AustralieFrV1, Main, Exploration, bibRecord, 001929

Post-hoc Analysis for Detecting Individual Rare Variant Risk Associations using Probit Regression Bayesian Variable Selection Methods in Case-Control Sequencing Studies

Identifieur interne : 001929 ( Main/Exploration ); précédent : 001928; suivant : 001930

Post-hoc Analysis for Detecting Individual Rare Variant Risk Associations using Probit Regression Bayesian Variable Selection Methods in Case-Control Sequencing Studies

Auteurs : Nicholas B. Larson [États-Unis] ; Shannon Mcdonnell [États-Unis] ; Lisa Cannon Albright [États-Unis] ; Craig Teerlink [États-Unis] ; Janet Stanford [États-Unis] ; Elaine A. Ostrander [États-Unis] ; William B. Isaacs [États-Unis] ; Jianfeng Xu [États-Unis] ; Kathleen A. Cooney [États-Unis] ; Ethan Lange [États-Unis] ; Johanna Schleutker [Finlande] ; John D. Carpten [États-Unis] ; Isaac Powell [États-Unis] ; Joan Bailey-Wilson [États-Unis] ; Olivier Cussenot [France] ; Geraldine Cancel-Tassin [France] ; Graham Giles [Australie] ; Robert Macinnis [Australie] ; Christiane Maier [Allemagne] ; Alice S. Whittemore [États-Unis] ; Chih-Lin Hsieh [États-Unis] ; Fredrik Wiklund [Suède] ; William J. Catolona [États-Unis] ; William Foulkes [Canada] ; Diptasri Mandal [États-Unis] ; Rosalind Eeles [Royaume-Uni] ; Zsofia Kote-Jarai [Royaume-Uni] ; Michael J. Ackerman [États-Unis] ; Timothy M. Olson [États-Unis] ; Christopher J. Klein [États-Unis] ; Stephen N. Thibodeau [États-Unis] ; Daniel J. Schaid [États-Unis]

Source :

Genetic epidemiology [ 0741-0395 ] ; 2016.

RBID : PMC:5063501

Descripteurs français

English descriptors

KwdEn :
- Bayes Theorem, Case-Control Studies, Genetic Variation, High-Throughput Nucleotide Sequencing, Humans, Models, Genetic, Sequence Analysis, DNA.
MESH :
- Bayes Theorem, Case-Control Studies, Genetic Variation, High-Throughput Nucleotide Sequencing, Humans, Models, Genetic, Sequence Analysis, DNA.

Abstract

Rare variants have been shown to be significant contributors to complex disease risk. By definition, these variants have very low minor allele frequencies and traditional single-marker methods for statistical analysis are underpowered for typical sequencing study sample sizes. Multi-marker burden-type approaches attempt to identify aggregation of rare variants across case-control status by analyzing relatively small partitions of the genome, such as genes. However, it is generally the case that the aggregative measure would be a mixture of causal and neutral variants, and these omnibus tests do not directly provide any indication of which rare variants may be driving a given association. Recently, Bayesian variable selection approaches have been proposed to identify rare variant associations from a large set of rare variants under consideration. While these approaches have been shown to be powerful at detecting associations at the rare variant level, there are often computational limitations on the total quantity of rare variants under consideration and compromises are necessary for large-scale application. Here, we propose a computationally efficient alternative formulation of this method using a probit regression approach specifically capable of simultaneously analyzing hundreds to thousands of rare variants. We evaluate our approach to detect causal variation on simulated data and examine sensitivity and specificity in instances of high rare variant dimensionality as well as apply it to pathway-level rare variant analysis results from a prostate cancer risk case-control sequencing study. Finally, we discuss potential extensions and future directions of this work.

