gsSKAT: Rapid gene set analysis and multiple testing correction for rare-variant association studies using weighted linear kernels.
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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 E. Bailey-Wilson [États-Unis] ; Olivier Cussenot [France] ; Geraldine Cancel-Tassin [France] ; Graham G. Giles [Australie] ; Robert J. 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 [ 1098-2272 ] ; 2017.
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Abstract
Next-generation sequencing technologies have afforded unprecedented characterization of low-frequency and rare genetic variation. Due to low power for single-variant testing, aggregative methods are commonly used to combine observed rare variation within a single gene. Causal variation may also aggregate across multiple genes within relevant biomolecular pathways. Kernel-machine regression and adaptive testing methods for aggregative rare-variant association testing have been demonstrated to be powerful approaches for pathway-level analysis, although these methods tend to be computationally intensive at high-variant dimensionality and require access to complete data. An additional analytical issue in scans of large pathway definition sets is multiple testing correction. Gene set definitions may exhibit substantial genic overlap, and the impact of the resultant correlation in test statistics on Type I error rate control for large agnostic gene set scans has not been fully explored. Herein, we first outline a statistical strategy for aggregative rare-variant analysis using component gene-level linear kernel score test summary statistics as well as derive simple estimators of the effective number of tests for family-wise error rate control. We then conduct extensive simulation studies to characterize the behavior of our approach relative to direct application of kernel and adaptive methods under a variety of conditions. We also apply our method to two case-control studies, respectively, evaluating rare variation in hereditary prostate cancer and schizophrenia. Finally, we provide open-source R code for public use to facilitate easy application of our methods to existing rare-variant analysis results.
DOI: 10.1002/gepi.22036
PubMed: 28211093
Affiliations:
- Allemagne, Australie, Canada, Finlande, France, Royaume-Uni, Suède, États-Unis
- Angleterre, Bade-Wurtemberg, Californie, Caroline du Nord, District de Tübingen, Finlande occidentale, Grand Londres, Illinois, Louisiane, Maryland, Michigan, Minnesota, Svealand, Utah, Victoria (État), Washington (État), Île-de-France
- Londres, Los Angeles, Melbourne, Paris, Stockholm, Turku, Ulm
- Université d'Ulm, Université de Californie du Sud, Université de Turku
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Catolona</name><affiliation wicri:level="2"><nlm:affiliation>Department of Urology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Urology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois</wicri:regionArea><placeName><region type="state">Illinois</region></placeName></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:affiliation>Department of Oncology, Montreal General Hospital, Montreal, Quebec, Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Department of Oncology, Montreal General Hospital, Montreal, Quebec</wicri:regionArea><wicri:noRegion>Quebec</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:affiliation>Department of Genetics, LSU Health Sciences Center, New Orleans, Louisiana, United States of America.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Genetics, LSU Health Sciences Center, New Orleans, Louisiana</wicri:regionArea><placeName><region type="state">Louisiane</region></placeName></affiliation></author><author><name sortKey="Eeles, Rosalind" sort="Eeles, Rosalind" uniqKey="Eeles R" first="Rosalind" last="Eeles">Rosalind Eeles</name><affiliation wicri:level="3"><nlm:affiliation>The Institute of Cancer Research, London, UK.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>The Institute of Cancer Research, London</wicri:regionArea><placeName><settlement type="city">Londres</settlement><region type="country">Angleterre</region><region type="région" nuts="1">Grand Londres</region></placeName></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="3"><nlm:affiliation>The Institute of Cancer Research, London, UK.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>The Institute of Cancer Research, London</wicri:regionArea><placeName><settlement type="city">Londres</settlement><region type="country">Angleterre</region><region type="région" nuts="1">Grand Londres</region></placeName></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:affiliation>Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, Minnesota, United States of America.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, Minnesota</wicri:regionArea><placeName><region type="state">Minnesota</region></placeName></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:affiliation>Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, Minnesota, United States of America.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, Minnesota</wicri:regionArea><placeName><region type="state">Minnesota</region></placeName></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:affiliation>Department of Neurology, Mayo Clinic, Rochester, Minnesota, United States of America.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Neurology, Mayo Clinic, Rochester, Minnesota</wicri:regionArea><placeName><region type="state">Minnesota</region></placeName></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:affiliation>Department of Laboratory Medicine/Pathology, Mayo Clinic, Rochester, Minnesota, United States of America.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Laboratory Medicine/Pathology, Mayo Clinic, Rochester, Minnesota</wicri:regionArea><placeName><region type="state">Minnesota</region></placeName></affiliation></author><author><name sortKey="Schaid, Daniel J" sort="Schaid, Daniel J" uniqKey="Schaid D" first="Daniel J" last="Schaid">Daniel J. 