology, comprise a 1928 Cutter lecture on a theory of epidemics, a survey-based study of tonsillectomy and immunity to Corynebacterium diphtheriae (1931), 2 papers from a longitudinal study of the incidence of minor respiratory diseases (1933 and 1935), an attack rate ratio analysis of the decline of diphtheria in Baltimore (1936), and a 1936 lecture on the age, time, and cohort analysis of tuberculosis mortality. These 6 American Journal of Hygiene /American Journal of Epidemiology papers attest that Frost's personal evolution mirrored that of the emerging "early" epidemiology: The scope of epidemiology extended beyond the study of epidemics of acute infectious diseases, and rigorous comparative study designs and their associated quantitative methods came to light.

Microsatellite DNA analysis revealed a drastic genetic change of Plasmodium vivax population in the Republic of Korea during 2002 and 2003.

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Moritoshi Iwagami

Full Text Available Vivax malaria was successfully eliminated in the Republic of Korea (South Korea in the late 1970s, but it was found to have re-emerged from 1993. In order to control malaria and evaluate the effectiveness of malaria controls, it is important to develop a spatiotemporal understanding of the genetic structure of the parasite population. Here, we estimated the population structure and temporal dynamics of the transmission of Plasmodium vivax in South Korea by analyzing microsatellite DNA markers of the parasite.We analyzed 14 microsatellite DNA loci of the P. vivax genome from 163 South Korean isolates collected from 1994 to 2008. Allelic data were used to analyze linkage disequilibrium (LD, genetic differentiation and population structure, in order to make a detailed estimate of temporal change in the parasite population. The LD analysis showed a gradual decrease in LD levels, while the levels of genetic differentiation between successive years and analysis of the population structure based on the Bayesian approach suggested that a drastic genetic change occurred in the South Korean population during 2002 and 2003.Although relapse and asymptomatic parasite carriage might influence the population structure to some extent, our results suggested the continual introduction of P. vivax into South Korea through other parasite population sources. One possible source, particularly during 2002 and 2003, is North Korea. Molecular epidemiology using microsatellite DNA of the P. vivax population is effective for assessing the population structure and temporal dynamics of parasite transmission; information that can assist in the elimination of vivax malaria in endemic areas.

Genetic Simulation Tools for Post-Genome Wide Association Studies of Complex Diseases

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Amos, Christopher I.; Bafna, Vineet; Hauser, Elizabeth R.; Hernandez, Ryan D.; Li, Chun; Liberles, David A.; McAllister, Kimberly; Moore, Jason H.; Paltoo, Dina N.; Papanicolaou, George J.; Peng, Bo; Ritchie, Marylyn D.; Rosenfeld, Gabriel; Witte, John S.

2014-01-01

Genetic simulation programs are used to model data under specified assumptions to facilitate the understanding and study of complex genetic systems. Standardized data sets generated using genetic simulation are essential for the development and application of novel analytical tools in genetic epidemiology studies. With continuing advances in high-throughput genomic technologies and generation and analysis of larger, more complex data sets, there is a need for updating current approaches in genetic simulation modeling. To provide a forum to address current and emerging challenges in this area, the National Cancer Institute (NCI) sponsored a workshop, entitled “Genetic Simulation Tools for Post-Genome Wide Association Studies of Complex Diseases” at the National Institutes of Health (NIH) in Bethesda, Maryland on March 11-12, 2014. The goals of the workshop were to: (i) identify opportunities, challenges and resource needs for the development and application of genetic simulation models; (ii) improve the integration of tools for modeling and analysis of simulated data; and (iii) foster collaborations to facilitate development and applications of genetic simulation. During the course of the meeting the group identified challenges and opportunities for the science of simulation, software and methods development, and collaboration. This paper summarizes key discussions at the meeting, and highlights important challenges and opportunities to advance the field of genetic simulation. PMID:25371374

Genetic variation of the riparian pioneer tree species populus nigra. II. Variation In susceptibility to the foliar rust melampsora larici-populina

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Legionnet; Muranty; Lefevre

1999-04-01

Partial resistance of Populus nigra L. to three races of the foliar rust Melampsora larici-populina Kleb. was studied in a field trial and in laboratory tests, using a collection of P. nigra originating from different places throughout France. No total resistance was found. The partial resistance was split into epidemiological components, which proved to be under genetic control. Various patterns of association of epidemiological components values were found. Principal components analysis revealed their relationships. Only 24% of the variance of the field susceptibility could be explained by the variation of the epidemiological components of susceptibility. This variable was significantly correlated with susceptibility to the most ancient and widespread race of the pathogen, and with the variables related to the size of the lesions of the different races. Analysis of variance showed significant differences in susceptibility between regions and between stands within one region. Up to 20% of variation was between regions, and up to 22% between stands, so that these genetic factors appeared to be more differentiated than the neutral diversity (up to 3.5% Legionnet & Lefevre, 1996). However, no clear pattern of geographical distribution of diversity was detected.

Analysis of genetic relationships of mulberry (Morus L.) germplasm ...

African Journals Online (AJOL)

STORAGESEVER

2009-06-03

Jun 3, 2009 ... Full Length Research Paper. Analysis of genetic ... Key words: Mulberry, molecular marker, genetic diversity, SRAP. ... Europe, North and South America, and Africa, and it is cultivated ... Xingjiang autonomous region, China.

A HIV-1 heterosexual transmission chain in Guangzhou, China: a molecular epidemiological study.

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Han, Zhigang; Leung, Tommy W C; Zhao, Jinkou; Wang, Ming; Fan, Lirui; Li, Kai; Pang, Xinli; Liang, Zhenbo; Lim, Wilina W L; Xu, Huifang

2009-09-25

We conducted molecular analyses to confirm four clustering HIV-1 infections (Patient A, B, C & D) in Guangzhou, China. These cases were identified by epidemiological investigation and suspected to acquire the infection through a common heterosexual transmission chain. Env C2V3V4 region, gag p17/p24 junction and partial pol gene of HIV-1 genome from serum specimens of these infected cases were amplified by reverse transcription polymerase chain reaction (RT-PCR) and nucleotide sequenced. Phylogenetic analyses indicated that their viral nucleotide sequences were significantly clustered together (bootstrap value is 99%, 98% and 100% in env, gag and pol tree respectively). Evolutionary distance analysis indicated that their genetic diversities of env, gag and pol genes were significantly lower than non-clustered controls, as measured by unpaired t-test (env gene comparison: p Epidemiological results and molecular analyses consistently illustrated these four cases represented a transmission chain which dispersed in the locality through heterosexual contact involving commercial sex worker.

Statistical methods for the time-to-event analysis of individual participant data from multiple epidemiological studies

DEFF Research Database (Denmark)

Thompson, Simon; Kaptoge, Stephen; White, Ian

2010-01-01

Meta-analysis of individual participant time-to-event data from multiple prospective epidemiological studies enables detailed investigation of exposure-risk relationships, but involves a number of analytical challenges....

Genetic Epidemiology of Spontaneous Subarachnoid Hemorrhage

DEFF Research Database (Denmark)

Korja, Miikka; Silventoinen, Karri; McCarron, Peter

2010-01-01

and 1 opposite sex) and 492 discordant twin pairs for SAH. The concordance for SAH in monozygotic twins was 3.1% compared with 0.27% in dizygotic twins, suggesting at most a modest role for genetic factors in the etiology of SAH. The population-based probability estimate for SAH in dizygotic siblings...... of a patient with SAH is 0.54%, and only 1 of 185 full siblings experience familial SAH. The corresponding risk of SAH in monozygotic twins is 5.9%. Model-fitting, which was based on the comparison of the few monozygotic and dizygotic pairs, suggested that the estimated heritability of SAH is 41%. CONCLUSIONS...

Genetic analysis of repeated, biparental, diploid, hydatidiform moles

DEFF Research Database (Denmark)

Sunde, Lone; Vejerslev, Lars O.; Jensen, Mie Poulsen

1993-01-01

for the abnormal development can be envisaged, environmental as well as genetic. To conform to current ideas of molar pathogenesis, it is suggested that the present conceptuses might have arisen from imbalances in imprinted genomic regions. This could be a consequence of uniparental disomy in critical regions......A woman presented with five consecutive pregnancies displaying molar morphology. In the fifth pregnancy, a non-malformed, liveborn infant was delivered. Genetic analyses (RFLP analysis, cytogenetics, flow cytometry) were performed in pregnancies II-V. It was demonstrated that these pregnancies...... originated in separate conceptions, all conceptuses were diploid, and all had maternally as well as paternally derived genetic markers. By cytogenetic analysis, aberrant heteromorphisms were noted; no other abnormalities were observed in chromosome structure or in DNA sequence. Many different causes...

Genetic Diversity in Natural Populations of New World Leishmania

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Cupolillo Elisa

1998-01-01

Full Text Available Our results have shown the wide diversity of parasites within New World Leishmania. Biochemical and molecular characterization of species within the genus has revealed that much of the population heterogeneity has a genetic basis. The source of genetic diversity among Leishmania appears to arise from predominantly asexual, clonal reproduction, although occasional bouts of sexual reproduction can not be ruled out. Genetic variation is extensive with some clones widely distributed and others seemingly unique and localized to a particular endemic focus. Epidemiological studies of leishmaniasis has been directed to the ecology and dynamics of transmission of Leishmania species/variants, particularly in localized areas. Future research using molecular techniques should aim to identify and follow Leishmania types in nature and correlate genetic typing with important clinical characteristics such as virulence, pathogenicity, drug resistance and antigenic variation. The epidemiological significance of such variation not only has important implications for the control of the leishmaniases, but would also help to elucidate the evolutionary biology of the causative agents.

Genetic diversity of popcorn genotypes using molecular analysis.

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Resh, F S; Scapim, C A; Mangolin, C A; Machado, M F P S; do Amaral, A T; Ramos, H C C; Vivas, M

2015-08-19

In this study, we analyzed dominant molecular markers to estimate the genetic divergence of 26 popcorn genotypes and evaluate whether using various dissimilarity coefficients with these dominant markers influences the results of cluster analysis. Fifteen random amplification of polymorphic DNA primers produced 157 amplified fragments, of which 65 were monomorphic and 92 were polymorphic. To calculate the genetic distances among the 26 genotypes, the complements of the Jaccard, Dice, and Rogers and Tanimoto similarity coefficients were used. A matrix of Dij values (dissimilarity matrix) was constructed, from which the genetic distances among genotypes were represented in a more simplified manner as a dendrogram generated using the unweighted pair-group method with arithmetic average. Clusters determined by molecular analysis generally did not group material from the same parental origin together. The largest genetic distance was between varieties 17 (UNB-2) and 18 (PA-091). In the identification of genotypes with the smallest genetic distance, the 3 coefficients showed no agreement. The 3 dissimilarity coefficients showed no major differences among their grouping patterns because agreement in determining the genotypes with large, medium, and small genetic distances was high. The largest genetic distances were observed for the Rogers and Tanimoto dissimilarity coefficient (0.74), followed by the Jaccard coefficient (0.65) and the Dice coefficient (0.48). The 3 coefficients showed similar estimations for the cophenetic correlation coefficient. Correlations among the matrices generated using the 3 coefficients were positive and had high magnitudes, reflecting strong agreement among the results obtained using the 3 evaluated dissimilarity coefficients.

Epidemiology of bronchial asthma and diabetes mellitus in children and teenagers of Ozyorsk town situated in the area of mayak nuclear enter-prise supervision zone

International Nuclear Information System (INIS)

Vologodskaya, I.A.; Kurbatov, A.V.; Kaminskaya, O.Yu.

2004-01-01

The epidemiology of bronchial asthma and diabetes mellitus in children and teenagers living in Ozyorsk town, which is situated in Mayak nuclear enterprise supervision zone, was studied. By the medical and statistical data in Ozyorsk for the studying forms of multifactorial diseases the trends to the increase both for primary incidence and prevalence were marked. By using the genetic and epidemiological analysis we marked the higher ratio of accumulated incidence as a probability to fall ill with multifactorial diseases (bronchial asthma and diabetes mellitus) in population of Ozyorsk city till 20 years old in comparison with Moscow population

Epidemiology, molecular epidemiology, and risk factors for renal cell carcinoma

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Chiara Paglino

2011-12-01

Full Text Available Despite only accounting for approximately 2% of all new primary cancer cases, renal cell carcinoma (RCC incidence has dramatically increased over time. Incidence rates vary greatly according to geographic areas, so that it is extremely likely that exogenous risk factors could play an important role in the development of this cancer. Several risk factors have been linked with RCC, including cigarette smoking, obesity, hypertension (and antihypertensive drugs, chronic kidney diseases (also dialysis and transplantation, as well as the use of certain analgesics. Furthermore, although RCC has not generally been considered an occupational cancer, several types of occupationally-derived exposures have been implicated in its pathogenesis. These include exposure to asbestos, chlorinated solvents, gasoline, diesel exhaust fumes, polycyclic aromatic hydrocarbons, printing inks and dyes, cadmium and lead. Finally, families with a predisposition to the development of renal neoplasms were identified and the genes involved discovered and characterized. Therefore, there are now four well-characterized, genetically determined syndromes associated with an increased incidence of kidney tumors, i.e., Von Hippel Lindau (VHL, Hereditary Papillary Renal Carcinoma (HPRC, Birt-Hogg-Dubé Syndrome (BHD, and Hereditary Leiomyomatosis and Renal Cell Cancer (HLRCC. This review will address present knowledge about the epidemiology, molecular epidemiology and risk factors of RCC.

Detailed Molecular Epidemiologic Characterization of HIV-1 Infection in Bulgaria Reveals Broad Diversity and Evolving Phylodynamics

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Ivanov, Ivailo Alexiev; Beshkov, Danail; Shankar, Anupama; Hanson, Debra L.; Paraskevis, Dimitrios; Georgieva, Viara; Karamacheva, Lyudmila; Taskov, Hristo; Varleva, Tonka; Elenkov, Ivaylo; Stoicheva, Mariana; Nikolova, Daniela; Switzer, William M.

2013-01-01

Limited information is available to describe the molecular epidemiology of HIV-1 in Bulgaria. To better understand the genetic diversity and the epidemiologic dynamics of HIV-1 we analyzed 125 new polymerase (pol) sequences from Bulgarians diagnosed through 2009 and 77 pol sequences available from our previous study from persons infected prior to 2007. Epidemiologic and demographic information was obtained from each participant and phylogenetic analysis was used to infer HIV-1 evolutionary histories. 120 (59.5%) persons were infected with one of five different HIV-1 subtypes (A1, B, C, F1 and H) and 63 (31.2%) persons were infected with one of six different circulating recombinant forms (CRFs; 01_AE, 02_AG, 04_cpx, 05_DF, 14_BG, and 36_cpx). We also for the first time identified infection with two different clusters of unique A-like and F-like sub-subtype variants in 12 persons (5.9%) and seven unique recombinant forms (3.5%), including a novel J/C recombinant. While subtype B was the major genotype identified and was more prevalent in MSM and increased between 2000–2005, most non-B subtypes were present in persons ≥45 years old. CRF01_AE was the most common non-B subtype and was higher in women and IDUs relative to other risk groups combined. Our results show that HIV-1 infection in Bulgaria reflects the shifting distribution of genotypes coincident with the changing epidemiology of the HIV-1 epidemic among different risk groups. Our data support increased public health interventions targeting IDUs and MSM. Furthermore, the substantial and increasing HIV-1 genetic heterogeneity, combined with fluctuating infection dynamics, highlights the importance of sustained and expanded surveillance to prevent and control HIV-1 infection in Bulgaria. PMID:23527245

RESEARCH NOTE Molecular genetic analysis of consanguineous ...

Indian Academy of Sciences (India)

Navya

Molecular genetic analysis of consanguineous families with primary microcephaly ... Translational Research Institute, Academic Health System, Hamad Medical ..... bridging the gap between homozygosity mapping and deep sequencing.

Profesi Epidemiologi

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Buchari Lapau

2011-01-01

Full Text Available Makalah ini pertama kali menjelaskan perlu adanya profesi kesehatan masyarakat dalam rangka pembangunan kesehatan. Lalu dijelaskan apa profesi itu dan standar keberadaan profesi, atas dasar mana dapat ditetapkan bahwa pelayanan epidemiologi merupakan salah satu profesi. Dalam rangka pembinaan profesi kesehatan masyarakat, IAKMI dan APTKMI telah membentuk Majelis Kolegium Kesehatan Masyarakat Indonesia (MKKMI yang terdiri atas 8 kolegium antara lain Kolegium Epidemiologi, yang telah menyusun Standar Profesi Epidemiologi yang terdiri atas beberapa standar. Masing-masing standar dijelaskan mulai dari kurikulum, standar pelayanan epidmiologi, profil epidemiolog kesehatan, peran epidemiolog kesehatan, fungsi epidemiolog kesehatan, standar kompetensi epidemiologi, dan standar pendidikan profesi epidemiologi.

Genetics of diabetic nephropathy

DEFF Research Database (Denmark)

Parving, H H; Tarnow, L; Rossing, P

1996-01-01

factor for cardiovascular disease in diabetic patients. However, a meta-analysis does not support the suggestion that this factor plays any role for the initiation of diabetic nephropathy. Similar negative results have been obtained in relation to polymorphisms of the genes encoding for angiotensinogen......Diabetic nephropathy is a clinical syndrome characterized by persistent albuminuria, a relentless decline in GFR, raised arterial blood pressure, and increased relative mortality for cardiovascular diseases. Diabetic nephropathy is a leading cause of end-stage renal failure. The pathogenesis...... of diabetic nephropathy is multifactorial, with contributions from metabolic abnormalities, hemodynamic alterations, and various growth factors and genetic factors. Epidemiologic and family studies have demonstrated that only a subset of the patients develop this complication that family clustering...

Epidemiology of Zygomycosis: Analysis of National Data from Pathological Autopsy Cases in Japan.

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Suzuki, Yuhko; Kume, Hikaru; Togano, Tomiteru; Ohto, Hitoshi

2017-01-01

To identify recent trends in the frequency of zygomycosis in autopsy cases, we conducted epidemiological analysis every four years from 1989 to 2009 using national data reported in the "Annual of Pathological Autopsy Cases in Japan." 153,615 cases were autopsied, of which 6622 (4.3%) were found to have had mycosis. Among these, there were 243 cases (3.7%) of zygomycosis, which was the fourth most predominant causative agent of mycoses among the monopathogen mycoses. Of the complicated mycoses, zygomycosis accounted for 56 cases. A total of 299 cases with zygomycoses were observed. The frequency of zygomycosis appeared to be generally stable over the twenty-year period from 1989 to 2009, at around 4% of autopsy cases having mycosis. Younger patients tended to have severe and complicated infections that were characteristic of zygomycosis, compared with non-zygomycosis. The pulmonary and gastrointestinal (GI) systems were the most common foci in our analysis, reflecting the severity of zygomycosis in these sites. Hematological disease was the most frequent underlying disease, but there was a peak of neonatal infections in 2009, which was the first time that this was observed in our studies. These results of the epidemiological analysis of autopsy cases with mycosis demonstrate that clinicians should promptly recognize and treat zygomycosis.

Linking healthcare associated norovirus outbreaks: a molecular epidemiologic method for investigating transmission

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Andrews Nick

2006-07-01

Full Text Available Abstract Background Noroviruses are highly infectious pathogens that cause gastroenteritis in the community and in semi-closed institutions such as hospitals. During outbreaks, multiple units within a hospital are often affected, and a major question for control programs is: are the affected units part of the same outbreak or are they unrelated transmission events? In practice, investigators often assume a transmission link based on epidemiological observations, rather than a systematic approach to tracing transmission. Here, we present a combined molecular and statistical method for assessing: 1 whether observed clusters provide evidence of local transmission and 2 the probability that anecdotally|linked outbreaks truly shared a transmission event. Methods 76 healthcare associated outbreaks were observed in an active and prospective surveillance scheme of 15 hospitals in the county of Avon, England from April 2002 to March 2003. Viral RNA from 64 out of 76 specimens from distinct outbreaks was amplified by reverse transcription-PCR and was sequenced in the polymerase (ORF 1 and capsid (ORF 2 regions. The genetic diversity, at the nucleotide level, was analysed in relation to the epidemiological patterns. Results Two out of four genetic and epidemiological clusters of outbreaks were unlikely to have occurred by chance alone, thus suggesting local transmission. There was anecdotal epidemiological evidence of a transmission link among 5 outbreaks pairs. By combining this epidemiological observation with viral sequence data, the evidence of a link remained convincing in 3 of these pairs. These results are sensitive to prior beliefs of the strength of epidemiological evidence especially when the outbreak strains are common in the background population. Conclusion The evidence suggests that transmission between hospitals units does occur. Using the proposed criteria, certain hypothesized transmission links between outbreaks were supported while

Analysis of genetic structure in Melia volkensii (Gurke.) populations ...

African Journals Online (AJOL)

Administrator

2Farm Forestry Programme, Kenya Forestry Research Institute, P. O. Box 20412, Nairobi, Kenya. Accepted 5 ... were used to estimate genetic distances between populations and for construction of neighbour-joining phenograms. Analysis of Molecular Variance (AMOVA) indicated significant genetic differentiation between ...

The epidemiological characteristics and genetic diversity of dengue virus during the third largest historical outbreak of dengue in Guangdong, China, in 2014.

Science.gov (United States)

Sun, Jiufeng; Wu, De; Zhou, Huiqiong; Zhang, Huan; Guan, Dawei; He, Xiang; Cai, Songwu; Ke, Changwen; Lin, Jinyan

2016-01-01

The third largest historical outbreak of dengue occurred during July to December 2014, in 20 of 21 cities of Guangdong, China. The epidemiological and molecular characteristics of the introduction, expansion and phylogeny of the DENV isolates involved in this outbreak were investigated. A combination analyses of epidemiological characteristics and genetic diversity of dengue virus was performed in this study. In total, 45,236 cases and 6 fatalities were reported. Unemployed individuals, retirees and retailers were the most affected populations. A total of 6024 cases were verified to have DENV infections by nucleic acid detection, of which 5947, 74 and 3 were confirmed to have DENV-1, -2, and -3 infections, respectively. Phylogenetic analyses of DENV-1 isolates were assigned into three genotypes (I, IV, and V). Genotype V was the predominant genotype that likely originated from Singapore. The DENV-2 isolates were assigned to the Cosmopolitan and Asian I genotypes. A unique DENV-3 isolate (genotype III) shared high similarity with isolates obtained from Guangdong in 2013. A combination analyses demonstrated the multiple geographical origins of this outbreak, and highlight the importance of early detection, the case management and vector surveillance for preventing further dengue epidemics in Guangdong. Copyright © 2015 The British Infection Association. Published by Elsevier Ltd. All rights reserved.

Applied immuno-epidemiological research: an approach for integrating existing knowledge into the statistical analysis of multiple immune markers.

Science.gov (United States)

Genser, Bernd; Fischer, Joachim E; Figueiredo, Camila A; Alcântara-Neves, Neuza; Barreto, Mauricio L; Cooper, Philip J; Amorim, Leila D; Saemann, Marcus D; Weichhart, Thomas; Rodrigues, Laura C

2016-05-20

Immunologists often measure several correlated immunological markers, such as concentrations of different cytokines produced by different immune cells and/or measured under different conditions, to draw insights from complex immunological mechanisms. Although there have been recent methodological efforts to improve the statistical analysis of immunological data, a framework is still needed for the simultaneous analysis of multiple, often correlated, immune markers. This framework would allow the immunologists' hypotheses about the underlying biological mechanisms to be integrated. We present an analytical approach for statistical analysis of correlated immune markers, such as those commonly collected in modern immuno-epidemiological studies. We demonstrate i) how to deal with interdependencies among multiple measurements of the same immune marker, ii) how to analyse association patterns among different markers, iii) how to aggregate different measures and/or markers to immunological summary scores, iv) how to model the inter-relationships among these scores, and v) how to use these scores in epidemiological association analyses. We illustrate the application of our approach to multiple cytokine measurements from 818 children enrolled in a large immuno-epidemiological study (SCAALA Salvador), which aimed to quantify the major immunological mechanisms underlying atopic diseases or asthma. We demonstrate how to aggregate systematically the information captured in multiple cytokine measurements to immunological summary scores aimed at reflecting the presumed underlying immunological mechanisms (Th1/Th2 balance and immune regulatory network). We show how these aggregated immune scores can be used as predictors in regression models with outcomes of immunological studies (e.g. specific IgE) and compare the results to those obtained by a traditional multivariate regression approach. The proposed analytical approach may be especially useful to quantify complex immune

Invited commentary: genetic variants and individual- and societal-level risk factors.

Science.gov (United States)

Coughlin, Steven S

2010-01-01

Over the past decade, leading epidemiologists have noted the importance of social factors in studying and understanding the distribution and determinants of disease in human populations; but to what extent are epidemiologic studies integrating genetic information and other biologic variables with information about individual-level risk factors and group-level or societal factors related to the broader residential, behavioral, or cultural context? There remains a need to consider ways to integrate genetic information with social and contextual information in epidemiologic studies, partly to combat the overemphasis on the importance of genetic factors as determinants of disease in human populations. Even in genome-wide association studies of coronary heart disease and other common complex diseases, only a small proportion of heritability is explained by the genetic variants identified to date. It is possible that familial clustering due to genetic factors has been overestimated and that important environmental or social influences (acting alone or in combination with genetic variants) have been overlooked. The accompanying article by Bressler et al. (Am J Epidemiol. 2010;171(1):14-23) highlights some of these important issues.

Role of genomic typing in taxonomy, evolutionary genetics, and microbial epidemiology.

NARCIS (Netherlands)

A.F. van Belkum (Alex); M. Struelens; A. de Visser (Arjan); H.A. Verbrugh (Henri); M. Tibayrench

2001-01-01

textabstractCurrently, genetic typing of microorganisms is widely used in several major fields of microbiological research. Taxonomy, research aimed at elucidation of evolutionary dynamics or phylogenetic relationships, population genetics of microorganisms, and

MetaGenyo: a web tool for meta-analysis of genetic association studies.

Science.gov (United States)

Martorell-Marugan, Jordi; Toro-Dominguez, Daniel; Alarcon-Riquelme, Marta E; Carmona-Saez, Pedro

2017-12-16

Genetic association studies (GAS) aims to evaluate the association between genetic variants and phenotypes. In the last few years, the number of this type of study has increased exponentially, but the results are not always reproducible due to experimental designs, low sample sizes and other methodological errors. In this field, meta-analysis techniques are becoming very popular tools to combine results across studies to increase statistical power and to resolve discrepancies in genetic association studies. A meta-analysis summarizes research findings, increases statistical power and enables the identification of genuine associations between genotypes and phenotypes. Meta-analysis techniques are increasingly used in GAS, but it is also increasing the amount of published meta-analysis containing different errors. Although there are several software packages that implement meta-analysis, none of them are specifically designed for genetic association studies and in most cases their use requires advanced programming or scripting expertise. We have developed MetaGenyo, a web tool for meta-analysis in GAS. MetaGenyo implements a complete and comprehensive workflow that can be executed in an easy-to-use environment without programming knowledge. MetaGenyo has been developed to guide users through the main steps of a GAS meta-analysis, covering Hardy-Weinberg test, statistical association for different genetic models, analysis of heterogeneity, testing for publication bias, subgroup analysis and robustness testing of the results. MetaGenyo is a useful tool to conduct comprehensive genetic association meta-analysis. The application is freely available at http://bioinfo.genyo.es/metagenyo/ .

Quality control in the neutron activation analysis of biological markers for selenium in epidemiological investigations

International Nuclear Information System (INIS)

Morris, J.S.; Ngwenyama, R.A.; Guthrie, J.M.; Brockman, J.D.; Spate, V.L.; Robertson, J.D.

2008-01-01

Instrumental neutron activation analysis is routinely used at the MURR to quantify selenium in prospectively-collected biologic markers including blood serum and toenails. These specimens are typically collected from well-defined cohort populations participating in investigations assessing selenium intake and incidence of chronic disease endpoints. These epidemiological investigations, whether observational (case-control) or clinical (intervention), typically generate thousands of samples. The purpose of this paper is to assess, through evaluation of quality control results, if the achievable accuracy and precision in the measurement of selenium using NAA is adequate to determine a relative risk of 1.2 at high confidence in epidemiological studies. (author)

The CoLaus study: a population-based study to investigate the epidemiology and genetic determinants of cardiovascular risk factors and metabolic syndrome

Directory of Open Access Journals (Sweden)

Stirnadel Heide A

2008-03-01

Full Text Available Abstract Background Cardiovascular diseases and their associated risk factors remain the main cause of mortality in western societies. In order to assess the prevalence of cardiovascular risk factors (CVRFs in the Caucasian population of Lausanne, Switzerland, we conducted a population-based study (Colaus Study. A secondary aim of the CoLaus study will be to determine new genetic determinants associated with CVRFs. Methods Single-center, cross-sectional study including a random sample of 6,188 extensively phenotyped Caucasian subjects (3,251 women and 2,937 men aged 35 to 75 years living in Lausanne, and genotyped using the 500 K Affymetrix chip technology. Results Obesity (body mass index ≥ 30 kg/m2, smoking, hypertension (blood pressure ≥ 140/90 mmHg and/or treatment, dyslipidemia (high LDL-cholesterol and/or low HDL-cholesterol and/or high triglyceride levels and diabetes (fasting plasma glucose ≥ 7 mmol/l and/or treatment were present in 947 (15.7%, 1673 (27.0%, 2268 (36.7%, 2113 (34.2% and 407 (6.6% of the participants, respectively, and the prevalence was higher in men than in women. In both genders, the prevalence of obesity, hypertension and diabetes increased with age. Conclusion The prevalence of major CVRFs is high in the Lausanne population in particular in men. We anticipate that given its size, the depth of the phenotypic analysis and the availability of dense genome-wide genetic data, the CoLaus Study will be a unique resource to investigate not only the epidemiology of isolated, or aggregated CVRFs like the metabolic syndrome, but can also serve as a discovery set, as well as replication set, to identify novel genes associated with these conditions.

