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Modeling Linkage Disequilibrium Increases Accuracy of Polygenic Risk Scores

The American Journal of Human Genetics · 2015 · Vol. 97(4) · pp. 576–592

Bjarni J. Vilhjálmsson(Broad Institute)Jian Yang(Translational Research Institute)Hilary K. Finucane(Broad Institute)Alexander Gusev(Broad Institute)Sara Lindström(Harvard University)Stephan Ripke(Broad Institute)Giulio Genovese(Broad Institute)Po‐Ru Loh(Broad Institute)Gaurav Bhatia(Broad Institute)Ron Do(Icahn School of Medicine at Mount Sinai)Tristan J. Hayeck(Broad Institute)Hong‐Hee Won(Broad Institute)Sekar Kathiresan(Broad Institute)Michele T. Pato(University of Southern California)Carlos N. Pato(University of Southern California)Rulla M. Tamimi(Brigham and Women's Hospital)Eli A. Stahl(Broad Institute)Noah Zaitlen(University of California, San Francisco)Bogdan Paşaniuc(University of California, Los Angeles)Gillian M. Belbin(Icahn School of Medicine at Mount Sinai)Eimear E. Kenny(Icahn School of Medicine at Mount Sinai)Mikkel Heide Schierup(Aarhus University)Philip L. De Jager(Broad Institute)Nikolaos A. Patsopoulos(Broad Institute)Steve McCarroll(Broad Institute)Mark J. Daly(Broad Institute)Shaun Purcell(Broad Institute)Daniel I. Chasman(Brigham and Women's Hospital)Benjamin M. Neale(Broad Institute)Michael E. Goddard(The University of Melbourne)Peter M. Visscher(Translational Research Institute)Peter Kraft(Broad Institute)Nick Patterson(Broad Institute)Alkes L. Price(Broad Institute)Stephan Ripke(Broad Institute)Benjamin M. Neale(Broad Institute)Aiden CorvinJames WaltersKai-How FarhPeter Holmans(Broad Institute)Phil Lee(Broad Institute)Brendan Bulik‐SullivanDavid CollierHailiang HuangTune H. PersIngrid AgartzEsben AgerboMargot AlbusMadeline Alexander(Broad Institute)Farooq Amin(Broad Institute)Silviu‐Alin BacanuMartin BegemannRichard A. BelliveauJudit BeneSarah E. BergenElizabeth BevilacquaTim B. BigdeliDonald W. BlackRichard BruggemanNancy G. BuccolaRandy L. BucknerWilliam ByerleyWiepke CahnGuiqing CaiDominique CampionRita M. CantorVaughan J. Carr(Broad Institute)Noa Carrera(University of California, San Francisco)Stanley V. CattsKimberly D. ChambertRaymond ChanRonald Y.L. ChenEric ChenWei ChengEric F.C. CheungSiow Ann ChongC. Robert CloningerDavid CohenNadine CohenPaul CormicanNick Craddock(Broad Institute)James J. CrowleyDavid CurtisMichael Davidson(The University of Melbourne)Kenneth L. DavisFranziska DegenhardtJurgen Del‐FaveroLynn E. DeLisiDitte DemontisDimitris DikeosTimothy G. DinanSrdjan DjurovicGary DonohoeElodie DrapeauJubao DuanFrank DudbridgeNaser DurmishiPeter Eichhammer(Broad Institute)Johan G. ErikssonValentina Escott‐PriceLaurent EssiouxAyman H. FanousMartilias S. FarrellJosef FrankLude FrankeRobert FreedmanNelson B. FreimerMarion FriedlJoseph I. FriedmanMenachem FromerGiulio Genovese(Broad Institute)Lyudmila GeorgievaElliot S. GershonIna GieglingPaola Giusti-RodrguezStephanie GodardJacqueline I. GoldsteinВ. Е. ГолимбетSrihari GopalJacob GrattenJakob GroveLieuwe de HaanChristian HammerMarian L. HamshereThomas Folkmann Hansen(Broad Institute)Thomas Folkmann HansenVahram HaroutunianAnnette M. HartmannFrans A. HenskensStefan HermsJoel N. HirschhornPer HoffmannAndrea HofmanMads V. HollegaardDavid M. HougaardMasashi IkedaInge JoaAntonio JuliàRené S. KahnLuba KalaydjievaSena Karachanak-YankovaJuha KarjalainenDavid KavanaghMatthew C. KellerBrian KellyJames L. KennedyAndrey KhruninYunjung KimJānis KloviņšJames A. KnowlesBettina KonteVaidutis KučinskasZita Aušrelė KučinskienėHana Kuzelova-PtackovaAnna K. KählerClaudine LaurentJimmy Lee Chee KeongSang LeeSophie E. LeggeBernard LererMiaoxin Li(Broad Institute)Tao Li(Broad Institute)Kung-Yee LiangJeffrey A. LiebermanLimborskaia SaCarmel M. LoughlandJan LubińskiJouko LnnqvistMilan MaçekPatrik K. E. MagnussonBrion S. MaherWolfgang MaierJacques MalletSara Marsal(Harvard University)Manuel MattheisenMorten MattingsdalRobert W. McCarleyColm McDonaldAndrew M. McIntoshSandra MeierCarin J. MeijerBéla MeleghIngrid MelleRaquelle I. Mesholam‐GatelyAndres MetspaluPatricia T. MichieLili MilaniVihra MilanovaYounes MokrabDerek W. MorrisOle MorsPreben Bo MortensenKieran C. MurphyRobin MurrayInez