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Larson</name><affiliation wicri:level="2"><nlm:affiliation>Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota</wicri:regionArea><placeName><region type="state">Minnesota</region></placeName></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:affiliation>Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota</wicri:regionArea><placeName><region type="state">Minnesota</region></placeName></affiliation></author><author><name sortKey="Cannon Albright, Lisa" sort="Cannon Albright, Lisa" uniqKey="Cannon Albright L" first="Lisa" last="Cannon Albright">Lisa Cannon Albright</name><affiliation wicri:level="2"><nlm:affiliation>Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah, United States of America.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah</wicri:regionArea><placeName><region type="state">Utah</region></placeName></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:affiliation>Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah, United States of America.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah</wicri:regionArea><placeName><region type="state">Utah</region></placeName></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:affiliation>Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Fred Hutchinson Cancer Research Center, Seattle, Washington</wicri:regionArea><placeName><region type="state">Washington (État)</region></placeName></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:affiliation>National Human Genome Research Institute, Bethesda, Maryland, United States of America.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>National Human Genome Research Institute, Bethesda, Maryland</wicri:regionArea><placeName><region type="state">Maryland</region></placeName></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:affiliation>Brady Urological Institute, School of Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Brady Urological Institute, School of Medicine, Johns Hopkins University, Baltimore, Maryland</wicri:regionArea><placeName><region type="state">Maryland</region></placeName></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:affiliation>NorthShore University HealthSystem Research Institute, Chicago, Illinois, United States of America.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>NorthShore University HealthSystem Research Institute, Chicago, Illinois</wicri:regionArea><placeName><region type="state">Illinois</region></placeName></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:affiliation>Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah, United States of America.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah</wicri:regionArea><placeName><region type="state">Utah</region></placeName></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:affiliation>Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, United States of America.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Genetics, University of North Carolina, Chapel Hill, North Carolina</wicri:regionArea><placeName><region type="state">Caroline du Nord</region></placeName></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:affiliation>Department of Medical Biochemistry and Genetics, Institute of Biomedicine, University of Turku, Turku, Finland.</nlm:affiliation><country xml:lang="fr">Finlande</country><wicri:regionArea>Department of Medical Biochemistry and Genetics, Institute of Biomedicine, University of Turku, Turku</wicri:regionArea><placeName><settlement type="city">Turku</settlement><region type="région" nuts="2">Finlande occidentale</region><settlement type="city">Turku</settlement></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="4"><nlm:affiliation>Department of Translational Genomics, University of Southern California, Los Angeles, California, United States of America.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Translational Genomics, University of Southern California, Los Angeles, California</wicri:regionArea><placeName><region type="state">Californie</region><settlement type="city">Los Angeles</settlement></placeName><orgName type="university">Université de Californie du Sud</orgName></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:affiliation>Department of Urology, Wayne State University, Detroit, Michigan, United States of America.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Urology, Wayne State University, Detroit, Michigan</wicri:regionArea><placeName><region type="state">Michigan</region></placeName></affiliation></author><author><name sortKey="Bailey Wilson, Joan E" sort="Bailey Wilson, Joan E" uniqKey="Bailey Wilson J" first="Joan E" last="Bailey-Wilson">Joan E. Bailey-Wilson</name><affiliation wicri:level="2"><nlm:affiliation>Statistical Genetics Section, National Human Genome Research Institute, Bethesda, Maryland, United States of America.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Statistical Genetics Section, National Human Genome Research Institute, Bethesda, Maryland</wicri:regionArea><placeName><region type="state">Maryland</region></placeName></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:affiliation>CeRePP, Hopital Tenon, Paris, France.</nlm:affiliation><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:affiliation>CeRePP, Hopital Tenon, Paris, France.