The epidemiology of acne vulgaris in late adolescence

Directory of Open Access Journals (Sweden)

Lynn DD

2016-01-01

Full Text Available Darren D Lynn,1 Tamara Umari,1 Cory A Dunnick,2,3 Robert P Dellavalle2–4 1Department of Dermatology, University of Colorado School of Medicine, 2Department of Dermatology, University of Colorado Anschutz Medical Campus, Aurora, 3Dermatology Service, US Department of Veterans Affairs, Eastern Colorado Health Care System, Denver, 4Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA Importance: Acne vulgaris is the most common skin condition affecting late adolescents across the globe. Although prior studies have evaluated epidemiologic patterns of acne vulgaris in various ethnicities and regions, adequate understanding of the worldwide burden of the disease associated with patients in their late adolescence (15–19-year olds remains lacking. Objective: To assess the global burden of the disease associated with acne vulgaris for late adolescents (15–19-year olds and provide an overview of the epidemiology, pathophysiology, and treatment options for acne in this population. Design: Database summary study. Setting: Global Burden of Disease Study 2010 database. Participants: Global Burden of Disease regions comprised countries with prevalence of acne vulgaris between the ages of 15 and 19 years. Main outcomes and measures: Geographic region-level disability-adjusted life year rates (per 100,000 persons associated with acne vulgaris in years 1990 through 2010. Median percentage change in disability-adjusted life year rates was estimated for each region across the specified study period. Conclusion and relevance: Acne vulgaris-associated disease burden exhibits global distribution and has continued to grow in prevalence over time within this population. This continued growth suggests an unmet dermatologic need worldwide for this disorder and potential opportunities for improved access and delivery of dermatologic care. Our analysis of the literature reveals numerous

Whole genome sequencing options for bacterial strain typing and epidemiologic analysis based on single nucleotide polymorphism versus gene-by-gene-based approaches.

Science.gov (United States)

Schürch, A C; Arredondo-Alonso, S; Willems, R J L; Goering, R V

2018-04-01

Whole genome sequence (WGS)-based strain typing finds increasing use in the epidemiologic analysis of bacterial pathogens in both public health as well as more localized infection control settings. This minireview describes methodologic approaches that have been explored for WGS-based epidemiologic analysis and considers the challenges and pitfalls of data interpretation. Personal collection of relevant publications. When applying WGS to study the molecular epidemiology of bacterial pathogens, genomic variability between strains is translated into measures of distance by determining single nucleotide polymorphisms in core genome alignments or by indexing allelic variation in hundreds to thousands of core genes, assigning types to unique allelic profiles. Interpreting isolate relatedness from these distances is highly organism specific, and attempts to establish species-specific cutoffs are unlikely to be generally applicable. In cases where single nucleotide polymorphism or core gene typing do not provide the resolution necessary for accurate assessment of the epidemiology of bacterial pathogens, inclusion of accessory gene or plasmid sequences may provide the additional required discrimination. As with all epidemiologic analysis, realizing the full potential of the revolutionary advances in WGS-based approaches requires understanding and dealing with issues related to the fundamental steps of data generation and interpretation. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

Automated High-Throughput Genotyping for Study of Global Epidemiology of Mycobacterium tuberculosis Based on Mycobacterial Interspersed Repetitive Units

Science.gov (United States)

Supply, Philip; Lesjean, Sarah; Savine, Evgueni; Kremer, Kristin; van Soolingen, Dick; Locht, Camille

2001-01-01

Large-scale genotyping of Mycobacterium tuberculosis is especially challenging, as the current typing methods are labor-intensive and the results are difficult to compare among laboratories. Here, automated typing based on variable-number tandem repeats (VNTRs) of genetic elements named mycobacterial interspersed repetitive units (MIRUs) in 12 mammalian minisatellite-like loci of M. tuberculosis is presented. This system combines analysis of multiplex PCRs on a fluorescence-based DNA analyzer with computerized automation of the genotyping. Analysis of a blinded reference set of 90 strains from 38 countries (K. Kremer et al., J. Clin. Microbiol. 37:2607–2618, 1999) demonstrated that it is 100% reproducible, sensitive, and specific for M. tuberculosis complex isolates, a performance that has not been achieved by any other typing method tested in the same conditions. MIRU-VNTRs can be used for analysis of the global genetic diversity of M. tuberculosis complex strains at different levels of evolutionary divergence. To fully exploit the portability of this typing system, a website was set up for the analysis of M. tuberculosis MIRU-VNTR genotypes via the Internet. This opens the way for global epidemiological surveillance of tuberculosis and should lead to novel insights into the evolutionary and population genetics of this major pathogen. PMID:11574573

Local Genetic Correlation Gives Insights into the Shared Genetic Architecture of Complex Traits.

Science.gov (United States)

Shi, Huwenbo; Mancuso, Nicholas; Spendlove, Sarah; Pasaniuc, Bogdan

2017-11-02

Although genetic correlations between complex traits provide valuable insights into epidemiological and etiological studies, a precise quantification of which genomic regions disproportionately contribute to the genome-wide correlation is currently lacking. Here, we introduce ρ-HESS, a technique to quantify the correlation between pairs of traits due to genetic variation at a small region in the genome. Our approach requires GWAS summary data only and makes no distributional assumption on the causal variant effect sizes while accounting for linkage disequilibrium (LD) and overlapping GWAS samples. We analyzed large-scale GWAS summary data across 36 quantitative traits, and identified 25 genomic regions that contribute significantly to the genetic correlation among these traits. Notably, we find 6 genomic regions that contribute to the genetic correlation of 10 pairs of traits that show negligible genome-wide correlation, further showcasing the power of local genetic correlation analyses. Finally, we report the distribution of local genetic correlations across the genome for 55 pairs of traits that show putative causal relationships. Copyright © 2017 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

A genetic-epidemiologic study of Alzheimer’s disease

NARCIS (Netherlands)

A. Arias-Vásquez (Alejandro)

2006-01-01

textabstractAlzheimer's disease (AD) is the most frequent cause of dementia and thus is a major public-health problem. Age and genetic predisposition to the disease are the most important risk factors. In 2001 more than 24 million people in the western world had dementia. This number is expected to

How to use sequence analysis for life course epidemiology? An example on HIV-positive Sub-Saharan migrants in France.

Science.gov (United States)

Gosselin, Anne; Desgrées du Loû, Annabel; Lelièvre, Eva

2018-06-01

Life course epidemiology is now an established field in social epidemiology; in sociodemography, the quantitative analysis of biographies recently experienced significant trend from event history analysis to sequence analysis. The purpose of this article is to introduce and adapt this methodology to a social epidemiology question, taking the example of the impact of HIV diagnosis on Sub-Saharan migrants' residential trajectories in the Paris region. The sample consists of 640 migrants born in Sub-Saharan Africa receiving HIV care. They were interviewed in healthcare facilities in the Paris region within the PARCOURS project, conducted from 2012 to 2013, using life event history calendars, which recorded year by year their health, family and residential histories. We introduce a two-step methodological approach consisting of (1) sequence analysis by optimal matching to build a typology of migrants' residential pathways before and after diagnosis, and (2) a Cox model of the probability to experience changes in the residential situation. The seven-clusters typology shows that for a majority, the HIV diagnosis did not entail changes in residential situation. However 30% of the migrants experienced a change in their residential situation at time of diagnosis. The Cox model analysis reveals that this residential change was in fact moving in with one's partner (HR 2.99, P<0.000) rather than network rejection. This original combination of sequence analysis and Cox models is a powerful process that could be applied to other themes and constitutes a new approach in the life course epidemiology toolbox. NCT02566148. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

[The genetics of addictions].

Science.gov (United States)

Ibañez Cuadrado, Angela

2008-01-01

The addictions are common chronic psychiatric diseases which represent a serious worldwide public-health problem. They have a high prevalence and negative effects at individual, family and societal level, with a high sanitary cost. Epidemiological genetic research has revealed that addictions are moderately to highly heritable. Also the investigation has evidenced that environmental and genetic factors contribute to individual differences in vulnerability to addictions. Advances in the neurobiology of addiction joined to the development of new molecular genetic technologies, have led to the identification of a variety of underlying genes and pathways in addiction process, leading to the description of common molecular mechanisms in substance and behaviour dependencies. Identifying gene-environment interactions is a crucial issue in future research. Other major goal in genetic research is the identification of new therapeutic targets for treatment and prevention.

Application of Pulsed-Field Gel Electrophoresis and Binary Typing as Tools in Veterinary Clinical Microbiology and Molecular Epidemiologic Analysis of Bovine and Human Staphylococcus aureus Isolates

Science.gov (United States)

Zadoks, Ruth; van Leeuwen, Willem; Barkema, Herman; Sampimon, Otlis; Verbrugh, Henri; Schukken, Ynte Hein; van Belkum, Alex

2000-01-01

Thirty-eight bovine mammary Staphylococcus aureus isolates from diverse clinical, temporal, and geographical origins were genotyped by pulsed-field gel electrophoresis (PFGE) after SmaI digestion of prokaryotic DNA and by means of binary typing using 15 strain-specific DNA probes. Seven pulsed-field types and four subtypes were identified, as were 16 binary types. Concordant delineation of genetic relatedness was documented by both techniques, yet based on practical and epidemiological considerations, binary typing was the preferable method. Genotypes of bovine isolates were compared to 55 previously characterized human S. aureus isolates through cluster analysis of binary types. Genetic clusters containing strains of both human and bovine origin were found, but bacterial genotypes were predominantly associated with a single host species. Binary typing proved an excellent tool for comparison of S. aureus strains, including methicillin-resistant S. aureus, derived from different host species and from different databases. For 28 bovine S. aureus isolates, detailed clinical observations in vivo were compared to strain typing results in vitro. Associations were found between distinct genotypes and severity of disease, suggesting strain-specific bacterial virulence. Circumstantial evidence furthermore supports strain-specific routes of bacterial dissemination. We conclude that PFGE and binary typing can be successfully applied for genetic analysis of S. aureus isolates from bovine mammary secretions. Binary typing in particular is a robust and simple method and promises to become a powerful tool for strain characterization, for resolution of clonal relationships of bacteria within and between host species, and for identification of sources and transmission routes of bovine S. aureus. PMID:10790124

Event History Analysis in Quantitative Genetics

DEFF Research Database (Denmark)

Maia, Rafael Pimentel

Event history analysis is a clas of statistical methods specially designed to analyze time-to-event characteristics, e.g. the time until death. The aim of the thesis was to present adequate multivariate versions of mixed survival models that properly represent the genetic aspects related to a given...

Epidemiological and genetic data supporting the transmission of Ancylostoma ceylanicum among human and domestic animals.

Directory of Open Access Journals (Sweden)

Romano Ngui

Full Text Available BACKGROUND: Currently, information on species-specific hookworm infection is unavailable in Malaysia and is restricted worldwide due to limited application of molecular diagnostic tools. Given the importance of accurate identification of hookworms, this study was conducted as part of an ongoing molecular epidemiological investigation aimed at providing the first documented data on species-specific hookworm infection, associated risk factors and the role of domestic animals as reservoirs for hookworm infections in endemic communities of Malaysia. METHODS/FINDINGS: A total of 634 human and 105 domestic canine and feline fecal samples were randomly collected. The overall prevalence of hookworm in humans and animals determined via microscopy was 9.1% (95% CI = 7.0-11.7% and 61.9% (95% CI = 51.2-71.2%, respectively. Multivariate analysis indicated that participants without the provision of proper latrine systems (OR = 3.5; 95% CI = 1.53-8.00; p = 0.003, walking barefooted (OR = 5.6; 95% CI = 2.91-10.73; p<0.001 and in close contact with pets or livestock (OR = 2.9; 95% CI = 1.19-7.15; p = 0.009 were more likely to be infected with hookworms. Molecular analysis revealed that while most hookworm-positive individuals were infected with Necator americanus, Ancylostoma ceylanicum constituted 12.8% of single infections and 10.6% mixed infections with N. americanus. As for cats and dogs, 52.0% were positive for A. ceylanicum, 46.0% for Ancylostoma caninum and 2.0% for Ancylostoma braziliense and all were single infections. CONCLUSION: This present study provided evidence based on the combination of epidemiological, conventional diagnostic and molecular tools that A. ceylanicum infection is common and that its transmission dynamic in endemic areas in Malaysia is heightened by the close contact of human and domestic animal (i.e., dogs and cats populations.

Global epidemiology of hyperthyroidism and hypothyroidism.

Science.gov (United States)

Taylor, Peter N; Albrecht, Diana; Scholz, Anna; Gutierrez-Buey, Gala; Lazarus, John H; Dayan, Colin M; Okosieme, Onyebuchi E

2018-05-01

Thyroid hormones are essential for growth, neuronal development, reproduction and regulation of energy metabolism. Hypothyroidism and hyperthyroidism are common conditions with potentially devastating health consequences that affect all populations worldwide. Iodine nutrition is a key determinant of thyroid disease risk; however, other factors, such as ageing, smoking status, genetic susceptibility, ethnicity, endocrine disruptors and the advent of novel therapeutics, including immune checkpoint inhibitors, also influence thyroid disease epidemiology. In the developed world, the prevalence of undiagnosed thyroid disease is likely falling owing to widespread thyroid function testing and relatively low thresholds for treatment initiation. However, continued vigilance against iodine deficiency remains essential in developed countries, particularly in Europe. In this report, we review the global incidence and prevalence of hyperthyroidism and hypothyroidism, highlighting geographical differences and the effect of environmental factors, such as iodine supplementation, on these data. We also highlight the pressing need for detailed epidemiological surveys of thyroid dysfunction and iodine status in developing countries.

Epidemiologic research program: Selected bibliography

International Nuclear Information System (INIS)

1993-05-01

This bibliography is a current listing of scientific reports from epidemiologic and related activities sponsored by the Department of Energy. The Office of Epidemiology and Health Surveillance now is the departmental focal point for these activities and any others relating to the study of human health effects. The Office's mission is evolving to encompass the new role of the Department in environmental restoration, weapons dismantlement and nuclear material storage, and development of new energy technologies. Publications in these areas will be included in future editions of the bibliography. The present edition brings the listing up to date, and should facilitate access to specific reports. The program has been divided into several general areas of activity: the Radiation Effects Research Foundation, which supports studies of survivors of the atomic weapons in Hiroshima and Nagasaki; mortality and morbidity studies of DOE workers; studies on internally deposited alpha emitters; medical/histologic studies; studies on the genetic aspects of radiation damage; community health surveillance studies; and the development of computational techniques and of databases to make the results as widely useful as possible

Some aspects of cancer epidemiology

International Nuclear Information System (INIS)

Lilienfeld, A.M.

1982-01-01

Epidemiolgic studies have strongly suggested that a vast majority (80-90%) of cancers are caused by radiation, chemical and biologic agents; the remainder result from endogenous or genetic factors. Biologically, cancer is most probably the end result of a complex multistage process and therefore may be due to a sequence of exposures to different agents at each of these stages. This emphasizes the need to stress the study of interactions in epidemiologic studies to a greater extent than has been done thus far. Examples of the importance of interactions in several types of cancer are presented

Analysis of those national analytic epidemiological studies that by obtention the exposure-response functions

International Nuclear Information System (INIS)

Molina, E.; Meneses, E.

2003-01-01

The Impact Pathway methodology, developed in the frame of Extern E project for estimating of the external costs or externalities of the energy use, has as one of their main steps the health impact evaluation. This evaluation is carried out through exposure-response functions. In previous estimates of the external costs of power generation in Cuba, functions obtained in international studies were used. The main objective of this work was to carry out a summarized critical analysis of those national analytic epidemiological studies that, according the exposed methodology, consider the main aspects specialized with views to the possible preliminary proposal of functions exposure-response (FER) based own in epidemiologic evidences. In agreement with the analysis, the results show that the great majority of the studies are not useful for the FER establishment, at least in their present form. A minority studies exists that contributes limited evidence and their reanalysis could increase their contribution to the propose purpose. Finally the main problems found in the studies are enumerated revision object

HIV-TRACE (Transmission Cluster Engine): a tool for large scale molecular epidemiology of HIV-1 and other rapidly evolving pathogens.

Science.gov (United States)

Kosakovsky Pond, Sergei L; Weaver, Steven; Leigh Brown, Andrew J; Wertheim, Joel O

2018-01-31

In modern applications of molecular epidemiology, genetic sequence data are routinely used to identify clusters of transmission in rapidly evolving pathogens, most notably HIV-1. Traditional 'shoeleather' epidemiology infers transmission clusters by tracing chains of partners sharing epidemiological connections (e.g., sexual contact). Here, we present a computational tool for identifying a molecular transmission analog of such clusters: HIV-TRACE (TRAnsmission Cluster Engine). HIV-TRACE implements an approach inspired by traditional epidemiology, by identifying chains of partners whose viral genetic relatedness imply direct or indirect epidemiological connections. Molecular transmission clusters are constructed using codon-aware pairwise alignment to a reference sequence followed by pairwise genetic distance estimation among all sequences. This approach is computationally tractable and is capable of identifying HIV-1 transmission clusters in large surveillance databases comprising tens or hundreds of thousands of sequences in near real time, i.e., on the order of minutes to hours. HIV-TRACE is available at www.hivtrace.org and from github.com/veg/hivtrace, along with the accompanying result visualization module from github.com/veg/hivtrace-viz. Importantly, the approach underlying HIV-TRACE is not limited to the study of HIV-1 and can be applied to study outbreaks and epidemics of other rapidly evolving pathogens. © The Author 2018. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Parameter determination for quantitative PIXE analysis using genetic algorithms

International Nuclear Information System (INIS)

Aspiazu, J.; Belmont-Moreno, E.

1996-01-01

For biological and environmental samples, PIXE technique is in particular advantage for elemental analysis, but the quantitative analysis implies accomplishing complex calculations that require the knowledge of more than a dozen parameters. Using a genetic algorithm, the authors give here an account of the procedure to obtain the best values for the parameters necessary to fit the efficiency for a X-ray detector. The values for some variables involved in quantitative PIXE analysis, were manipulated in a similar way as the genetic information is treated in a biological process. The authors carried out the algorithm until they reproduce, within the confidence interval, the elemental concentrations corresponding to a reference material

Genetics and caries: prospects

Directory of Open Access Journals (Sweden)

Alexandre Rezende Vieira

2012-01-01

Full Text Available Caries remains the most prevalent non-contagious infectious disease in humans. It is clear that the current approaches to decrease the prevalence of caries in human populations, including water fluoridation and school-based programs, are not enough to protect everyone. The scientific community has suggested the need for innovative work in a number of areas in cariology, encompassing disease etiology, epidemiology, definition, prevention, and treatment. We have pioneered the work on genetic studies to identify genes and genetic markers of diagnostic, prognostic, and therapeutic value. This paper summarizes a presentation that elaborated on these initial findings.

The epidemiology of endometriosis.

Science.gov (United States)

Cramer, Daniel W; Missmer, Stacey A

2002-03-01

Advances in understanding the epidemiology of endometriosis have lagged behind other diseases because of methodologic problems related to disease definition and control selection. Nevertheless, a better picture of the epidemiology of endometriosis has emerged over the past few decades. Prevalence estimates of the disease in clinic populations vary from about a 4% occurrence of largely asymptomatic endometriosis found in women undergoing tubal ligation to 50% of teenagers with intractable dysmenorrhea. General population incidence during the 1970s in this country has been suggested to be 1.6 per 1000 white females aged 15-49, while a more current study based upon hospital discharges finds endometriosis as a first listed diagnosis in 1.3 per 1000 discharges in women aged 15-44. There is a clinical impression that blacks have lower rates of endometriosis and Orientals have higher rates than whites. A variety of personal risk factors for endometriosis have also been described. Women with endometriosis may be taller and thinner. Menstrual factors reported to increase risk include dysmenorrhea, early menarche, and shorter cycle lengths. There is support for the idea that lifestyle exposures that might raise or lower estrogen levels could affect risk, including a decreased risk associated with smoking and exercise and an increased risk associated with caffeine or alcohol use. These risk factors appear to be compatible with the central importance of retrograde menstruation influenced by outflow obstruction that might affect its amount, immune factors that might affect its ability to be cleared, or hormonal stimuli that might affect its growth. In this model, dysmenorrhea could be either a disease symptom or a manifestation of outflow obstruction. Nulliparity could be either a consequence of disease or a cause since nulliparous women would not have the benefit of cervical dilation associated with labor and delivery. Since there is evidence that family history is a risk

Local level epidemiological analysis of TB in people from a high incidence country of birth

OpenAIRE

Massey Peter D; Durrheim David N; Stephens Nicola; Christensen Amanda

2013-01-01

Abstract Background The setting for this analysis is the low tuberculosis (TB) incidence state of New South Wales (NSW), Australia. Local level analysis of TB epidemiology in people from high incidence countries-of-birth (HIC) in a low incidence setting has not been conducted in Australia and has not been widely reported. Local level analysis could inform measures such as active case finding and targeted earlier diagnosis. The aim of this study was to use a novel approach to identify local ar...

Genetic analysis of Myanmar Vigna species in responses to salt ...

African Journals Online (AJOL)

Genetic analysis of Myanmar Vigna species in responses to salt stress at the ... of reduction was highly dependent on different genotypes and salinity levels. ... the mechanism of salt tolerance and for the provision of genetic resources for ...

[A survey of willingness about genetic counseling and tests in patients of epithelial ovarian cancer].

Science.gov (United States)

Li, L; Qiu, L; Wu, M

2017-11-21

Objective: To analyze patients' tendency towards genetics counseling and tests based on a prospective cohort study on hereditary ovarian cancer. Methods: From February 2017 to June 2017, among 220 cases of epithelial ovarian cancer in Peking Union Medical College Hospital, we collected epidemiological, pathological and tendency towards genetics counseling and tests via medical records and questionnaire.All patients would get education about hereditary ovarian cancer by pamphlets and WeChat.If they would receive further counseling, a face to face interview and tests will be given. Results: Among all 220 patients, 10 (4.5%) denied further counseling.For 210 patients receiving genetic counseling, 170 (81%) accepted genetic tests.In multivariate analysis, risk factors relevant to acceptance of genetic tests included: being charged by physicians of gynecologic oncology for diagnosis and treatment, receiving counseling in genetic counseling clinics, and having family history of breast cancer.For patients denying genetic tests, there were many subjective reasons, among which, "still not understanding genetic tests" (25%) and "unable bear following expensive targeting medicine" . Conclusions: High proportion patients of epithelial ovarian cancer would accept genetic counseling and tests.Genetic counseling clinics for gynecologic oncology would further improve genetic tests for patients.

Molecular epidemiology of Corynebacterium pseudotuberculosis isolated from horses in California.

Science.gov (United States)

Haas, Dionei J; Dorneles, Elaine M S; Spier, Sharon J; Carroll, Scott P; Edman, Judy; Azevedo, Vasco A; Heinemann, Marcos B; Lage, Andrey P

2017-04-01

Corynebacterium pseudotuberculosis biovar Equi is an important pathogen of horses. It is increasing in frequency in the United States, and is responsible for various clinical forms of infection, including external abscesses, internal abscesses of the abdominal or thoracic cavities, and ulcerative lymphangitis. The host/pathogen factors dictating the form or severity of infection are currently unknown. Our recent investigations have shown that genotyping C. pseudotuberculosis isolates using enterobacterial repetitive intergenic consensus (ERIC)-PCR is useful for understanding the evolutionary genetics of the species as well for molecular epidemiology studies. The aims of the present study were to assess (i) the genetic diversity of C. pseudotuberculosis strains isolated from horses in California, United States and (ii) the epidemiologic relationships among isolates. One hundred and seven C. pseudotuberculosis biovar Equi isolates from ninety-five horses, and two C. pseudotuberculosis biovar Ovis strains, C. pseudotuberculosis ATCC 19410 T type strain and C. pseudotuberculosis 1002 vaccine strain, were fingerprinted using the ERIC 1+2-PCR. C. pseudotuberculosis isolated from horses showed a high genetic diversity, clustering in twenty-seven genotypes with a diversity index of 0.91. Minimal spanning tree showed four major clonal complexes with a pattern of temporal clustering. Strains isolated from the same horse showed identical ERIC 1+2-PCR genotype, with the exception of two strains isolated from the same animal that showed distinct genotypes, suggesting a co-infection. We found no strong genetic signals related to clinical form (including internal versus external infections). However, temporal clustering of genotypes was observed. Copyright © 2016. Published by Elsevier B.V.

Ethics, big data and computing in epidemiology and public health.

Science.gov (United States)

Salerno, Jennifer; Knoppers, Bartha M; Lee, Lisa M; Hlaing, WayWay M; Goodman, Kenneth W

2017-05-01

This article reflects on the activities of the Ethics Committee of the American College of Epidemiology (ACE). Members of the Ethics Committee identified an opportunity to elaborate on knowledge gained since the inception of the original Ethics Guidelines published by the ACE Ethics and Standards of Practice Committee in 2000. The ACE Ethics Committee presented a symposium session at the 2016 Epidemiology Congress of the Americas in Miami on the evolving complexities of ethics and epidemiology as it pertains to "big data." This article presents a summary and further discussion of that symposium session. Three topic areas were presented: the policy implications of big data and computing, the fallacy of "secondary" data sources, and the duty of citizens to contribute to big data. A balanced perspective is needed that provides safeguards for individuals but also furthers research to improve population health. Our in-depth review offers next steps for teaching of ethics and epidemiology, as well as for epidemiological research, public health practice, and health policy. To address contemporary topics in the area of ethics and epidemiology, the Ethics Committee hosted a symposium session on the timely topic of big data. Technological advancements in clinical medicine and genetic epidemiology research coupled with rapid advancements in data networks, storage, and computation at a lower cost are resulting in the growth of huge data repositories. Big data increases concerns about data integrity; informed consent; protection of individual privacy, confidentiality, and harm; data reidentification; and the reporting of faulty inferences. Copyright © 2017 Elsevier Inc. All rights reserved.

Psoriasis: epidemiology, natural history, and differential diagnosis

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Basko-Plluska JL

2012-09-01

Full Text Available Juliana L Basko-Plluska, Vesna Petronic-RosicDepartment of Medicine, Section of Dermatology, University of Chicago, Chicago, IL, USAAbstract: Psoriasis is a chronic, immune-mediated, inflammatory disease which affects primarily the skin and joints. It occurs worldwide, but its prevalence varies considerably between different regions of the world. Genetic susceptibility as well as environmental factors play an important role in determining the development and prognosis of psoriasis. Genome-wide association studies have identified many genetic loci as potential psoriasis susceptibility regions, including PSORS1 through PSORS7. Histocompatibility antigen (HLA studies have also identified several HLA antigens, with HLA-Cw6 being the most frequently associated antigen. Epidemiological studies identified several modifiable risk factors that may predispose individuals to developing psoriasis or exacerbate pre-existing disease. These include smoking, obesity, alcohol consumption, diet, infections, medications and stressful life events. The exact mechanism by which they trigger psoriasis remains to be elucidated; however, existing data suggest that they are linked through Th1-mediated immunological pathways. The natural history of psoriasis varies depending on the clinical subtype as well as special circumstances, including pregnancy and HIV infection. In general, psoriasis is a chronic disease with intermittent remissions and exacerbations. The differential diagnosis is vast and includes many other immune-mediated, inflammatory disorders.Keywords: psoriasis, epidemiology, natural history, differential diagnosis

Simulating Nationwide Pandemics: Applying the Multi-scale Epidemiologic Simulation and Analysis System to Human Infectious Diseases

Energy Technology Data Exchange (ETDEWEB)

Dombroski, M; Melius, C; Edmunds, T; Banks, L E; Bates, T; Wheeler, R

2008-09-24

This study uses the Multi-scale Epidemiologic Simulation and Analysis (MESA) system developed for foreign animal diseases to assess consequences of nationwide human infectious disease outbreaks. A literature review identified the state of the art in both small-scale regional models and large-scale nationwide models and characterized key aspects of a nationwide epidemiological model. The MESA system offers computational advantages over existing epidemiological models and enables a broader array of stochastic analyses of model runs to be conducted because of those computational advantages. However, it has only been demonstrated on foreign animal diseases. This paper applied the MESA modeling methodology to human epidemiology. The methodology divided 2000 US Census data at the census tract level into school-bound children, work-bound workers, elderly, and stay at home individuals. The model simulated mixing among these groups by incorporating schools, workplaces, households, and long-distance travel via airports. A baseline scenario with fixed input parameters was run for a nationwide influenza outbreak using relatively simple social distancing countermeasures. Analysis from the baseline scenario showed one of three possible results: (1) the outbreak burned itself out before it had a chance to spread regionally, (2) the outbreak spread regionally and lasted a relatively long time, although constrained geography enabled it to eventually be contained without affecting a disproportionately large number of people, or (3) the outbreak spread through air travel and lasted a long time with unconstrained geography, becoming a nationwide pandemic. These results are consistent with empirical influenza outbreak data. The results showed that simply scaling up a regional small-scale model is unlikely to account for all the complex variables and their interactions involved in a nationwide outbreak. There are several limitations of the methodology that should be explored in future

Genetic analysis for grain quality traits in pakistani wheat varieties

International Nuclear Information System (INIS)

Minhas, N.M.; Ajmal, S.U.; Iqbal, Z.; Munir, M.