Url:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5063501

DOI: 10.1002/gepi.21983
PubMed: 27312771
PubMed Central: 5063501

Affiliations:

Allemagne, Australie, Canada, Finlande, France, Royaume-Uni, Suède, États-Unis
Arizona, Bade-Wurtemberg, Californie, Caroline du Nord, District de Tübingen, Finlande occidentale, Illinois, Louisiane, Maryland, Michigan, Minnesota, Svealand, Utah, Victoria (État), Washington (État), Île-de-France
Melbourne, Paris, Stockholm, Turku, Ulm
Université d'Ulm, Université de Melbourne, Université de Turku

Le document en format XML

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<placeName><region type="state">Minnesota</region>
</placeName>
<wicri:cityArea>Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester</wicri:cityArea>
</affiliation>
</author>
<author><name sortKey="Mcdonnell, Shannon" sort="Mcdonnell, Shannon" uniqKey="Mcdonnell S" first="Shannon" last="Mcdonnell">Shannon Mcdonnell</name>
<affiliation wicri:level="2"><nlm:aff id="A1">Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<placeName><region type="state">Minnesota</region>
</placeName>
<wicri:cityArea>Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester</wicri:cityArea>
</affiliation>
</author>
<author><name sortKey="Albright, Lisa Cannon" sort="Albright, Lisa Cannon" uniqKey="Albright L" first="Lisa Cannon" last="Albright">Lisa Cannon Albright</name>
<affiliation wicri:level="2"><nlm:aff id="A2">Dept. Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<placeName><region type="state">Utah</region>
</placeName>
<wicri:cityArea>Dept. Internal Medicine, University of Utah School of Medicine, Salt Lake City</wicri:cityArea>
</affiliation>
</author>
<author><name sortKey="Teerlink, Craig" sort="Teerlink, Craig" uniqKey="Teerlink C" first="Craig" last="Teerlink">Craig Teerlink</name>
<affiliation wicri:level="2"><nlm:aff id="A2">Dept. Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<placeName><region type="state">Utah</region>
</placeName>
<wicri:cityArea>Dept. Internal Medicine, University of Utah School of Medicine, Salt Lake City</wicri:cityArea>
</affiliation>
</author>
<author><name sortKey="Stanford, Janet" sort="Stanford, Janet" uniqKey="Stanford J" first="Janet" last="Stanford">Janet Stanford</name>
<affiliation wicri:level="2"><nlm:aff id="A3">Fred Hutchinson Cancer Research Center, Seattle, WA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<placeName><region type="state">Washington (État)</region>
</placeName>
<wicri:cityArea>Fred Hutchinson Cancer Research Center, Seattle</wicri:cityArea>
</affiliation>
</author>
<author><name sortKey="Ostrander, Elaine A" sort="Ostrander, Elaine A" uniqKey="Ostrander E" first="Elaine A." last="Ostrander">Elaine A. Ostrander</name>
<affiliation wicri:level="2"><nlm:aff id="A4">National Human Genome Research Institute, Bethesda, MD</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<placeName><region type="state">Maryland</region>
</placeName>
<wicri:cityArea>National Human Genome Research Institute, Bethesda</wicri:cityArea>
</affiliation>
</author>
<author><name sortKey="Isaacs, William B" sort="Isaacs, William B" uniqKey="Isaacs W" first="William B." last="Isaacs">William B. Isaacs</name>
<affiliation wicri:level="2"><nlm:aff id="A5">Johns Hopkins Hospital, Department of Urology, Baltimore, MD</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<placeName><region type="state">Maryland</region>
</placeName>
<wicri:cityArea>Johns Hopkins Hospital, Department of Urology, Baltimore</wicri:cityArea>
</affiliation>
</author>
<author><name sortKey="Xu, Jianfeng" sort="Xu, Jianfeng" uniqKey="Xu J" first="Jianfeng" last="Xu">Jianfeng Xu</name>
<affiliation wicri:level="2"><nlm:aff id="A6">NorthShore University Health System Research Institute, Chicago, IL</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<placeName><region type="state">Illinois</region>
</placeName>
<wicri:cityArea>NorthShore University Health System Research Institute, Chicago</wicri:cityArea>
</affiliation>
