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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Post-hoc Analysis for Detecting Individual Rare Variant Risk Associations using Probit Regression Bayesian Variable Selection Methods in Case-Control Sequencing Studies</title><author><name sortKey="Larson, Nicholas B" sort="Larson, Nicholas B" uniqKey="Larson N" first="Nicholas B." last="Larson">Nicholas B. Larson</name><affiliation><nlm:aff id="A1">Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN</nlm:aff></affiliation></author><author><name sortKey="Mcdonnell, Shannon" sort="Mcdonnell, Shannon" uniqKey="Mcdonnell S" first="Shannon" last="Mcdonnell">Shannon Mcdonnell</name><affiliation><nlm:aff id="A1">Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN</nlm:aff></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><nlm:aff id="A2">Dept. Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT</nlm:aff></affiliation></author><author><name sortKey="Teerlink, Craig" sort="Teerlink, Craig" uniqKey="Teerlink C" first="Craig" last="Teerlink">Craig Teerlink</name><affiliation><nlm:aff id="A2">Dept. Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT</nlm:aff></affiliation></author><author><name sortKey="Stanford, Janet" sort="Stanford, Janet" uniqKey="Stanford J" first="Janet" last="Stanford">Janet Stanford</name><affiliation><nlm:aff id="A3">Fred Hutchinson Cancer Research Center, Seattle, WA</nlm:aff></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><nlm:aff id="A4">National Human Genome Research Institute, Bethesda, MD</nlm:aff></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><nlm:aff id="A5">Johns Hopkins Hospital, Department of Urology, Baltimore, MD</nlm:aff></affiliation></author><author><name sortKey="Xu, Jianfeng" sort="Xu, Jianfeng" uniqKey="Xu J" first="Jianfeng" last="Xu">Jianfeng Xu</name><affiliation><nlm:aff id="A6">NorthShore University Health System Research Institute, Chicago, IL</nlm:aff></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><nlm:aff id="A7">Depts. of Internal Medicine and Urology, University of Michigan Medical School, Ann Arbor, MI</nlm:aff></affiliation></author><author><name sortKey="Lange, Ethan" sort="Lange, Ethan" uniqKey="Lange E" first="Ethan" last="Lange">Ethan Lange</name><affiliation><nlm:aff id="A8">Dept. of Genetics, University of North Carolina, Chapel Hill, NC</nlm:aff></affiliation></author><author><name sortKey="Schleutker, Johanna" sort="Schleutker, Johanna" uniqKey="Schleutker J" first="Johanna" last="Schleutker">Johanna Schleutker</name><affiliation><nlm:aff id="A9">Dept. of Medical Biochemistry and Genetics, Institute of Biomedicine, University of Turku, Finland</nlm:aff></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><nlm:aff id="A10">Integrated Cancer Genomics Division, The Translational Genomics Research Institute, Phoenix, AZ</nlm:aff></affiliation></author><author><name sortKey="Powell, Isaac" sort="Powell, Isaac" uniqKey="Powell I" first="Isaac" last="Powell">Isaac Powell</name><affiliation><nlm:aff id="A11">Wayne State University, Detroit, MI</nlm:aff></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><nlm:aff id="A12">Statistical Genetics Section, National Human Genome Research Institute, Bethesda, MD</nlm:aff></affiliation></author><author><name sortKey="Cussenot, Olivier" sort="Cussenot, Olivier" uniqKey="Cussenot O" first="Olivier" last="Cussenot">Olivier Cussenot</name><affiliation><nlm:aff id="A13">CeRePP, Hopital Tenon, Paris, France</nlm:aff></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><nlm:aff id="A13">CeRePP, Hopital Tenon, Paris, France</nlm:aff></affiliation></author><author><name sortKey="Giles, Graham" sort="Giles, Graham" uniqKey="Giles G" first="Graham" last="Giles">Graham Giles</name><affiliation><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></affiliation></author><author><name sortKey="Macinnis, Robert" sort="Macinnis, Robert" uniqKey="Macinnis R" first="Robert" last="Macinnis">Robert