2014-01-01

A set of eight parental diallel involving seven commercial wheat cultivars and one breeding line was made to investigate the nature of gene action determining inheritance pattern of grain quality characters. Highly significant differences were observed among the genotypes for 1000 grain weight, protein content, wet gluten and lysine content. Adequacy tests were employed to estimate the fitness of data sets to additive dominance model. Both the tests i.e. analysis of uniformity of Wr, Vr and joint regression analysis validated the data of these traits for genetic analysis. Gene actions for grain quality traits were ascertained following Hayman's analysis of variance. Results of the genetic analysis revealed that both additive and dominance genetic components were involved in the manifestation of characters under study. However, additive gene effects were more pronounced in the genetic control of these traits. Non significance of b1, b2 and b3 values revealed the absence of directional dominance, symmetrical distribution of genes among the parental lines and absence of specific genes action respectively in all the traits. Maternal effects were also noted in 1000 grain weight, protein content and wet gluten percentage. It is concluded that additive effects are crucial in the expression of grain quality characters of wheat in germplasm under study and single plant selection may be recommended in segregating generations for effective improvement in these characters. (author)

Epidemiología de campo y epidemiología social Field epidemiology and social epidemiology

Directory of Open Access Journals (Sweden)

Javier Segura del Pozo

2006-03-01

Full Text Available Mediante la comparación de la epidemiología de campo y la epidemiología social, se pretende reflexionar sobre los imaginarios no explícitos que operan en ambos ámbitos, necesariamente convergentes, sobre los obstáculos de la práctica epidemiológica actual para alcanzar su función social y sobre la necesidad de cambiar las bases epistemológicas, metodológicas y prácticas que operan en la epidemiología, empezando por la formación del epidemiólogo de campo. La epidemiología de campo tiende a la acción sin marco teórico. La epidemiología social, por el contrario, tiende a los desarrollos teóricos (reflexión e investigación sobre los determinantes sociales alejados de la acción, debido a los limitantes para cambiar las políticas públicas. Otras diferencias se sitúan en el nivel de intervención (micro/macroespacios, el objeto de intervención (control del brote frente a control de las desigualdades y en la forma de articular la comunicación con la sociedad. Se asemejan en la preocupación por el método, la predominancia de una orientación positivista y condicionada por la estadística, aunque en proceso de cierta apertura epistemológica, la tensión experimentada entre relacionarse con un mundo virtual de bases de datos o con la sociedad real, su situación en la periferia del sistema político-social-institucional-profesional y por estar abocadas a la frustración profesional. Finalmente, se formulan 10 interrogantes a los epidemiólogos de campo sobre su práctica actual, a través de los cuales se podría evaluar si están realizando una epidemiología social, y se sugieren cambios para introducir en la formación y práctica del epidemiólogo.Comparing field epidemiology and social epidemiology, we pretend to think about the no explicit images and meanings operating in both necessary convergent fields, about the obstacles present in epidemiological practice to fulfil its social function and about the necessity of

Genetic data analysis for plant and animal breeding

Science.gov (United States)

This book is an advanced textbook covering the application of quantitative genetics theory to analysis of actual data (both trait and DNA marker information) for breeding populations of crops, trees, and animals. Chapter 1 is an introduction to basic software used for trait data analysis. Chapter 2 ...

Multilocus Sequence Typing of Pathogenic Candida albicans Isolates Collected from a Teaching Hospital in Shanghai, China: A Molecular Epidemiology Study

Science.gov (United States)

Li, Li; Zhang, Qiangqiang; Zhu, Junhao; Gao, Qian; Chen, Min; Zhu, Min

2015-01-01

Molecular typing of Candida albicans is important for studying the population structure and epidemiology of this opportunistic yeast, such as population dynamics, nosocomial infections, multiple infections and microevolution. The genetic diversity of C. albicans has been rarely studied in China. In the present study, multilocus sequence typing (MLST) was used to characterize the genetic diversity and population structure of 62 C. albicans isolates collected from 40 patients from Huashan Hospital in Shanghai, China. A total of 50 diploid sequence types (DSTs) were identified in the 62 C. albicans isolates, with 41 newly identified DSTs. Based on cluster analysis, the 62 isolates were classified into nine existing clades and two new clades (namely clades New 1 and New 2). The majority of the isolates were clustered into three clades, clade 6 (37.5%), clade 1 (15.0%) and clade 17 (15.0%). Isolates of clade New 2 were specifically identified in East Asia. We identified three cases of potential nosocomial transmission based on association analysis between patients’ clinical data and the genotypes of corresponding isolates. Finally, by analyzing the genotypes of serial isolates we further demonstrated that the microevolution of C. albicans was due to loss of heterozygosity. Our study represents the first molecular typing of C. albicans in eastern China, and we confirmed that MLST is a useful tool for studying the epidemiology and evolution of C. albicans. PMID:25919124

Genetics and epigenetics of eating disorders

Directory of Open Access Journals (Sweden)

Yilmaz Z

2015-03-01

Full Text Available Zeynep Yilmaz,1 J Andrew Hardaway,1 Cynthia M Bulik1–3 1Department of Psychiatry, 2Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; 3Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden Abstract: Eating disorders (EDs are serious psychiatric conditions influenced by biological, psychological, and sociocultural factors. A better understanding of the genetics of these complex traits and the development of more sophisticated molecular biology tools have advanced our understanding of the etiology of EDs. The aim of this review is to critically evaluate the literature on the genetic research conducted on three major EDs: anorexia nervosa, bulimia nervosa, and binge eating disorder. We will first review the diagnostic criteria, clinical features, prevalence, and prognosis of anorexia nervosa, bulimia nervosa, and binge eating disorder, followed by a review of family, twin, and adoption studies. We then review the history of genetic studies of EDs covering linkage analysis, candidate-gene association studies, genome-wide association studies, and the study of rare variants in EDs. Our review also incorporates a translational perspective by covering animal models of ED-related phenotypes. Finally, we review the nascent field of epigenetics of EDs and a look forward to future directions for ED genetic research. Keywords: anorexia nervosa, binge eating disorder, bulimia nervosa, animal models, genome-wide association studies, high-throughput sequencing

A roadmap for the genetic analysis of renal aging.

Science.gov (United States)

Noordmans, Gerda A; Hillebrands, Jan-Luuk; van Goor, Harry; Korstanje, Ron

2015-10-01

Several studies show evidence for the genetic basis of renal disease, which renders some individuals more prone than others to accelerated renal aging. Studying the genetics of renal aging can help us to identify genes involved in this process and to unravel the underlying pathways. First, this opinion article will give an overview of the phenotypes that can be observed in age-related kidney disease. Accurate phenotyping is essential in performing genetic analysis. For kidney aging, this could include both functional and structural changes. Subsequently, this article reviews the studies that report on candidate genes associated with renal aging in humans and mice. Several loci or candidate genes have been found associated with kidney disease, but identification of the specific genetic variants involved has proven to be difficult. CUBN, UMOD, and SHROOM3 were identified by human GWAS as being associated with albuminuria, kidney function, and chronic kidney disease (CKD). These are promising examples of genes that could be involved in renal aging, and were further mechanistically evaluated in animal models. Eventually, we will provide approaches for performing genetic analysis. We should leverage the power of mouse models, as testing in humans is limited. Mouse and other animal models can be used to explain the underlying biological mechanisms of genes and loci identified by human GWAS. Furthermore, mouse models can be used to identify genetic variants associated with age-associated histological changes, of which Far2, Wisp2, and Esrrg are examples. A new outbred mouse population with high genetic diversity will facilitate the identification of genes associated with renal aging by enabling high-resolution genetic mapping while also allowing the control of environmental factors, and by enabling access to renal tissues at specific time points for histology, proteomics, and gene expression. © 2015 The Authors. Aging Cell published by the Anatomical Society and John

A roadmap for the genetic analysis of renal aging

Science.gov (United States)

Noordmans, Gerda A; Hillebrands, Jan-Luuk; van Goor, Harry; Korstanje, Ron

2015-01-01

Several studies show evidence for the genetic basis of renal disease, which renders some individuals more prone than others to accelerated renal aging. Studying the genetics of renal aging can help us to identify genes involved in this process and to unravel the underlying pathways. First, this opinion article will give an overview of the phenotypes that can be observed in age-related kidney disease. Accurate phenotyping is essential in performing genetic analysis. For kidney aging, this could include both functional and structural changes. Subsequently, this article reviews the studies that report on candidate genes associated with renal aging in humans and mice. Several loci or candidate genes have been found associated with kidney disease, but identification of the specific genetic variants involved has proven to be difficult. CUBN, UMOD, and SHROOM3 were identified by human GWAS as being associated with albuminuria, kidney function, and chronic kidney disease (CKD). These are promising examples of genes that could be involved in renal aging, and were further mechanistically evaluated in animal models. Eventually, we will provide approaches for performing genetic analysis. We should leverage the power of mouse models, as testing in humans is limited. Mouse and other animal models can be used to explain the underlying biological mechanisms of genes and loci identified by human GWAS. Furthermore, mouse models can be used to identify genetic variants associated with age-associated histological changes, of which Far2, Wisp2, and Esrrg are examples. A new outbred mouse population with high genetic diversity will facilitate the identification of genes associated with renal aging by enabling high-resolution genetic mapping while also allowing the control of environmental factors, and by enabling access to renal tissues at specific time points for histology, proteomics, and gene expression. PMID:26219736

Epidemiology & social costs of haemophilia in India

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Anita Kar

2014-01-01

Full Text Available India lacks a national policy on the prevention and control of genetic disorders. Although the haemoglobinopathies have received some attention, there are scarce data on the epidemiology of other genetic disorders in India. Haemophilia, an inherited single gene disorder with an incidence of 1 per 10,000 births, manifests as spontaneous or trauma-induced haemorrhagic episodes in patients, progressing to chronic disability and premature mortality in untreated patients or patients with sub-optimal treatment. Although the genetic basis of this disorder has been well studied in India, data on the number of patients, trends of the disorder in India, social costs of the condition and opportunities and competencies for offering genetic counselling through a public health programme have not been reported. This review article summarizes the available Indian data, which show that the country harbours the second highest number of global patients with haemophilia A. The reported number of patients with haemophilia A is 11,586 while the estimated prevalence could be around 50,000 patients. This review also identifies the need to immediately initiate a national programme for haemophilia, with components of prevention, care for patients, surveillance and education and support for families.

Epidemiologic analysis: Prophylaxis and multidrug-resistance in surgery.

Science.gov (United States)

Solís-Téllez, H; Mondragón-Pinzón, E E; Ramírez-Marino, M; Espinoza-López, F R; Domínguez-Sosa, F; Rubio-Suarez, J F; Romero-Morelos, R D

Surgical site infection is defined as an infection related to the surgical procedure in the area of manipulation occurring within the first 30 postoperative days. The diagnostic criteria include: purulent drainage, isolation of microorganisms, and signs of infection. To describe the epidemiologic characteristics and differences among the types of prophylactic regimens associated with hospital-acquired infections at the general surgery service of a tertiary care hospital. The electronic case records of patients that underwent general surgery at a tertiary care hospital within the time frame of January 1, 2013 and December 31, 2014 were reviewed. A convenience sample of 728 patients was established and divided into the following groups: Group 1: n=728 for the epidemiologic study; Group 2: n=638 for the evaluation of antimicrobial prophylaxis; and Group 3: n=50 for the evaluation of multidrug-resistant bacterial strains in the intensive care unit. The statistical analysis was carried out with the SPSS 19 program, using the Mann-Whitney U test and the chi-square test. A total of 728 procedures were performed (65.9% were elective surgeries). Three hundred twelve of the patients were males and 416 were females. Only 3.98% of the patients complied with the recommended antimicrobial prophylaxis, and multidrug-resistant bacterial strains were found in the intensive care unit. A single prophylactic dose is effective, but adherence to this recommendation was not adequate. The prophylactic guidelines are not strictly adhered to in our environment. There was a significant association between the development of nosocomial infections from multidrug-resistant germs and admission to the intensive care unit. Copyright © 2016 Asociación Mexicana de Gastroenterología. Publicado por Masson Doyma México S.A. All rights reserved.

Polyglot programming in applications used for genetic data analysis.

Science.gov (United States)

Nowak, Robert M

2014-01-01

Applications used for the analysis of genetic data process large volumes of data with complex algorithms. High performance, flexibility, and a user interface with a web browser are required by these solutions, which can be achieved by using multiple programming languages. In this study, I developed a freely available framework for building software to analyze genetic data, which uses C++, Python, JavaScript, and several libraries. This system was used to build a number of genetic data processing applications and it reduced the time and costs of development.

Premium adjustment: actuarial analysis on epidemiological models ...

African Journals Online (AJOL)

In this paper, we analyse insurance premium adjustment in the context of an epidemiological model where the insurer's future financial liability is greater than the premium from patients. In this situation, it becomes extremely difficult for the insurer since a negative reserve would severely increase its risk of insolvency, ...

Analysis of epidemiological indicators: Bovine brucellosis on the Atlantic coast and Antioquia - Colombia, 2005-2013

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Misael Oviedo-Pastrana

2017-05-01

Full Text Available Objective. Describe the situation of the bovine brucellosis in the Atlantic Coast and Antioquia (CAA by analysis of epidemiological indicators during 2005-2013. Materials and methods. The data was obtained from epidemiological reports of the Colombian Agricultural Institute and the National Agricultural Census 2014. The annual departmental average of the variables studied was compared and it was performed a temporal analysis through graphical representation. Results. 44% of the positive farms were focused on the CAA; the positivity rate of farms in the CAA (27.9% was higher and statistically significant when related to the average rate in the country (24.8% being promoted by the least producing departments. Regarding to the cattle population, the CAA concentrated 47.0% of positive cattle in the country; however, the bovine positivity rate (5.8% was statistically equal to the national average (5.3%; yet, the departments with lower cattle population had the highest rates. The best surveillance for bovine brucellosis was observed between 2005 and 2009, in contrast, during 2010, 2011 and 2013 there was a considerable reduction in the number of diagnoses, in both farms and cattle. In the least producing departments the temporary distribution of epidemiological indicators favored more the presence of the disease. Conclusions. The National Prevention Control and Eradication Program of Bovine Brucellosis in the CAA presented promising results, however, the lack of continuity in the diagnostic surveillance during some years and mainly in the least producing departments affected negatively their development.

GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research--an update.

Science.gov (United States)

Peakall, Rod; Smouse, Peter E

2012-10-01

GenAlEx: Genetic Analysis in Excel is a cross-platform package for population genetic analyses that runs within Microsoft Excel. GenAlEx offers analysis of diploid codominant, haploid and binary genetic loci and DNA sequences. Both frequency-based (F-statistics, heterozygosity, HWE, population assignment, relatedness) and distance-based (AMOVA, PCoA, Mantel tests, multivariate spatial autocorrelation) analyses are provided. New features include calculation of new estimators of population structure: G'(ST), G''(ST), Jost's D(est) and F'(ST) through AMOVA, Shannon Information analysis, linkage disequilibrium analysis for biallelic data and novel heterogeneity tests for spatial autocorrelation analysis. Export to more than 30 other data formats is provided. Teaching tutorials and expanded step-by-step output options are included. The comprehensive guide has been fully revised. GenAlEx is written in VBA and provided as a Microsoft Excel Add-in (compatible with Excel 2003, 2007, 2010 on PC; Excel 2004, 2011 on Macintosh). GenAlEx, and supporting documentation and tutorials are freely available at: http://biology.anu.edu.au/GenAlEx. rod.peakall@anu.edu.au.

International Veterinary Epilepsy Task Force's current understanding of idiopathic epilepsy of genetic or suspected genetic origin in purebred dogs

DEFF Research Database (Denmark)

Hülsmeyer, Velia-Isabel; Fischer, Andrea; Mandigers, Paul J. J.

2015-01-01

Canine idiopathic epilepsy is a common neurological disease affecting both purebred and crossbred dogs. Various breed-specific cohort, epidemiological and genetic studies have been conducted to date, which all improved our knowledge and general understanding of canine idiopathic epilepsy, and in ...

Identifying genetic variants that affect viability in large cohorts.

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Hakhamanesh Mostafavi

2017-09-01

Full Text Available A number of open questions in human evolutionary genetics would become tractable if we were able to directly measure evolutionary fitness. As a step towards this goal, we developed a method to examine whether individual genetic variants, or sets of genetic variants, currently influence viability. The approach consists in testing whether the frequency of an allele varies across ages, accounting for variation in ancestry. We applied it to the Genetic Epidemiology Research on Adult Health and Aging (GERA cohort and to the parents of participants in the UK Biobank. Across the genome, we found only a few common variants with large effects on age-specific mortality: tagging the APOE ε4 allele and near CHRNA3. These results suggest that when large, even late-onset effects are kept at low frequency by purifying selection. Testing viability effects of sets of genetic variants that jointly influence 1 of 42 traits, we detected a number of strong signals. In participants of the UK Biobank of British ancestry, we found that variants that delay puberty timing are associated with a longer parental life span (P~6.2 × 10-6 for fathers and P~2.0 × 10-3 for mothers, consistent with epidemiological studies. Similarly, variants associated with later age at first birth are associated with a longer maternal life span (P~1.4 × 10-3. Signals are also observed for variants influencing cholesterol levels, risk of coronary artery disease (CAD, body mass index, as well as risk of asthma. These signals exhibit consistent effects in the GERA cohort and among participants of the UK Biobank of non-British ancestry. We also found marked differences between males and females, most notably at the CHRNA3 locus, and variants associated with risk of CAD and cholesterol levels. Beyond our findings, the analysis serves as a proof of principle for how upcoming biomedical data sets can be used to learn about selection effects in contemporary humans.

Association between exposure to noise and risk of hypertension: a meta-analysis of observational epidemiological studies.

Science.gov (United States)

Fu, Wenning; Wang, Chao; Zou, Li; Liu, Qiaoyan; Gan, Yong; Yan, Shijiao; Song, Fujian; Wang, Zhihong; Lu, Zuxun; Cao, Shiyi

2017-12-01

An increasing amount of original studies suggested that exposure to noise could be associated with the risk of hypertension, but the results remain inconsistent and inconclusive. We aimed to synthesize available epidemiological evidence about the relationship between various types of noise and hypertension, and to explore the potential dose-response relationship between them in an up-to-date meta-analysis. We conducted a literature search of PubMed and Embase from these databases' inception through December 2016 to identify observational epidemiological studies examining the association between noise and risk of hypertension. A random effects model was used to combine the results of included studies. Dose-response meta-analysis was conducted to examine the potential dose-response relationship. In total, 32 studies (five cohort studies, one case-control study, and 26 cross-section studies) involving 264 678 participants were eligible for inclusion. Pooled result showed that living or working in environment with noise exposure was significantly associated with increased risk of hypertension (odds ratio 1.62; 95% confidence interval: 1.40-1.88). We found no evidence of a curve linear association between noise and risk of hypertension. A dose-response analysis suggested that, for an increment of per 10 dB(A) of noise, the combined odds ratio of hypertension was 1.06 (95% confidence interval: 1.04-1.08). Integrated epidemiological evidence supports the hypothesis that exposure to noise may be a risk factor of hypertension, and there is a positive dose-response association between them.

Aetiology of Depression: Insights from epidemiological and genetic research

NARCIS (Netherlands)

O. Story-Jovanova (Olivera)

2018-01-01

markdownabstractThis thesis includes several population-based studies that explore the aetiology of depression, with a specific interest on biological factors, genetics and epigenetics, and physical health factors for depression. Unravelling the aetiology of depression could potentially answer some

Epidemiological data and radiation risk estimates

International Nuclear Information System (INIS)

Cardis, E.

2002-01-01

The results of several major epidemiology studies on populations with particular exposure to ionizing radiation should become available during the first years of the 21. century. These studies are expected to provide answers to a number of questions concerning public health and radiation protection. Most of the populations concerned were accidentally exposed to radiation in ex-USSR or elsewhere or in a nuclear industrial context. The results will complete and test information on risk coming from studies among survivors of the Hiroshima and Nagasaki atomic bombs, particularly studies on the effects of low dose exposure and prolonged low-dose exposure, of different types of radiation, and environmental and host-related factors which could modify the risk of radiation-induced effects. These studies are thus important to assess the currently accepted scientific evidence on radiation protection for workers and the general population. In addition, supplementary information on radiation protection could be provided by formal comparisons and analyses combining data from populations with different types of exposure. Finally, in order to provide pertinent information for public health and radiation protection, future epidemiology studies should be targeted and designed to answer specific questions, concerning, for example, the risk for specific populations (children, patients, people with genetic predisposition). An integrated approach, combining epidemiology and studies on the mechanisms of radiation induction should provide particularly pertinent information. (author)

Pitfalls in genetic analysis of pheochromocytomas/paragangliomas-case report.

Science.gov (United States)

Canu, Letizia; Rapizzi, Elena; Zampetti, Benedetta; Fucci, Rossella; Nesi, Gabriella; Richter, Susan; Qin, Nan; Giachè, Valentino; Bergamini, Carlo; Parenti, Gabriele; Valeri, Andrea; Ercolino, Tonino; Eisenhofer, Graeme; Mannelli, Massimo

2014-07-01

About 35% of patients with pheochromocytoma/paraganglioma carry a germline mutation in one of the 10 main susceptibility genes. The recent introduction of next-generation sequencing will allow the analysis of all these genes in one run. When positive, the analysis is generally unequivocal due to the association between a germline mutation and a concordant clinical presentation or positive family history. When genetic analysis reveals a novel mutation with no clinical correlates, particularly in the presence of a missense variant, the question arises whether the mutation is pathogenic or a rare polymorphism. We report the case of a 35-year-old patient operated for a pheochromocytoma who turned out to be a carrier of a novel SDHD (succinate dehydrogenase subunit D) missense mutation. With no positive family history or clinical correlates, we decided to perform additional analyses to test the clinical significance of the mutation. We performed in silico analysis, tissue loss of heterozygosity analysis, immunohistochemistry, Western blot analysis, SDH enzymatic assay, and measurement of the succinate/fumarate concentration ratio in the tumor tissue by tandem mass spectrometry. Although the in silico analysis gave contradictory results according to the different methods, all the other tests demonstrated that the SDH complex was conserved and normally active. We therefore came to the conclusion that the variant was a nonpathogenic polymorphism. Advancements in technology facilitate genetic analysis of patients with pheochromocytoma but also offer new challenges to the clinician who, in some cases, needs clinical correlates and/or functional tests to give significance to the results of the genetic assay.

Genetic epidemiology of coronary artery disease: an Asian Indian ...

Indian Academy of Sciences (India)

The present review aims to consolidate the available literature on the genetics of. CAD in Asian Indians ... India and the US who were participating in the Sikh Diabetes ..... to undertake systematic large-scale studies in order to under- stand the ...

Genetic factors and molecular mechanisms in dry eye disease.

Science.gov (United States)

Lee, Ling; Garrett, Qian; Flanagan, Judith; Chakrabarti, Subhabrata; Papas, Eric

2018-04-01

Dry eye disease (DED) is a complex condition with a multifactorial etiology that can be difficult to manage successfully. While external factors are modifiable, treatment success is limited if genetic factors contribute to the disease. The purpose of this review is to compile research describing normal and abnormal ocular surface function on a molecular level, appraise genetic studies involving DED or DED-associated diseases, and introduce the basic methods used for conducting genetic epidemiology studies. Copyright © 2018 Elsevier Inc. All rights reserved.

Genetic diversity analysis of common beans based on molecular markers

Directory of Open Access Journals (Sweden)

Homar R. Gill-Langarica

2011-01-01

Full Text Available A core collection of the common bean (Phaseolus vulgaris L., representing genetic diversity in the entire Mexican holding, is kept at the INIFAP (Instituto Nacional de Investigaciones Forestales, Agricolas y Pecuarias, Mexico Germplasm Bank. After evaluation, the genetic structure of this collection (200 accessions was compared with that of landraces from the states of Oaxaca, Chiapas and Veracruz (10 genotypes from each, as well as a further 10 cultivars, by means of four amplified fragment length polymorphisms (AFLP +3/+3 primer combinations and seven simple sequence repeats (SSR loci, in order to define genetic diversity, variability and mutual relationships. Data underwent cluster (UPGMA and molecular variance (AMOVA analyses. AFLP analysis produced 530 bands (88.5% polymorphic while SSR primers amplified 174 alleles, all polymorphic (8.2 alleles per locus. AFLP indicated that the highest genetic diversity was to be found in ten commercial-seed classes from two major groups of accessions from Central Mexico and Chiapas, which seems to be an important center of diversity in the south. A third group included genotypes from Nueva Granada, Mesoamerica, Jalisco and Durango races. Here, SSR analysis indicated a reduced number of shared haplotypes among accessions, whereas the highest genetic components of AMOVA variation were found within accessions. Genetic diversity observed in the common-bean core collection represents an important sample of the total Phaseolus genetic variability at the main Germplasm Bank of INIFAP. Molecular marker strategies could contribute to a better understanding of the genetic structure of the core collection as well as to its improvement and validation.

Genetic diversity analysis of common beans based on molecular markers

Directory of Open Access Journals (Sweden)

Homar R. Gill-Langarica

Full Text Available A core collection of the common bean (Phaseolus vulgaris L., representing genetic diversity in the entire Mexican holding, is kept at the INIFAP (Instituto Nacional de Investigaciones Forestales, Agricolas y Pecuarias, Mexico Germplasm Bank. After evaluation, the genetic structure of this collection (200 accessions was compared with that of landraces from the states of Oaxaca, Chiapas and Veracruz (10 genotypes from each, as well as a further 10 cultivars, by means of four amplified fragment length polymorphisms (AFLP +3/+3 primer combinations and seven simple sequence repeats (SSR loci, in order to define genetic diversity, variability and mutual relationships. Data underwent cluster (UPGMA and molecular variance (AMOVA analyses. AFLP analysis produced 530 bands (88.5% polymorphic while SSR primers amplified 174 alleles, all polymorphic (8.2 alleles per locus. AFLP indicated that the highest genetic diversity was to be found in ten commercial-seed classes from two major groups of accessions from Central Mexico and Chiapas, which seems to be an important center of diversity in the south. A third group included genotypes from Nueva Granada, Mesoamerica, Jalisco and Durango races. Here, SSR analysis indicated a reduced number of shared haplotypes among accessions, whereas the highest genetic components of AMOVA variation were found within accessions. Genetic diversity observed in the common-bean core collection represents an important sample of the total Phaseolus genetic variability at the main Germplasm Bank of INIFAP. Molecular marker strategies could contribute to a better understanding of the genetic structure of the core collection as well as to its improvement and validation.

Genetic diversity analysis of common beans based on molecular markers.

Science.gov (United States)

Gill-Langarica, Homar R; Muruaga-Martínez, José S; Vargas-Vázquez, M L Patricia; Rosales-Serna, Rigoberto; Mayek-Pérez, Netzahualcoyotl

2011-10-01

A core collection of the common bean (Phaseolus vulgaris L.), representing genetic diversity in the entire Mexican holding, is kept at the INIFAP (Instituto Nacional de Investigaciones Forestales, Agricolas y Pecuarias, Mexico) Germplasm Bank. After evaluation, the genetic structure of this collection (200 accessions) was compared with that of landraces from the states of Oaxaca, Chiapas and Veracruz (10 genotypes from each), as well as a further 10 cultivars, by means of four amplified fragment length polymorphisms (AFLP) +3/+3 primer combinations and seven simple sequence repeats (SSR) loci, in order to define genetic diversity, variability and mutual relationships. Data underwent cluster (UPGMA) and molecular variance (AMOVA) analyses. AFLP analysis produced 530 bands (88.5% polymorphic) while SSR primers amplified 174 alleles, all polymorphic (8.2 alleles per locus). AFLP indicated that the highest genetic diversity was to be found in ten commercial-seed classes from two major groups of accessions from Central Mexico and Chiapas, which seems to be an important center of diversity in the south. A third group included genotypes from Nueva Granada, Mesoamerica, Jalisco and Durango races. Here, SSR analysis indicated a reduced number of shared haplotypes among accessions, whereas the highest genetic components of AMOVA variation were found within accessions. Genetic diversity observed in the common-bean core collection represents an important sample of the total Phaseolus genetic variability at the main Germplasm Bank of INIFAP. Molecular marker strategies could contribute to a better understanding of the genetic structure of the core collection as well as to its improvement and validation.

A Fantastic Epidemiology Journey: from China to Africa and back

Science.gov (United States)

Dr. Ann Hsing is a professor of medicine at Stanford University and a co-leader of the Population Sciences Program at Stanford Cancer Institute. She is also a professor in the Department of Health Research and Policy (epidemiology, by courtesy) and a faculty fellow for the Center for Innovation in Global Health. In addition, she chairs the Pacific Rim Alliance for Population Health at Stanford’s Center for Population Health Sciences. Prior to joining Stanford School of Medicine, Dr. Hsing served four years as Chief Scientific Officer at the Cancer Prevention Institute of California and 22 years as an intramural scientist (tenured senior investigator) at the Division of Cancer Epidemiology and Genetics, National Cancer Institute. Dr. Hsing received her PhD in epidemiology from the Johns Hopkins University and is widely recognized as a leading expert in the epidemiology of prostate and hepatobiliary cancer, as well as hormonal carcinogenesis and molecular epidemiology. She has authored more than 280 peer-reviewed articles and mentored over 60 pre- and post-doctoral fellows and junior scholars. At Stanford, she leads the Liver Cancer Working Group and the LDCT Screening Group, and serves as the principal investigator (PI) for wellness cohort studies in China, Taiwan, and Singapore as well as liver cancer studies in the Bay area, Taiwan, Mongolia, and Africa.

Epidemiological analysis of Salmonella clusters identified by whole genome sequencing, England and Wales 2014.