</author>
<author><name sortKey="Cooney, Kathleen A" sort="Cooney, Kathleen A" uniqKey="Cooney K" first="Kathleen A." last="Cooney">Kathleen A. Cooney</name>
<affiliation wicri:level="2"><nlm:aff id="A7">Depts. of Internal Medicine and Urology, University of Michigan Medical School, Ann Arbor, MI</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<placeName><region type="state">Michigan</region>
</placeName>
<wicri:cityArea>Depts. of Internal Medicine and Urology, University of Michigan Medical School, Ann Arbor</wicri:cityArea>
</affiliation>
</author>
<author><name sortKey="Lange, Ethan" sort="Lange, Ethan" uniqKey="Lange E" first="Ethan" last="Lange">Ethan Lange</name>
<affiliation wicri:level="2"><nlm:aff id="A8">Dept. of Genetics, University of North Carolina, Chapel Hill, NC</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<placeName><region type="state">Caroline du Nord</region>
</placeName>
<wicri:cityArea>Dept. of Genetics, University of North Carolina, Chapel Hill</wicri:cityArea>
</affiliation>
</author>
<author><name sortKey="Schleutker, Johanna" sort="Schleutker, Johanna" uniqKey="Schleutker J" first="Johanna" last="Schleutker">Johanna Schleutker</name>
<affiliation wicri:level="4"><nlm:aff id="A9">Dept. of Medical Biochemistry and Genetics, Institute of Biomedicine, University of Turku, Finland</nlm:aff>
<country xml:lang="fr">Finlande</country>
<wicri:regionArea>Dept. of Medical Biochemistry and Genetics, Institute of Biomedicine, University of Turku</wicri:regionArea>
<placeName><settlement type="city">Turku</settlement>
<region type="région" nuts="2">Finlande occidentale</region>
</placeName>
<orgName type="university">Université de Turku</orgName>
</affiliation>
</author>
<author><name sortKey="Carpten, John D" sort="Carpten, John D" uniqKey="Carpten J" first="John D." last="Carpten">John D. Carpten</name>
<affiliation wicri:level="2"><nlm:aff id="A10">Integrated Cancer Genomics Division, The Translational Genomics Research Institute, Phoenix, AZ</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<placeName><region type="state">Arizona</region>
</placeName>
<wicri:cityArea>Integrated Cancer Genomics Division, The Translational Genomics Research Institute, Phoenix</wicri:cityArea>
</affiliation>
</author>
<author><name sortKey="Powell, Isaac" sort="Powell, Isaac" uniqKey="Powell I" first="Isaac" last="Powell">Isaac Powell</name>
<affiliation wicri:level="2"><nlm:aff id="A11">Wayne State University, Detroit, MI</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<placeName><region type="state">Michigan</region>
</placeName>
<wicri:cityArea>Wayne State University, Detroit</wicri:cityArea>
</affiliation>
</author>
<author><name sortKey="Bailey Wilson, Joan" sort="Bailey Wilson, Joan" uniqKey="Bailey Wilson J" first="Joan" last="Bailey-Wilson">Joan Bailey-Wilson</name>
<affiliation wicri:level="2"><nlm:aff id="A12">Statistical Genetics Section, National Human Genome Research Institute, Bethesda, MD</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<placeName><region type="state">Maryland</region>
</placeName>
<wicri:cityArea>Statistical Genetics Section, National Human Genome Research Institute, Bethesda</wicri:cityArea>
</affiliation>
</author>
<author><name sortKey="Cussenot, Olivier" sort="Cussenot, Olivier" uniqKey="Cussenot O" first="Olivier" last="Cussenot">Olivier Cussenot</name>
<affiliation wicri:level="3"><nlm:aff id="A13">CeRePP, Hopital Tenon, Paris, France</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea>CeRePP, Hopital Tenon, Paris</wicri:regionArea>
<placeName><region type="region">Île-de-France</region>
<region type="old region">Île-de-France</region>
<settlement type="city">Paris</settlement>
</placeName>
</affiliation>
</author>
<author><name sortKey="Cancel Tassin, Geraldine" sort="Cancel Tassin, Geraldine" uniqKey="Cancel Tassin G" first="Geraldine" last="Cancel-Tassin">Geraldine Cancel-Tassin</name>
