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@ARTICLE{Ni:897092,
author = {Ni, Guiyan and Zeng, Jian and Revez, Joana A. and Wang,
Ying and Zheng, Zhili and Ge, Tian and Restuadi, Restuadi
and Kiewa, Jacqueline and Nyholt, Dale R. and Coleman,
Jonathan R. I. and Smoller, Jordan W. and Yang, Jian and
Visscher, Peter M. and Wray, Naomi R. and Ripke, Stephan and
Neale, Benjamin M. and Corvin, Aiden and Walters, James T.
R. and Farh, Kai-How and Holmans, Peter A. and Lee, Phil and
Bulik-Sullivan, Brendan and Collier, David A. and Huang,
Hailiang and Pers, Tune H. and Agartz, Ingrid and Agerbo,
Esben and Albus, Margot and Alexander, Madeline and Amin,
Farooq and Bacanu, Silviu A. and Begemann, Martin and
Belliveau, Richard A. and Bene, Judit and Bergen, Sarah E.
and Bevilacqua, Elizabeth and Bigdeli, Tim B. and Black,
Donald W. and Bruggeman, Richard and Buccola, Nancy G. and
Buckner, Randy L. and Byerley, William and Cahn, Wiepke and
Cai, Guiqing and Campion, Dominique and Cantor, Rita M. and
Carr, Vaughan J. and Carrera, Noa and Catts, Stanley V. and
Chambert, Kimberley D. and Chan, Raymond C. K. and Chen,
Ronald Y. L. and Chen, Eric Y. H. and Cheng, Wei and Cheung,
Eric F. C. and Chong, Siow Ann and Cloninger, C. Robert and
Cohen, David and Cohen, Nadine and Cormican, Paul and
Craddock, Nick and Crowley, James J. and Davidson, Michael
and Davis, Kenneth L. and Degenhardt, Franziska and Del
Favero, Jurgen and Demontis, Ditte and Dikeos, Dimitris and
Dinan, Timothy and Djurovic, Srdjan and Donohoe, Gary and
Drapeau, Elodie and Duan, Jubao and Dudbridge, Frank and
Durmishi, Naser and Eichhammer, Peter and Eriksson, Johan
and Escott-Price, Valentina and Essioux, Laurent and Fanous,
Ayman H. and Farrell, Martilias S. and Frank, Josef and
Franke, Lude and Freedman, Robert and Freimer, Nelson B. and
Friedl, Marion and Friedman, Joseph I. and Fromer, Menachem
and Genovese, Giulio and Georgieva, Lyudmila and Giegling,
Ina and Giusti-Rodríguez, Paola and Godard, Stephanie and
Goldstein, Jacqueline I. and Golimbet, Vera and Gopal,
Srihari and Gratten, Jacob and de Haan, Lieuwe and Hammer,
Christian and Hamshere, Marian L. and Hansen, Mark and
Hansen, Thomas and Haroutunian, Vahram and Hartmann, Annette
M. and Henskens, Frans A. and Herms, Stefan and Hirschhorn,
Joel N. and Hoffmann, Per and Hofman, Andrea and Hollegaard,
Mads V. and Hougaard, David M. and Ikeda, Masashi and Joa,
Inge and Julià, Antonio and Kahn, René S. and Kalaydjieva,
Luba and Karachanak-Yankova, Sena and Karjalainen, Juha and
Kavanagh, David and Keller, Matthew C. and Kennedy, James L.