Macinnis</name><affiliation><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></affiliation></author><author><name sortKey="Maier, Christiane" sort="Maier, Christiane" uniqKey="Maier C" first="Christiane" last="Maier">Christiane Maier</name><affiliation><nlm:aff id="A15">Dept. of Urology, University of Ulm, Ulm, Germany</nlm:aff></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><nlm:aff id="A16">Dept. Health Research and Policy, Stanford University, Stanford, CA</nlm:aff></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><nlm:aff id="A17">Dept. of Urology, University of Southern California, Los Angeles, CA</nlm:aff></affiliation></author><author><name sortKey="Wiklund, Fredrik" sort="Wiklund, Fredrik" uniqKey="Wiklund F" first="Fredrik" last="Wiklund">Fredrik Wiklund</name><affiliation><nlm:aff id="A18">Dept. of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden</nlm:aff></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><nlm:aff id="A19">Northwestern University Feinberg School of Medicine, Chicago, IL</nlm:aff></affiliation></author><author><name sortKey="Foulkes, William" sort="Foulkes, William" uniqKey="Foulkes W" first="William" last="Foulkes">William Foulkes</name><affiliation><nlm:aff id="A20">Depts. Of Oncology and Human Genetics, Montreal General Hospital, Montreal QC, Canada</nlm:aff></affiliation></author><author><name sortKey="Mandal, Diptasri" sort="Mandal, Diptasri" uniqKey="Mandal D" first="Diptasri" last="Mandal">Diptasri Mandal</name><affiliation><nlm:aff id="A21">Dept. of Genetics, LSU Health Sciences Center, New Orleans, LA</nlm:aff></affiliation></author><author><name sortKey="Eeles, Rosalind" sort="Eeles, Rosalind" uniqKey="Eeles R" first="Rosalind" last="Eeles">Rosalind Eeles</name><affiliation><nlm:aff id="A22">Genetics and Epidemiology, Institute of Cancer Research, Sutton Surrey, UK</nlm:aff></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><nlm:aff id="A22">Genetics and Epidemiology, Institute of Cancer Research, Sutton Surrey, UK</nlm:aff></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><nlm:aff id="A23">Dept. of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN</nlm:aff></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><nlm:aff id="A23">Dept. of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN</nlm:aff></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><nlm:aff id="A24">Dept. of Neurology, Mayo Clinic, Rochester, MN</nlm:aff></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><nlm:aff id="A25">Dept. of Laboratory Medicine/Pathology, Mayo Clinic, Rochester, MN</nlm:aff></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><nlm:aff id="A1">Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN</nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">27312771</idno><idno type="pmc">5063501</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5063501</idno><idno type="RBID">PMC:5063501</idno><idno type="doi">10.1002/gepi.21983</idno><date when="2016">2016</date><idno type="wicri:Area/Pmc/Corpus">002027</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">002027</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Post-hoc Analysis for Detecting Individual Rare Variant Risk Associations using Probit Regression Bayesian Variable Selection Methods in Case-Control Sequencing Studies</title><author><name sortKey="Larson, Nicholas B" sort="Larson, Nicholas B" uniqKey="Larson N" first="Nicholas B." last="Larson">Nicholas B. Larson</name><affiliation><nlm:aff id="A1">Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN</nlm:aff></affiliation></author><author><name sortKey="Mcdonnell, Shannon" sort="Mcdonnell, Shannon" uniqKey="Mcdonnell S" first="Shannon" last="Mcdonnell">Shannon Mcdonnell</name><affiliation><nlm:aff id="A1">Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN</nlm:aff></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><nlm:aff id="A2">Dept. Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT</nlm:aff></affiliation></author><author><name sortKey="Teerlink, Craig" sort="Teerlink, Craig" uniqKey="Teerlink C" first="Craig" last="Teerlink">Craig Teerlink</name><affiliation><nlm:aff id="A2">Dept. Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT</nlm:aff></affiliation></author><author><name sortKey="Stanford, Janet" sort="Stanford, Janet" uniqKey="Stanford J" first="Janet" last="Stanford">Janet Stanford</name><affiliation><nlm:aff id="A3">Fred Hutchinson Cancer Research Center, Seattle, WA</nlm:aff></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><nlm:aff id="A4">National Human Genome Research Institute, Bethesda, MD</nlm:aff></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><nlm:aff id="A5">Johns Hopkins Hospital, Department of Urology, Baltimore, MD</nlm:aff></affiliation></author><author><name sortKey="Xu, Jianfeng" sort="Xu, Jianfeng" uniqKey="Xu J" first="Jianfeng" last="Xu">Jianfeng Xu</name><affiliation><nlm:aff id="A6">NorthShore University Health System Research Institute, Chicago, IL</nlm:aff></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><nlm:aff id="A7">Depts. of Internal Medicine and Urology, University of Michigan Medical School, Ann Arbor, MI</nlm:aff></affiliation></author><author><name sortKey="Lange, Ethan" sort="Lange, Ethan" uniqKey="Lange E" first="Ethan" last="Lange">Ethan Lange</name><affiliation><nlm:aff id="A8">Dept. of Genetics, University of North Carolina, Chapel Hill, NC</nlm:aff></affiliation></author><author><name sortKey="Schleutker, Johanna" sort="Schleutker, Johanna" uniqKey="Schleutker J" first="Johanna" last="Schleutker">Johanna Schleutker</name><affiliation><nlm:aff id="A9">Dept. of Medical Biochemistry and Genetics, Institute of Biomedicine, University of Turku, Finland</nlm:aff></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><nlm:aff id="A10">Integrated Cancer Genomics Division, The Translational Genomics Research Institute, Phoenix, AZ</nlm:aff></affiliation></author><author><name sortKey="Powell, Isaac" sort="Powell, Isaac" uniqKey="Powell I" first="Isaac" last="Powell">Isaac Powell</name><affiliation><nlm:aff id="A11">Wayne State University, Detroit, MI</nlm:aff></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><nlm:aff id="A12">Statistical Genetics Section, National Human Genome Research Institute, Bethesda, MD</nlm:aff></affiliation></author><author><name sortKey="Cussenot, Olivier" sort="Cussenot, Olivier" uniqKey="Cussenot O" first="Olivier" last="Cussenot">Olivier Cussenot</name><affiliation><nlm:aff id="A13">CeRePP, Hopital Tenon, Paris, France</nlm:aff></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><nlm:aff id="A13">CeRePP, Hopital Tenon, Paris, France</nlm:aff></affiliation></author><author><name sortKey="Giles, Graham" sort="Giles, Graham" uniqKey="Giles G" first="Graham" last="Giles">Graham Giles</name><affiliation><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></affiliation></author><author><name sortKey="Macinnis, Robert" sort="Macinnis, Robert" uniqKey="Macinnis R" first="Robert" last="Macinnis">Robert Macinnis</name><affiliation><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></affiliation></author><author><name sortKey="Maier, Christiane" sort="Maier, Christiane" uniqKey="Maier C" first="Christiane" last="Maier">Christiane Maier</name><affiliation><nlm:aff id="A15">Dept. of Urology, University of Ulm, Ulm, Germany</nlm:aff></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><nlm:aff id="A16">Dept. Health Research and Policy, Stanford University, Stanford, CA</nlm:aff></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><nlm:aff id="A17">Dept. of Urology, University of Southern California, Los Angeles, CA</nlm:aff></affiliation></author><author><name sortKey="Wiklund, Fredrik" sort="Wiklund, Fredrik" uniqKey="Wiklund F" first="Fredrik" last="Wiklund">Fredrik Wiklund</name><affiliation><nlm:aff id="A18">Dept. of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden</nlm:aff></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><nlm:aff