<affiliation wicri:level="3"><nlm:aff id="A13">CeRePP, Hopital Tenon, Paris, France</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea>CeRePP, Hopital Tenon, Paris</wicri:regionArea>
<placeName><region type="region">Île-de-France</region>
<region type="old region">Île-de-France</region>
<settlement type="city">Paris</settlement>
</placeName>
</affiliation>
</author>
<author><name sortKey="Giles, Graham" sort="Giles, Graham" uniqKey="Giles G" first="Graham" last="Giles">Graham Giles</name>
<affiliation wicri:level="4"><nlm:aff id="A14">Cancer Epidemiology Centre, Cancer Council Victoria, and Centre for Epidemiology and Biostatistics, School of Population and Global Health, University of Melbourne, Melbourne, Australia</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>Cancer Epidemiology Centre, Cancer Council Victoria, and Centre for Epidemiology and Biostatistics, School of Population and Global Health, University of Melbourne, Melbourne</wicri:regionArea>
<placeName><settlement type="city">Melbourne</settlement>
<region type="état">Victoria (État)</region>
<settlement type="city">Melbourne</settlement>
</placeName>
<orgName type="university">Université de Melbourne</orgName>
</affiliation>
</author>
<author><name sortKey="Macinnis, Robert" sort="Macinnis, Robert" uniqKey="Macinnis R" first="Robert" last="Macinnis">Robert Macinnis</name>
<affiliation wicri:level="4"><nlm:aff id="A14">Cancer Epidemiology Centre, Cancer Council Victoria, and Centre for Epidemiology and Biostatistics, School of Population and Global Health, University of Melbourne, Melbourne, Australia</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>Cancer Epidemiology Centre, Cancer Council Victoria, and Centre for Epidemiology and Biostatistics, School of Population and Global Health, University of Melbourne, Melbourne</wicri:regionArea>
<placeName><settlement type="city">Melbourne</settlement>
<region type="état">Victoria (État)</region>
<settlement type="city">Melbourne</settlement>
</placeName>
<orgName type="university">Université de Melbourne</orgName>
</affiliation>
</author>
<author><name sortKey="Maier, Christiane" sort="Maier, Christiane" uniqKey="Maier C" first="Christiane" last="Maier">Christiane Maier</name>
<affiliation wicri:level="4"><nlm:aff id="A15">Dept. of Urology, University of Ulm, Ulm, Germany</nlm:aff>
<country xml:lang="fr">Allemagne</country>
<wicri:regionArea>Dept. of Urology, University of Ulm, Ulm</wicri:regionArea>
<placeName><region type="land" nuts="1">Bade-Wurtemberg</region>
<region type="district" nuts="2">District de Tübingen</region>
<settlement type="city">Ulm</settlement>
<settlement type="city">Ulm</settlement>
</placeName>
<orgName type="university">Université d'Ulm</orgName>
</affiliation>
</author>
<author><name sortKey="Whittemore, Alice S" sort="Whittemore, Alice S" uniqKey="Whittemore A" first="Alice S." last="Whittemore">Alice S. Whittemore</name>
<affiliation wicri:level="2"><nlm:aff id="A16">Dept. Health Research and Policy, Stanford University, Stanford, CA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<placeName><region type="state">Californie</region>
</placeName>
<wicri:cityArea>Dept. Health Research and Policy, Stanford University, Stanford</wicri:cityArea>
</affiliation>
</author>
<author><name sortKey="Hsieh, Chih Lin" sort="Hsieh, Chih Lin" uniqKey="Hsieh C" first="Chih-Lin" last="Hsieh">Chih-Lin Hsieh</name>
<affiliation wicri:level="2"><nlm:aff id="A17">Dept. of Urology, University of Southern California, Los Angeles, CA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<placeName><region type="state">Californie</region>
</placeName>
<wicri:cityArea>Dept. of Urology, University of Southern California, Los Angeles</wicri:cityArea>
</affiliation>
</author>
<author><name sortKey="Wiklund, Fredrik" sort="Wiklund, Fredrik" uniqKey="Wiklund F" first="Fredrik" last="Wiklund">Fredrik Wiklund</name>
<affiliation wicri:level="3"><nlm:aff id="A18">Dept. of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden</nlm:aff>
<country xml:lang="fr">Suède</country>