and Khrunin, Andrey and Kim, Yunjung and Klovins, Janis and
Knowles, James A. and Konte, Bettina and Kucinskas, Vaidutis
and Kucinskiene, Zita Ausrele and Kuzelova-Ptackova, Hana
and Kähler, Anna K. and Laurent, Claudine and Lee, Jimmy
and Lee, S. Hong and Legge, Sophie E. and Lerer, Bernard and
Li, Miaoxin and Li, Tao and Liang, Kung-Yee and Lieberman,
Jeffrey and Limborska, Svetlana and Loughland, Carmel M. and
Lubinski, Jan and Lönnqvist, Jouko and Macek, Milan and
Magnusson, Patrik K. E. and Maher, Brion S. and Maier,
Wolfgang and Mallet, Jacques and Marsal, Sara and
Mattheisen, Manuel and Mattingsdal, Morten and McCarley,
Robert W. and McDonald, Colm and McIntosh, Andrew M. and
Meier, Sandra and Meijer, Carin J. and Melegh, Bela and
Melle, Ingrid and Mesholam-Gately, Raquelle I. and Metspalu,
Andres and Michie, Patricia T. and Milani, Lili and
Milanova, Vihra and Mokrab, Younes and Morris, Derek W. and
Mors, Ole and Murphy, Kieran C. and Murray, Robin M. and
Myin-Germeys, Inez and Müller-Myhsok, Bertram and Nelis,
Mari and Nenadic, Igor and Nertney, Deborah A. and Nestadt,
Gerald and Nicodemus, Kristin K. and Nikitina-Zake, Liene
and Nisenbaum, Laura and Nordin, Annelie and O’Callaghan,
Eadbhard and O’Dushlaine, Colm and O’Neill, F. Anthony
and Oh, Sang-Yun and Olincy, Ann and Olsen, Line and Van Os,
Jim and International Consortium, Psychosis Endophenotypes
and Pantelis, Christos and Papadimitriou, George N. and
Papiol, Sergi and Parkhomenko, Elena and Pato, Michele T.
and Paunio, Tiina and Pejovic-Milovancevic, Milica and
Perkins, Diana O. and Pietiläinen, Olli and Pimm, Jonathan
and Pocklington, Andrew J. and Powell, John and Price, Alkes
and Pulver, Ann E. and Purcell, Shaun M. and Quested, Digby
and Rasmussen, Henrik B. and Reichenberg, Abraham and
Reimers, Mark A. and Richards, Alexander L. and Roffman,
Joshua L. and Roussos, Panos and Ruderfer, Douglas M. and
Salomaa, Veikko and Sanders, Alan R. and Schall, Ulrich and
Schubert, Christian R. and Schulze, Thomas G. and Schwab,
Sibylle G. and Scolnick, Edward M. and Scott, Rodney J. and
Seidman, Larry J. and Shi, Jianxin and Sigurdsson, Engilbert
and Silagadze, Teimuraz and Silverman, Jeremy M. and Sim,
Kang and Slominsky, Petr and Smoller, Jordan W. and So,
Hon-Cheong and Spencer, Chris C. A. and Stahl, Eli A. and
Stefansson, Hreinn and Steinberg, Stacy and Stogmann,
Elisabeth and Straub, Richard E. and Strengman, Eric and
Strohmaier, Jana and Stroup, T. Scott and Subramaniam,
Mythily and Suvisaari, Jaana and Svrakic, Dragan M. and
Szatkiewicz, Jin P. and Söderman, Erik and Thirumalai,
Srinivas and Toncheva, Draga and Tosato, Sarah and Veijola,
Juha and Waddington, John and Walsh, Dermot and Wang, Dai
and Wang, Qiang and Webb, Bradley T. and Weiser, Mark and
Wildenauer, Dieter B. and Williams, Nigel M. and Williams,
Stephanie and Witt, Stephanie H. and Wolen, Aaron R. and
Wong, Emily H. M. and Wormley, Brandon K. and Xi, Hualin
Simon and Zai, Clement C. and Zheng, Xuebin and Zimprich,
Fritz and Wray, Naomi R. and Stefansson, Kari and Visscher,
Peter M. and Case-Control Consortium, Wellcome Trust and
Adolfsson, Rolf and Andreassen, Ole A. and Blackwood,
Douglas H. R. and Bramon, Elvira and Buxbaum, Joseph D. and
Børglum, Anders D. and Cichon, Sven and Darvasi, Ariel and
Domenici, Enrico and Ehrenreich, Hannelore and Esko, Tõnu
and Gejman, Pablo V. and Gill, Michael and Gurling, Hugh and
Hultman, Christina M. and Iwata, Nakao and Jablensky, Assen
V. and Jönsson, Erik G. and Kendler, Kenneth S. and Kirov,
George and Knight, Jo and Lencz, Todd and Levinson, Douglas
F. and Li, Qingqin S. and Liu, Jianjun and Malhotra, Anil K.
and McCarroll, Steven A. and McQuillin, Andrew and Moran,
Jennifer L. and Mortensen, Preben B. and Mowry, Bryan J. and
Nöthen, Markus M. and Ophoff, Roel A. and Owen, Michael J.
