Global Biobank analyses provide lessons for developing polygenic risk scores across diverse cohorts.
Global Biobank analyses provide lessons for developing polygenic risk scores across diverse cohorts.
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全球生物库分析为在各种队列中发展多基因风险评分提供了教训。
DOI:
10.1016/j.xgen.2022.100241
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发表时间:
2023-01-11
期刊:
影响因子:
--
通讯作者:
Hirbo, Jibril
中科院分区:
文献类型:
--
作者:
Wang, Ying;Namba, Shinichi;Lopera, Esteban;Kerminen, Sini;Tsuo, Kristin;Lall, Kristi;Kanai, Masahiro;Zhou, Wei;Wu, Kuan-Han;Fave, Marie-Julie;Bhatta, Laxmi;Awadalla, Philip;Brumpton, Ben;Deelen, Patrick;Hveem, Kristian;Lo Faro, Valeria;Magi, Reedik;Murakami, Yoshinori;Sanna, Serena;Smoller, Jordan W.;Uzunovic, Jasmina;Wolford, Brooke N.;Willer, Cristen;Gamazon, Eric R.;Cox, Nancy J.;Surakka, Ida;Okada, Yukinori;Martin, Alicia R.;Hirbo, Jibril
Polygenic risk scores (PRSs) have been widely explored in precision medicine. However, few studies have thoroughly investigated their best practices in global populations across different diseases. We here utilized data from Global Biobank Meta-analysis Initiative (GBMI) to explore methodological considerations and PRS performance in 9 different biobanks for 14 disease endpoints. Specifically, we constructed PRSs using pruning and thresholding (P + T) and PRS-continuous shrinkage (CS). For both methods, using a European-based linkage disequilibrium (LD) reference panel resulted in comparable or higher prediction accuracy compared with several other non-European-based panels. PRS-CS overall outperformed the classic P + T method, especially for endpoints with higher SNP-based heritability. Notably, prediction accuracy is heterogeneous across endpoints, biobanks, and ancestries, especially for asthma, which has known variation in disease prevalence across populations. Overall, we provide lessons for PRS construction, evaluation, and interpretation using GBMI resources and highlight the importance of best practices for PRS in the biobank-scale genomics era. PRS accuracy is heterogeneous across disease endpoints, ancestries, and biobanks Larger sample sizes and greater diversity of GBMI improves PRS accuracy Lessons and guidelines for developing PRS with multi-ancestry GWASs are provided Wang et al. used the unique resource from Global Biobank Meta-analysis Initiative to develop and evaluate PRSs for 14 disease endpoints with varying genetic architectures and prevalences. They developed guidelines regarding the effects of multi-ancestry and heterogeneous GWASs, trait-specific genetic architecture, and PRS methods on prediction performance across diverse populations.
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影响因子:
2.1
作者:
Dudbridge F;Pashayan N;Yang J
通讯作者:
Yang J
影响因子:
64.8
作者:
Bycroft C;Freeman C;Petkova D;Band G;Elliott LT;Sharp K;Motyer A;Vukcevic D;Delaneau O;O'Connell J;Cortes A;Welsh S;Young A;Effingham M;McVean G;Leslie S;Allen N;Donnelly P;Marchini J
通讯作者:
Marchini J
影响因子:
30.8
作者:
Atkinson EG;Maihofer AX;Kanai M;Martin AR;Karczewski KJ;Santoro ML;Ulirsch JC;Kamatani Y;Okada Y;Finucane HK;Koenen KC;Nievergelt CM;Daly MJ;Neale BM
通讯作者:
Neale BM
影响因子:
30.8
作者:
Bulik-Sullivan, Brendan K.;Loh, Po-Ru;Finucane, Hilary K.;Ripke, Stephan;Yang, Jian;Patterson, Nick;Daly, Mark J.;Price, Alkes L.;Neale, Benjamin M.
通讯作者:
Neale, Benjamin M.