<wicri:regionArea>Dept. of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm</wicri:regionArea>
<placeName><settlement type="city">Stockholm</settlement>
<region nuts="2">Svealand</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Catolona, William J" sort="Catolona, William J" uniqKey="Catolona W" first="William J." last="Catolona">William J. Catolona</name>
<affiliation wicri:level="2"><nlm:aff id="A19">Northwestern University Feinberg School of Medicine, Chicago, IL</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<placeName><region type="state">Illinois</region>
</placeName>
<wicri:cityArea>Northwestern University Feinberg School of Medicine, Chicago</wicri:cityArea>
</affiliation>
</author>
<author><name sortKey="Foulkes, William" sort="Foulkes, William" uniqKey="Foulkes W" first="William" last="Foulkes">William Foulkes</name>
<affiliation wicri:level="1"><nlm:aff id="A20">Depts. Of Oncology and Human Genetics, Montreal General Hospital, Montreal QC, Canada</nlm:aff>
<country xml:lang="fr">Canada</country>
<wicri:regionArea>Depts. Of Oncology and Human Genetics, Montreal General Hospital, Montreal QC</wicri:regionArea>
<wicri:noRegion>Montreal QC</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Mandal, Diptasri" sort="Mandal, Diptasri" uniqKey="Mandal D" first="Diptasri" last="Mandal">Diptasri Mandal</name>
<affiliation wicri:level="2"><nlm:aff id="A21">Dept. of Genetics, LSU Health Sciences Center, New Orleans, LA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<placeName><region type="state">Louisiane</region>
</placeName>
<wicri:cityArea>Dept. of Genetics, LSU Health Sciences Center, New Orleans</wicri:cityArea>
</affiliation>
</author>
<author><name sortKey="Eeles, Rosalind" sort="Eeles, Rosalind" uniqKey="Eeles R" first="Rosalind" last="Eeles">Rosalind Eeles</name>
<affiliation wicri:level="1"><nlm:aff id="A22">Genetics and Epidemiology, Institute of Cancer Research, Sutton Surrey, UK</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Genetics and Epidemiology, Institute of Cancer Research, Sutton Surrey</wicri:regionArea>
<wicri:noRegion>Sutton Surrey</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Kote Jarai, Zsofia" sort="Kote Jarai, Zsofia" uniqKey="Kote Jarai Z" first="Zsofia" last="Kote-Jarai">Zsofia Kote-Jarai</name>
<affiliation wicri:level="1"><nlm:aff id="A22">Genetics and Epidemiology, Institute of Cancer Research, Sutton Surrey, UK</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Genetics and Epidemiology, Institute of Cancer Research, Sutton Surrey</wicri:regionArea>
<wicri:noRegion>Sutton Surrey</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Ackerman, Michael J" sort="Ackerman, Michael J" uniqKey="Ackerman M" first="Michael J." last="Ackerman">Michael J. Ackerman</name>
<affiliation wicri:level="2"><nlm:aff id="A23">Dept. of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<placeName><region type="state">Minnesota</region>
</placeName>
<wicri:cityArea>Dept. of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester</wicri:cityArea>
</affiliation>
</author>
<author><name sortKey="Olson, Timothy M" sort="Olson, Timothy M" uniqKey="Olson T" first="Timothy M." last="Olson">Timothy M. Olson</name>
<affiliation wicri:level="2"><nlm:aff id="A23">Dept. of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<placeName><region type="state">Minnesota</region>
</placeName>
<wicri:cityArea>Dept. of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester</wicri:cityArea>
</affiliation>
</author>
<author><name sortKey="Klein, Christopher J" sort="Klein, Christopher J" uniqKey="Klein C" first="Christopher J." last="Klein">Christopher J. Klein</name>
<affiliation wicri:level="2"><nlm:aff id="A24">Dept. of Neurology, Mayo Clinic, Rochester, MN</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<placeName><region type="state">Minnesota</region>
</placeName>
<wicri:cityArea>Dept. of Neurology, Mayo Clinic, Rochester</wicri:cityArea>
</affiliation>
</author>