id="A19">Northwestern University Feinberg School of Medicine, Chicago, IL</nlm:aff></affiliation></author><author><name sortKey="Foulkes, William" sort="Foulkes, William" uniqKey="Foulkes W" first="William" last="Foulkes">William Foulkes</name><affiliation><nlm:aff id="A20">Depts. Of Oncology and Human Genetics, Montreal General Hospital, Montreal QC, Canada</nlm:aff></affiliation></author><author><name sortKey="Mandal, Diptasri" sort="Mandal, Diptasri" uniqKey="Mandal D" first="Diptasri" last="Mandal">Diptasri Mandal</name><affiliation><nlm:aff id="A21">Dept. of Genetics, LSU Health Sciences Center, New Orleans, LA</nlm:aff></affiliation></author><author><name sortKey="Eeles, Rosalind" sort="Eeles, Rosalind" uniqKey="Eeles R" first="Rosalind" last="Eeles">Rosalind Eeles</name><affiliation><nlm:aff id="A22">Genetics and Epidemiology, Institute of Cancer Research, Sutton Surrey, UK</nlm:aff></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><nlm:aff id="A22">Genetics and Epidemiology, Institute of Cancer Research, Sutton Surrey, UK</nlm:aff></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><nlm:aff id="A23">Dept. of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN</nlm:aff></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><nlm:aff id="A23">Dept. of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN</nlm:aff></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><nlm:aff id="A24">Dept. of Neurology, Mayo Clinic, Rochester, MN</nlm:aff></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><nlm:aff id="A25">Dept. of Laboratory Medicine/Pathology, Mayo Clinic, Rochester, MN</nlm:aff></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><nlm:aff id="A1">Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN</nlm:aff></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></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></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><pmc article-type="research-article"><pmc-comment>The publisher of this article does not allow downloading of the full text in XML form.</pmc-comment>
<pmc-dir>properties manuscript</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-journal-id">8411723</journal-id><journal-id journal-id-type="pubmed-jr-id">3864</journal-id><journal-id journal-id-type="nlm-ta">Genet Epidemiol</journal-id><journal-id journal-id-type="iso-abbrev">Genet. Epidemiol.</journal-id><journal-title-group><journal-title>Genetic epidemiology</journal-title></journal-title-group><issn pub-type="ppub">0741-0395</issn><issn pub-type="epub">1098-2272</issn></journal-meta><article-meta><article-id pub-id-type="pmid">27312771</article-id><article-id pub-id-type="pmc">5063501</article-id><article-id pub-id-type="doi">10.1002/gepi.21983</article-id><article-id pub-id-type="manuscript">NIHMS820987</article-id><article-categories><subj-group subj-group-type="heading"><subject>Article</subject></subj-group></article-categories><title-group><article-title>Post-hoc Analysis for Detecting Individual Rare Variant Risk Associations using Probit Regression Bayesian Variable Selection Methods in Case-Control Sequencing Studies</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Larson</surname><given-names>Nicholas B.</given-names></name><xref ref-type="aff" rid="A1">1</xref><xref rid="FN1" ref-type="author-notes">§</xref></contrib><contrib contrib-type="author"><name><surname>McDonnell</surname><given-names>Shannon</given-names></name><xref ref-type="aff" rid="A1">1</xref></contrib><contrib contrib-type="author"><name><surname>Albright</surname><given-names>Lisa Cannon</given-names></name><xref ref-type="aff" rid="A2">2</xref></contrib><contrib contrib-type="author"><name><surname>Teerlink</surname><given-names>Craig</given-names></name><xref ref-type="aff" rid="A2">2</xref></contrib><contrib contrib-type="author"><name><surname>Stanford</surname><given-names>Janet</given-names></name><xref ref-type="aff" rid="A3">3</xref></contrib><contrib contrib-type="author"><name><surname>Ostrander</surname><given-names>Elaine A.