影响因子:
64.8
作者:
Graham SE;Clarke SL;Wu KH;Kanoni S;Zajac GJM;Ramdas S;Surakka I;Ntalla I;Vedantam S;Winkler TW;Locke AE;Marouli E;Hwang MY;Han S;Narita A;Choudhury A;Bentley AR;Ekoru K;Verma A;Trivedi B;Martin HC;Hunt KA;Hui Q;Klarin D;Zhu X;Thorleifsson G;Helgadottir A;Gudbjartsson DF;Holm H;Olafsson I;Akiyama M;Sakaue S;Terao C;Kanai M;Zhou W;Brumpton BM;Rasheed H;Ruotsalainen SE;Havulinna AS;Veturi Y;Feng Q;Rosenthal EA;Lingren T;Pacheco JA;Pendergrass SA;Haessler J;Giulianini F;Bradford Y;Miller JE;Campbell A;Lin K;Millwood IY;Hindy G;Rasheed A;Faul JD;Zhao W;Weir DR;Turman C;Huang H;Graff M;Mahajan A;Brown MR;Zhang W;Yu K;Schmidt EM;Pandit A;Gustafsson S;Yin X;Luan J;Zhao JH;Matsuda F;Jang HM;Yoon K;Medina-Gomez C;Pitsillides A;Hottenga JJ;Willemsen G;Wood AR;Ji Y;Gao Z;Haworth S;Mitchell RE;Chai JF;Aadahl M;Yao J;Manichaikul A;Warren HR;Ramirez J;Bork-Jensen J;Kårhus LL;Goel A;Sabater-Lleal M;Noordam R;Sidore C;Fiorillo E;McDaid AF;Marques-Vidal P;Wielscher M;Trompet S;Sattar N;Møllehave LT;Thuesen BH;Munz M;Zeng L;Huang J;Yang B;Poveda A;Kurbasic A;Lamina C;Forer L;Scholz M;Galesloot TE;Bradfield JP;Daw EW;Zmuda JM;Mitchell JS;Fuchsberger C;Christensen H;Brody JA;Feitosa MF;Wojczynski MK;Preuss M;Mangino M;Christofidou P;Verweij N;Benjamins JW;Engmann J;Kember RL;Slieker RC;Lo KS;Zilhao NR;Le P;Kleber ME;Delgado GE;Huo S;Ikeda DD;Iha H;Yang J;Liu J;Leonard HL;Marten J;Schmidt B;Arendt M;Smyth LJ;Cañadas-Garre M;Wang C;Nakatochi M;Wong A;Hutri-Kähönen N;Sim X;Xia R;Huerta-Chagoya A;Fernandez-Lopez JC;Lyssenko V;Ahmed M;Jackson AU;Yousri NA;Irvin MR;Oldmeadow C;Kim HN;Ryu S;Timmers PRHJ;Arbeeva L;Dorajoo R;Lange LA;Chai X;Prasad G;Lorés-Motta L;Pauper M;Long J;Li X;Theusch E;Takeuchi F;Spracklen CN;Loukola A;Bollepalli S;Warner SC;Wang YX;Wei WB;Nutile T;Ruggiero D;Sung YJ;Hung YJ;Chen S;Liu F;Yang J;Kentistou KA;Gorski M;Brumat M;Meidtner K;Bielak LF;Smith JA;Hebbar P;Farmaki AE;Hofer E;Lin M;Xue C;Zhang J;Concas MP;Vaccargiu S;van der Most PJ;Pitkänen N;Cade BE;Lee J;van der Laan SW;Chitrala KN;Weiss S;Zimmermann ME;Lee JY;Choi HS;Nethander M;Freitag-Wolf S;Southam L;Rayner NW;Wang CA;Lin SY;Wang JS;Couture C;Lyytikäinen LP;Nikus K;Cuellar-Partida G;Vestergaard H;Hildalgo B;Giannakopoulou O;Cai Q;Obura MO;van Setten J;Li X;Schwander K;Terzikhan N;Shin JH;Jackson RD;Reiner AP;Martin LW;Chen Z;Li L;Highland HM;Young KL;Kawaguchi T;Thiery J;Bis JC;Nadkarni GN;Launer LJ;Li H;Nalls MA;Raitakari OT;Ichihara S;Wild SH;Nelson CP;Campbell H;Jäger S;Nabika T;Al-Mulla F;Niinikoski