and Palotie, Aarno and Pato, Carlos N. and Petryshen, Tracey
L. and Posthuma, Danielle and Rietschel, Marcella and Riley,
Brien P. and Rujescu, Dan and Sham, Pak C. and Sklar, Pamela
and St Clair, David and Weinberger, Daniel R. and Wendland,
Jens R. and Werge, Thomas and Daly, Mark J. and Sullivan,
Patrick F. and O’Donovan, Michael C. and Wray, Naomi R.
and Ripke, Stephan and Mattheisen, Manuel and Trzaskowski,
Maciej and Byrne, Enda M. and Abdellaoui, Abdel and Adams,
Mark J. and Agerbo, Esben and Air, Tracy M. and Andlauer,
Till F. M. and Bacanu, Silviu-Alin and Bækvad-Hansen, Marie
and Beekman, Aartjan T. F. and Bigdeli, Tim B. and Binder,
Elisabeth B. and Bryois, Julien and Buttenschøn, Henriette
N. and Bybjerg-Grauholm, Jonas and Cai, Na and Castelao,
Enrique and Christensen, Jane Hvarregaard and Clarke,
Toni-Kim and Coleman, Jonathan R. I. and Colodro-Conde,
Lucía and Couvy-Duchesne, Baptiste and Craddock, Nick and
Crawford, Gregory E. and Davies, Gail and Deary, Ian J. and
Degenhardt, Franziska and Derks, Eske M. and Direk, Nese and
Dolan, Conor V. and Dunn, Erin C. and Eley, Thalia C. and
Escott-Price, Valentina and Hassan Kiadeh, Farnush Farhadi
and Finucane, Hilary K. and Foo, Jerome C. and Forstner,
Andreas J. and Frank, Josef and Gaspar, Héléna A. and
Gill, Michael and Goes, Fernando S. and Gordon, Scott D. and
Grove, Jakob and Hall, Lynsey S. and Hansen, Christine
Søholm and Hansen, Thomas F. and Herms, Stefan and Hickie,
Ian B. and Hoffmann, Per and Homuth, Georg and Horn, Carsten
and Hottenga, Jouke-Jan and Hougaard, David M. and Howard,
David M. and Ising, Marcus and Jansen, Rick and Jones, Ian
and Jones, Lisa A. and Jorgenson, Eric and Knowles, James A.
and Kohane, Isaac S. and Kraft, Julia and Kretzschmar,
Warren W. and Kutalik, Zoltán and Li, Yihan and Lind,
Penelope A. and MacIntyre, Donald J. and MacKinnon, Dean F.
and Maier, Robert M. and Maier, Wolfgang and Marchini,
Jonathan and Mbarek, Hamdi and McGrath, Patrick and
McGuffin, Peter and Medland, Sarah E. and Mehta, Divya and
Middeldorp, Christel M. and Mihailov, Evelin and Milaneschi,
Yuri and Milani, Lili and Mondimore, Francis M. and
Montgomery, Grant W. and Mostafavi, Sara and Mullins, Niamh
and Nauck, Matthias and Ng, Bernard and Nivard, Michel G.
and Nyholt, Dale R. and O’Reilly, Paul F. and Oskarsson,
Hogni and Owen, Michael J. and Painter, Jodie N. and
Pedersen, Carsten Bøcker and Pedersen, Marianne Giørtz and
Peterson, Roseann E. and Peyrot, Wouter J. and Pistis,
Giorgio and Posthuma, Danielle and Quiroz, Jorge A. and
Qvist, Per and Rice, John P. and Riley, Brien P. and Rivera,
Margarita and Mirza, Saira Saeed and Schoevers, Robert and
Schulte, Eva C. and Shen, Ling and Shi, Jianxin and Shyn,
Stanley I. and Sigurdsson, Engilbert and Sinnamon, Grant C.