Science.gov (United States)

Waldram, Alison; Dolan, Gayle; Ashton, Philip M; Jenkins, Claire; Dallman, Timothy J

2018-05-01

The unprecedented level of bacterial strain discrimination provided by whole genome sequencing (WGS) presents new challenges with respect to the utility and interpretation of the data. Whole genome sequences from 1445 isolates of Salmonella belonging to the most commonly identified serotypes in England and Wales isolated between April and August 2014 were analysed. Single linkage single nucleotide polymorphism thresholds at the 10, 5 and 0 level were explored for evidence of epidemiological links between clustered cases. Analysis of the WGS data organised 566 of the 1445 isolates into 32 clusters of five or more. A statistically significant epidemiological link was identified for 17 clusters. The clusters were associated with foreign travel (n = 8), consumption of Chinese takeaways (n = 4), chicken eaten at home (n = 2), and one each of the following; eating out, contact with another case in the home and contact with reptiles. In the same time frame, one cluster was detected using traditional outbreak detection methods. WGS can be used for the highly specific and highly sensitive detection of biologically related isolates when epidemiological links are obscured. Improvements in the collection of detailed, standardised exposure information would enhance cluster investigations. Copyright © 2017 Elsevier Ltd. All rights reserved.

A molecular epidemiology survey of respiratory adenoviruses circulating in children residing in Southern Palestine.

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Lina Qurei

Full Text Available A molecular epidemiology survey was performed in order to establish and document the respiratory adenovirus pathogen profiles among children in Southern Palestine. Three hundred and thirty-eight hospitalized pediatric cases with adenovirus-associated respiratory tract infections were analyzed. Forty four cases out of the 338 were evaluated in more detail for the adenoviruses types present. All of the children resided in Southern Palestine, that is, in city, village and refugee camp environments within the districts of Hebron and Bethlehem. Human adenoviruses circulated throughout 2005-2010, with major outbreaks occurring in the spring months. A larger percent of the children diagnosed with adenoviral infections were male infants. DNA sequence analysis of the hexon genes from 44 samples revealed that several distinct adenovirus types circulated in the region; these were HAdV-C1, HAdV-C2, HAdV-B3 and HAdV-C5. However, not all of these types were detected within each year. This is the first study ever conducted in Palestine of the genetic epidemiology of respiratory adenovirus infections.

Epidemiological correlates of breast cancer in South India.

Science.gov (United States)

Babu, Giridhara Rathnaiah; Lakshmi, Srikanthi Bodapati; Thiyagarajan, Jotheeswaran Amuthavalli

2013-01-01

Breast cancer is the most frequent cancer in women globally and represents the second leading cause of cancer death among women (after lung cancer). India is going through epidemiologic transition. It is reported that the incidence of breast cancer is rising rapidly as a result of changes in reproductive risk factors, dietary habits and increasing life expectancy, acting in concert with genetic factors. In order to understand the existing epidemiological correlates of breast cancer in South India, a systematic review of evidence available on epidemiologic correlates of breast cancer addressing incidence, prevalence, and associated factors like age, reproductive factors, cultural and religious factors was performed with specific focus on screening procedures in southern India. An increase in breast cancer incidence due to various modifiable risk factors was noted, especially in women over 40 years of age, with late stage of presentation, lack of awareness about screening, costs, fear and stigma associated with the disease serving as major barriers for early presentation. Educational strategies should be aimed at modifying the life style, early planning of pregnancy, promoting breast feeding and physical activity. It is very important to obtain reliable data for planning policies, decision-making and setting up the priorities.

A markerless protocol for genetic analysis of Aggregatibacter actinomycetemcomitans

Science.gov (United States)

Cheng, Ya-An; Jee, Jason; Hsu, Genie; Huang, Yanyan; Chen, Casey; Lin, Chun-Pin

2015-01-01

Background/Purpose The genomes of different Aggregatibacter actinomycetemcomitans strains contain many strain-specific genes and genomic islands (defined as DNA found in some but not all strains) of unknown functions. Genetic analysis for the functions of these islands will be constrained by the limited availability of genetic markers and vectors for A. actinomycetemcomitans. In this study we tested a novel genetic approach of gene deletion and restoration in a naturally competent A. actinomycetemcomitans strain D7S-1. Methods Specific genes’ deletion mutants and mutants restored with the deleted genes were constructed by a markerless loxP/Cre system. In mutants with sequential deletion of multiple genes loxP with different spacer regions were used to avoid unwanted recombinations between loxP sites. Results Eight single-gene deletion mutants, four multiple-gene deletion mutants, and two mutants with restored genes were constructed. No unintended non-specific deletion mutants were generated by this protocol. The protocol did not negatively affect the growth and biofilm formation of A. actinomycetemcomitans. Conclusion The protocol described in this study is efficient and specific for genetic manipulation of A. actinomycetemcomitans, and will be amenable for functional analysis of multiple genes in A. actinomycetemcomitans. PMID:24530245

Genetics of gallstone disease.

Directory of Open Access Journals (Sweden)

Mittal B

2002-04-01

Full Text Available Gallstone disease is a complex disorder where both environmental and genetic factors contribute towards susceptibility to the disease. Epidemiological and family studies suggest a strong genetic component in the causation of this disease. Several genetically derived phenotypes in the population are responsible for variations in lipoprotein types, which in turn affect the amount of cholesterol available in the gall bladder. The genetic polymorphisms in various genes for apo E, apo B, apo A1, LDL receptor, cholesteryl ester transfer and LDL receptor-associated protein have been implicated in gallstone formation. However, presently available information on genetic differences is not able to account for a large number of gallstone patients. The molecular studies in the animal models have not only confirmed the present paradigm of gallstone formation but also helped in identification of novel genes in humans, which might play an important role in pathogenesis of the disease. Precise understanding of such genes and their molecular mechanisms may provide the basis of new targets for rational drug designs and dietary interventions.

Genetic basis of atrial fibrillation

Directory of Open Access Journals (Sweden)

Oscar Campuzano

2016-12-01

Full Text Available Atrial fibrillation is the most common sustained arrhythmia and remains as one of main challenges in current clinical practice. The disease may be induced secondary to other diseases such as hypertension, valvular heart disease, and heart failure, conferring an increased risk of stroke and sudden death. Epidemiological studies have provided evidence that genetic factors play an important role and up to 30% of clinically diagnosed patients may have a family history of atrial fibrillation. To date, several rare variants have been identified in a wide range of genes associated with ionic channels, calcium handling protein, fibrosis, conduction and inflammation. Important advances in clinical, genetic and molecular basis have been performed over the last decade, improving diagnosis and treatment. However, the genetics of atrial fibrillation is complex and pathophysiological data remains still unraveling. A better understanding of the genetic basis will induce accurate risk stratification and personalized clinical treatment. In this review, we have focused on current genetics basis of atrial fibrillation.

Pervasive Sharing of Genetic Effects in Autoimmune Disease

DEFF Research Database (Denmark)

Cotsapas, Chris; Voight, Benjamin F.; Rossin, Elizabeth

2011-01-01

Genome-wide association (GWA) studies have identified numerous, replicable, genetic associations between common single nucleotide polymorphisms (SNPs) and risk of common autoimmune and inflammatory (immune-mediated) diseases, some of which are shared between two diseases. Along with epidemiologic...

Applications of artificial intelligence systems in the analysis of epidemiological data.

Science.gov (United States)

Flouris, Andreas D; Duffy, Jack

2006-01-01

A brief review of the germane literature suggests that the use of artificial intelligence (AI) statistical algorithms in epidemiology has been limited. We discuss the advantages and disadvantages of using AI systems in large-scale sets of epidemiological data to extract inherent, formerly unidentified, and potentially valuable patterns that human-driven deductive models may miss.

Genetic and epidemiological aspect of Complex Regional Pain Syndrome

NARCIS (Netherlands)

Rooij, Annetje Monique de

2010-01-01

Complex Regional Pain Syndrome (CRPS) is a painful disorder affecting one or more extremities. CRPS is characterized by various combinations of sensory, autonomic and motor disturbances. Genetic factors are suggested to play a role in CRPS, but this has not been extensively studied. Therefore the

Pleiotropic Analysis of Lung Cancer and Blood Triglycerides.

Science.gov (United States)

Zuber, Verena; Marconett, Crystal N; Shi, Jianxin; Hua, Xing; Wheeler, William; Yang, Chenchen; Song, Lei; Dale, Anders M; Laplana, Marina; Risch, Angela; Witoelar, Aree; Thompson, Wesley K; Schork, Andrew J; Bettella, Francesco; Wang, Yunpeng; Djurovic, Srdjan; Zhou, Beiyun; Borok, Zea; van der Heijden, Henricus F M; de Graaf, Jacqueline; Swinkels, Dorine; Aben, Katja K; McKay, James; Hung, Rayjean J; Bikeböller, Heike; Stevens, Victoria L; Albanes, Demetrius; Caporaso, Neil E; Han, Younghun; Wei, Yongyue; Panadero, Maria Angeles; Mayordomo, Jose I; Christiani, David C; Kiemeney, Lambertus; Andreassen, Ole A; Houlston, Richard; Amos, Christopher I; Chatterjee, Nilanjan; Laird-Offringa, Ite A; Mills, Ian G; Landi, Maria Teresa

2016-12-01

Epidemiologically related traits may share genetic risk factors, and pleiotropic analysis could identify individual loci associated with these traits. Because of their shared epidemiological associations, we conducted pleiotropic analysis of genome-wide association studies of lung cancer (12 160 lung cancer case patients and 16 838 control subjects) and cardiovascular disease risk factors (blood lipids from 188 577 subjects, type 2 diabetes from 148 821 subjects, body mass index from 123 865 subjects, and smoking phenotypes from 74 053 subjects). We found that 6p22.1 (rs6904596, ZNF184) was associated with both lung cancer (P = 5.50x10(-6)) and blood triglycerides (P = 1.39x10(-5)). We replicated the association in 6097 lung cancer case patients and 204 657 control subjects (P = 2.40 × 10(-4)) and in 71 113 subjects with triglycerides data (P = .01). rs6904596 reached genome-wide significance in lung cancer meta-analysis (odds ratio = 1.15, 95% confidence interval = 1.10 to 1.21 ,: Pcombined = 5.20x10(-9)). The large sample size provided by the lipid GWAS data and the shared genetic risk factors between the two traits contributed to the uncovering of a hitherto unidentified genetic locus for lung cancer. Published by Oxford University Press 2016. This work is written by US Government employees and is in the public domain in the United States.

The epidemiology of acne vulgaris in late adolescence.

Science.gov (United States)

Lynn, Darren D; Umari, Tamara; Dunnick, Cory A; Dellavalle, Robert P

2016-01-01

Acne vulgaris is the most common skin condition affecting late adolescents across the globe. Although prior studies have evaluated epidemiologic patterns of acne vulgaris in various ethnicities and regions, adequate understanding of the worldwide burden of the disease associated with patients in their late adolescence (15-19-year olds) remains lacking. To assess the global burden of the disease associated with acne vulgaris for late adolescents (15-19-year olds) and provide an overview of the epidemiology, pathophysiology, and treatment options for acne in this population. Database summary study. Global Burden of Disease Study 2010 database. Global Burden of Disease regions comprised countries with prevalence of acne vulgaris between the ages of 15 and 19 years. Geographic region-level disability-adjusted life year rates (per 100,000 persons) associated with acne vulgaris in years 1990 through 2010. Median percentage change in disability-adjusted life year rates was estimated for each region across the specified study period. Acne vulgaris-associated disease burden exhibits global distribution and has continued to grow in prevalence over time within this population. This continued growth suggests an unmet dermatologic need worldwide for this disorder and potential opportunities for improved access and delivery of dermatologic care. Our analysis of the literature reveals numerous opportunities for enhanced patient care. To that end, we highlight some of the effective and promising treatments currently available and address important factors, such as sex, nationality, genetics, pathophysiology, and diet, as they relate to acne vulgaris in late adolescence.

Osteoarthritis of the first carpometacarpal joint: a study of radiology and clinical epidemiology:

DEFF Research Database (Denmark)

Sonne-Holm, Stig; Jacobsen, J

2006-01-01

Epidemiological studies show an increased prevalence of osteoarthritis of the knee and hand with increased body mass index [BMI]. Osteoarthritis of the hip joint is not related to BMI. The connection between obesity and osteoarthritis cannot exclusively be explained by genetic factors or by the a...

Spatial epidemiological techniques in cholera mapping and analysis towards a local scale predictive modelling

Science.gov (United States)

Rasam, A. R. A.; Ghazali, R.; Noor, A. M. M.; Mohd, W. M. N. W.; Hamid, J. R. A.; Bazlan, M. J.; Ahmad, N.

2014-02-01

Cholera spatial epidemiology is the study of the spread and control of the disease spatial pattern and epidemics. Previous studies have shown that multi-factorial causation such as human behaviour, ecology and other infectious risk factors influence the disease outbreaks. Thus, understanding spatial pattern and possible interrelationship factors of the outbreaks are crucial to be explored an in-depth study. This study focuses on the integration of geographical information system (GIS) and epidemiological techniques in exploratory analyzing the cholera spatial pattern and distribution in the selected district of Sabah. Spatial Statistic and Pattern tools in ArcGIS and Microsoft Excel software were utilized to map and analyze the reported cholera cases and other data used. Meanwhile, cohort study in epidemiological technique was applied to investigate multiple outcomes of the disease exposure. The general spatial pattern of cholera was highly clustered showed the disease spread easily at a place or person to others especially 1500 meters from the infected person and locations. Although the cholera outbreaks in the districts are not critical, it could be endemic at the crowded areas, unhygienic environment, and close to contaminated water. It was also strongly believed that the coastal water of the study areas has possible relationship with the cholera transmission and phytoplankton bloom since the areas recorded higher cases. GIS demonstrates a vital spatial epidemiological technique in determining the distribution pattern and elucidating the hypotheses generating of the disease. The next research would be applying some advanced geo-analysis methods and other disease risk factors for producing a significant a local scale predictive risk model of the disease in Malaysia.

Spatial epidemiological techniques in cholera mapping and analysis towards a local scale predictive modelling

International Nuclear Information System (INIS)

Rasam, A R A; Ghazali, R; Noor, A M M; Mohd, W M N W; Hamid, J R A; Bazlan, M J; Ahmad, N

2014-01-01

Cholera spatial epidemiology is the study of the spread and control of the disease spatial pattern and epidemics. Previous studies have shown that multi-factorial causation such as human behaviour, ecology and other infectious risk factors influence the disease outbreaks. Thus, understanding spatial pattern and possible interrelationship factors of the outbreaks are crucial to be explored an in-depth study. This study focuses on the integration of geographical information system (GIS) and epidemiological techniques in exploratory analyzing the cholera spatial pattern and distribution in the selected district of Sabah. Spatial Statistic and Pattern tools in ArcGIS and Microsoft Excel software were utilized to map and analyze the reported cholera cases and other data used. Meanwhile, cohort study in epidemiological technique was applied to investigate multiple outcomes of the disease exposure. The general spatial pattern of cholera was highly clustered showed the disease spread easily at a place or person to others especially 1500 meters from the infected person and locations. Although the cholera outbreaks in the districts are not critical, it could be endemic at the crowded areas, unhygienic environment, and close to contaminated water. It was also strongly believed that the coastal water of the study areas has possible relationship with the cholera transmission and phytoplankton bloom since the areas recorded higher cases. GIS demonstrates a vital spatial epidemiological technique in determining the distribution pattern and elucidating the hypotheses generating of the disease. The next research would be applying some advanced geo-analysis methods and other disease risk factors for producing a significant a local scale predictive risk model of the disease in Malaysia

The Genetics of Stress-Related Disorders: PTSD, Depression, and Anxiety Disorders

Science.gov (United States)

Smoller, Jordan W

2016-01-01

Research into the causes of psychopathology has largely focused on two broad etiologic factors: genetic vulnerability and environmental stressors. An important role for familial/heritable factors in the etiology of a broad range of psychiatric disorders was established well before the modern era of genomic research. This review focuses on the genetic basis of three disorder categories—posttraumatic stress disorder (PTSD), major depressive disorder (MDD), and the anxiety disorders—for which environmental stressors and stress responses are understood to be central to pathogenesis. Each of these disorders aggregates in families and is moderately heritable. More recently, molecular genetic approaches, including genome-wide studies of genetic variation, have been applied to identify specific risk variants. In this review, I summarize evidence for genetic contributions to PTSD, MDD, and the anxiety disorders including genetic epidemiology, the role of common genetic variation, the role of rare and structural variation, and the role of gene–environment interaction. Available data suggest that stress-related disorders are highly complex and polygenic and, despite substantial progress in other areas of psychiatric genetics, few risk loci have been identified for these disorders. Progress in this area will likely require analysis of much larger sample sizes than have been reported to date. The phenotypic complexity and genetic overlap among these disorders present further challenges. The review concludes with a discussion of prospects for clinical translation of genetic findings and future directions for research. PMID:26321314

Molecular epidemiology of human rhinoviruses

OpenAIRE

Savolainen-Kopra, Carita

2006-01-01

The first part of this work investigates the molecular epidemiology of a human enterovirus (HEV), echovirus 30 (E-30). This project is part of a series of studies performed in our research team analyzing the molecular epidemiology of HEV-B viruses. A total of 129 virus strains had been isolated in different parts of Europe. The sequence analysis was performed in three different genomic regions: 420 nucleotides (nt) in the VP4/VP2 capsid protein coding region, the entire VP1 capsid protein cod...

Genetic analysis of PAX3 for diagnosis of Waardenburg syndrome type I.

Science.gov (United States)

Matsunaga, Tatsuo; Mutai, Hideki; Namba, Kazunori; Morita, Noriko; Masuda, Sawako

2013-04-01

PAX3 genetic analysis increased the diagnostic accuracy for Waardenburg syndrome type I (WS1). Analysis of the three-dimensional (3D) structure of PAX3 helped verify the pathogenicity of a missense mutation, and multiple ligation-dependent probe amplification (MLPA) analysis of PAX3 increased the sensitivity of genetic diagnosis in patients with WS1. Clinical diagnosis of WS1 is often difficult in individual patients with isolated, mild, or non-specific symptoms. The objective of the present study was to facilitate the accurate diagnosis of WS1 through genetic analysis of PAX3 and to expand the spectrum of known PAX3 mutations. In two Japanese families with WS1, we conducted a clinical evaluation of symptoms and genetic analysis, which involved direct sequencing, MLPA analysis, quantitative PCR of PAX3, and analysis of the predicted 3D structure of PAX3. The normal-hearing control group comprised 92 subjects who had normal hearing according to pure tone audiometry. In one family, direct sequencing of PAX3 identified a heterozygous mutation, p.I59F. Analysis of PAX3 3D structures indicated that this mutation distorted the DNA-binding site of PAX3. In the other family, MLPA analysis and subsequent quantitative PCR detected a large, heterozygous deletion spanning 1759-2554 kb that eliminated 12-18 genes including a whole PAX3 gene.

DMPD: The Toll-like receptors: analysis by forward genetic methods. [Dynamic Macrophage Pathway CSML Database

Lifescience Database Archive (English)

Full Text Available 16001129 The Toll-like receptors: analysis by forward genetic methods. Beutler B. I...mmunogenetics. 2005 Jul;57(6):385-92. (.png) (.svg) (.html) (.csml) Show The Toll-like receptors: analysis by forwar...d genetic methods. PubmedID 16001129 Title The Toll-like receptors: analysis by forward genetic meth

Molecular epidemiology of Klebsiella pneumoniae K1 and K2 isolates in Japan.

Science.gov (United States)

Harada, Sohei; Ishii, Yoshikazu; Saga, Tomoo; Aoki, Kotaro; Tateda, Kazuhiro

2018-03-20

Although severe infections caused by hypervirulent Klebsiella pneumoniae isolates, such as K1 isolates belonging to sequence type (ST) 23, have been a significant problem in Asian countries, epidemiology of these isolates in Japan remains unclear. We performed a nationwide molecular epidemiological study of K. pneumoniae K1 and K2 isolates in Japan. Of the 259K. pneumoniae isolates collected, 14 and 16 isolates were identified as capsular genotypes K1 and K2, respectively. All K1 isolates were ST23 or its closely related clones and showed high genetic similarity by pulsed-field gel electrophoresis (PFGE) and the DiversiLab system (DL). K2 isolates, belonging to ST14, ST25, ST65, ST86, and ST110, were more genetically diverse than K1 isolates. Isolates belonging to a specific ST showed identical virulence gene profiles with a few exceptions. PFGE and DL results using K1 and K2 isolates were generally in agreement. Copyright © 2018. Published by Elsevier Inc.

Analysis of genetic effects of nuclear-cytoplasmic interaction on quantitative traits: genetic model for diploid plants.

Science.gov (United States)

Han, Lide; Yang, Jian; Zhu, Jun

2007-06-01

A genetic model was proposed for simultaneously analyzing genetic effects of nuclear, cytoplasm, and nuclear-cytoplasmic interaction (NCI) as well as their genotype by environment (GE) interaction for quantitative traits of diploid plants. In the model, the NCI effects were further partitioned into additive and dominance nuclear-cytoplasmic interaction components. Mixed linear model approaches were used for statistical analysis. On the basis of diallel cross designs, Monte Carlo simulations showed that the genetic model was robust for estimating variance components under several situations without specific effects. Random genetic effects were predicted by an adjusted unbiased prediction (AUP) method. Data on four quantitative traits (boll number, lint percentage, fiber length, and micronaire) in Upland cotton (Gossypium hirsutum L.) were analyzed as a worked example to show the effectiveness of the model.

Genetic, Maternal, and Environmental Risk Factors for Cryptorchidism

DEFF Research Database (Denmark)

Barthold, Julia Spencer; Reinhardt, Susanne; Thorup, Jorgen

2016-01-01

genetic risk, multiple susceptibility loci, and a role for the maternal environment. Epidemiologic studies have identified low birth weight or intrauterine growth retardation as factors most strongly associated with cryptorchidism, with additional evidence suggesting that maternal smoking and gestational...

GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research—an update

Science.gov (United States)

Peakall, Rod; Smouse, Peter E.

2012-01-01

Summary: GenAlEx: Genetic Analysis in Excel is a cross-platform package for population genetic analyses that runs within Microsoft Excel. GenAlEx offers analysis of diploid codominant, haploid and binary genetic loci and DNA sequences. Both frequency-based (F-statistics, heterozygosity, HWE, population assignment, relatedness) and distance-based (AMOVA, PCoA, Mantel tests, multivariate spatial autocorrelation) analyses are provided. New features include calculation of new estimators of population structure: G′ST, G′′ST, Jost’s Dest and F′ST through AMOVA, Shannon Information analysis, linkage disequilibrium analysis for biallelic data and novel heterogeneity tests for spatial autocorrelation analysis. Export to more than 30 other data formats is provided. Teaching tutorials and expanded step-by-step output options are included. The comprehensive guide has been fully revised. Availability and implementation: GenAlEx is written in VBA and provided as a Microsoft Excel Add-in (compatible with Excel 2003, 2007, 2010 on PC; Excel 2004, 2011 on Macintosh). GenAlEx, and supporting documentation and tutorials are freely available at: http://biology.anu.edu.au/GenAlEx. Contact: rod.peakall@anu.edu.au PMID:22820204

EMBO Course “Formal Analysis of Genetic Regulation”

CERN Document Server

1979-01-01

The E M B 0 course on "Formal Analysis of Genetic Regulation" A course entitled "Formal analysis of Genetic Regulation" was held at the University of Brussels from 6 to 16 September 1977 under the auspices of EMBO (European Molecular Biology Organization). As indicated by the title of the book (but not explicitly enough by the title of the course), the main emphasis was put on a dynamic analysis of systems using logical methods, that is, methods in which functions and variables take only a limited number of values - typically two. In this respect, this course was complementary to an EMBO course using continuous methods which was held some months later in Israel by Prof. Segel. People from four very different laboratories took an active part in teaching our course in Brussels : Drs Anne LEUSSLER and Philippe VAN HAM, from the Laboratory of Prof. Jean FLORINE (Laboratoire des Systemes logiques et numeriques, Faculte des Sciences appliquees, Universite Libre de Bruxelles). Dr Stuart KAUFFMAN (Dept. of Biochemist...

Phenotypic and molecular genetic analysis of Pyruvate Kinase ...

African Journals Online (AJOL)

Phenotypic and molecular genetic analysis of Pyruvate Kinase deficiency in a Tunisian family. Jaouani Mouna, Hamdi Nadia, Chaouch Leila, Kalai Miniar, Mellouli Fethi, Darragi Imen, Boudriga Imen, Chaouachi Dorra, Bejaoui Mohamed, Abbes Salem ...

Temporal stability in the genetic structure of Sarcoptes scabiei under the host-taxon law: empirical evidences from wildlife-derived Sarcoptes mite in Asturias, Spain

Directory of Open Access Journals (Sweden)

Rossi Luca

2011-07-01

Full Text Available Abstract Background Implicitly, parasite molecular studies assume temporal genetic stability. In this study we tested, for the first time to our knowledge, the extent of changes in genetic diversity and structure of Sarcoptes mite populations from Pyrenean chamois (Rupicapra pyrenaica in Asturias (Spain, using one multiplex of 9 microsatellite markers and Sarcoptes samples from sympatric Pyrenean chamois, red deer (Cervus elaphus, roe deer (Capreolus capreolus and red fox (Vulpes vulpes. Results The analysis of an 11-years interval period found little change in the genetic diversity (allelic diversity, and observed and expected heterozygosity. The temporal stability in the genetic diversity was confirmed by population structure analysis, which was not significantly variable over time. Population structure analysis revealed temporal stability in the genetic diversity of Sarcoptes mite under the host-taxon law (herbivore derived- and carnivore derived-Sarcoptes mite among the sympatric wild animals from Asturias. Conclusions The confirmation of parasite temporal genetic stability is of vital interest to allow generalizations to be made, which have further implications regarding the genetic structure, epidemiology and monitoring protocols of the ubiquitous Sarcoptes mite. This could eventually be applied to other parasite species.

Oropouche Virus: Clinical, Epidemiological, and Molecular Aspects of a Neglected Orthobunyavirus.

Science.gov (United States)

Travassos da Rosa, Jorge Fernando; de Souza, William Marciel; Pinheiro, Francisco de Paula; Figueiredo, Mário Luiz; Cardoso, Jedson Ferreira; Acrani, Gustavo Olszanski; Nunes, Márcio Roberto Teixeira

2017-05-01

AbstractOropouche virus (OROV) is an important cause of arboviral illness in Latin American countries, more specifically in the Amazon region of Brazil, Venezuela and Peru, as well as in other countries such as Panama. In the past decades, the clinical, epidemiological, pathological, and molecular aspects of OROV have been published and provide the basis for a better understanding of this important human pathogen. Here, we describe the milestones in a comprehensive review of OROV epidemiology, pathogenesis, and molecular biology, including a description of the first isolation of the virus, the outbreaks during the past six decades, clinical aspects of OROV infection, diagnostic methods, genome and genetic traits, evolution, and viral dispersal.

ANALYSIS OF THE INCIDENCE OF LYMPHOMAS IN THE REPUBLIC OF KHAKASSIA FOR 2014 AND ITS EPIDEMIOLOGICAL FEATURES

Directory of Open Access Journals (Sweden)

Olga Valentinovna Smirnova

2016-05-01

Full Text Available The aim of the study was to study patterns in the incidence of lymphomas and its epidemiological characteristics in the Republic of Khakassia for 2014. The research was conducted by retrospective analysis. The following epidemiological features are revealed: NHL is more common; LGM often ill persons young and middle age, and the NHL people in the older age groups; incidence among men is higher than women’s; among refined morphological variants LGM disseminated sclerosis and nodular lymphoid predominance, among the NHL is most prevalent diffuse non-Hodgkin’s lymphoma; it is noted that the NHL is more common in urban populations.

Adaptive divergence despite strong genetic drift: genomic analysis of the evolutionary mechanisms causing genetic differentiation in the island fox (Urocyon littoralis)

Science.gov (United States)

FUNK, W. CHRIS; LOVICH, ROBERT E.; HOHENLOHE, PAUL A.; HOFMAN, COURTNEY A.; MORRISON, SCOTT A.; SILLETT, T. SCOTT; GHALAMBOR, CAMERON K.; MALDONADO, JESUS E.; RICK, TORBEN C.; DAY, MITCH D.; POLATO, NICHOLAS R.; FITZPATRICK, SARAH W.; COONAN, TIMOTHY J.; CROOKS, KEVIN R.; DILLON, ADAM; GARCELON, DAVID K.; KING, JULIE L.; BOSER, CHRISTINA L.; GOULD, NICHOLAS; ANDELT, WILLIAM F.

2016-01-01

The evolutionary mechanisms generating the tremendous biodiversity of islands have long fascinated evolutionary biologists. Genetic drift and divergent selection are predicted to be strong on islands and both could drive population divergence and speciation. Alternatively, strong genetic drift may preclude adaptation. We conducted a genomic analysis to test the roles of genetic drift and divergent selection in causing genetic differentiation among populations of the island fox (Urocyon littoralis). This species consists of 6 subspecies, each of which occupies a different California Channel Island. Analysis of 5293 SNP loci generated using Restriction-site Associated DNA (RAD) sequencing found support for genetic drift as the dominant evolutionary mechanism driving population divergence among island fox populations. In particular, populations had exceptionally low genetic variation, small Ne (range = 2.1–89.7; median = 19.4), and significant genetic signatures of bottlenecks. Moreover, islands with the lowest genetic variation (and, by inference, the strongest historical genetic drift) were most genetically differentiated from mainland gray foxes, and vice versa, indicating genetic drift drives genome-wide divergence. Nonetheless, outlier tests identified 3.6–6.6% of loci as high FST outliers, suggesting that despite strong genetic drift, divergent selection contributes to population divergence. Patterns of similarity among populations based on high FST outliers mirrored patterns based on morphology, providing additional evidence that outliers reflect adaptive divergence. Extremely low genetic variation and small Ne in some island fox populations, particularly on San Nicolas Island, suggest that they may be vulnerable to fixation of deleterious alleles, decreased fitness, and reduced adaptive potential. PMID:26992010

Adaptive divergence despite strong genetic drift: genomic analysis of the evolutionary mechanisms causing genetic differentiation in the island fox (Urocyon littoralis).