<author><name sortKey="Thibodeau, Stephen N" sort="Thibodeau, Stephen N" uniqKey="Thibodeau S" first="Stephen N." last="Thibodeau">Stephen N. Thibodeau</name>
<affiliation wicri:level="2"><nlm:aff id="A25">Dept. of Laboratory Medicine/Pathology, Mayo Clinic, Rochester, MN</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<placeName><region type="state">Minnesota</region>
</placeName>
<wicri:cityArea>Dept. of Laboratory Medicine/Pathology, Mayo Clinic, Rochester</wicri:cityArea>
</affiliation>
</author>
<author><name sortKey="Schaid, Daniel J" sort="Schaid, Daniel J" uniqKey="Schaid D" first="Daniel J." last="Schaid">Daniel J. Schaid</name>
<affiliation wicri:level="2"><nlm:aff id="A1">Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<placeName><region type="state">Minnesota</region>
</placeName>
<wicri:cityArea>Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester</wicri:cityArea>
</affiliation>
</author>
</analytic>
<series><title level="j">Genetic epidemiology</title>
<idno type="ISSN">0741-0395</idno>
<idno type="eISSN">1098-2272</idno>
<imprint><date when="2016">2016</date>
</imprint>
</series>
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<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Bayes Theorem</term>
<term>Case-Control Studies</term>
<term>Genetic Variation</term>
<term>High-Throughput Nucleotide Sequencing</term>
<term>Humans</term>
<term>Models, Genetic</term>
<term>Sequence Analysis, DNA</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de séquence d'ADN</term>
<term>Humains</term>
<term>Modèles génétiques</term>
<term>Séquençage nucléotidique à haut débit</term>
<term>Théorème de Bayes</term>
<term>Variation génétique</term>
<term>Études cas-témoins</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Bayes Theorem</term>
<term>Case-Control Studies</term>
<term>Genetic Variation</term>
<term>High-Throughput Nucleotide Sequencing</term>
<term>Humans</term>
<term>Models, Genetic</term>
<term>Sequence Analysis, DNA</term>
</keywords>
<keywords scheme="MESH" xml:lang="fr"><term>Analyse de séquence d'ADN</term>
<term>Humains</term>
<term>Modèles génétiques</term>
<term>Séquençage nucléotidique à haut débit</term>
<term>Théorème de Bayes</term>
<term>Variation génétique</term>
<term>Études cas-témoins</term>
</keywords>
</textClass>
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</teiHeader>
<front><div type="abstract" xml:lang="en"><p id="P1">Rare variants have been shown to be significant contributors to complex disease risk. By definition, these variants have very low minor allele frequencies and traditional single-marker methods for statistical analysis are underpowered for typical sequencing study sample sizes. Multi-marker burden-type approaches attempt to identify aggregation of rare variants across case-control status by analyzing relatively small partitions of the genome, such as genes. However, it is generally the case that the aggregative measure would be a mixture of causal and neutral variants, and these omnibus tests do not directly provide any indication of which rare variants may be driving a given association. Recently, Bayesian variable selection approaches have been proposed to identify rare variant associations from a large set of rare variants under consideration. While these approaches have been shown to be powerful at detecting associations at the rare variant level, there are often computational limitations on the total quantity of rare variants under consideration and compromises are necessary for large-scale application. Here, we propose a computationally efficient alternative formulation of this method using a probit regression approach specifically capable of simultaneously analyzing hundreds to thousands of rare variants. We evaluate our approach to detect causal variation on simulated data and examine sensitivity and specificity in instances of high rare variant dimensionality as well as apply it to pathway-level rare variant analysis results from a prostate cancer risk case-control sequencing study. Finally, we discuss potential extensions and future directions of this work.</p>