</nlm:affiliation><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 G" sort="Giles, Graham G" uniqKey="Giles G" first="Graham G" last="Giles">Graham G. Giles</name><affiliation wicri:level="3"><nlm:affiliation>Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne</wicri:regionArea><placeName><settlement type="city">Melbourne</settlement><region type="état">Victoria (État)</region></placeName></affiliation></author><author><name sortKey="Macinnis, Robert J" sort="Macinnis, Robert J" uniqKey="Macinnis R" first="Robert J" last="Macinnis">Robert J. Macinnis</name><affiliation wicri:level="3"><nlm:affiliation>Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne</wicri:regionArea><placeName><settlement type="city">Melbourne</settlement><region type="état">Victoria (État)</region></placeName></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:affiliation>Department of Urology, University of Ulm, Ulm, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Department 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:affiliation>Department of Health Research and Policy, Stanford University, Stanford, California, United States of America.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Health Research and Policy, Stanford University, Stanford, California</wicri:regionArea><placeName><region type="state">Californie</region></placeName></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="4"><nlm:affiliation>Department of Urology, University of Southern California, Los Angeles, California, United States of America.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Urology, University of Southern California, Los Angeles, California</wicri:regionArea><placeName><region type="state">Californie</region><settlement type="city">Los Angeles</settlement></placeName><orgName type="university">Université de Californie du Sud</orgName></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:affiliation>Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.</nlm:affiliation><country xml:lang="fr">Suède</country><wicri:regionArea>Department 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:affiliation>Department of Urology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Urology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois</wicri:regionArea><placeName><region type="state">Illinois</region></placeName></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:affiliation>Department of Oncology, Montreal General Hospital, Montreal, Quebec, Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Department of Oncology, Montreal General Hospital, Montreal, Quebec</wicri:regionArea><wicri:noRegion>Quebec</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:affiliation>Department of Genetics, LSU Health Sciences Center, New Orleans, Louisiana, United States of America.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Genetics, LSU Health Sciences Center, New Orleans, Louisiana</wicri:regionArea><placeName><region type="state">Louisiane</region></placeName></affiliation></author><author><name sortKey="Eeles, Rosalind" sort="Eeles, Rosalind" uniqKey="Eeles R" first="Rosalind" last="Eeles">Rosalind Eeles</name><affiliation wicri:level="3"><nlm:affiliation>The Institute of Cancer Research, London, UK.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>The Institute of Cancer Research, London</wicri:regionArea><placeName><settlement type="city">Londres</settlement><region type="country">Angleterre</region><region type="région" nuts="1">Grand Londres</region></placeName></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="3"><nlm:affiliation>The Institute of Cancer Research, London, UK.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>The Institute of Cancer Research, London</wicri:regionArea><placeName><settlement type="city">Londres</settlement><region type="country">Angleterre</region><region type="région" nuts="1">Grand Londres</region></placeName></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:affiliation>Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, Minnesota, United States of America.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, Minnesota</wicri:regionArea><placeName><region type="state">Minnesota</region></placeName></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:affiliation>Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, Minnesota, United States of America.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, Minnesota</wicri:regionArea><placeName><region type="state">Minnesota</region></placeName></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:affiliation>Department of Neurology, Mayo Clinic, Rochester, Minnesota, United States of America.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Neurology, Mayo Clinic, Rochester, Minnesota</wicri:regionArea><placeName><region type="state">Minnesota</region></placeName></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:affiliation>Department of Laboratory Medicine/Pathology, Mayo Clinic, Rochester, Minnesota, United States of America.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Laboratory Medicine/Pathology, Mayo Clinic, Rochester, Minnesota</wicri:regionArea><placeName><region type="state">Minnesota</region></placeName></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:affiliation>Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota</wicri:regionArea><placeName><region type="state">Minnesota</region></placeName></affiliation></author></analytic><series><title level="j">Genetic epidemiology</title><idno type="eISSN">1098-2272</idno><imprint><date when="2017" type="published">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms</term><term>Computer Simulation</term><term>Genetic Association Studies (methods)</term><term>Genetic Variation</term><term>Humans</term><term>Models, Genetic</term><term>Sample Size</term><term>Statistics, Nonparametric</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Algorithmes</term><term>Humains</term><term>Modèles génétiques</term><term>Simulation numérique</term><term>Statistique non paramétrique</term><term>Taille d'échantillon</term><term>Variation génétique</term><term>Études d'associations génétiques ()</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Genetic Association Studies</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Algorithms</term><term>Computer Simulation</term><term>Genetic Variation</term><term>Humans</term><term>Models, Genetic</term><term>Sample Size</term><term>Statistics, Nonparametric</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Algorithmes</term><term>Humains</term><term>Modèles