B. and Smit, Johannes H. and Smith, Daniel J. and
Stefansson, Hreinn and Steinberg, Stacy and Streit, Fabian
and Strohmaier, Jana and Tansey, Katherine E. and Teismann,
Henning and Teumer, Alexander and Thompson, Wesley and
Thomson, Pippa A. and Thorgeirsson, Thorgeir E. and Traylor,
Matthew and Treutlein, Jens and Trubetskoy, Vassily and
Uitterlinden, André G. and Umbricht, Daniel and Van der
Auwera, Sandra and van Hemert, Albert M. and Viktorin,
Alexander and Visscher, Peter M. and Wang, Yunpeng and Webb,
Bradley T. and Weinsheimer, Shantel Marie and Wellmann,
Jürgen and Willemsen, Gonneke and Witt, Stephanie H. and
Wu, Yang and Xi, Hualin S. and Yang, Jian and Zhang, Futao
and Arolt, Volker and Baune, Bernhard T. and Berger, Klaus
and Boomsma, Dorret I. and Cichon, Sven and Dannlowski, Udo
and de Geus, E. J. C. and DePaulo, J. Raymond and Domenici,
Enrico and Domschke, Katharina and Esko, Tõnu and Grabe,
Hans J. and Hamilton, Steven P. and Hayward, Caroline and
Heath, Andrew C. and Kendler, Kenneth S. and Kloiber, Stefan
and Lewis, Glyn and Li, Qingqin S. and Lucae, Susanne and
Madden, Pamela A. F. and Magnusson, Patrik K. and Martin,
Nicholas G. and McIntosh, Andrew M. and Metspalu, Andres and
Mors, Ole and Mortensen, Preben Bo and Müller-Myhsok,
Bertram and Nordentoft, Merete and Nöthen, Markus M. and
O’Donovan, Michael C. and Paciga, Sara A. and Pedersen,
Nancy L.},
title = {{A} {C}omparison of {T}en {P}olygenic {S}core {M}ethods for
{P}sychiatric {D}isorders {A}pplied {A}cross {M}ultiple
{C}ohorts},
journal = {Biological psychiatry},
volume = {90},
number = {9},
issn = {0006-3223},
address = {Amsterdam [u.a.]},
publisher = {Elsevier Science},
reportid = {FZJ-2021-03591},
pages = {611-620},
year = {2021},
abstract = {BackgroundPolygenic scores (PGSs), which assess the genetic
risk of individuals for a disease, are calculated as a
weighted count of risk alleles identified in genome-wide
association studies. PGS methods differ in which DNA
variants are included and the weights assigned to them; some
require an independent tuning sample to help inform these
choices. PGSs are evaluated in independent target cohorts
with known disease status. Variability between target
cohorts is observed in applications to real data sets, which
could reflect a number of factors, e.g., phenotype
definition or technical factors.MethodsThe Psychiatric
Genomics Consortium Working Groups for schizophrenia and
major depressive disorder bring together many independently
collected case-control cohorts. We used these resources
(31,328 schizophrenia cases, 41,191 controls; 248,750 major
depressive disorder cases, 563,184 controls) in repeated
application of leave-one-cohort-out meta-analyses, each used
to calculate and evaluate PGS in the left-out (target)
cohort. Ten PGS methods (the baseline PC+T method and 9
methods that model genetic architecture more formally:
SBLUP, LDpred2-Inf, LDpred-funct, LDpred2, Lassosum, PRS-CS,
PRS-CS-auto, SBayesR, MegaPRS) were compared.ResultsCompared
with PC+T, the other 9 methods gave higher prediction
statistics, MegaPRS, LDPred2, and SBayesR significantly so,
explaining up to $9.2\%$ variance in liability for
schizophrenia across 30 target cohorts, an increase of
$44\%.$ For major depressive disorder across 26 target
cohorts, these statistics were $3.5\%$ and $59\%,$
respectively.},
cin = {INM-1},
ddc = {610},
cid = {I:(DE-Juel1)INM-1-20090406},
pnm = {5251 - Multilevel Brain Organization and Variability
(POF4-525)},
pid = {G:(DE-HGF)POF4-5251},
typ = {PUB:(DE-HGF)16},
pubmed = {pmid:34304866},
UT = {WOS:000719390100006},
doi = {10.1016/j.biopsych.2021.04.018},
url = {https://juser.fz-juelich.de/record/897092},
}
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