Myin‐GermeysBertram Mller-MyhsokMari NelisIgor NenadićDeborah A. NertneyGerald NestadtKristin K. NicodemusLiene Ņikitina-ZaķeLaura NisenbaumAnnelie NordinEadbhard O’CallaghanColm O’DushlaineF. Anthony O’NeillSang-Yun Oh(Broad Institute)Ann OlincyLine OlsenJim van OsChristos PantelisGeorge N. PapadimitriouSergi PapiolElena ParkhomenkoMichele T. Pato(University of Southern California)Tiina PaunioMilica Pejović-MilovančevićDiana O. PerkinsOlli PietilinenJonathan PimmAndrew PocklingtonJohn PowellAlkes L. Price✉(Broad Institute)Ann E. PulverShaun Purcell(Broad Institute)Digby QuestedHenrik Berg RasmussenAbraham ReichenbergMark A. Reimers(Broad Institute)Alexander RichardsJoshua L. RoffmanPanos RoussosDouglas M. RuderferVeikko SalomaaAlan R. SandersUlrich SchallChristian SchubertThomas G. SchulzeSibylle G. SchwabEdward M. ScolnickRodney J. ScottLarry J. SeidmanJianxin ShiEngilbert SigurðssonTeimuraz SilagadzeJeremy M. SilvermanKang SimP. A. SlominskyJordan W. SmollerHon‐Cheong So(Broad Institute)Chris C. A. SpencerEli A. Stahl(Broad Institute)Hreinn StefánssonStacy SteinbergElisabeth StögmannRichard E. StraubEric StrengmanJana StrohmaierT. Scott StroupMythily SubramaniamJaana SuvisaariDragan M. ŠvrakićJin SzatkiewiczErik SdermanSrinivas ThirumalaiДрага ТончеваPaul A. TooneySarah TosatoJuha VeijolaJohn L. WaddingtonDermot WalshDai WangQiang WangBradley T. WebbMark Weiser(Broad Institute)Dieter B. WildenauerNigel WilliamsStephanie WilliamsStephanie H. WittAaron R. WolenEmily WongBrandon K. WormleyJing WuHualin Simon XiClement C. Zai(University of California, San Francisco)Xuebin ZhengFritz ZimprichNaomi R. WrayKāri StefánssonPeter M. Visscher(Translational Research Institute)Rolf AdolfssonOle A. AndreassenDouglas BlackwoodElvira BramonJoseph D. BuxbaumAnders D. BørglumSven CichonAriel DarvasiEnrico DomeniciHannelore EhrenreichTōnu EskoPablo V. GejmanMichael Gill(Icahn School of Medicine at Mount Sinai)Hugh GurlingChristina M. HultmanNakao IwataAssen JablenskyErik G. JönssonKenneth S. KendlerGeorge KirovJo KnightTodd LenczDouglas F. LevinsonQingqin S. Li(Broad Institute)Jianjun LiuAnil K. MalhotraSteven A. McCarroll(Broad Institute)Andrew McQuillinJennifer L. MoranPreben Bo MortensenBryan MowryMarkus M. NthenRoel A. OphoffMichael J. OwenAarno PalotieCarlos N. Pato(University of Southern California)Tracey L. PetryshenDaniëlle PosthumaMarcella RietschelBrien P. RileyDan Rujescu(Brigham and Women's Hospital)Pak C. ShamPamela SklarDavid St ClairDaniel R. WeinbergerJens R. WendlandThomas WergeMark J. Daly(Broad Institute)Patrick F. SullivanMichael O’DonovanPeter Kraft(Broad Institute)David J. HunterMuriel A. AdankHabibul AhsanKristiina AittomäkiLaura BagliettoSonja I. BerndtCarl Blomquist(University of Southern California)Federico CanzianJenny Chang‐ClaudeStephen J. ChanockLaura CrisponiKamila CzeneNorbert DahmenIsabel dos‐Santos‐SilvaDouglas F. EastonA. Heather EliassenJonine D. FigueroaOlivia FletcherMontserrat García‐ClosasMia M. GaudetLorna J. GibsonChristopher A. HaimanPer HallAditi HazraRebecca HeinBrian E. HendersonAlbert HofmanJohn L. HopperAstrid IrwantoMattias JohanssonRudolf KaaksMuhammad G. KibriyaPeter Lichtner(Broad Institute)Sara Lindström(Harvard University)Jianjun LiuEiliv LundEnes MakalicAlfons MeindlHanne Meijers‐HeijboerBertram Müller‐MyhsokTaru MuranenHeli NevanlinnaPetra H. PeetersJulian PetoRoss L. PrenticeNazneen RahmanMaría‐José SánchezDaniel F. SchmidtRita K. SchmutzlerMelissa C. SoutheyRulla M. Tamimi(Brigham and Women's Hospital)Ruth C. TravisClare TurnbullAndré G. UitterlindenRob B. van der LuijtQuinten WaisfiszThomas J. WangAlice S. WhittemoreRose Yang(Translational Research Institute)Wei Zheng

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Genetic Associations and Epidemiology Bioinformatics and Genomic Networks Advanced Causal Inference TechniquesLinkage disequilibriumDisequilibriumPolygenic risk scorePruningComputer scienceStatisticsSample size determinationThresholdingArtificial intelligenceSample (material)

MeSH terms

GenotypeHumansModels, TheoreticalMultiple SclerosisPhenotypePrognosisSchizophreniaLinkage DisequilibriumMultifactorial InheritancePolymorphism, Single NucleotideQuantitative Trait LociGenome-Wide Association Study