Science.gov (United States)

Funk, W Chris; Lovich, Robert E; Hohenlohe, Paul A; Hofman, Courtney A; Morrison, Scott A; Sillett, T Scott; Ghalambor, Cameron K; Maldonado, Jesus E; Rick, Torben C; Day, Mitch D; Polato, Nicholas R; Fitzpatrick, Sarah W; Coonan, Timothy J; Crooks, Kevin R; Dillon, Adam; Garcelon, David K; King, Julie L; Boser, Christina L; Gould, Nicholas; Andelt, William F

2016-05-01

The evolutionary mechanisms generating the tremendous biodiversity of islands have long fascinated evolutionary biologists. Genetic drift and divergent selection are predicted to be strong on islands and both could drive population divergence and speciation. Alternatively, strong genetic drift may preclude adaptation. We conducted a genomic analysis to test the roles of genetic drift and divergent selection in causing genetic differentiation among populations of the island fox (Urocyon littoralis). This species consists of six subspecies, each of which occupies a different California Channel Island. Analysis of 5293 SNP loci generated using Restriction-site Associated DNA (RAD) sequencing found support for genetic drift as the dominant evolutionary mechanism driving population divergence among island fox populations. In particular, populations had exceptionally low genetic variation, small Ne (range = 2.1-89.7; median = 19.4), and significant genetic signatures of bottlenecks. Moreover, islands with the lowest genetic variation (and, by inference, the strongest historical genetic drift) were most genetically differentiated from mainland grey foxes, and vice versa, indicating genetic drift drives genome-wide divergence. Nonetheless, outlier tests identified 3.6-6.6% of loci as high FST outliers, suggesting that despite strong genetic drift, divergent selection contributes to population divergence. Patterns of similarity among populations based on high FST outliers mirrored patterns based on morphology, providing additional evidence that outliers reflect adaptive divergence. Extremely low genetic variation and small Ne in some island fox populations, particularly on San Nicolas Island, suggest that they may be vulnerable to fixation of deleterious alleles, decreased fitness and reduced adaptive potential. © 2016 John Wiley & Sons Ltd.

Stability analysis on an economic epidemiological model with vaccination Pages : - , and.

Science.gov (United States)

Avusuglo, Wisdom S; Abdella, Kenzu; Feng, Wenying

2017-08-01

In this paper, an economic epidemiological model with vaccination is studied. The stability of the endemic steady-state is analyzed and some bifurcation properties of the system are investigated. It is established that the system exhibits saddle-point and period-doubling bifurcations when adult susceptible individuals are vaccinated. Furthermore, it is shown that susceptible individuals also have the tendency of opting for more number of contacts even if the vaccine is inefficacious and thus causes the disease endemic to increase in the long run. Results from sensitivity analysis with specific disease parameters are also presented. Finally, it is shown that the qualitative behaviour of the system is affected by contact levels.

Population Genetic Analysis of Theileria annulata from Six Geographical Regions in China, Determined on the Basis of Micro- and Mini-satellite Markers.

Science.gov (United States)

Yin, Fangyuan; Liu, Zhijie; Liu, Junlong; Liu, Aihong; Salih, Diaeldin A; Li, Youquan; Liu, Guangyuan; Luo, Jianxun; Guan, Guiquan; Yin, Hong

2018-01-01

Theileria annulata , a tick-borne apicomplexan protozoan, causes a lymphoproliferative disease of cattle with high prevalence in tropical and sub-tropical regions. Understanding the genetic diversity and structure of local populations will provide more fundamental knowledge for the population genetics and epidemics of protozoa. In this study, 78 samples of T. annulata collected from cattle/yaks representing 6 different geographic populations in China were genotyped using eight micro- and mini-satellite markers. High genetic variation within population, moderate genetic differentiation, and high level of diversity co-occurring with significant linkage disequilibrium were observed, which indicates there is gene flow between these populations in spite of the existence of reproductive and geographical barriers among populations. Furthermore, some degree of genetic differentiation was also found between samples from China and Oman. These findings provide a first glimpse of the genetic diversity of the T. annulata populations in China, and might contribute to the knowledge of distribution, dynamics, and epidemiology of T. annulata populations and optimize the management strategies for control.

Genetic epidemiology of coronary artery disease: an Asian Indian ...

Indian Academy of Sciences (India)

Coronary artery disease (CAD) has emerged as a major cause of morbidity and mortality worldwide. Recent findings on the role of genetic factors in the aetiopathology of CAD have implicated novel genes and variants in addition to those involved in lipid and lipoprotein metabolism. However, our present knowledge is ...

[THE EPIZOOTIC AND EPIDEMIC ACTIVITY OF NATURAL TULAREMIA FOCI OF DIFFERENT LANDSCAPE EPIDEMIOLOGICAL TYPES IN 2009-2014].

Science.gov (United States)

Meshcheryakova, I S; Mikhailova, T V; Demidova, T N; Kormilitsyna, M I

2016-01-01

to assess the present state of the natural tularemia foci of different landscape epidemiological types, by using individual focal areas as an example. Epizootological monitoring and epidemiological analysis were conducted in the areas of natural tularemia foci of tundra (Wrangel Island), meadow-field (Central Federal District of the Russian Federation), flood-swamp (Arkhangelsk Region, Khanty-Mansi Autonomous District), and steppe (Mongolii) types. Small mammals (organs, blood), tularemia patients' sera, and environniental objects were examined. Molecular genetic and immune serological diagnostic assays were used. The incidence of tularemia in the past decade was analyzed using the maps for the epidemiological examinations of tularemia cases and medical reports. The natural foci of tularemia were established to continue to actively operate. There were 2913 cases of tularemia in the Russian Federation in 2001 to 2014. The flood-swamp natural foci, in which there were summer transmissive tularemia outbreaks, the largest of high occurred in Khanti-Mansiysk in 2013 when a total of 1005 people fell ill, are a special epidemic hazard. Analysis of the tularemia outbreaks suggests that there is a need for continuous epizootological monitoring of the areas of natural tularemia foci for the timely prediction and prevention of epidemic complications. It is noted that there is an unfounded reduction in the scope of preventive measures, and immunoprevention in particular, and a weaker control of the antitularemia immune status in the population residing in the area of active natural foci of tularemia.

Pauci- and Multibacillary Leprosy: Two Distinct, Genetically Neglected Diseases

Science.gov (United States)

Gaschignard, Jean; Grant, Audrey Virginia; Thuc, Nguyen Van; Orlova, Marianna; Cobat, Aurélie; Huong, Nguyen Thu; Ba, Nguyen Ngoc; Thai, Vu Hong; Abel, Laurent; Schurr, Erwin; Alcaïs, Alexandre

2016-01-01

After sustained exposure to Mycobacterium leprae, only a subset of exposed individuals develops clinical leprosy. Moreover, leprosy patients show a wide spectrum of clinical manifestations that extend from the paucibacillary (PB) to the multibacillary (MB) form of the disease. This “polarization” of leprosy has long been a major focus of investigation for immunologists because of the different immune response in these two forms. But while leprosy per se has been shown to be under tight human genetic control, few epidemiological or genetic studies have focused on leprosy subtypes. Using PubMed, we collected available data in English on the epidemiology of leprosy polarization and the possible role of human genetics in its pathophysiology until September 2015. At the genetic level, we assembled a list of 28 genes from the literature that are associated with leprosy subtypes or implicated in the polarization process. Our bibliographical search revealed that improved study designs are needed to identify genes associated with leprosy polarization. Future investigations should not be restricted to a subanalysis of leprosy per se studies but should instead contrast MB to PB individuals. We show the latter approach to be the most powerful design for the identification of genetic polarization determinants. Finally, we bring to light the important resource represented by the nine-banded armadillo model, a unique animal model for leprosy. PMID:27219008

Stroke genetics: prospects for personalized medicine

Directory of Open Access Journals (Sweden)

Markus Hugh S

2012-09-01

Full Text Available Abstract Epidemiologic evidence supports a genetic predisposition to stroke. Recent advances, primarily using the genome-wide association study approach, are transforming what we know about the genetics of multifactorial stroke, and are identifying novel stroke genes. The current findings are consistent with different stroke subtypes having different genetic architecture. These discoveries may identify novel pathways involved in stroke pathogenesis, and suggest new treatment approaches. However, the already identified genetic variants explain only a small proportion of overall stroke risk, and therefore are not currently useful in predicting risk for the individual patient. Such risk prediction may become a reality as identification of a greater number of stroke risk variants that explain the majority of genetic risk proceeds, and perhaps when information on rare variants, identified by whole-genome sequencing, is also incorporated into risk algorithms. Pharmacogenomics may offer the potential for earlier implementation of 'personalized genetic' medicine. Genetic variants affecting clopidogrel and warfarin metabolism may identify non-responders and reduce side-effects, but these approaches have not yet been widely adopted in clinical practice.

Genetic and environmental factors in experimental and human cancer

Energy Technology Data Exchange (ETDEWEB)

Takayama, S.; Takebe, H.; Gelboin, H.V.; MaChahon, B.; Matsushima, T.; Sugimura, T.

1980-01-01

Recently technological advances in assaying mutagenic principles have revealed that there are many mutagens in the environment, some of which might be carcinogenic to human beings. Other advances in genetics have shown that genetic factors might play an important role in the induction of cancer in human beings, e.g., the high incidence of skin cancers in patients with xeroderma pigmentosum. These proceedings deal with the relationships between genetic and environmental factors in carcinogenesis. The contributors cover mixed-function oxidases, pharmacogenetics, twin studies, DNA repair, immunology, and epidemiology.

A novel genetic tool for clonal analysis of fourth chromosome mutations

OpenAIRE

Sousa-Neves, Rui; Schinaman, Joseph M.

2012-01-01

The fourth chromosome of Drosophila remains one of the most intractable regions of the fly genome to genetic analysis. The main difficulty posed to the genetic analyses of mutations on this chromosome arises from the fact that it does not undergo meiotic recombination, which makes recombination mapping impossible, and also prevents clonal analysis of mutations, a technique which relies on recombination to introduce the prerequisite recessive markers and FLP-recombinase recognition targets (FR...

Analysis of genetic polymorphism of nine short tandem repeat loci in ...

African Journals Online (AJOL)

Yomi

2012-03-15

Mar 15, 2012 ... Key words: short tandem repeat, repeat motif, genetic polymorphism, Han population, forensic genetics. INTRODUCTION. Short tandem repeat (STR) is widely .... Data analysis. The exact test of Hardy-Weinberg equilibrium was conducted with. Arlequin version 3.5 software (Computational and Molecular.

Genetic Code Analysis Toolkit: A novel tool to explore the coding properties of the genetic code and DNA sequences

Science.gov (United States)

Kraljić, K.; Strüngmann, L.; Fimmel, E.; Gumbel, M.

2018-01-01

The genetic code is degenerated and it is assumed that redundancy provides error detection and correction mechanisms in the translation process. However, the biological meaning of the code's structure is still under current research. This paper presents a Genetic Code Analysis Toolkit (GCAT) which provides workflows and algorithms for the analysis of the structure of nucleotide sequences. In particular, sets or sequences of codons can be transformed and tested for circularity, comma-freeness, dichotomic partitions and others. GCAT comes with a fertile editor custom-built to work with the genetic code and a batch mode for multi-sequence processing. With the ability to read FASTA files or load sequences from GenBank, the tool can be used for the mathematical and statistical analysis of existing sequence data. GCAT is Java-based and provides a plug-in concept for extensibility. Availability: Open source Homepage:http://www.gcat.bio/

Human T-cell Lymphotropic Virus types I and II (HTLV-I/II in French Guiana: clinical and molecular epidemiology

Directory of Open Access Journals (Sweden)

Kazanji Mirdad

2003-01-01

Full Text Available We review here the epidemiological studies performed by our group on human retrovirus HTLV-I and HTLV-II infections and the associated diseases in French Guiana since 1984. French Guiana is an overseas French administrative district located between Brazil and Surinam. Its population is characterized by a large variety of ethnic groups, including several populations of African origin and various populations of Amerindian origin. Several epidemiological studies of large samples of pregnant women and in remote villages showed that HTLV-I is highly endemic in this area but is restricted to groups of African origin, especially the Noir-Marrons. In this endemic population, the results of segregation analysis in a genetic epidemiological study were consistent with the presence of a dominant major gene predisposing to HTLV-I infection, especially in children. In contrast, HTLV-II infection appears to be rare in French Guiana, having been found in only a few individuals of Brazilian origin. From a molecular point of view, the HTLV-I strains present in the Noir-Marrons, Creoles and Amerindians appear to originate from Africa, as they belong to the large cosmopolitan molecular subtype A.

mec-associated dru typing in the epidemiological analysis of ST239 MRSA in Malaysia.

Science.gov (United States)

Ghaznavi-Rad, E; Goering, R V; Nor Shamsudin, M; Weng, P L; Sekawi, Z; Tavakol, M; van Belkum, A; Neela, V

2011-11-01

The usefulness of mec-associated dru typing in the epidemiological analysis of methicillin-resistant Staphylococcus aureus (MRSA) isolated in Malaysia was investigated and compared with pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), and spa and SCCmec typing. The isolates studied included all MRSA types in Malaysia. Multilocus sequence type ST188 and ST1 isolates were highly clonal by all typing methods. However, the dru typing of ST239 isolates produced the clearest discrimination between SCCmec IIIa and III isolates, yielding more subtypes than any other method. Evaluation of the discriminatory power for each method identified dru typing and PFGE as the most discriminatory, with Simpson's index of diversity (SID) values over 89%, including an isolate which was non-typeable by spa, but dru-typed as dt13j. The discriminatory ability of dru typing, especially with closely related MRSA ST239 strains (e.g., Brazilian and Hungarian), underscores its utility as a tool for the epidemiological investigation of MRSA.

Logic analysis and verification of n-input genetic logic circuits

DEFF Research Database (Denmark)

Baig, Hasan; Madsen, Jan

2017-01-01

. In this paper, we present an approach to analyze and verify the Boolean logic of a genetic circuit from the data obtained through stochastic analog circuit simulations. The usefulness of this analysis is demonstrated through different case studies illustrating how our approach can be used to verify the expected......Nature is using genetic logic circuits to regulate the fundamental processes of life. These genetic logic circuits are triggered by a combination of external signals, such as chemicals, proteins, light and temperature, to emit signals to control other gene expressions or metabolic pathways...... accordingly. As compared to electronic circuits, genetic circuits exhibit stochastic behavior and do not always behave as intended. Therefore, there is a growing interest in being able to analyze and verify the logical behavior of a genetic circuit model, prior to its physical implementation in a laboratory...

Analysis and design of a genetic circuit for dynamic metabolic engineering.

Science.gov (United States)

Anesiadis, Nikolaos; Kobayashi, Hideki; Cluett, William R; Mahadevan, Radhakrishnan

2013-08-16

Recent advances in synthetic biology have equipped us with new tools for bioprocess optimization at the genetic level. Previously, we have presented an integrated in silico design for the dynamic control of gene expression based on a density-sensing unit and a genetic toggle switch. In the present paper, analysis of a serine-producing Escherichia coli mutant shows that an instantaneous ON-OFF switch leads to a maximum theoretical productivity improvement of 29.6% compared to the mutant. To further the design, global sensitivity analysis is applied here to a mathematical model of serine production in E. coli coupled with a genetic circuit. The model of the quorum sensing and the toggle switch involves 13 parameters of which 3 are identified as having a significant effect on serine concentration. Simulations conducted in this reduced parameter space further identified the optimal ranges for these 3 key parameters to achieve productivity values close to the maximum theoretical values. This analysis can now be used to guide the experimental implementation of a dynamic metabolic engineering strategy and reduce the time required to design the genetic circuit components.

[Analytical procedure of variable number of tandem repeats (VNTR) analysis and effective use of analysis results for tuberculosis control].

Science.gov (United States)

Hachisu, Yushi; Hashimoto, Ruiko; Kishida, Kazunori; Yokoyama, Eiji

2013-12-01

Variable number of tandem repeats (VNTR) analysis is one of the methods for molecular epidemiological studies of Mycobacterium tuberculosis. VNTR analysis is a method based on PCR, provides rapid highly reproducible results and higher strain discrimination power than the restriction fragment length polymorphism (RFLP) analysis widely used in molecular epidemiological studies of Mycobacterium tuberculosis. Genetic lineage compositions of Mycobacterium tuberculosis clinical isolates differ among the regions from where they are isolated, and allelic diversity at each locus also differs among the genetic lineages of Mycobacterium tuberculosis. Therefore, the combination of VNTR loci that can provide high discrimination capacity for analysis is not common in every region. The Japan Anti-Tuberculosis Association (JATA) 12 (15) reported a standard combination of VNTR loci for analysis in Japan, and the combination with hypervariable (HV) loci added to JATA12 (15), which has very high discrimination capacity, was also reported. From these reports, it is thought that data sharing between institutions and construction of a nationwide database will progress from now on. Using database construction of VNTR profiles, VNTR analysis has become an effective tool to trace the route of tuberculosis infection, and also helps in decision-making in the treatment course. However, in order to utilize the results of VNTR analysis effectively, it is important that each related organization cooperates closely, and analysis should be appropriately applied in the system in which accurate control and private information protection are ensured.

Landscape Epidemiology of Tularemia Outbreaks in Sweden

Science.gov (United States)

Svensson, Kerstin; Bäck, Erik; Eliasson, Henrik; Berglund, Lennart; Granberg, Malin; Karlsson, Linda; Larsson, Pär; Forsman, Mats

2009-01-01

Summer outbreaks of tularemia that occurred from 1995 through 2005 in 2 locations in Sweden affected 441 persons. We performed an epidemiologic investigation of these outbreaks using a novel strategy, involving high-resolution genotyping of Francisella tularensis isolates obtained from 136 patients (using 18 genetic markers developed from 6 F. tularensis genome sequences) and interviews with the patients. Strong spatial associations were found between F. tularensis subpopulations and the places of disease transmission; infection by some subpopulations occurred within areas as small as 2 km2, indicating unidentified environmental point sources of tularemia. In both locations, disease clusters were associated with recreational areas beside water, and genetic subpopulations were present throughout the tularemia season and persisted over years. High-resolution genotyping in combination with patients’ statements about geographic places of disease transmission provided valuable indications of likely sources of infection and the causal genotypes during these tularemia outbreaks. PMID:19961673

Safety of natural radiation exposure. A meta-analysis of epidemiological studies on natural radiation

International Nuclear Information System (INIS)

Osaki, S.

2000-01-01

. Furthermore, the combine of these studies, a meta-analysis, is expected to decrease the confidence limit and to countervail the confounding factors. This study reviewed the epidemiological studies on natural radiation exposure and tried to combine their results to prove the safety of natural radiation exposure. (author)

Chondrosarcoma of the Osseous Spine: An Analysis of Epidemiology, Patient Outcomes, and Prognostic Factors Using the SEER Registry From 1973 to 2012.

Science.gov (United States)

Arshi, Armin; Sharim, Justin; Park, Don Y; Park, Howard Y; Bernthal, Nicholas M; Yazdanshenas, Hamed; Shamie, Arya N

2017-05-01

Retrospective analysis. To determine the epidemiology and prognostic indicators in patients with chondrosarcoma of the osseous spine. Chondrosarcoma of the spine is rare, with limited data on its epidemiology, clinicopathologic features, and treatment outcomes. Therapy centers on complete en bloc resection with radiotherapy reserved for subtotal resection or advanced disease. The Surveillance, Epidemiology, and End Results Registry was queried for patients with chondrosarcoma of the osseous spine from 1973 to 2012. Study variables included age, sex, race, year of diagnosis, size, grade, extent of disease, and treatment modality. The search identified 973 cases of spinal chondrosarcoma. Mean age at diagnosis was 51.6 years, and 627% of patients were males. Surgical resection and radiotherapy were performed in 75.2% and 21.3% of cases, respectively. Kaplan-Meier analysis demonstrated overall survival (OS) and disease-specific survival (DSS) of 53% and 64%, respectively, at 5 years. Multivariate Cox regression analysis showed that age (OS, P chondrosarcoma of the spine independent of extent of disease. Radiotherapy improves survival in patients with metastatic disease and worsens outcomes in patients with confined and locally invasive disease. 4.

Population genetic analysis and trichothecene profiling of Fusarium graminearum from wheat in Uruguay.

Science.gov (United States)

Pan, D; Mionetto, A; Calero, N; Reynoso, M M; Torres, A; Bettucci, L

2016-03-11

Fusarium graminearum sensu stricto (F. graminearum s.s.) is the major causal agent of Fusarium head blight of wheat worldwide, and contaminates grains with trichothecene mycotoxins that cause serious threats to food safety and animal health. An important aspect of managing this pathogen and reducing mycotoxin contamination of wheat is knowledge regarding its population genetics. Therefore, isolates of F. graminearum s.s. from the major wheat-growing region of Uruguay were analyzed by amplified fragment length polymorphism assays, PCR genotyping, and chemical analysis of trichothecene production. Of the 102 isolates identified as having the 15-ADON genotype via PCR genotyping, all were DON producers, but only 41 strains were also 15-ADON producers, as determined by chemical analysis. The populations were genotypically diverse but genetically similar, with significant genetic exchange occurring between them. Analysis of molecular variance indicated that most of the genetic variability resulted from differences between isolates within populations. Multilocus linkage disequilibrium analysis suggested that the isolates had a panmictic population genetic structure and that there is significant recombination occurs in F. graminearum s.s. In conclusion, tour findings provide the first detailed description of the genetic structure and trichothecene production of populations of F. graminearum s.s. from Uruguay, and expands our understanding of the agroecology of F. graminearum and of the correlation between genotypes and trichothecene chemotypes.

Epidemiology of fibromyalgia.

Science.gov (United States)

Neumann, Lily; Buskila, Dan

2003-10-01

Chronic widespread pain, the cardinal symptom of fibromyalgia (FM), is common in the general population, with comparable prevalence rates of 7.3% to 12.9% across different countries. The prevalence of FM in the general population was reported to range from 0.5% to 5% and up to 15.7% in the clinic. The common association of FM with other rheumatic disorders, chronic viral infections, and systemic illnesses has been well documented in several studies. Up to 65% of patients with systemic lupus erythematosus meet the criteria for FM. FM is considered a member of the family of functional somatic syndromes. These syndromes are very common and share a similar phenomenology, epidemiologic characteristics, high rates of occurrence, a common pathogenesis, and similar management strategies. A high prevalence of FM was demonstrated among relatives of patients with FM and it may be attributed to genetic and environmental factors.

[Occupational epidemiology: some methodological considerations].

Science.gov (United States)

Alvear-Galindo, María Guadalupe; del Pilar Paz-Román, María

2006-01-01

During the last decade, occupational epidemiology has gained a great importance, not only because of the increase of pollutants and their noxiousness, but also because it has gone from the descriptive to the analytic level. The purpose of this work is to present what has been reported on epidemiological studies, different ways of characterizing and measuring occupational exposure, by emphasizing slants of exposure and selection measurement. In the reviewed studies, an interest in improving the exposure evaluation has been shown. The mainly reported measurement slants are the ways of measuring and classifying the exposure. The main designs were transversal with the use of matrixes to improve the evaluation of exposure. Conditions of hygiene and security were considered in order to control the quality of the information. This information was analyzed with different criteria. Some of the elements that hinder the research on occupational epidemiology are a mixed exposure, small populations, lack of exposure data, low levels of exposure and long periods of illness latency. Some breakthroughs in the strategies of epidemiological analysis and some other areas of knowledge have made possible a better understanding of work and health conditions of workers.

Shared genetic contribution to ischemic stroke and Alzheimer's disease

Science.gov (United States)

Adib‐Samii, Poneh; Harold, Denise; Dichgans, Martin; Williams, Julie; Lewis, Cathryn M.; Markus, Hugh S.; Fornage, Myriam; Holliday, Elizabeth G; Sharma, Pankaj; Bis, Joshua C; Psaty, Bruce M; Seshadri, Sudha; Nalls, Mike A; Devan, William J; Boncoraglio, Giorgio; Malik, Rainer; Mitchell, Braxton D; Kittner, Steven J; Ikram, M Arfan; Clarke, Robert; Rosand, Jonathan; Meschia, James F; Sudlow, Cathie; Rothwell, Peter M; Levi, Christopher; Bevan, Steve; Kilarski, Laura L; Walters, Matthew; Thijs, Vincent; Slowik, Agnieszka; Lindgren, Arne; de Bakker, Paul I W; Lambert, Jean‐Charles; Ibrahim‐Verbaas, Carla A; Harold, Denise; Naj, Adam C; Sims, Rebecca; Bellenguez, Céline; Jun, Gyungah; DeStefano, Anita L; Bis, Joshua C; Beecham, Gary W; Grenier‐Boley, Benjamin; Russo, Giancarlo; Thornton‐Wells, Tricia A; Jones, Nicola; Smith, Albert V; Chouraki, Vincent; Thomas, Charlene; Ikram, M Arfan; Zelenika, Diana; Vardarajan, Badri N; Kamatani, Yoichiro; Lin, Chiao‐Feng; Gerrish, Amy; Schmidt, Helena; Kunkle, Brian; Dunstan, Melanie L; Ruiz, Agustin; Bihoreau, Marie‐Thçrèse; Choi, Seung‐Hoan; Reitz, Christiane; Pasquier, Florence; Hollingworth, Paul; Ramirez, Alfredo; Hanon, Olivier; Fitzpatrick, Annette L; Buxbaum, Joseph D; Campion, Dominique; Crane, Paul K; Baldwin, Clinton; Becker, Tim; Gudnason, Vilmundur; Cruchaga, Carlos; Craig, David; Amin, Najaf; Berr, Claudine; Lopez, Oscar L; De Jager, Philip L; Deramecourt, Vincent; Johnston, Janet A; Evans, Denis; Lovestone, Simon; Letenneur, Luc; Morón, Francisco J; Rubinsztein, David C; Eiriksdottir, Gudny; Sleegers, Kristel; Goate, Alison M; Fiçvet, Nathalie; Huentelman, Matthew J; Gill, Michael; Brown, Kristelle; Kamboh, M Ilyas; Keller, Lina; Barberger‐Gateau, Pascale; McGuinness, Bernadette; Larson, Eric B; Green, Robert; Myers, Amanda J; Dufouil, Carole; Todd, Stephen; Wallon, David; Love, Seth; Rogaeva, Ekaterina; Gallacher, John; St George‐Hyslop, Peter; Clarimon, Jordi; Lleo, Alberto; Bayer, Anthony; Tsuang, Debby W; Yu, Lei; Tsolaki, Magda; Bossù, Paola; Spalletta, Gianfranco; Proitsi, Petroula; Collinge, John; Sorbi, Sandro; Sanchez‐Garcia, Florentino; Fox, Nick C; Hardy, John; Deniz Naranjo, Maria Candida; Bosco, Paolo; Clarke, Robert; Brayne, Carol; Galimberti, Daniela; Mancuso, Michelangelo; Matthews, Fiona; Moebus, Susanne; Mecocci, Patrizia; Del Zompo, Maria; Maier, Wolfgang; Hampel, Harald; Pilotto, Alberto; Bullido, Maria; Panza, Francesco; Caffarra, Paolo; Nacmias, Benedetta; Gilbert, John R; Mayhaus, Manuel; Lannfelt, Lars; Hakonarson, Hakon; Pichler, Sabrina; Carrasquillo, Minerva M; Ingelsson, Martin; Beekly, Duane; Alvarez, Victoria; Zou, Fanggeng; Valladares, Otto; Younkin, Steven G; Coto, Eliecer; Hamilton‐Nelson, Kara L; Gu, Wei; Razquin, Cristina; Pastor, Pau; Mateo, Ignacio; Owen, Michael J; Faber, Kelley M; Jonsson, Palmi V; Combarros, Onofre; O'Donovan, Michael C; Cantwell, Laura B; Soininen, Hilkka; Blacker, Deborah; Mead, Simon; Mosley, Thomas H; Bennett, David A; Harris, Tamara B; Fratiglioni, Laura; Holmes, Clive; de Bruijn, Renee F A G; Passmore, Peter; Montine, Thomas J; Bettens, Karolien; Rotter, Jerome I; Brice, Alexis; Morgan, Kevin; Foroud, Tatiana M; Kukull, Walter A; Hannequin, Didier; Powell, John F; Nalls, Michael A; Ritchie, Karen; Lunetta, Kathryn L; Kauwe, John S K; Boerwinkle, Eric; Riemenschneider, Matthias; Boada, Mercè; Hiltunen, Mikko; Martin, Eden R; Schmidt, Reinhold; Rujescu, Dan; Wang, Li‐San; Dartigues, Jean‐François; Mayeux, Richard; Tzourio, Christophe; Hofman, Albert; Nöthen, Markus M; Graff, Caroline; Psaty, Bruce M; Jones, Lesley; Haines, Jonathan L; Holmans, Peter A; Lathrop, Mark; Pericak‐Vance, Margaret A; Launer, Lenore J; Farrer, Lindsay A; van Duijn, Cornelia M; Van Broeckhoven, Christine; Moskvina, Valentina; Seshadri, Sudha; Williams, Julie; Schellenberg, Gerard D; Amouyel, Philippe

2016-01-01

Objective Increasing evidence suggests epidemiological and pathological links between Alzheimer's disease (AD) and ischemic stroke (IS). We investigated the evidence that shared genetic factors underpin the two diseases. Methods Using genome‐wide association study (GWAS) data from METASTROKE + (15,916 IS cases and 68,826 controls) and the International Genomics of Alzheimer's Project (IGAP; 17,008 AD cases and 37,154 controls), we evaluated known associations with AD and IS. On the subset of data for which we could obtain compatible genotype‐level data (4,610 IS cases, 1,281 AD cases, and 14,320 controls), we estimated the genome‐wide genetic correlation (rG) between AD and IS, and the three subtypes (cardioembolic, small vessel, and large vessel), using genome‐wide single‐nucleotide polymorphism (SNP) data. We then performed a meta‐analysis and pathway analysis in the combined AD and small vessel stroke data sets to identify the SNPs and molecular pathways through which disease risk may be conferred. Results We found evidence of a shared genetic contribution between AD and small vessel stroke (rG [standard error] = 0.37 [0.17]; p = 0.011). Conversely, there was no evidence to support shared genetic factors in AD and IS overall or with the other stroke subtypes. Of the known GWAS associations with IS or AD, none reached significance for association with the other trait (or stroke subtypes). A meta‐analysis of AD IGAP and METASTROKE + small vessel stroke GWAS data highlighted a region (ATP5H/KCTD2/ICT1) associated with both diseases (p = 1.8 × 10−8). A pathway analysis identified four associated pathways involving cholesterol transport and immune response. Interpretation Our findings indicate shared genetic susceptibility to AD and small vessel stroke and highlight potential causal pathways and loci. Ann Neurol 2016;79:739–747 PMID:26913989

Common Genetic Variants Found in HLA and KIR Immune Genes in Autism Spectrum Disorder

OpenAIRE

Torres, Anthony R.; Sweeten, Thayne L.; Johnson, Randall C.; Odell, Dennis; Westover, Jonna B.; Bray-Ward, Patricia; Ward, David C.; Davies, Christopher J.; Thomas, Aaron J.; Croen, Lisa A.; Benson, Michael

2016-01-01

The common variant - common disease hypothesis was proposed to explain diseases with strong inheritance. This model suggests that a genetic disease is the result of the combination of several common genetic variants. Common genetic variants are described as a 5% frequency differential between diseased versus matched control populations. This theory was recently supported by an epidemiology paper stating that about 50% of genetic risk for autism resides in common variants. However, rare va...