H;Braund PS;Kolcic I;Kovacs P;Giardoglou T;Katsuya T;Bhatti KF;de Kleijn D;de Borst GJ;Kim EK;Adams HHH;Ikram MA;Zhu X;Asselbergs FW;Kraaijeveld AO;Beulens JWJ;Shu XO;Rallidis LS;Pedersen O;Hansen T;Mitchell P;Hewitt AW;Kähönen M;Pérusse L;Bouchard C;Tönjes A;Chen YI;Pennell CE;Mori TA;Lieb W;Franke A;Ohlsson C;Mellström D;Cho YS;Lee H;Yuan JM;Koh WP;Rhee SY;Woo JT;Heid IM;Stark KJ;Völzke H;Homuth G;Evans MK;Zonderman AB;Polasek O;Pasterkamp G;Hoefer IE;Redline S;Pahkala K;Oldehinkel AJ;Snieder H;Biino G;Schmidt R;Schmidt H;Chen YE;Bandinelli S;Dedoussis G;Thanaraj TA;Kardia SLR;Kato N;Schulze MB;Girotto G;Jung B;Böger CA;Joshi PK;Bennett DA;De Jager PL;Lu X;Mamakou V;Brown M;Caulfield MJ;Munroe PB;Guo X;Ciullo M;Jonas JB;Samani NJ;Kaprio J;Pajukanta P;Adair LS;Bechayda SA;de Silva HJ;Wickremasinghe AR;Krauss RM;Wu JY;Zheng W;den Hollander AI;Bharadwaj D;Correa A;Wilson JG;Lind L;Heng CK;Nelson AE;Golightly YM;Wilson JF;Penninx B;Kim HL;Attia J;Scott RJ;Rao DC;Arnett DK;Hunt SC;Walker M;Koistinen HA;Chandak GR;Yajnik CS;Mercader JM;Tusié-Luna T;Aguilar-Salinas CA;Villalpando CG;Orozco L;Fornage M;Tai ES;van Dam RM;Lehtimäki T;Chaturvedi N;Yokota M;Liu J;Reilly DF;McKnight AJ;Kee F;Jöckel KH;McCarthy MI;Palmer CNA;Vitart V;Hayward C;Simonsick E;van Duijn CM;Lu F;Qu J;Hishigaki H;Lin X;März W;Parra EJ;Cruz M;Gudnason V;Tardif JC;Lettre G;'t Hart LM;Elders PJM;Damrauer SM;Kumari M;Kivimaki M;van der Harst P;Spector TD;Loos RJF;Province MA;Psaty BM;Brandslund I;Pramstaller PP;Christensen K;Ripatti S;Widén E;Hakonarson H;Grant SFA;Kiemeney LALM;de Graaf J;Loeffler M;Kronenberg F;Gu D;Erdmann J;Schunkert H;Franks PW;Linneberg A;Jukema JW;Khera AV;Männikkö M;Jarvelin MR;Kutalik Z;Cucca F;Mook-Kanamori DO;van Dijk KW;Watkins H;Strachan DP;Grarup N;Sever P;Poulter N;Rotter JI;Dantoft TM;Karpe F;Neville MJ;Timpson NJ;Cheng CY;Wong TY;Khor CC;Sabanayagam C;Peters A;Gieger C;Hattersley AT;Pedersen NL;Magnusson PKE;Boomsma DI;de Geus EJC;Cupples LA;van Meurs JBJ;Ghanbari M;Gordon-Larsen P;Huang W;Kim YJ;Tabara Y;Wareham NJ;Langenberg C;Zeggini E;Kuusisto J;Laakso M;Ingelsson E;Abecasis G;Chambers JC;Kooner JS;de Vries PS;Morrison AC;North KE;Daviglus M;Kraft P;Martin NG;Whitfield JB;Abbas S;Saleheen D;Walters RG;Holmes MV;Black C;Smith BH;Justice AE;Baras A;Buring JE;Ridker PM;Chasman DI;Kooperberg C;Wei WQ;Jarvik GP;Namjou B;Hayes MG;Ritchie MD;Jousilahti P;Salomaa V;Hveem K;Åsvold BO;Kubo M;Kamatani Y;Okada Y;Murakami 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通讯作者:
Willer CJ