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An Evolutionary Framework for Association Testing in Resequencing Studies 英文参考文献
AnEvolutionaryFrameworkforAssociationTestingin
ResequencingStudies
C.RyanKing1*,PaulJ.Rathouz1,2,DanL.Nicolae3
1Department ofHealthStudies,UniversityofChicago,Chicago,Illinois,United StatesofAmerica, 2Department ofBiostatisticsandMedicalInformatics, Universityof
Wisconsin-Madison,Madison,Wisconsin,UnitedStatesofAmerica,3DepartmentsofMedicine,Statistics,andHumanGenetics,UniversityofChicago,Chicago,Illinois,
UnitedStatesofAmerica
Abstract
Sequencing technologies are becoming cheap enough to apply to large numbers of study participants and promise to
provide new insights into human phenotypes by bringing to light rare and previously unknown genetic variants. We
develop a new framework for the analysis of sequence data that incorporates all of the major features of previously
proposed approaches, including those focused on allele counts and allele burden, but is both more general and more
powerful.Weharnesspopulationgenetictheorytoprovidepriorinformationoneffectsizesandtocreateapoolingstrategy
for information from rare variants. Our method, EMMPAT (Evolutionary Mixed Model for Pooled Association Testing),
generates a single test per gene (substantially reducing multiple testing concerns), facilitates graphical summaries, and
improves the interpretation of results by allowing calculation of attributable variance. Simulations show that, relative to
previouslyusedapproaches,ourmethodincreasesthepowertodetectgenesthataffectphenotypewhennaturalselection
haskeptalleleswithlargeeffectsizesrare.Wedemonstrateourapproachonapopulation-basedre-sequencingstudyof
associationbetweenserumtriglyceridesandvariationinANGPTL4.
Citation: King CR, Rathouz PJ, Nicolae DL (2010) An Evolutionary Framework for Association Testing in Resequencing Studies. PLoS Genet 6(11): e1001202.
doi:10.1371/journal.pgen.1001202
Editor:JonathanMarchini,UniversityofOxford,UnitedKingdom
ReceivedMay12,2010;AcceptedOctober7,2010;PublishedNovember11,2010
Copyright:?2010Kingetal.Thisisanopen-accessarticledist
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