Genetic Diversity of Rose germplasm based on RAPD analysis

African Journals Online (AJOL)

AHSAN IQBAL

2012-06-12

Jun 12, 2012 ... identification and analysis of genetic variation within a collection of 4 species and 30 accessions of rose using RAPD analysis technique. The results showed the molecular distinctions among the ... that range in colour from white and yellow to many shades of pink and red have been developed. Since.

Insights to genetic characterization tools for epidemiological tracking of Francisella tularensis in Sweden.

Directory of Open Access Journals (Sweden)

Tara Wahab

Full Text Available Tularaemia, caused by the bacterium Francisella tularensis, is endemic in Sweden and is poorly understood. The aim of this study was to evaluate the effectiveness of three different genetic typing systems to link a genetic type to the source and place of tularemia infection in Sweden. Canonical single nucleotide polymorphisms (canSNPs, MLVA including five variable number of tandem repeat loci and PmeI-PFGE were tested on 127 F. tularensis positive specimens collected from Swedish case-patients. All three typing methods identified two major genetic groups with near-perfect agreement. Higher genetic resolution was obtained with canSNP and MLVA compared to PFGE; F. tularensis samples were first assigned into ten phylogroups based on canSNPs followed by 33 unique MLVA types. Phylogroups were geographically analysed to reveal complex phylogeographic patterns in Sweden. The extensive phylogenetic diversity found within individual counties posed a challenge to linking specific genetic types with specific geographic locations. Despite this, a single phylogroup (B.22, defined by a SNP marker specific to a lone Swedish sequenced strain, did link genetic type with a likely geographic place. This result suggests that SNP markers, highly specific to a particular reference genome, may be found most frequently among samples recovered from the same location where the reference genome originated. This insight compels us to consider whole-genome sequencing (WGS as the appropriate tool for effectively linking specific genetic type to geography. Comparing the WGS of an unknown sample to WGS databases of archived Swedish strains maximizes the likelihood of revealing those rare geographically informative SNPs.

Multicollinearity in Regression Analyses Conducted in Epidemiologic Studies.

Science.gov (United States)

Vatcheva, Kristina P; Lee, MinJae; McCormick, Joseph B; Rahbar, Mohammad H

2016-04-01

The adverse impact of ignoring multicollinearity on findings and data interpretation in regression analysis is very well documented in the statistical literature. The failure to identify and report multicollinearity could result in misleading interpretations of the results. A review of epidemiological literature in PubMed from January 2004 to December 2013, illustrated the need for a greater attention to identifying and minimizing the effect of multicollinearity in analysis of data from epidemiologic studies. We used simulated datasets and real life data from the Cameron County Hispanic Cohort to demonstrate the adverse effects of multicollinearity in the regression analysis and encourage researchers to consider the diagnostic for multicollinearity as one of the steps in regression analysis.

An evidence-based analysis of epidemiologic associations between lymphatic and hematopoietic cancers and occupational exposure to gasoline.

Science.gov (United States)

Keenan, J J; Gaffney, S; Gross, S A; Ronk, C J; Paustenbach, D J; Galbraith, D; Kerger, B D

2013-10-01

The presence of benzene in motor gasoline has been a health concern for potential increased risk of acute myelogenous leukemia and perhaps other lymphatic/hematopoietic cancers for approximately 40 years. Because of the widespread and increasing use of gasoline by consumers and the high exposure potential of occupational cohorts, a thorough understanding of this issue is important. The current study utilizes an evidence-based approach to examine whether or not the available epidemiologic studies demonstrate a strong and consistent association between occupational exposure to gasoline and lymphatic/hematopoietic cancers. Among 67 epidemiologic studies initially identified, 54 were ranked according to specific criteria relating to the relevance and robustness of each study for answering the research question. The 30 highest-ranked studies were sorted into three tiers of evidence and were analyzed for strength, specificity, consistency, temporality, dose-response trends and coherence. Meta statistics were also calculated for each general and specific lymphatic/hematopoietic cancer category with adequate data. The evidence-based analysis did not confirm any strong and consistent association between occupational exposure to gasoline and lymphatic/hematopoietic cancers based on the epidemiologic studies available to date. These epidemiologic findings, combined with the evidence showing relatively low occupational benzene vapor exposures associated with gasoline formulations during the last three decades, suggest that current motor gasoline formulations are not associated with increased lymphatic/hematopoietic cancer risks related to benzene.

A genetic epidemiology approach to cyber-security.

Science.gov (United States)

Gil, Santiago; Kott, Alexander; Barabási, Albert-László

2014-07-16

While much attention has been paid to the vulnerability of computer networks to node and link failure, there is limited systematic understanding of the factors that determine the likelihood that a node (computer) is compromised. We therefore collect threat log data in a university network to study the patterns of threat activity for individual hosts. We relate this information to the properties of each host as observed through network-wide scans, establishing associations between the network services a host is running and the kinds of threats to which it is susceptible. We propose a methodology to associate services to threats inspired by the tools used in genetics to identify statistical associations between mutations and diseases. The proposed approach allows us to determine probabilities of infection directly from observation, offering an automated high-throughput strategy to develop comprehensive metrics for cyber-security.

Methodological exploratory study applied to occupational epidemiology

Energy Technology Data Exchange (ETDEWEB)

Carneiro, Janete C.G. Gaburo; Vasques, MOnica Heloisa B.; Fontinele, Ricardo S.; Sordi, Gian Maria A. [Instituto de Pesquisas Energeticas e Nucleares (IPEN/CNEN-SP), Sao Paulo, SP (Brazil)]. E-mail: janetegc@ipen.br

2007-07-01

The utilization of epidemiologic methods and techniques has been object of practical experimentation and theoretical-methodological reflection in health planning and programming process. Occupational Epidemiology is the study of the causes and prevention of diseases and injuries from exposition and risks in the work environment. In this context, there is no intention to deplete such a complex theme but to deal with basic concepts of Occupational Epidemiology, presenting the main characteristics of the analysis methods used in epidemiology, as investigate the possible determinants of exposition (chemical, physical and biological agents). For this study, the social-demographic profile of the IPEN-CNEN/SP work force was used. The knowledge of this reference population composition is based on sex, age, educational level, marital status and different occupations, aiming to know the relation between the health aggravating factors and these variables. The methodology used refers to a non-experimental research based on a theoretical methodological practice. The work performed has an exploratory character, aiming a later survey of indicators in the health area in order to analyze possible correlations related to epidemiologic issues. (author)

Methodological exploratory study applied to occupational epidemiology

International Nuclear Information System (INIS)

Carneiro, Janete C.G. Gaburo; Vasques, MOnica Heloisa B.; Fontinele, Ricardo S.; Sordi, Gian Maria A.

2007-01-01

The utilization of epidemiologic methods and techniques has been object of practical experimentation and theoretical-methodological reflection in health planning and programming process. Occupational Epidemiology is the study of the causes and prevention of diseases and injuries from exposition and risks in the work environment. In this context, there is no intention to deplete such a complex theme but to deal with basic concepts of Occupational Epidemiology, presenting the main characteristics of the analysis methods used in epidemiology, as investigate the possible determinants of exposition (chemical, physical and biological agents). For this study, the social-demographic profile of the IPEN-CNEN/SP work force was used. The knowledge of this reference population composition is based on sex, age, educational level, marital status and different occupations, aiming to know the relation between the health aggravating factors and these variables. The methodology used refers to a non-experimental research based on a theoretical methodological practice. The work performed has an exploratory character, aiming a later survey of indicators in the health area in order to analyze possible correlations related to epidemiologic issues. (author)

The Co-Occurrence of Reading Disorder and ADHD: Epidemiology, Treatment, Psychosocial Impact, and Economic Burden

Science.gov (United States)

Sexton, Chris C.; Gelhorn, Heather L.; Bell, Jill A.; Classi, Peter M.

2012-01-01

The co-occurrence of reading disorder (RD) and attention-deficit/hyperactivity disorder (ADHD) has received increasing attention. This review summarizes the epidemiology, treatment strategies, psychosocial impact, and economic burden associated with the co-occurrence of these conditions. Common genetic and neuropsychological deficits may partially…

Causal diagrams in systems epidemiology

Directory of Open Access Journals (Sweden)

Joffe Michael

2012-03-01

Full Text Available Abstract Methods of diagrammatic modelling have been greatly developed in the past two decades. Outside the context of infectious diseases, systematic use of diagrams in epidemiology has been mainly confined to the analysis of a single link: that between a disease outcome and its proximal determinant(s. Transmitted causes ("causes of causes" tend not to be systematically analysed. The infectious disease epidemiology modelling tradition models the human population in its environment, typically with the exposure-health relationship and the determinants of exposure being considered at individual and group/ecological levels, respectively. Some properties of the resulting systems are quite general, and are seen in unrelated contexts such as biochemical pathways. Confining analysis to a single link misses the opportunity to discover such properties. The structure of a causal diagram is derived from knowledge about how the world works, as well as from statistical evidence. A single diagram can be used to characterise a whole research area, not just a single analysis - although this depends on the degree of consistency of the causal relationships between different populations - and can therefore be used to integrate multiple datasets. Additional advantages of system-wide models include: the use of instrumental variables - now emerging as an important technique in epidemiology in the context of mendelian randomisation, but under-used in the exploitation of "natural experiments"; the explicit use of change models, which have advantages with respect to inferring causation; and in the detection and elucidation of feedback.

Causal diagrams in systems epidemiology.

Science.gov (United States)

Joffe, Michael; Gambhir, Manoj; Chadeau-Hyam, Marc; Vineis, Paolo

2012-03-19

Methods of diagrammatic modelling have been greatly developed in the past two decades. Outside the context of infectious diseases, systematic use of diagrams in epidemiology has been mainly confined to the analysis of a single link: that between a disease outcome and its proximal determinant(s). Transmitted causes ("causes of causes") tend not to be systematically analysed.The infectious disease epidemiology modelling tradition models the human population in its environment, typically with the exposure-health relationship and the determinants of exposure being considered at individual and group/ecological levels, respectively. Some properties of the resulting systems are quite general, and are seen in unrelated contexts such as biochemical pathways. Confining analysis to a single link misses the opportunity to discover such properties.The structure of a causal diagram is derived from knowledge about how the world works, as well as from statistical evidence. A single diagram can be used to characterise a whole research area, not just a single analysis - although this depends on the degree of consistency of the causal relationships between different populations - and can therefore be used to integrate multiple datasets.Additional advantages of system-wide models include: the use of instrumental variables - now emerging as an important technique in epidemiology in the context of mendelian randomisation, but under-used in the exploitation of "natural experiments"; the explicit use of change models, which have advantages with respect to inferring causation; and in the detection and elucidation of feedback.

Poisson versus threshold models for genetic analysis of clinical mastitis in US Holsteins.

Science.gov (United States)

Vazquez, A I; Weigel, K A; Gianola, D; Bates, D M; Perez-Cabal, M A; Rosa, G J M; Chang, Y M

2009-10-01

Typically, clinical mastitis is coded as the presence or absence of disease in a given lactation, and records are analyzed with either linear models or binary threshold models. Because the presence of mastitis may include cows with multiple episodes, there is a loss of information when counts are treated as binary responses. Poisson models are appropriated for random variables measured as the number of events, and although these models are used extensively in studying the epidemiology of mastitis, they have rarely been used for studying the genetic aspects of mastitis. Ordinal threshold models are pertinent for ordered categorical responses; although one can hypothesize that the number of clinical mastitis episodes per animal reflects a continuous underlying increase in mastitis susceptibility, these models have rarely been used in genetic analysis of mastitis. The objective of this study was to compare probit, Poisson, and ordinal threshold models for the genetic evaluation of US Holstein sires for clinical mastitis. Mastitis was measured as a binary trait or as the number of mastitis cases. Data from 44,908 first-parity cows recorded in on-farm herd management software were gathered, edited, and processed for the present study. The cows were daughters of 1,861 sires, distributed over 94 herds. Predictive ability was assessed via a 5-fold cross-validation using 2 loss functions: mean squared error of prediction (MSEP) as the end point and a cost difference function. The heritability estimates were 0.061 for mastitis measured as a binary trait in the probit model and 0.085 and 0.132 for the number of mastitis cases in the ordinal threshold and Poisson models, respectively; because of scale differences, only the probit and ordinal threshold models are directly comparable. Among healthy animals, MSEP was smallest for the probit model, and the cost function was smallest for the ordinal threshold model. Among diseased animals, MSEP and the cost function were smallest

Epidemiology, radiology, and genetics of nicotine dependence in COPD

Directory of Open Access Journals (Sweden)

Hokanson John E

2011-01-01

Full Text Available Abstract Background Cigarette smoking is the principal environmental risk factor for developing COPD, and nicotine dependence strongly influences smoking behavior. This study was performed to elucidate the relationship between nicotine dependence, genetic susceptibility to nicotine dependence, and volumetric CT findings in smokers. Methods Current smokers with COPD (GOLD stage ≥ 2 or normal spirometry were analyzed from the COPDGene Study, a prospective observational study. Nicotine dependence was determined by the Fagerstrom test for nicotine dependence (FTND. Volumetric CT acquisitions measuring the percent of emphysema on inspiratory CT (% of lung Results Among 842 currently smoking subjects (335 COPD cases and 507 controls, 329 subjects (39.1% showed high nicotine dependence. Subjects with high nicotine dependence had greater cumulative and current amounts of smoking. However, emphysema severity was negatively correlated with the FTND score in controls (ρ = -0.19, p Conclusions Nicotine dependence was a negative predictor for emphysema on CT in COPD and control smokers. Increased inflammation in more highly addicted current smokers could influence the CT lung density distribution, which may influence genetic association studies of emphysema phenotypes. Trial registration ClinicalTrials (NCT: NCT00608764

The epidemiology of acne vulgaris in late adolescence

Science.gov (United States)

Lynn, Darren D; Umari, Tamara; Dunnick, Cory A; Dellavalle, Robert P

2016-01-01

Importance Acne vulgaris is the most common skin condition affecting late adolescents across the globe. Although prior studies have evaluated epidemiologic patterns of acne vulgaris in various ethnicities and regions, adequate understanding of the worldwide burden of the disease associated with patients in their late adolescence (15–19-year olds) remains lacking. Objective To assess the global burden of the disease associated with acne vulgaris for late adolescents (15–19-year olds) and provide an overview of the epidemiology, pathophysiology, and treatment options for acne in this population. Design Database summary study. Setting Global Burden of Disease Study 2010 database. Participants Global Burden of Disease regions comprised countries with prevalence of acne vulgaris between the ages of 15 and 19 years. Main outcomes and measures Geographic region-level disability-adjusted life year rates (per 100,000 persons) associated with acne vulgaris in years 1990 through 2010. Median percentage change in disability-adjusted life year rates was estimated for each region across the specified study period. Conclusion and relevance Acne vulgaris-associated disease burden exhibits global distribution and has continued to grow in prevalence over time within this population. This continued growth suggests an unmet dermatologic need worldwide for this disorder and potential opportunities for improved access and delivery of dermatologic care. Our analysis of the literature reveals numerous opportunities for enhanced patient care. To that end, we highlight some of the effective and promising treatments currently available and address important factors, such as sex, nationality, genetics, pathophysiology, and diet, as they relate to acne vulgaris in late adolescence. PMID:26955297

Overview of Epidemiology, Genetics, Birth Defects, and Chromosome Abnormalities Associated With CDH

Science.gov (United States)

Pober, Barbara R.

2010-01-01

Congenital diaphragmatic hernia (CDH) is a common and well-studied birth defect. The etiology of most cases remains unknown but increasing evidence points to genetic causation. The data supporting genetic etiologies which are detailed below include the association of CDH with recurring chromosome abnormalities, the existence of CDH-multiplex families, and the co-occurrence of CDH with additional congenital malformations. PMID:17436298

EWET: Data collection and interface for the genetic analysis of Echinococcus multilocularis based on EmsB microsatellite

Science.gov (United States)

Damy, Sylvie; Brillaud, Jonathan; Tissot, Jean-Daniel; Navion, Jérémy; Mélior, Raphael; Afonso, Eve; Hormaz, Vanessa; Gottstein, Bruno; Umhang, Gérald; Casulli, Adriano; Dadeau, Frédéric; Millon, Laurence; Raoul, Francis

2017-01-01

Evolution and dispersion history on Earth of organisms can best be studied through biological markers in molecular epidemiological studies. The biological diversity of the cestode Echinococcus multilocularis was investigated in different cladistic approaches. First the morphological aspects were explored in connection with its ecology. More recently, molecular aspects were investigated to better understand the nature of the variations observed among isolates. The study of the tandemly repeated multilocus microsatellite EmsB allowed us to attain a high genetic diversity level where other classic markers have failed. Since 2006, EmsB data have been collected on specimens from various endemic foci of the parasite in Europe (in historic and newly endemic areas), Asia (China, Japan and Kyrgyzstan), and North America (Canada and Alaska). Biological data on the isolates and metadata were also recorded (e.g. host, geographical location, EmsB analysis, citation in the literature). In order to make available the data set of 1,166 isolates from classic and aberrant domestic and wild animal hosts (larval lesions and adult worms) and from human origin, an open web access interface, developed in PHP, and connected to a PostgreSQL database, was developed in the EmsB Website for the Echinococcus Typing (EWET) project. It allows researchers to access data collection, perform genetic analyses online (e.g. defining the genetic distance between their own samples and the samples in the database), consult distribution maps of EmsB profiles, and record and share their new EmsB genotyping data. In order to standardize the EmsB analyses performed in the different laboratories throughout the world, a calibrator was developed. The final aim of this project was to gather and arrange available data to permit to better understand the dispersion and transmission patterns of the parasite among definitive and intermediate hosts, in order to organize control strategies on the ground. PMID:28972978

EWET: Data collection and interface for the genetic analysis of Echinococcus multilocularis based on EmsB microsatellite.

Directory of Open Access Journals (Sweden)

Jenny Knapp

Full Text Available Evolution and dispersion history on Earth of organisms can best be studied through biological markers in molecular epidemiological studies. The biological diversity of the cestode Echinococcus multilocularis was investigated in different cladistic approaches. First the morphological aspects were explored in connection with its ecology. More recently, molecular aspects were investigated to better understand the nature of the variations observed among isolates. The study of the tandemly repeated multilocus microsatellite EmsB allowed us to attain a high genetic diversity level where other classic markers have failed. Since 2006, EmsB data have been collected on specimens from various endemic foci of the parasite in Europe (in historic and newly endemic areas, Asia (China, Japan and Kyrgyzstan, and North America (Canada and Alaska. Biological data on the isolates and metadata were also recorded (e.g. host, geographical location, EmsB analysis, citation in the literature. In order to make available the data set of 1,166 isolates from classic and aberrant domestic and wild animal hosts (larval lesions and adult worms and from human origin, an open web access interface, developed in PHP, and connected to a PostgreSQL database, was developed in the EmsB Website for the Echinococcus Typing (EWET project. It allows researchers to access data collection, perform genetic analyses online (e.g. defining the genetic distance between their own samples and the samples in the database, consult distribution maps of EmsB profiles, and record and share their new EmsB genotyping data. In order to standardize the EmsB analyses performed in the different laboratories throughout the world, a calibrator was developed. The final aim of this project was to gather and arrange available data to permit to better understand the dispersion and transmission patterns of the parasite among definitive and intermediate hosts, in order to organize control strategies on the ground.

EWET: Data collection and interface for the genetic analysis of Echinococcus multilocularis based on EmsB microsatellite.

Science.gov (United States)

Knapp, Jenny; Damy, Sylvie; Brillaud, Jonathan; Tissot, Jean-Daniel; Navion, Jérémy; Mélior, Raphael; Afonso, Eve; Hormaz, Vanessa; Gottstein, Bruno; Umhang, Gérald; Casulli, Adriano; Dadeau, Frédéric; Millon, Laurence; Raoul, Francis

2017-01-01

Evolution and dispersion history on Earth of organisms can best be studied through biological markers in molecular epidemiological studies. The biological diversity of the cestode Echinococcus multilocularis was investigated in different cladistic approaches. First the morphological aspects were explored in connection with its ecology. More recently, molecular aspects were investigated to better understand the nature of the variations observed among isolates. The study of the tandemly repeated multilocus microsatellite EmsB allowed us to attain a high genetic diversity level where other classic markers have failed. Since 2006, EmsB data have been collected on specimens from various endemic foci of the parasite in Europe (in historic and newly endemic areas), Asia (China, Japan and Kyrgyzstan), and North America (Canada and Alaska). Biological data on the isolates and metadata were also recorded (e.g. host, geographical location, EmsB analysis, citation in the literature). In order to make available the data set of 1,166 isolates from classic and aberrant domestic and wild animal hosts (larval lesions and adult worms) and from human origin, an open web access interface, developed in PHP, and connected to a PostgreSQL database, was developed in the EmsB Website for the Echinococcus Typing (EWET) project. It allows researchers to access data collection, perform genetic analyses online (e.g. defining the genetic distance between their own samples and the samples in the database), consult distribution maps of EmsB profiles, and record and share their new EmsB genotyping data. In order to standardize the EmsB analyses performed in the different laboratories throughout the world, a calibrator was developed. The final aim of this project was to gather and arrange available data to permit to better understand the dispersion and transmission patterns of the parasite among definitive and intermediate hosts, in order to organize control strategies on the ground.

Epidemiology and treatment of psoriasis: a Brazilian perspective

Directory of Open Access Journals (Sweden)

Duarte GV

2015-04-01

Full Text Available Gleison V Duarte,1 Larissa Porto-Silva,2 Maria de Fátima Paim de Oliveira1 1Dermatology Department, Federal University of Bahia, Salvador, 2Escola Bahiana de Medicina e Saúde Pública, Salvador, BA, Brazil Abstract: Psoriasis is a chronic immune-mediated systemic disease that is influenced by genetic and environmental factors, is associated with comorbidities, and has a negative impact on the quality of life of affected individuals. The prevalence of psoriasis varies among different ethnic groups, but this topic has not been studied in Brazil to date. In this review, we evaluate the epidemiology and treatment of psoriasis from a Brazilian perspective. We focused on studies that involved Brazilian subjects. The prevalence of psoriasis in Brazil is estimated to be 2.5%, but no population study has been performed previously. Environmental factors, such as tropical climate, in association with genetic factors, such as miscegenation, may exert a beneficial impact on the course and frequency of psoriasis in Brazil. A number of studies have advanced our understanding of the cardiovascular, ophthalmic, and oral comorbidities that are associated with psoriasis. Concerns about biological therapy, such as endemic leprosy, human T-cell lymphotropic virus (HTLV, and tuberculosis infections, are discussed. The nonavailability of treatment options for psoriasis in the public health system contradicts the Brazilian Society of Dermatology guidelines, stimulating the judicialization of access to medicines in psoriasis care. Keywords: psoriasis, epidemiology, comorbidities, health services accessibility, health care disparities, insurance, health care costs

Novel molecular markers of Chlamydia pecorum genetic diversity in the koala (Phascolarctos cinereus)

Science.gov (United States)

2011-01-01

-detailed molecular marker for epidemiological analysis appears justified, the tarP and ORF663 genes also appear to be valuable markers of phylogenetic or biogeographic divisions at the C. pecorum intra-species level. This research has significant implications for future typing studies to understand the phylogeny, genetic diversity, and epidemiology of C. pecorum infections in the koala and other animal species. PMID:21496349

Novel molecular markers of Chlamydia pecorum genetic diversity in the koala (Phascolarctos cinereus

Directory of Open Access Journals (Sweden)

Timms Peter

2011-04-01

ompA as a fine-detailed molecular marker for epidemiological analysis appears justified, the tarP and ORF663 genes also appear to be valuable markers of phylogenetic or biogeographic divisions at the C. pecorum intra-species level. This research has significant implications for future typing studies to understand the phylogeny, genetic diversity, and epidemiology of C. pecorum infections in the koala and other animal species.

Hierarchical linear modeling of longitudinal pedigree data for genetic association analysis

DEFF Research Database (Denmark)

Tan, Qihua; B Hjelmborg, Jacob V; Thomassen, Mads

2014-01-01

-effect models to explicitly model the genetic relationship. These have proved to be an efficient way of dealing with sample clustering in pedigree data. Although current algorithms implemented in popular statistical packages are useful for adjusting relatedness in the mixed modeling of genetic effects...... associated with blood pressure with estimated inflation factors of 0.99, suggesting that our modeling of random effects efficiently handles the genetic relatedness in pedigrees. Application to simulated data captures important variants specified in the simulation. Our results show that the method is useful......Genetic association analysis on complex phenotypes under a longitudinal design involving pedigrees encounters the problem of correlation within pedigrees, which could affect statistical assessment of the genetic effects. Approaches have been proposed to integrate kinship correlation into the mixed...

Dairy consumption and body mass index among adults: Mendelian randomization analysis of 184802 individuals from 25 studies

Science.gov (United States)

Associations between dairy intake and body mass index (BMI) have been inconsistently observed in epidemiological studies, and the causal relationship remains ill defined. We performed Mendelian randomization (MR) analysis using an established dairy intake-associated genetic polymorphism located upst...

Genetics of Human and Canine Dilated Cardiomyopathy.

Science.gov (United States)

Simpson, Siobhan; Edwards, Jennifer; Ferguson-Mignan, Thomas F N; Cobb, Malcolm; Mongan, Nigel P; Rutland, Catrin S

2015-01-01

Cardiovascular disease is a leading cause of death in both humans and dogs. Dilated cardiomyopathy (DCM) accounts for a large number of these cases, reported to be the third most common form of cardiac disease in humans and the second most common in dogs. In human studies of DCM there are more than 50 genetic loci associated with the disease. Despite canine DCM having similar disease progression to human DCM studies into the genetic basis of canine DCM lag far behind those of human DCM. In this review the aetiology, epidemiology, and clinical characteristics of canine DCM are examined, along with highlighting possible different subtypes of canine DCM and their potential relevance to human DCM. Finally the current position of genetic research into canine and human DCM, including the genetic loci, is identified and the reasons many studies may have failed to find a genetic association with canine DCM are reviewed.

Raps markers for genetic diversity analysis in rice (Oryza sativa L)

Energy Technology Data Exchange (ETDEWEB)

Alvarez, A; Fuentes, Jorge L [Centro de Estudios Aplicados al Desarrollo Nuclear, La Habana (Cuba); Deus, Juan E [Instituto de Investigaciones del Arroz, Habana (Cuba); Duque, Maria C [Centro Internacional de la Agricultura Tropical. Proyecto de Arroz , Cali (Colombia)

1999-07-01

The establishment of relationships between genotypes existing in gene banks that may be used in new crosses, and about genetic diversity in available germplasm, is very useful for plant breeders. In this work, a genetic diversity analysis among 20 varieties of the Cuban rice germplasm bank was performed by using RAPD markers. Twenty four decamer primers were screened which produced 61 polymorphic bands out of 105 consistent and reproducible amplified fragments (58.1 %). The proportion of polymorphic bands varied for each primer, with an average of 3 polymorphic bands per primer, these results agreed with previous reports on RAPD polymorphism in rice germplasm. Depending on the primer, 1 to 7 distinct patterns were obtained among the screened genotypes. Pair-wise genetic distances between genotypes were computed based on Dice's coefficient. Three major, statistically robust groups were obtained in the UPGMA dendrogram (A, B and C) which clearly corresponded to different genetic pools. Additionally, more insight could be gained according to the sub-grouping pattern within group A, which included the principal semi-dwarf commercial varieties. The present study allowed to prove the efficiency of RAPD markers for genetic diversity analysis in closely related germplasm, particularly for the semi-dwarf Cuban commercial rice cultivars. Also, the existence of a narrow genetic base among these varieties has been confirmed, pointing at the urgent necessity of widen it.