génétiques</term><term>Simulation numérique</term><term>Statistique non paramétrique</term><term>Taille d'échantillon</term><term>Variation génétique</term><term>Études d'associations génétiques</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Next-generation sequencing technologies have afforded unprecedented characterization of low-frequency and rare genetic variation. Due to low power for single-variant testing, aggregative methods are commonly used to combine observed rare variation within a single gene. Causal variation may also aggregate across multiple genes within relevant biomolecular pathways. Kernel-machine regression and adaptive testing methods for aggregative rare-variant association testing have been demonstrated to be powerful approaches for pathway-level analysis, although these methods tend to be computationally intensive at high-variant dimensionality and require access to complete data. An additional analytical issue in scans of large pathway definition sets is multiple testing correction. Gene set definitions may exhibit substantial genic overlap, and the impact of the resultant correlation in test statistics on Type I error rate control for large agnostic gene set scans has not been fully explored. Herein, we first outline a statistical strategy for aggregative rare-variant analysis using component gene-level linear kernel score test summary statistics as well as derive simple estimators of the effective number of tests for family-wise error rate control. We then conduct extensive simulation studies to characterize the behavior of our approach relative to direct application of kernel and adaptive methods under a variety of conditions. We also apply our method to two case-control studies, respectively, evaluating rare variation in hereditary prostate cancer and schizophrenia. Finally, we provide open-source R code for public use to facilitate easy application of our methods to existing rare-variant analysis results.</div></front></TEI><affiliations><list><country><li>Allemagne</li><li>Australie</li><li>Canada</li><li>Finlande</li><li>France</li><li>Royaume-Uni</li><li>Suède</li><li>États-Unis</li></country><region><li>Angleterre</li><li>Bade-Wurtemberg</li><li>Californie</li><li>Caroline du Nord</li><li>District de Tübingen</li><li>Finlande occidentale</li><li>Grand Londres</li><li>Illinois</li><li>Louisiane</li><li>Maryland</li><li>Michigan</li><li>Minnesota</li><li>Svealand</li><li>Utah</li><li>Victoria (État)</li><li>Washington (État)</li><li>Île-de-France</li></region><settlement><li>Londres</li><li>Los Angeles</li><li>Melbourne</li><li>Paris</li><li>Stockholm</li><li>Turku</li><li>Ulm</li></settlement><orgName><li>Université d'Ulm</li><li>Université de Californie du Sud</li><li>Université de Turku</li></orgName></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="Bailey Wilson, Joan E" sort="Bailey Wilson, Joan E" uniqKey="Bailey Wilson J" first="Joan E" last="Bailey-Wilson">Joan E. Bailey-Wilson</name><name sortKey="Cannon Albright, Lisa" sort="Cannon Albright, Lisa" uniqKey="Cannon Albright L" first="Lisa" last="Cannon Albright">Lisa Cannon Albright</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><name sortKey="Schaid, Daniel J" sort="Schaid, Daniel J" uniqKey="Schaid D" first="Daniel J" last="Schaid">Daniel J. Schaid</name><name sortKey="Stanford, Janet" sort="Stanford, Janet" uniqKey="Stanford J" first="Janet" last="Stanford">Janet Stanford</name><name sortKey="Teerlink, Craig" sort="Teerlink, Craig" uniqKey="Teerlink C" first="Craig" last="Teerlink">Craig Teerlink</name><name sortKey="Thibodeau, Stephen N" sort="Thibodeau, Stephen N" uniqKey="Thibodeau S" first="Stephen N" last="Thibodeau">Stephen N. Thibodeau</name><name sortKey="Whittemore, Alice S" sort="Whittemore, Alice S" uniqKey="Whittemore A" first="Alice S" last="Whittemore">Alice S. Whittemore</name><name sortKey="Xu, Jianfeng" sort="Xu, Jianfeng" uniqKey="Xu J" first="Jianfeng" last="Xu">Jianfeng Xu</name></country><country name="Finlande"><region name="Finlande occidentale"><name sortKey="Schleutker, Johanna" sort="Schleutker, Johanna" uniqKey="Schleutker J" first="Johanna" last="Schleutker">Johanna Schleutker</name></region></country><country name="France"><region name="Île-de-France"><name sortKey="Cussenot, Olivier" sort="Cussenot, Olivier" uniqKey="Cussenot O" first="Olivier" last="Cussenot">Olivier Cussenot</name></region><name sortKey="Cancel Tassin, Geraldine" sort="Cancel Tassin, Geraldine" uniqKey="Cancel Tassin G" first="Geraldine" last="Cancel-Tassin">Geraldine Cancel-Tassin</name></country><country name="Australie"><region name="Victoria (État)"><name sortKey="Giles, Graham G" sort="Giles, Graham G" uniqKey="Giles G" first="Graham G" last="Giles">Graham G. Giles</name></region><name sortKey="Macinnis, Robert J" sort="Macinnis, Robert J" uniqKey="Macinnis R" first="Robert J" last="Macinnis">Robert J. Macinnis</name></country><country name="Allemagne"><region name="Bade-Wurtemberg"><name sortKey="Maier, Christiane" sort="Maier, Christiane" uniqKey="Maier C" first="Christiane" last="Maier">Christiane Maier</name></region></country><country name="Suède"><region name="Svealand"><name sortKey="Wiklund, Fredrik" sort="Wiklund, Fredrik" uniqKey="Wiklund F" first="Fredrik" last="Wiklund">Fredrik Wiklund</name></region></country><country name="Canada"><noRegion><name sortKey="Foulkes, William" sort="Foulkes, William" uniqKey="Foulkes W" first="William" last="Foulkes">William Foulkes</name></noRegion></country><country name="Royaume-Uni"><region name="Angleterre"><name sortKey="Eeles, Rosalind" sort="Eeles, Rosalind" uniqKey="Eeles R" first="Rosalind" last="Eeles">Rosalind Eeles</name></region><name sortKey="Kote Jarai, Zsofia" sort="Kote Jarai, Zsofia" uniqKey="Kote Jarai Z" first="Zsofia" last="Kote-Jarai">Zsofia Kote-Jarai</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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