</div>
</front>
</TEI>
<affiliations><list><country><li>Allemagne</li>
<li>Australie</li>
<li>Canada</li>
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<li>Suède</li>
<li>États-Unis</li>
</country>
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<li>Bade-Wurtemberg</li>
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<li>Paris</li>
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<li>Université de Melbourne</li>
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</list>
<tree><country name="États-Unis"><region name="Minnesota"><name sortKey="Larson, Nicholas B" sort="Larson, Nicholas B" uniqKey="Larson N" first="Nicholas B." last="Larson">Nicholas B. Larson</name>
</region>
<name sortKey="Ackerman, Michael J" sort="Ackerman, Michael J" uniqKey="Ackerman M" first="Michael J." last="Ackerman">Michael J. Ackerman</name>
<name sortKey="Albright, Lisa Cannon" sort="Albright, Lisa Cannon" uniqKey="Albright L" first="Lisa Cannon" last="Albright">Lisa Cannon Albright</name>
<name sortKey="Bailey Wilson, Joan" sort="Bailey Wilson, Joan" uniqKey="Bailey Wilson J" first="Joan" last="Bailey-Wilson">Joan Bailey-Wilson</name>
<name sortKey="Carpten, John D" sort="Carpten, John D" uniqKey="Carpten J" first="John D." last="Carpten">John D. Carpten</name>
<name sortKey="Catolona, William J" sort="Catolona, William J" uniqKey="Catolona W" first="William J." last="Catolona">William J. Catolona</name>
<name sortKey="Cooney, Kathleen A" sort="Cooney, Kathleen A" uniqKey="Cooney K" first="Kathleen A." last="Cooney">Kathleen A. Cooney</name>
<name sortKey="Hsieh, Chih Lin" sort="Hsieh, Chih Lin" uniqKey="Hsieh C" first="Chih-Lin" last="Hsieh">Chih-Lin Hsieh</name>
<name sortKey="Isaacs, William B" sort="Isaacs, William B" uniqKey="Isaacs W" first="William B." last="Isaacs">William B. Isaacs</name>
<name sortKey="Klein, Christopher J" sort="Klein, Christopher J" uniqKey="Klein C" first="Christopher J." last="Klein">Christopher J. Klein</name>
<name sortKey="Lange, Ethan" sort="Lange, Ethan" uniqKey="Lange E" first="Ethan" last="Lange">Ethan Lange</name>
<name sortKey="Mandal, Diptasri" sort="Mandal, Diptasri" uniqKey="Mandal D" first="Diptasri" last="Mandal">Diptasri Mandal</name>
<name sortKey="Mcdonnell, Shannon" sort="Mcdonnell, Shannon" uniqKey="Mcdonnell S" first="Shannon" last="Mcdonnell">Shannon Mcdonnell</name>
<name sortKey="Olson, Timothy M" sort="Olson, Timothy M" uniqKey="Olson T" first="Timothy M." last="Olson">Timothy M. Olson</name>
<name sortKey="Ostrander, Elaine A" sort="Ostrander, Elaine A" uniqKey="Ostrander E" first="Elaine A." last="Ostrander">Elaine A. Ostrander</name>
<name sortKey="Powell, Isaac" sort="Powell, Isaac" uniqKey="Powell I" first="Isaac" last="Powell">Isaac Powell</name>
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<name sortKey="Stanford, Janet" sort="Stanford, Janet" uniqKey="Stanford J" first="Janet" last="Stanford">Janet Stanford</name>
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   |area=    AustralieFrV1
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   |étape=   Exploration
   |type=    RBID
   |clé=     PMC:5063501
   |texte=   Post-hoc Analysis for Detecting Individual Rare Variant Risk Associations using Probit Regression Bayesian Variable Selection Methods in Case-Control Sequencing Studies
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Serveur d'exploration sur les relations entre la France et l'Australie

Post-hoc Analysis for Detecting Individual Rare Variant Risk Associations using Probit Regression Bayesian Variable Selection Methods in Case-Control Sequencing Studies

Post-hoc Analysis for Detecting Individual Rare Variant Risk Associations using Probit Regression Bayesian Variable Selection Methods in Case-Control Sequencing Studies

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	Serveur d'exploration sur les relations entre la France et l'Australie
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