Raps markers for genetic diversity analysis in rice (Oryza sativa L)

International Nuclear Information System (INIS)

Alvarez, A.; Fuentes, Jorge L.; Deus, Juan E.; Duque, Maria C.

1999-01-01

The establishment of relationships between genotypes existing in gene banks that may be used in new crosses, and about genetic diversity in available germplasm, is very useful for plant breeders. In this work, a genetic diversity analysis among 20 varieties of the Cuban rice germplasm bank was performed by using RAPD markers. Twenty four decamer primers were screened which produced 61 polymorphic bands out of 105 consistent and reproducible amplified fragments (58.1 %). The proportion of polymorphic bands varied for each primer, with an average of 3 polymorphic bands per primer, these results agreed with previous reports on RAPD polymorphism in rice germplasm. Depending on the primer, 1 to 7 distinct patterns were obtained among the screened genotypes. Pair-wise genetic distances between genotypes were computed based on Dice's coefficient. Three major, statistically robust groups were obtained in the UPGMA dendrogram (A, B and C) which clearly corresponded to different genetic pools. Additionally, more insight could be gained according to the sub-grouping pattern within group A, which included the principal semi-dwarf commercial varieties. The present study allowed to prove the efficiency of RAPD markers for genetic diversity analysis in closely related germplasm, particularly for the semi-dwarf Cuban commercial rice cultivars. Also, the existence of a narrow genetic base among these varieties has been confirmed, pointing at the urgent necessity of widen it

The Current Status of the Disease Caused by Enterovirus 71 Infections: Epidemiology, Pathogenesis, Molecular Epidemiology, and Vaccine Development

Science.gov (United States)

Chang, Ping-Chin; Chen, Shou-Chien; Chen, Kow-Tong

2016-01-01

Enterovirus 71 (EV71) infections have a major public health impact in the Asia-Pacific region. We reviewed the epidemiology, pathogenesis, and molecular epidemiology of EV71 infection as well as EV71 vaccine development. Previous studies were found using the search terms “enterovirus 71” and “epidemiology” or “pathogenesis” or “molecular epidemiology” or “vaccine” in Medline and PubMed. Articles that were not published in the English language, manuscripts without an abstract, and opinion articles were excluded from the review. The reported epidemiology of cases caused by EV71 infection varied from country to country; seasonal variations in incidence were observed. Most cases of EV71 infection that resulted in hospitalization for complications occurred in children less than five years old. The brainstem was the most likely major target of EV71 infection. The emergence of the EV71 epidemic in the Asia-Pacific region has been associated with the circulation of different genetic lineages (genotypes B3, B4, C1, C2, and C4) that appear to be undergoing rapid evolutionary changes. The relationship between the gene structure of the EV71 virus and the factors that ensure its survival, circulation, and evasion of immunity is still unknown. EV71 infection has emerged as an important global public health problem. Vaccine development, including the development of inactivated whole-virus live attenuated, subviral particles, and DNA vaccines, has been progressing. PMID:27618078

Analysis of epidemiological indices of type 2 diabetes mellitus in the adult population of Moscow

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Marina Fedorovna Kalashnikova

2014-07-01

Full Text Available Diabetes mellitus is a disease that presents a global medical problem. It is necessary to implement an in-depth analysis of the epidemiological situation of type 2 diabetes mellitus for planning and organizing specialized medical help to patients with type 2 diabetes mellitus.AimTo rate the basic epidemiological indices of type 2 diabetes mellitus in actual clinical practice using the informational database of national registry of diabetic patients.Materials and methodsEpidemiological analyses were performed in two administrative districts of Moscow. From 1999 to 2011 48978 adult patients with type 2 diabetes mellitus who were aged 18 years and older were registered. We used methods of clinical, analytical and statistical epidemiology with elements of descriptive research.ResultsThe prevalence rate of type 2 diabetes mellitus was 1590 per hundred thousand, most patients were in the 60–64 and 70–74 age groups, and approximately 80% of patients were older than 55 years. The morbidity rate of type 2 diabetes mellitus was 138,72 per hundred thousand and was found to be higher in women at 1,89. The mortality rate of adult patients with diabetes mellitus was 0,83, mostly in men of all ages. Cardiovascular diseases accounted for most of the registered cases of deaths (34,4%. The average life expectancy appeared to be 75,24±0,45 years, although women lived 6 years longer than men. The average duration of the disease was 10,04±0,34 years. A total of 0,4% of patients underwent hospital treatment and the average length of treatment was 17–18 days. The total number of days of disablement was an average of 307,33±30,13 days (80% of patients were older than 55 years. In the study group, a mean grade of НbА1c <7% was observed in 56,6% of patients. The prevalence rate of detected chronic complications was considerably lower compared to other epidemiological studies.ConclusionsOur epidemiological analyses revealed a number of features and consistent

Genetic studies of the Roma (Gypsies: a review

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Gresham David

2001-04-01

Full Text Available Abstract Background Data provided by the social sciences as well as genetic research suggest that the 8-10 million Roma (Gypsies who live in Europe today are best described as a conglomerate of genetically isolated founder populations. The relationship between the traditional social structure observed by the Roma, where the Group is the primary unit, and the boundaries, demographic history and biological relatedness of the diverse founder populations appears complex and has not been addressed by population genetic studies. Results Recent medical genetic research has identified a number of novel, or previously known but rare conditions, caused by private founder mutations. A summary of the findings, provided in this review, should assist diagnosis and counselling in affected families, and promote future collaborative research. The available incomplete epidemiological data suggest a non-random distribution of disease-causing mutations among Romani groups. Conclusion Although far from systematic, the published information indicates that medical genetics has an important role to play in improving the health of this underprivileged and forgotten people of Europe. Reported carrier rates for some Mendelian disorders are in the range of 5 -15%, sufficient to justify newborn screening and early treatment, or community-based education and carrier testing programs for disorders where no therapy is currently available. To be most productive, future studies of the epidemiology of single gene disorders should take social organisation and cultural anthropology into consideration, thus allowing the targeting of public health programs and contributing to the understanding of population structure and demographic history of the Roma.

Microsatellite DNA analysis of northern pike ( Esox lucius L.) populations: insights into the genetic structure and demographic history of a genetically depauperate species

DEFF Research Database (Denmark)

Jacobsen, B. H.; Hansen, Michael Møller; Loeschcke, V.

2005-01-01

The northern pike Esox lucius L. is a freshwater fish exhibiting pronounced population subdivision and low genetic variability. However, there is limited knowledge on phylogeographical patterns within the species, and it is not known whether the low genetic variability reflects primarily current...... low effective population sizes or historical bottlenecks. We analysed six microsatellite loci in ten populations from Europe and North America. Genetic variation was low, with the average number of alleles within populations ranging from 2.3 to 4.0 per locus. Genetic differentiation among populations...... was high (overall theta(ST) = 0.51; overall rho(ST) = 0.50). Multidimensional scaling analysis of genetic distances between populations and spatial analysis of molecular variance suggested a single phylogeographical race within the sampled populations from northern Europe, whereas North American...

Late radiation effects: status and needs of epidemiologic research

International Nuclear Information System (INIS)

Miller, R.W.

1974-01-01

Epidemiologic studies of late radiation effects in man are reviewed, based on exposure to the atomic bomb, radiotherapy, diagnostic radiations, and occupational or accidental exposures. Areas studied include: genetic effects, fertility, immunology, cancer, congenital malformations, growth and development, aging, cataracts, psychiatric effects, interactions with drugs or viruses, host susceptibility, and radiation factors. Cancer areas discussed include leukemia; thyroid, lung, breast, bone, and liver cancers; lymphoma; salivary gland tumors; brain tumors; nonleukemia cancers; intrauterine exposures; and preconception irradiation and childhood cancers. (U.S.)

Analysis of conditional genetic effects and variance components in developmental genetics.

Science.gov (United States)

Zhu, J

1995-12-01

A genetic model with additive-dominance effects and genotype x environment interactions is presented for quantitative traits with time-dependent measures. The genetic model for phenotypic means at time t conditional on phenotypic means measured at previous time (t-1) is defined. Statistical methods are proposed for analyzing conditional genetic effects and conditional genetic variance components. Conditional variances can be estimated by minimum norm quadratic unbiased estimation (MINQUE) method. An adjusted unbiased prediction (AUP) procedure is suggested for predicting conditional genetic effects. A worked example from cotton fruiting data is given for comparison of unconditional and conditional genetic variances and additive effects.

TFOS DEWS II Epidemiology Report

NARCIS (Netherlands)

Stapleton, Fiona; Alves, Monica; Bunya, Vatinee Y.; Jalbert, Isabelle; Lekhanont, Kaevalin; Malet, Florence; Na, Kyung-Sun; Schaumberg, Debra; Uchino, Miki; Vehof, Jelle; Viso, Eloy; Vitale, Susan; Jones, Lyndon

The subcommittee reviewed the prevalence, incidence, risk factors, natural history, morbidity and questionnaires reported in epidemiological studies of dry eye disease (DED). A meta-analysis of published prevalence data estimated the impact of age and sex. Global mapping of prevalence was

Multivariate Survival Mixed Models for Genetic Analysis of Longevity Traits

DEFF Research Database (Denmark)

Pimentel Maia, Rafael; Madsen, Per; Labouriau, Rodrigo

2014-01-01

A class of multivariate mixed survival models for continuous and discrete time with a complex covariance structure is introduced in a context of quantitative genetic applications. The methods introduced can be used in many applications in quantitative genetics although the discussion presented co...... applications. The methods presented are implemented in such a way that large and complex quantitative genetic data can be analyzed......A class of multivariate mixed survival models for continuous and discrete time with a complex covariance structure is introduced in a context of quantitative genetic applications. The methods introduced can be used in many applications in quantitative genetics although the discussion presented...... concentrates on longevity studies. The framework presented allows to combine models based on continuous time with models based on discrete time in a joint analysis. The continuous time models are approximations of the frailty model in which the hazard function will be assumed to be piece-wise constant...

Multivariate Survival Mixed Models for Genetic Analysis of Longevity Traits

DEFF Research Database (Denmark)

Pimentel Maia, Rafael; Madsen, Per; Labouriau, Rodrigo

2013-01-01

A class of multivariate mixed survival models for continuous and discrete time with a complex covariance structure is introduced in a context of quantitative genetic applications. The methods introduced can be used in many applications in quantitative genetics although the discussion presented co...... applications. The methods presented are implemented in such a way that large and complex quantitative genetic data can be analyzed......A class of multivariate mixed survival models for continuous and discrete time with a complex covariance structure is introduced in a context of quantitative genetic applications. The methods introduced can be used in many applications in quantitative genetics although the discussion presented...... concentrates on longevity studies. The framework presented allows to combine models based on continuous time with models based on discrete time in a joint analysis. The continuous time models are approximations of the frailty model in which the hazard function will be assumed to be piece-wise constant...

Genetic predisposition to increased blood cholesterol and triglyceride lipid levels and risk of Alzheimer disease: a Mendelian randomization analysis.

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Petroula Proitsi

2014-09-01

Full Text Available Although altered lipid metabolism has been extensively implicated in the pathogenesis of Alzheimer disease (AD through cell biological, epidemiological, and genetic studies, the molecular mechanisms linking cholesterol and AD pathology are still not well understood and contradictory results have been reported. We have used a Mendelian randomization approach to dissect the causal nature of the association between circulating lipid levels and late onset AD (LOAD and test the hypothesis that genetically raised lipid levels increase the risk of LOAD.We included 3,914 patients with LOAD, 1,675 older individuals without LOAD, and 4,989 individuals from the general population from six genome wide studies drawn from a white population (total n=10,578. We constructed weighted genotype risk scores (GRSs for four blood lipid phenotypes (high-density lipoprotein cholesterol [HDL-c], low-density lipoprotein cholesterol [LDL-c], triglycerides, and total cholesterol using well-established SNPs in 157 loci for blood lipids reported by Willer and colleagues (2013. Both full GRSs using all SNPs associated with each trait at p<5×10-8 and trait specific scores using SNPs associated exclusively with each trait at p<5 × 10-8 were developed. We used logistic regression to investigate whether the GRSs were associated with LOAD in each study and results were combined together by meta-analysis. We found no association between any of the full GRSs and LOAD (meta-analysis results: odds ratio [OR]=1.005, 95% CI 0.82-1.24, p = 0.962 per 1 unit increase in HDL-c; OR=0.901, 95% CI 0.65-1.25, p=0.530 per 1 unit increase in LDL-c; OR=1.104, 95% CI 0.89-1.37, p=0.362 per 1 unit increase in triglycerides; and OR=0.954, 95% CI 0.76-1.21, p=0.688 per 1 unit increase in total cholesterol. Results for the trait specific scores were similar; however, the trait specific scores explained much smaller phenotypic variance.Genetic predisposition to increased blood cholesterol and

Multivariate Meta-Analysis of Genetic Association Studies: A Simulation Study.

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Binod Neupane

Full Text Available In a meta-analysis with multiple end points of interests that are correlated between or within studies, multivariate approach to meta-analysis has a potential to produce more precise estimates of effects by exploiting the correlation structure between end points. However, under random-effects assumption the multivariate estimation is more complex (as it involves estimation of more parameters simultaneously than univariate estimation, and sometimes can produce unrealistic parameter estimates. Usefulness of multivariate approach to meta-analysis of the effects of a genetic variant on two or more correlated traits is not well understood in the area of genetic association studies. In such studies, genetic variants are expected to roughly maintain Hardy-Weinberg equilibrium within studies, and also their effects on complex traits are generally very small to modest and could be heterogeneous across studies for genuine reasons. We carried out extensive simulation to explore the comparative performance of multivariate approach with most commonly used univariate inverse-variance weighted approach under random-effects assumption in various realistic meta-analytic scenarios of genetic association studies of correlated end points. We evaluated the performance with respect to relative mean bias percentage, and root mean square error (RMSE of the estimate and coverage probability of corresponding 95% confidence interval of the effect for each end point. Our simulation results suggest that multivariate approach performs similarly or better than univariate method when correlations between end points within or between studies are at least moderate and between-study variation is similar or larger than average within-study variation for meta-analyses of 10 or more genetic studies. Multivariate approach produces estimates with smaller bias and RMSE especially for the end point that has randomly or informatively missing summary data in some individual studies, when

Coffee consumption and risk of esophageal cancer incidence: A meta-analysis of epidemiologic studies.

Science.gov (United States)

Zhang, Juan; Zhou, Bin; Hao, Chuanzheng

2018-04-01

In epidemiologic studies, association between coffee consumption and esophageal cancer risk is inconsistent. The aim of tjis study was to evaluate the effect of coffee on esophageal cancer by combining several similar studies. We conducted a meta-analysis for association of coffee intake and esophageal cancer incidence. Eleven studies, including 457,010 participants and 2628 incident cases, were identified. A relative risk (RR, for cohort study) or odds ratio (OR, for case-control study) of heavy coffee drinkers was calculated, compared with light coffee drinkers or non-drinkers. The analysis was also stratified by cancer types (esophageal squamous cell carcinoma and esophageal adenocarcinoma), sex, and geographic region. The summarized OR of having esophageal cancer in heavy coffee drinkers was 0.93 (95% confidence interval [CI]: 0.73-1.12), compared with light coffee drinkers. When stratified by sex, pathologic type of esophageal cancer, and type of epidemiologic study, we did not find any association of coffee consumption and esophageal cancer incidence. However, an inverse association between coffee consumption and incidence of esophageal cancer was found in East Asia participants with OR of 0.64 (95% CI: 0.44-0.83), but not in Euro-America participants (OR = 1.05; 95% CI: 0.81-1.29). There is a protective role of coffee consumption against esophageal cancer in East Asians, but not in Euro-Americans.

Analysis of genetic diversity in Bolivian llama populations using microsatellites.

Science.gov (United States)

Barreta, J; Gutiérrez-Gil, B; Iñiguez, V; Romero, F; Saavedra, V; Chiri, R; Rodríguez, T; Arranz, J J

2013-08-01

South American camelids (SACs) have a major role in the maintenance and potential future of rural Andean human populations. More than 60% of the 3.7 million llamas living worldwide are found in Bolivia. Due to the lack of studies focusing on genetic diversity in Bolivian llamas, this analysis investigates both the genetic diversity and structure of 12 regional groups of llamas that span the greater part of the range of distribution for this species in Bolivia. The analysis of 42 microsatellite markers in the considered regional groups showed that, in general, there were high levels of polymorphism (a total of 506 detected alleles; average PIC across per marker: 0.66), which are comparable with those reported for other populations of domestic SACs. The estimated diversity parameters indicated that there was high intrapopulational genetic variation (average number of alleles and average expected heterozygosity per marker: 12.04 and 0.68, respectively) and weak genetic differentiation among populations (FST range: 0.003-0.052). In agreement with these estimates, Bolivian llamas showed a weak genetic structure and an intense gene flow between all the studied regional groups, which is due to the exchange of reproductive males between the different flocks. Interestingly, the groups for which the largest pairwise FST estimates were observed, Sud Lípez and Nor Lípez, showed a certain level of genetic differentiation that is probably due to the pattern of geographic isolation and limited communication infrastructures of these southern localities. Overall, the population parameters reported here may serve as a reference when establishing conservation policies that address Bolivian llama populations. © 2012 Blackwell Verlag GmbH.

A genetic analysis of segregation distortion revealed by molecular ...

Indian Academy of Sciences (India)

Journal of Genetics, Vol. 90, No. ... Segregation analysis was based on 64 molecular markers, including 26 .... FHB of RIL populations was controlled by quantitative trait ... The authors acknowledge financial support by the National Basic.

Epidemiology of Usher syndrome in Valencia and Spain.

Science.gov (United States)

Espinós, C; Millán, J M; Beneyto, M; Nájera, C

1998-01-01

To obtain epidemiological data on the prevalence of the different types of Usher syndrome (US) in Spain, since these data were missing; to estimate the proportion of sporadic cases among simplex families, and calculate the prevalence of the Usher syndrome in a homogeneous population from Eastern Spain (3,875,234 inhabitants) that is representative of the Spanish population. Otological, ophthalmological and genetic studies were performed in 89 US patients from 46 families and subjected to statistical and segregation analysis. 41.6% of them suffered US type I, 46.1% type II, and in 12.3% the classification remains unclear. The estimated prevalence for the Province of Valencia was 4.2/100,000. There was a notable excess of male-only affected multiplex sibships in our sample that could be attributable to an X-linked inheritance. The number of families with USI type was similar to that of families with USII type. The estimated prevalence for the Province of Valencia is in agreement with other reports in which the estimate for the prevalence of US ranges from 1.8 to 6.2/100,000.

Epidemiology of cardiomyopathy - A clinical and genetic study of dilated cardiomyopathy: The EPOCH-D study

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Soumi Das

2015-01-01

Full Text Available Background: Dilated Cardiomyopathy (DCM is a genetic disorder where a heterogeneous group of cardiac-muscles are involved and is characterized by ventricular dilatation, impaired systolic function, reduced myocardial contractility with left ventricular ejection fraction (LVEF less than 40%. Our study aims to report the Demographic, Clinical and Genetic profile of Indian Dilated Cardiomyopathy patients. Methodology: All patients were recruited with prior written informed consent and are of Indian origin. Results: In a total of 80 DCM patients, the prevalence was higher among males. In males, mean age of onset was comparatively less than females. In this cohort, 40% had familial inheritance. Sixty two percent of DCM patients belong to NYHA functional class II with ejection fraction (EF ranging between 21-30% and, around one third of the patients had atrial fibrillation (AF. Genetic screening revealed a novel splice site mutation LMNA (c.639+ G>C and a rare variant MYH7 (c.2769 C>T in a patient and insilico analysis of both variants suggested functional changes that were considered pathogenic. We report 3% and 4% occurance of variants, each in LMNA and MYH7, where as reported frequencies of these genes are 6% LMNA and 4% MYH7. Conclusions: DCM is often familial and all possible candidate genes should be screened to identify mutations. Such type of exercise may help in the identification of mechanistic pathways. Next generation sequencing platforms may play an important role in this respect in future.

Radiobiology and Epidemiology

International Nuclear Information System (INIS)

Desaintes, C; Holmstock, L.

2001-01-01

The main objectives of research in the field of radiobiology and epidemiology performed at the Belgian Nuclear Research Centre SCK-CEN are: (1) to study cancer mortality in nuclear workers in Belgium and to co-ordinate the Belgian contribution to the 'International Collaborative Study of Cancer Risk among Radiation Workers in the Nuclear Industry'; (2) to elucidate the molecular basis of individual susceptibility to ionizing radiation in mammalian embryo during the early phases of its development; (3) to assess the genetic risk of maternal exposure to ionizing radiation; (4) to elucidate the cellular mechanisms leading to brain damage after prenatal irradiation; (5) to monitor the early variations of gene expression induced by ionising radiation and cytokines; (6) to evaluate the use of cytokines and natural substances for improving radiotherapy protocols; (6) to advise authorities and to provide the general population with adequate information concerning the health risk arising from radiation exposure. Progress and major achievements in these topical areas in 2000 are reported

Radiobiology and Epidemiology

Energy Technology Data Exchange (ETDEWEB)

Desaintes, C; Holmstock, L

2001-04-01

The main objectives of research in the field of radiobiology and epidemiology performed at the Belgian Nuclear Research Centre SCK-CEN are: (1) to study cancer mortality in nuclear workers in Belgium and to co-ordinate the Belgian contribution to the 'International Collaborative Study of Cancer Risk among Radiation Workers in the Nuclear Industry'; (2) to elucidate the molecular basis of individual susceptibility to ionizing radiation in mammalian embryo during the early phases of its development; (3) to assess the genetic risk of maternal exposure to ionizing radiation; (4) to elucidate the cellular mechanisms leading to brain damage after prenatal irradiation; (5) to monitor the early variations of gene expression induced by ionising radiation and cytokines; (6) to evaluate the use of cytokines and natural substances for improving radiotherapy protocols; (6) to advise authorities and to provide the general population with adequate information concerning the health risk arising from radiation exposure. Progress and major achievements in these topical areas in 2000 are reported.

Protein and genetic diagnosis of limb girdle muscular dystrophy type 2A: The yield and the pitfalls.

Science.gov (United States)

Fanin, Marina; Angelini, Corrado

2015-08-01

Limb girdle muscular dystrophy type 2A (LGMD2A) is the most frequent form of LGMD worldwide. Comprehensive clinical assessment and laboratory testing is essential for diagnosis of LGMD2A. Muscle immunoblot analysis of calpain-3 is the most useful tool to direct genetic testing, as detection of calpain-3 deficiency has high diagnostic value. However, calpain-3 immunoblot testing lacks sensitivity in about 30% of cases due to gene mutations that inactivate the enzyme. The best diagnostic strategy should be determined on a case-by-case basis, depending on which tissues are available, and which molecular and/or genetic methods are adopted. In this work we survey the current knowledge, advantages, limitations, and pitfalls of protein testing and mutation detection in LGMD2A and provide an update of genetic epidemiology. © 2015 Wiley Periodicals, Inc.

The heterogeneous HLA genetic makeup of the Swiss population.

Science.gov (United States)

Buhler, Stéphane; Nunes, José Manuel; Nicoloso, Grazia; Tiercy, Jean-Marie; Sanchez-Mazas, Alicia

2012-01-01

This study aims at investigating the HLA molecular variation across Switzerland in order to determine possible regional differences, which would be highly relevant to several purposes: optimizing donor recruitment strategies in hematopoietic stem cell transplantation (HSCT), providing reliable reference data in HLA and disease association studies, and understanding the population genetic background(s) of this culturally heterogeneous country. HLA molecular data of more than 20,000 HSCT donors from 9-13 recruitment centers of the whole country were analyzed. Allele and haplotype frequencies were estimated by using new computer tools adapted to the heterogeneity and ambiguity of the data. Non-parametric and resampling statistical tests were performed to assess Hardy-Weinberg equilibrium, selective neutrality and linkage disequilibrium among different loci, both in each recruitment center and in the whole national registry. Genetic variation was explored through genetic distance and hierarchical analysis of variance taking into account both geographic and linguistic subdivisions in Switzerland. The results indicate a heterogeneous genetic makeup of the Swiss population: first, allele frequencies estimated on the whole national registry strongly deviate from Hardy-Weinberg equilibrium, by contrast with the results obtained for individual centers; second, a pronounced differentiation is observed for Ticino, Graubünden, and, to a lesser extent, Wallis, suggesting that the Alps represent(ed) a barrier to gene flow; finally, although cultural (linguistic) boundaries do not represent a main genetic differentiation factor in Switzerland, the genetic relatedness between population from south-eastern Switzerland and Italy agrees with historical and linguistic data. Overall, this study justifies the maintenance of a decentralized donor recruitment structure in Switzerland allowing increasing the genetic diversity of the national--and hence global--donor registry. It also

The Epidemiology of Sarcoma

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Burningham Zachary

2012-10-01

Full Text Available Abstract Sarcomas account for over 20% of all pediatric solid malignant cancers and less than 1% of all adult solid malignant cancers. The vast majority of diagnosed sarcomas will be soft tissue sarcomas, while malignant bone tumors make up just over 10% of sarcomas. The risks for sarcoma are not well-understood. We evaluated the existing literature on the epidemiology and etiology of sarcoma. Risks for sarcoma development can be divided into environmental exposures, genetic susceptibility, and an interaction between the two. HIV-positive individuals are at an increased risk for Kaposi’s sarcoma, even though HHV8 is the causative virus. Radiation exposure from radiotherapy has been strongly associated with secondary sarcoma development in certain cancer patients. In fact, the risk of malignant bone tumors increases as the cumulative dose of radiation to the bone increases (p for trend

Analysis of epidemiological indices of type 2 diabetes mellitus in the adult population of Moscow

Directory of Open Access Journals (Sweden)

Marina Fedorovna Kalashnikova

2014-07-01

Full Text Available Diabetes mellitus is a disease that presents a global medical problem. It is necessary to implement an in-depth analysis of the epidemiological situation of type 2 diabetes mellitus for planning and organizing specialized medical help to patients with type 2 diabetes mellitus. Aim. To rate the basic epidemiological indices of type 2 diabetes mellitus in actual clinical practice using the informational database of national registry of diabetic patients. Materials and methods. Epidemiological analyses were performed in two administrative districts of Moscow. From 1999 to 2011 48978 adult patients with type 2 diabetes mellitus who were aged 18 years and older were registered. We used methods of clinical, analytical and statistical epidemiology with elements of descriptive research. Results. The prevalence rate of type 2 diabetes mellitus was 1590 per hundred thousand, most patients were in the 60?64 and 70?74 age groups, and approximately 80% of patients were older than 55 years. The morbidity rate of type 2 diabetes mellitus was 138,72 per hundred thousand and was found to be higher in women at 1,89. The mortality rate of adult patients with diabetes mellitus was 0,83, mostly in men of all ages. Cardiovascular diseases accounted for most of the registered cases of deaths (34,4%. The average life expectancy appeared to be 75,24?0,45 years, although women lived 6 years longer than men. The average duration of the disease was 10,04?0,34 years. A total of 0,4% of patients underwent hospital treatment and the average length of treatment was 17?18 days. The total number of days of disablement was an average of 307,33?30,13 days (80% of patients were older than 55 years. In the study group, a mean grade of НbА1c

Analysis of epidemiological situation of iodine deficiency in Tomsk region from 1998 to 2014

Science.gov (United States)

Samoilova, Y. G.; Oleynik, O. A.; Yurchenko, E. V.; Zinchuk, S. F.; Sivolobova, T. V.; Rotkank, M. A.; Mazhitova, D. S.

2017-08-01

The purpose of the present research is the comparative analysis of the epidemiological situation of iodine deficiency in the Tomsk region from 1998 to 2014. There were examined 9901 and 15174 children of the school age including within the medical examination of the children’s population in 1998 and 2014 in Tomsk. At all school pupils there were analyzed anamnestic data and carried out anthropometrical measurements, ultrasonography of the thyroid gland was carried out using the portable scanner "Aloka SSD 500" with the linear sensor of 7,5 MHz frequency in the real time, the thyroid volume was evaluated according to Delange (1997). The excretion of inorganic iodine was determined at 264 in 1998 and at 120 children in 2014, respectively, in a one-time portion of urine by the cerium-arsenic method. There was additionally carried out the analysis of results of determination of TSH at 10717 in 1998, and at 15091 in 2014 in a spot of the whole blood at newborn children on the 4-5 day after birth at full-term and on the 7-14 day at prematurely born children. Neonatal TSH in the dried-up samples of capillary blood was determined by the method of the fluorometric immune-ferment analysis with the use of sets of TSH-Neonatal: Delfia, Finland. Statistical processing of the data obtained was carried out with the use of the applied software package pspp. The descriptive analysis included calculation of the median for the quantitative and the calculation of frequencies for qualitative data. The comparative analysis included calculation of distinctions reliability by the Mann-Whitney criterion for independent and to Wilcoxon’s criterion for dependent data. The comparative analysis of epidemiological situation of iodine deficiency in Tomsk and the Tomsk region in 1998 and 2014 specifies decreasing the iodine deficiency diseases in the Tomsk region, increasing the iodine provision of the population within 15 years by 27%, decreasing neonatal hyperthyroidism by 1.5 times.