</given-names></name><xref ref-type="aff" rid="A4">4</xref></contrib><contrib contrib-type="author"><name><surname>Isaacs</surname><given-names>William B.</given-names></name><xref ref-type="aff" rid="A5">5</xref></contrib><contrib contrib-type="author"><name><surname>Xu</surname><given-names>Jianfeng</given-names></name><xref ref-type="aff" rid="A6">6</xref></contrib><contrib contrib-type="author"><name><surname>Cooney</surname><given-names>Kathleen A.</given-names></name><xref ref-type="aff" rid="A7">7</xref></contrib><contrib contrib-type="author"><name><surname>Lange</surname><given-names>Ethan</given-names></name><xref ref-type="aff" rid="A8">8</xref></contrib><contrib contrib-type="author"><name><surname>Schleutker</surname><given-names>Johanna</given-names></name><xref ref-type="aff" rid="A9">9</xref></contrib><contrib contrib-type="author"><name><surname>Carpten</surname><given-names>John D.</given-names></name><xref ref-type="aff" rid="A10">10</xref></contrib><contrib contrib-type="author"><name><surname>Powell</surname><given-names>Isaac</given-names></name><xref ref-type="aff" rid="A11">11</xref></contrib><contrib contrib-type="author"><name><surname>Bailey-Wilson</surname><given-names>Joan</given-names></name><xref ref-type="aff" rid="A12">12</xref></contrib><contrib contrib-type="author"><name><surname>Cussenot</surname><given-names>Olivier</given-names></name><xref ref-type="aff" rid="A13">13</xref></contrib><contrib contrib-type="author"><name><surname>Cancel-Tassin</surname><given-names>Geraldine</given-names></name><xref ref-type="aff" rid="A13">13</xref></contrib><contrib contrib-type="author"><name><surname>Giles</surname><given-names>Graham</given-names></name><xref ref-type="aff" rid="A14">14</xref></contrib><contrib contrib-type="author"><name><surname>MacInnis</surname><given-names>Robert</given-names></name><xref ref-type="aff" rid="A14">14</xref></contrib><contrib contrib-type="author"><name><surname>Maier</surname><given-names>Christiane</given-names></name><xref ref-type="aff" rid="A15">15</xref></contrib><contrib contrib-type="author"><name><surname>Whittemore</surname><given-names>Alice S.</given-names></name><xref ref-type="aff" rid="A16">16</xref></contrib><contrib contrib-type="author"><name><surname>Hsieh</surname><given-names>Chih-Lin</given-names></name><xref ref-type="aff" rid="A17">17</xref></contrib><contrib contrib-type="author"><name><surname>Wiklund</surname><given-names>Fredrik</given-names></name><xref ref-type="aff" rid="A18">18</xref></contrib><contrib contrib-type="author"><name><surname>Catolona</surname><given-names>William J.</given-names></name><xref ref-type="aff" rid="A19">19</xref></contrib><contrib contrib-type="author"><name><surname>Foulkes</surname><given-names>William</given-names></name><xref ref-type="aff" rid="A20">20</xref></contrib><contrib contrib-type="author"><name><surname>Mandal</surname><given-names>Diptasri</given-names></name><xref ref-type="aff" rid="A21">21</xref></contrib><contrib contrib-type="author"><name><surname>Eeles</surname><given-names>Rosalind</given-names></name><xref ref-type="aff" rid="A22">22</xref></contrib><contrib contrib-type="author"><name><surname>Kote-Jarai</surname><given-names>Zsofia</given-names></name><xref ref-type="aff" rid="A22">22</xref></contrib><contrib contrib-type="author"><name><surname>Ackerman</surname><given-names>Michael J.</given-names></name><xref ref-type="aff" rid="A23">23</xref></contrib><contrib contrib-type="author"><name><surname>Olson</surname><given-names>Timothy M.</given-names></name><xref ref-type="aff" rid="A23">23</xref></contrib><contrib contrib-type="author"><name><surname>Klein</surname><given-names>Christopher J.</given-names></name><xref ref-type="aff" rid="A24">24</xref></contrib><contrib contrib-type="author"><name><surname>Thibodeau</surname><given-names>Stephen N.