Epidemiological Distribution and Subtype Analysis of Premenstrual Dysphoric Disorder Syndromes and Symptoms Based on TCM Theories

Directory of Open Access Journals (Sweden)

Mingqi Qiao

2017-01-01

Full Text Available We performed an epidemiological investigation of subjects with premenstrual dysphoric disorder (PMDD to identify the clinical distribution of the major syndromes and symptoms. The pathogenesis of PMDD mainly involves the dysfunction of liver conveyance and dispersion. Excessive liver conveyance and dispersion are associated with liver-qi invasion syndrome, while insufficient liver conveyance and dispersion are expressed as liver-qi depression syndrome. Additionally, a nonconditional logistic regression was performed to analyze the symptomatic features of liver-qi invasion and liver-qi depression. As a result of this analysis, two subtypes of PMDD are proposed, namely, excessive liver conveyance and dispersion (liver-qi invasion syndrome and insufficient liver conveyance and dispersion (liver-qi depression syndrome. Our findings provide an epidemiological foundation for the clinical diagnosis and treatment of PMDD based on the identification of different types.

Genetically Predicted Body Mass Index and Breast Cancer Risk

DEFF Research Database (Denmark)

Guo, Yan; Warren Andersen, Shaneda; Shu, Xiao-Ou

2016-01-01

BACKGROUND: Observational epidemiological studies have shown that high body mass index (BMI) is associated with a reduced risk of breast cancer in premenopausal women but an increased risk in postmenopausal women. It is unclear whether this association is mediated through shared genetic or enviro...

Epidemiologic analysis of sporadic Salmonella typhi isolates and those from outbreaks by pulsed-field gel electrophoresis.

Science.gov (United States)

Thong, K L; Cheong, Y M; Puthucheary, S; Koh, C L; Pang, T

1994-05-01

Pulsed-field gel electrophoresis (PFGE) was used to compare and analyze 158 isolates of Salmonella typhi from five well-defined outbreaks of typhoid fever in Malaysia and also isolates involved in sporadic cases of typhoid fever occurring during the same period. Digestion of chromosomal DNAs from these S. typhi isolates with the restriction endonucleases XbaI (5'-TCTAGA-3'), SpeI (5'-ACTAGT-3'), and AvrII (5'-CCTAGG-3') and then PFGE produced restriction endonuclease analysis (REA) patterns consisting of 11 to 24 DNA fragments ranging in size from 20 to 630 kbp. Analysis of the REA patterns generated by PFGE after digestion with XbaI and SpeI indicated that the S. typhi isolates obtained from sporadic cases of infection were much more heterogeneous (at least 13 different REA patterns were detected; Dice coefficient, between 0.73 and 1.0) than those obtained during outbreaks of typhoid fever. The clonal nature and the close genetic identities of isolates from outbreaks in Alor Setar, Penang, Kota Kinabalu, Johor Bahru, and Kota Bahru were suggested by the fact that only a limited number of REA patterns, which mostly differed by only a single band, were detected (one to four patterns; Dice coefficient, between 0.82 and 1.0), although a different pattern was associated with each of these outbreaks. Comparison of REA patterns with ribotyping for 18 S. typhi isolates involved in sporadic cases of infection showed a good correlation, in that 72% of the isolates were in the same group. There was no clear correlation of phage types with a specific REA pattern. We conclude that PFGE of s. typhi chromosomal DNA digested with infrequently cutting restriction endonucleases is a useful method for comparing and differentiating S. typhi isolates for epidemiological purposes.

Pervasive sharing of genetic effects in autoimmune disease.

Directory of Open Access Journals (Sweden)

Chris Cotsapas

2011-08-01

Full Text Available Genome-wide association (GWA studies have identified numerous, replicable, genetic associations between common single nucleotide polymorphisms (SNPs and risk of common autoimmune and inflammatory (immune-mediated diseases, some of which are shared between two diseases. Along with epidemiological and clinical evidence, this suggests that some genetic risk factors may be shared across diseases-as is the case with alleles in the Major Histocompatibility Locus. In this work we evaluate the extent of this sharing for 107 immune disease-risk SNPs in seven diseases: celiac disease, Crohn's disease, multiple sclerosis, psoriasis, rheumatoid arthritis, systemic lupus erythematosus, and type 1 diabetes. We have developed a novel statistic for Cross Phenotype Meta-Analysis (CPMA which detects association of a SNP to multiple, but not necessarily all, phenotypes. With it, we find evidence that 47/107 (44% immune-mediated disease risk SNPs are associated to multiple-but not all-immune-mediated diseases (SNP-wise P(CPMA<0.01. We also show that distinct groups of interacting proteins are encoded near SNPs which predispose to the same subsets of diseases; we propose these as the mechanistic basis of shared disease risk. We are thus able to leverage genetic data across diseases to construct biological hypotheses about the underlying mechanism of pathogenesis.

Genetic Analysis of Oncorhynchus Nerka : Life History and Genetic Analysis of Redfish Lake Oncorhynchus Nerka, 1993-1994 Completion Report.

Energy Technology Data Exchange (ETDEWEB)

Brannon, E.L.; Thorgaard, G.H.; Cummings, S.A.

1994-10-01

The study has shown through life history examination and DNA analysis that three forms of O. nerka are present in Redfish Lake. The three forms are closely related, but may be sufficiently different to be considered three separate stocks. Fishhook Creek kokanee are temporally isolated from the beach spawners, and may represent the gene pool most similar to the historic sockeye population that once spawned there. Fishhook Creek offers the best spawning area available in the lake system, and should be considered for use in reestablishing an anadromous Fishhook Creek sockeye swain. The resident beach spawning strain of O. nerka is likewise the most similar genetic form of the companion anadromous beach spawning O. nerka, and needs to be considered the most appropriate genetic source to help minimize reduced fitness of the sockeye from inbreeding.

Analysis of genetic diversity of Piper spp. in Hainan Island (China ...

African Journals Online (AJOL)

Inter-simple sequence repeat (ISSR) analysis was used to evaluate the genetic variation of Piper spp. from Hainan, China. 247 polymorphic bands out of a total of 248 (99.60%) were generated from 74 individual plants of Piper spp. The overall level of genetic diversity among Piper spp. in Hainan was high, with the mean ...

Genetic analysis of a consanguineous Pakistani family with Leber ...

Indian Academy of Sciences (India)

2014-08-01

Aug 1, 2014 ... RESEARCH NOTE. Genetic analysis of a consanguineous Pakistani family with Leber .... representation of the deleterious mutation at genomic and protein level. ... In the last couple of years, numerous mutations in. GUCY2D ...

Molecular epidemiology of Mycobacterium tuberculosis complex in Brussels, 2010-2013.

Directory of Open Access Journals (Sweden)

Christelle Vluggen

Full Text Available The tuberculosis (TB incidence rate in Brussels-Capital Region is 3-fold higher than in Belgium as a whole. Eight years after the realization of initial prospective population-based molecular epidemiology investigations in this Region, a similar study over the period 2010-2013 was conducted. TB strains isolated from 945 patients were submitted to genotyping by standardized 24-locus-MIRU-VNTR typing and spoligotyping. The phylogenetic analysis showed that the LAM (16.7% and Haarlem (15.7% branches are the two most prevalent TB lineages circulating in Brussels. Analysis of the MDR subgroup showed an association with Beijing strains (39.9% and patients native of Eastern Europe (40.7%. Genotyping detected 113 clusters involving 321 patients, giving a recent transmission index of 22.9%. Molecular-guided epidemiological investigations and routine surveillance activities revealed family transmission or social contact for patients distributed over 34 clusters. Most of the patients were foreign-born (75.7%. However, cluster analysis revealed only limited trans-national transmission. Comparison with the previous study shows a stable epidemiological situation except for the mean age difference between Belgian-born and foreign-born patients which has disappeared. This study confirms that molecular epidemiology has become an important determinant for TB control programs. However, sufficient financial means need to be available to perform all required epidemiological investigations.

A theoretical analysis of population genetics of plants on restored habitats

Energy Technology Data Exchange (ETDEWEB)

Bogoliubov, A.G. [Botanical Institute, Russian Academy of Science, St. Petersburg (Russian Federation); Loehle, C. [Argonne National Lab., IL (United States)

1995-02-01

Seed and propagules used for habitat restoration are not likely to be closely adapted to local site conditions. Rapid changes of genotypes frequencies on local microsites and/or microevolution would allow plants to become better adapted to a site. These same factors would help to maintain genetic diversity and ensure the survival of small endangered populations. We used population genetics models to examine the selection of genotypes during establishment on restored sites. Vegetative spread was shown to affect selection and significantly reduce genetic diversity. To study general microevolution, we linked a model of resource usage with a genetics model and analyzed competition between genotypes. A complex suite of feasible ecogenetic states was shown to result. The state actually resulting would depend strongly on initial conditions. This analysis indicated that genetic structure can vary locally and can produce overall genetic variability that is not simply the result of microsite adaptations. For restoration activities, the implication is that small differences in seed source could lead to large differences in local genetic structure after selection.

A theoretical analysis of population genetics of plants on restored habitats

Energy Technology Data Exchange (ETDEWEB)

Bogoliubov, A.G. [Russian Academy of Science, St. Petersburg (Russian Federation). Botanical Inst.; Loehle, C. [Argonne National Lab., IL (United States). Environmental Research Div.

1997-07-01

Seed and propagules used for habitat restoration are not likely to be closely adapted to local site conditions. Rapid changes of genotypes frequencies on local microsites and/or microevolution would allow plants to become better adapted to a site. These same factors would help to maintain genetic diversity and ensure the survival of small endangered populations. The authors used population genetics models to examine the selection of genotypes during establishment on restored sites. Vegetative spread was shown to affect selection and significantly reduce genetic diversity. To study general microevolution, the authors linked a model of resource usage with a genetics model and analyzed competition between genotypes. A complex suite of feasible ecogenetic states was shown to result. The state actually resulting would depend strongly on initial conditions. This analysis indicated that genetic structure can vary locally and can produce overall genetic variability that is not simply the result of microsite adaptations. For restoration activities, the implication is that small differences in seed source could lead to large differences in local genetic structure after selection.

Genetics of Human and Canine Dilated Cardiomyopathy

Directory of Open Access Journals (Sweden)

Siobhan Simpson

2015-01-01

Full Text Available Cardiovascular disease is a leading cause of death in both humans and dogs. Dilated cardiomyopathy (DCM accounts for a large number of these cases, reported to be the third most common form of cardiac disease in humans and the second most common in dogs. In human studies of DCM there are more than 50 genetic loci associated with the disease. Despite canine DCM having similar disease progression to human DCM studies into the genetic basis of canine DCM lag far behind those of human DCM. In this review the aetiology, epidemiology, and clinical characteristics of canine DCM are examined, along with highlighting possible different subtypes of canine DCM and their potential relevance to human DCM. Finally the current position of genetic research into canine and human DCM, including the genetic loci, is identified and the reasons many studies may have failed to find a genetic association with canine DCM are reviewed.

Demographic and epidemiological characteristics of HIV ...

African Journals Online (AJOL)

Department of Epidemiology and Medical Statistics, College of Medicine, University of Ibadan, Ibadan, Nigeria ... Methods: Analysis of data extracted from electronic records of 17, 312 .... system for the purpose of privacy and confidentiality of.

Genetic evidence linking lung cancer and COPD: a new perspective

Directory of Open Access Journals (Sweden)

Crapo JD

2011-07-01

Full Text Available Robert P Young1,4, Raewyn J Hopkins1, Gregory D Gamble1, Carol Etzel2, Randa El-Zein2, James D Crapo31Department of Medicine and School of Biological Sciences, University of Auckland, Auckland, New Zealand; 2Department of Epidemiology, UT MD Anderson Cancer Center, Houston, TX, USA; 3National Jewish Health, Denver, CO, USA; 4Synergenz Biosciences Ltd, Auckland, New ZealandAbstract: Epidemiological studies indicate that tobacco smoke exposure accounts for nearly 90% of cases of chronic obstructive pulmonary disease (COPD and lung cancer. However, genetic factors may explain why 10%–30% of smokers develop these complications. This perspective reviews the evidence suggesting that COPD is closely linked to susceptibility to lung cancer and outlines the potential relevance of this observation. Epidemiological studies show that COPD is the single most important risk factor for lung cancer among smokers and predates lung cancer in up to 80% of cases. Genome-wide association studies of lung cancer, lung function, and COPD have identified a number of overlapping “susceptibility” loci. With stringent phenotyping, it has recently been shown that several of these overlapping loci are independently associated with both COPD and lung cancer. These loci implicate genes underlying pulmonary inflammation and apoptotic processes mediated by the bronchial epithelium, and link COPD with lung cancer at a molecular genetic level. It is currently possible to derive risk models for lung cancer that incorporate lung cancer-specific genetic variants, recently identified “COPD-related” genetic variants, and clinical variables. Early studies suggest that single nucleotide polymorphism-based risk stratification of smokers might help better target novel prevention and early diagnostic strategies in lung cancer.Keywords: lung cancer, chronic obstructive pulmonary disease, association study, single nucleotide polymorphism, risk model

Transcriptomic identification of ADH1B as a novel candidate gene for obesity and insulin resistance in human adipose tissue in Mexican Americans from the Veterans Administration Genetic Epidemiology Study (VAGES.

Directory of Open Access Journals (Sweden)

Deidre A Winnier

Full Text Available Type 2 diabetes (T2D is a complex metabolic disease that is more prevalent in ethnic groups such as Mexican Americans, and is strongly associated with the risk factors obesity and insulin resistance. The goal of this study was to perform whole genome gene expression profiling in adipose tissue to detect common patterns of gene regulation associated with obesity and insulin resistance. We used phenotypic and genotypic data from 308 Mexican American participants from the Veterans Administration Genetic Epidemiology Study (VAGES. Basal fasting RNA was extracted from adipose tissue biopsies from a subset of 75 unrelated individuals, and gene expression data generated on the Illumina BeadArray platform. The number of gene probes with significant expression above baseline was approximately 31,000. We performed multiple regression analysis of all probes with 15 metabolic traits. Adipose tissue had 3,012 genes significantly associated with the traits of interest (false discovery rate, FDR ≤ 0.05. The significance of gene expression changes was used to select 52 genes with significant (FDR ≤ 10(-4 gene expression changes across multiple traits. Gene sets/Pathways analysis identified one gene, alcohol dehydrogenase 1B (ADH1B that was significantly enriched (P < 10(-60 as a prime candidate for involvement in multiple relevant metabolic pathways. Illumina BeadChip derived ADH1B expression data was consistent with quantitative real time PCR data. We observed significant inverse correlations with waist circumference (2.8 x 10(-9, BMI (5.4 x 10(-6, and fasting plasma insulin (P < 0.001. These findings are consistent with a central role for ADH1B in obesity and insulin resistance and provide evidence for a novel genetic regulatory mechanism for human metabolic diseases related to these traits.

Genetic characterization, species differentiation and detection of Fasciola spp. by molecular approaches.

Science.gov (United States)

Ai, Lin; Chen, Mu-Xin; Alasaad, Samer; Elsheikha, Hany M; Li, Juan; Li, Hai-Long; Lin, Rui-Qing; Zou, Feng-Cai; Zhu, Xing-Quan; Chen, Jia-Xu

2011-06-10

Liver flukes belonging to the genus Fasciola are among the causes of foodborne diseases of parasitic etiology. These parasites cause significant public health problems and substantial economic losses to the livestock industry. Therefore, it is important to definitively characterize the Fasciola species. Current phenotypic techniques fail to reflect the full extent of the diversity of Fasciola spp. In this respect, the use of molecular techniques to identify and differentiate Fasciola spp. offer considerable advantages. The advent of a variety of molecular genetic techniques also provides a powerful method to elucidate many aspects of Fasciola biology, epidemiology, and genetics. However, the discriminatory power of these molecular methods varies, as does the speed and ease of performance and cost. There is a need for the development of new methods to identify the mechanisms underpinning the origin and maintenance of genetic variation within and among Fasciola populations. The increasing application of the current and new methods will yield a much improved understanding of Fasciola epidemiology and evolution as well as more effective means of parasite control. Herein, we provide an overview of the molecular techniques that are being used for the genetic characterization, detection and genotyping of Fasciola spp..

Is the development of nuclear energy likely to increase the incidence of genetic diseases for mankind

International Nuclear Information System (INIS)

Leonard, A.

1976-01-01

In a normal human population a relatively high number of individuals (+10%) are bearing genetic and chromosomal deficiencies. As a result of the difficulties encountered when carrying out valid epidemiological investigations, the observations made on the descent of irradiated subjects have not demonstrated that an exposure for a man to ionizing radiations increases the incidence of his deficiencies. That explains the need of having to use the results of experiments conducted on animals in order to evaluate this kind of hazard for mankind. The analysis of these experimental data allows us to conclude that under normal conditions of exploitation the expected development of the nuclear energy is not likely to increase significantly the incidence of genetic deficiencies for mankind. (G.C.)

Genetic analysis of floating Enteromorpha prolifera in the Yellow Sea with AFLP marker

Science.gov (United States)

Liu, Cui; Zhang, Jing; Sun, Xiaoyu; Li, Jian; Zhang, Xi; Liu, Tao

2011-09-01

Extremely large accumulation of green algae Enteromorpha prolifera floated along China' coastal region of the Yellow Sea ever since the summer of 2008. Amplified Fragment Length Polymorphism (AFLP) analysis was applied to assess the genetic diversity and relationships among E. prolifera samples collected from 9 affected areas of the Yellow Sea. Two hundred reproducible fragments were generated with 8 AFLP primer combinations, of which 194 (97%) were polymorphic. The average Nei's genetic diversity, the coefficiency of genetic differentiation (Gst), and the average gene flow estimated from Gst in the 9 populations were 0.4018, 0.6404 and 0.2807 respectively. Cluster analysis based on the unweighed pair group method with arithmetic averages (UPGMA) showed that the genetic relationships within one population or among different populations were all related to their collecting locations and sampling time. Large genetic differentiation was detected among the populations. The E. prolifera originated from different areas and were undergoing a course of mixing.

Epidemiology and risk factors for drug allergy.

Science.gov (United States)

Thong, Bernard Y-H; Tan, Teck-Choon

2011-05-01

The aim of this review was to describe the current evidence-based knowledge of the epidemiology, prevalence, incidence, risk factors and genetic associations of drug allergy. Articles published between 1966 and 2010 were identified in MEDLINE using the key words adult, adverse drug reaction reporting systems, age factors, anaphylactoid, anaphylaxis, anaesthetics, antibiotics, child, drug allergy, drug eruptions, ethnic groups, hypersensitivity, neuromuscular depolarizing agents, neuromuscular nondepolarizing agents, sex factors, Stevens Johnson syndrome and toxic epidermal necrolysis. Additional studies were identified from article reference lists. Relevant, peer-reviewed original research articles, case series and reviews were considered for review. Current epidemiological studies on adverse drug reactions (ADRs) have used different definitions for ADR-related terminology, often do not differentiate immunologically and non-immunologically mediated drug hypersensitivity, study different study populations (different ethnicities, inpatients or outpatients, adults or children), utilize different methodologies (spontaneous vs. non-spontaneous reporting, cohort vs. case-control studies), different methods of assessing drug imputability and different methods of data analyses. Potentially life-threatening severe cutaneous adverse reactions (SCAR) are associated with a high risk of morbidity and mortality. HLA associations for SCAR associated with allopurinol, carbamazepine and abacavir have been reported with the potential for clinical use in screening prior to prescription. Identification of risk factors for drug allergy and appropriate genetic screening of at-risk ethnic groups may improve the outcomes of drug-specific SCAR. Research and collaboration are necessary for the generation of clinically-relevant, translational pharmacoepidemiological and pharmacogenomic knowledge, and success of health outcomes research and policies on drug allergies. © 2011 The Authors

Parity among interpretation methods of MLEE patterns and disparity among clustering methods in epidemiological typing of Candida albicans.

Science.gov (United States)

Boriollo, Marcelo Fabiano Gomes; Rosa, Edvaldo Antonio Ribeiro; Gonçalves, Reginaldo Bruno; Höfling, José Francisco

2006-03-01

The typing of C. albicans by MLEE (multilocus enzyme electrophoresis) is dependent on the interpretation of enzyme electrophoretic patterns, and the study of the epidemiological relationships of these yeasts can be conducted by cluster analysis. Therefore, the aims of the present study were to first determine the discriminatory power of genetic interpretation (deduction of the allelic composition of diploid organisms) and numerical interpretation (mere determination of the presence and absence of bands) of MLEE patterns, and then to determine the concordance (Pearson product-moment correlation coefficient) and similarity (Jaccard similarity coefficient) of the groups of strains generated by three cluster analysis models, and the discriminatory power of such models as well [model A: genetic interpretation, genetic distance matrix of Nei (d(ij)) and UPGMA dendrogram; model B: genetic interpretation, Dice similarity matrix (S(D1)) and UPGMA dendrogram; model C: numerical interpretation, Dice similarity matrix (S(D2)) and UPGMA dendrogram]. MLEE was found to be a powerful and reliable tool for the typing of C. albicans due to its high discriminatory power (>0.9). Discriminatory power indicated that numerical interpretation is a method capable of discriminating a greater number of strains (47 versus 43 subtypes), but also pointed to model B as a method capable of providing a greater number of groups, suggesting its use for the typing of C. albicans by MLEE and cluster analysis. Very good agreement was only observed between the elements of the matrices S(D1) and S(D2), but a large majority of the groups generated in the three UPGMA dendrograms showed similarity S(J) between 4.8% and 75%, suggesting disparities in the conclusions obtained by the cluster assays.

A Genetic Analysis of Mortality in Pigs

DEFF Research Database (Denmark)

Varona, Luis; Sorensen, Daniel

2010-01-01

to investigate whether there is support for genetic variation for mortality and to study the quality of fit and predictive properties of the various models. In both breeds, the model that provided the best fit to the data was the standard binomial hierarchical model. The model that performed best in terms......An analysis of mortality is undertaken in two breeds of pigs: Danish Landrace and Yorkshire. Zero-inflated and standard versions of hierarchical Poisson, binomial, and negative binomial Bayesian models were fitted using Markov chain Monte Carlo (MCMC). The objectives of the study were...... of the ability to predict the distribution of stillbirths was the hierarchical zero-inflated negative binomial model. The best fit of the binomial hierarchical model and of the zero-inflated hierarchical negative binomial model was obtained when genetic variation was included as a parameter. For the hierarchical...

Epidemiology: past, present and future.

Science.gov (United States)

Kesteloot, H

2004-01-01

Epidemiology in the past was concerned essentially by the study of infectious diseases which were the cause of huge mortalities especially since urbanisation was initiated. Epidemics of pest, typhus, cholera, influenza a.o. were common. The epidemics were halted by better hygiene, vaccination and antibiotics. Since the second world war epidemiology was dominated by an "epidemic" of new chronic diseases, especially heart disease and cancer. This was due to an increase in life span and to an increase in smoking habits and in the intake of saturated fat and a too small intake of fruit and vegetables combined with a too high intake of salt (NaCl). Gradually epidemiology evolved as the study of the causes, the distribution, the risk factors and the prevention of chronic diseases, but also including accidents, suicide, depression a.o., diseases with a mass occurrence at the population level. The importance of nutrition as a determinant of health gradually became recognized, but remains undervalued by the medical profession. Mortality at the population level follows some simple mathematical laws and can be represented accurately (r2>0.99) between the ages of 35 and 84 year by either Gompertz equations (ln mortality versus age) or by a polynomial equation (ln mortality versus age, age2). This is valid for all populations and both sexes and remains valid at times of great and rapid changes in mortality. This shows that measures for prevention should be directed towards the total population. The future of epidemiology should be directed towards the slowing of the ageing process at the population level by a healthy life style consisting of: not smoking, avoiding obesity, a fair amount of physical activity and a healthy nutrition i.e little salt, little saturated fat, an adequate amount of omega-3 fatty acids and a large amount of fruit and vegetables, with an occasional glass of red wine. This contains the secret of a long and healthy life. Conceptually it will be important

Molecular genetic analysis of activation-tagged transcription factors thought to be involved in photomorphogenesis

Energy Technology Data Exchange (ETDEWEB)

Neff, Michael M.

2011-06-23

This is a final report for Department of Energy Grant No. DE-FG02-08ER15927 entitled “Molecular Genetic Analysis of Activation-Tagged Transcription Factors Thought to be Involved in Photomorphogenesis”. Based on our preliminary photobiological and genetic analysis of the sob1-D mutant, we hypothesized that OBP3 is a transcription factor involved in both phytochrome and cryptochrome-mediated signal transduction. In addition, we hypothesized that OBP3 is involved in auxin signaling and root development. Based on our preliminary photobiological and genetic analysis of the sob2-D mutant, we also hypothesized that a related gene, LEP, is involved in hormone signaling and seedling development.

Analysis of the Threat of Genetically Modified Organisms for Biological Warfare

Science.gov (United States)

2011-05-01

biological warfare. The primary focus of the framework are those aspects of the technology directly affecting humans by inducing virulent infectious disease...applications. Simple organisms such as fruit flies have been used to study the effects of genetic changes across generations. Transgenic mice are...Analysis * Multi-cell pathogens * Toxins (Chemical products of living cells.) * Fungi (Robust organism; no genetic manipulation needed

Epidemiological analysis of data for scrapie in Great Britain

NARCIS (Netherlands)

Hagenaars, T.H.J.; Donnelly, C.; Ferguson, N.M.

2006-01-01

In recent years, the control or eradication of scrapie and any other transmissible spongiform encephalopathies (TSEs) possibly circulating in the sheep population has become a priority in Britain and elsewhere in Europe. A better understanding of the epidemiology of scrapie would greatly aid the

Red and processed meat intake and risk of colorectal adenomas: a systematic review and meta-analysis of epidemiological studies

NARCIS (Netherlands)

Aune, D.; Chan, D.S.M.; Vieira, A.; Navarro Rosenblatt, D.; Vieira, R.; Greenwood, D.C.; Kampman, E.; Norat, T.

2013-01-01

Background Current evidence indicates that red and processed meat intake increases the risk of colorectal cancer; however, the association with colorectal adenomas is unclear. Objective To conduct a systematic review and meta-analysis of epidemiological studies of red and processed meat intake and

The Information Content of Discrete Functions and Their Application in Genetic Data Analysis.

Science.gov (United States)

Sakhanenko, Nikita A; Kunert-Graf, James; Galas, David J

2017-12-01

The complex of central problems in data analysis consists of three components: (1) detecting the dependence of variables using quantitative measures, (2) defining the significance of these dependence measures, and (3) inferring the functional relationships among dependent variables. We have argued previously that an information theory approach allows separation of the detection problem from the inference of functional form problem. We approach here the third component of inferring functional forms based on information encoded in the functions. We present here a direct method for classifying the functional forms of discrete functions of three variables represented in data sets. Discrete variables are frequently encountered in data analysis, both as the result of inherently categorical variables and from the binning of continuous numerical variables into discrete alphabets of values. The fundamental question of how much information is contained in a given function is answered for these discrete functions, and their surprisingly complex relationships are illustrated. The all-important effect of noise on the inference of function classes is found to be highly heterogeneous and reveals some unexpected patterns. We apply this classification approach to an important area of biological data analysis-that of inference of genetic interactions. Genetic analysis provides a rich source of real and complex biological data analysis problems, and our general methods provide an analytical basis and tools for characterizing genetic problems and for analyzing genetic data. We illustrate the functional description and the classes of a number of common genetic interaction modes and also show how different modes vary widely in their sensitivity to noise.

SecureMA: protecting participant privacy in genetic association meta-analysis.

Science.gov (United States)

Xie, Wei; Kantarcioglu, Murat; Bush, William S; Crawford, Dana; Denny, Joshua C; Heatherly, Raymond; Malin, Bradley A

2014-12-01

Sharing genomic data is crucial to support scientific investigation such as genome-wide association studies. However, recent investigations suggest the privacy of the individual participants in these studies can be compromised, leading to serious concerns and consequences, such as overly restricted access to data. We introduce a novel cryptographic strategy to securely perform meta-analysis for genetic association studies in large consortia. Our methodology is useful for supporting joint studies among disparate data sites, where privacy or confidentiality is of concern. We validate our method using three multisite association studies. Our research shows that genetic associations can be analyzed efficiently and accurately across substudy sites, without leaking information on individual participants and site-level association summaries. Our software for secure meta-analysis of genetic association studies, SecureMA, is publicly available at http://github.com/XieConnect/SecureMA. Our customized secure computation framework is also publicly available at http://github.com/XieConnect/CircuitService. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Geoepidemiology, Genetic and Environmental Risk Factors for PBC.

Science.gov (United States)

Zhang, Haiyan; Carbone, Marco; Lleo, Ana; Invernizzi, Pietro

2015-01-01

Primary biliary cirrhosis (PBC) is the most paradigmatic autoimmune liver disease with still several controversial issues in epidemiology, diagnosis, causation, and therapy. Although we are witnessing an enormous increase in the quantum of our basic knowledge of the disease with an initial translation in clinical practice, there are still a number of key open questions in PBC. Among them are the following questions: Why are there vast geographical variations in disease frequency? What are the reasons for female preponderance? Why do only small-size bile ducts get affected: What is the real role of genetics and epigenetics in its development? In particular, the prevalence of PBC is known to vary both on an international and a regional level, suggesting the existence of substantive geographical differences in terms of genetic susceptibility and environmental factors. New theories on potential environmental triggers, such as chemical xenobiotics, which lead to the breaking of self-tolerance within a unique immunological milieu of the liver, have been suggested. On the other hand, new and solid data on the genetic architecture of PBC are now obtained from recent high-throughput studies, together with data on sex chromosomes defects, and epigenetic abnormalities, thus strongly suggesting a role of genetic and epigenetic factors in the triggering and perpetuation of the autoimmune aggression in PBC. Based on these evidences, a number of novel drugs directed against specific immune-related molecules are currently under development. In this paper, we review a comprehensive collection of current epidemiological reports from various world regions. We also discuss here the most recent data regarding candidate genetic and environmental risk factors for PBC. © 2015 S. Karger AG, Basel.

Analysis of genetic polymorphism and genetic distance among four ...

African Journals Online (AJOL)

use

2011-11-21