</given-names></name><xref ref-type="aff" rid="A25">25</xref></contrib><contrib contrib-type="author"><name><surname>Schaid</surname><given-names>Daniel J.</given-names></name><xref ref-type="aff" rid="A1">1</xref></contrib></contrib-group><aff id="A1"><label>1</label>Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN</aff><aff id="A2"><label>2</label>Dept. Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT</aff><aff id="A3"><label>3</label>Fred Hutchinson Cancer Research Center, Seattle, WA</aff><aff id="A4"><label>4</label>National Human Genome Research Institute, Bethesda, MD</aff><aff id="A5"><label>5</label>Johns Hopkins Hospital, Department of Urology, Baltimore, MD</aff><aff id="A6"><label>6</label>NorthShore University Health System Research Institute, Chicago, IL</aff><aff id="A7"><label>7</label>Depts. of Internal Medicine and Urology, University of Michigan Medical School, Ann Arbor, MI</aff><aff id="A8"><label>8</label>Dept. of Genetics, University of North Carolina, Chapel Hill, NC</aff><aff id="A9"><label>9</label>Dept. of Medical Biochemistry and Genetics, Institute of Biomedicine, University of Turku, Finland</aff><aff id="A10"><label>10</label>Integrated Cancer Genomics Division, The Translational Genomics Research Institute, Phoenix, AZ</aff><aff id="A11"><label>11</label>Wayne State University, Detroit, MI</aff><aff id="A12"><label>12</label>Statistical Genetics Section, National Human Genome Research Institute, Bethesda, MD</aff><aff id="A13"><label>13</label>CeRePP, Hopital Tenon, Paris, France</aff><aff id="A14"><label>14</label>Cancer Epidemiology Centre, Cancer Council Victoria, and Centre for Epidemiology and Biostatistics, School of Population and Global Health, University of Melbourne, Melbourne, Australia</aff><aff id="A15"><label>15</label>Dept. of Urology, University of Ulm, Ulm, Germany</aff><aff id="A16"><label>16</label>Dept. Health Research and Policy, Stanford University, Stanford, CA</aff><aff id="A17"><label>17</label>Dept. of Urology, University of Southern California, Los Angeles, CA</aff><aff id="A18"><label>18</label>Dept. of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden</aff><aff id="A19"><label>19</label>Northwestern University Feinberg School of Medicine, Chicago, IL</aff><aff id="A20"><label>20</label>Depts. Of Oncology and Human Genetics, Montreal General Hospital, Montreal QC, Canada</aff><aff id="A21"><label>21</label>Dept. of Genetics, LSU Health Sciences Center, New Orleans, LA</aff><aff id="A22"><label>22</label>Genetics and Epidemiology, Institute of Cancer Research, Sutton Surrey, UK</aff><aff id="A23"><label>23</label>Dept. of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN</aff><aff id="A24"><label>24</label>Dept. of Neurology, Mayo Clinic, Rochester, MN</aff><aff id="A25"><label>25</label>Dept. of Laboratory Medicine/Pathology, Mayo Clinic, Rochester, MN</aff><author-notes><corresp id="FN1"><label>§</label>Corresponding author: Nicholas B. Larson, PhD, Department of Health Sciences Research, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, <email>Larson.nicholas@mayo.edu</email>, Phone: (507) – 293 – 1700, Fax: (507) – 284 – 1516</corresp></author-notes><pub-date pub-type="nihms-submitted"><day>6</day><month>10</month><year>2016</year></pub-date><pub-date pub-type="epub"><day>17</day><month>6</month><year>2016</year></pub-date><pub-date pub-type="ppub"><month>9</month><year>2016</year></pub-date><pub-date pub-type="pmc-release"><day>01</day><month>9</month><year>2017</year></pub-date><volume>40</volume><issue>6</issue><fpage>461</fpage><lpage>469</lpage><pmc-comment>elocation-id from pubmed: 10.1002/gepi.21983</pmc-comment>
<abstract><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></abstract><kwd-group><kwd>next-generation sequencing</kwd><kwd>MCMC</kwd><kwd>prostate cancer</kwd><kwd>burden testing</kwd></kwd-group></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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