Genetic Epidemiology, Translational Neurogenomics, Psychiatric Genetics and Statistical Genetics Laboratories investigate the pattern of disease in families, particularly identical and non-identical twins, to assess the relative importance of genes and environment in a variety of important health problems.
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34304866
TITLE
A Comparison of Ten Polygenic Score Methods for Psychiatric Disorders Applied Across Multiple Cohorts.
ABSTRACT
BACKGROUND NlmCategory: BACKGROUND
Polygenic 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.
METHODS NlmCategory: METHODS
Polygenic 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. The 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.
RESULTS NlmCategory: RESULTS
Polygenic 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. The 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. Compared 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.
CONCLUSIONS NlmCategory: CONCLUSIONS
Polygenic 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. The 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. Compared 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. Although the methods that more formally model genetic architecture have similar performance, MegaPRS, LDpred2, and SBayesR rank highest in most comparisons and are recommended in applications to psychiatric disorders.
Copyright © 2021 Society of Biological Psychiatry. Published by Elsevier Inc. All rights reserved.
DATE PUBLISHED
2021 May 04
HISTORY
PUBSTATUS PUBSTATUSDATE
received 2020/09/15
revised 2021/04/26
accepted 2021/04/26
entrez 2021/07/26 05:32
pubmed 2021/07/27 06:00
medline 2021/07/27 06:00
AUTHORS
NAME COLLECTIVENAME LASTNAME FORENAME INITIALS AFFILIATION AFFILIATIONINFO
Ni G Ni Guiyan G Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia.
Zeng J Zeng Jian J Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia.
Revez JA Revez Joana A JA Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia.
Wang Y Wang Ying Y Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia.
Zheng Z Zheng Zhili Z Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia.
Ge T Ge Tian T Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts.
Restuadi R Restuadi Restuadi R Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia.
Kiewa J Kiewa Jacqueline J Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia.
Nyholt DR Nyholt Dale R DR Faculty of Health, School of Biomedical Sciences, Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, Queensland, Australia.
Coleman JRI Coleman Jonathan R I JRI Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom.
Smoller JW Smoller Jordan W JW Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts; Department of Psychiatry, Massachusetts General Hospital, Boston, Massachusetts; Stanley Center for Psychiatric Research, Broad Institute, Cambridge, Massachusetts.
Schizophrenia Working Group of the Psychiatric Genomics Consortium
Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium
Yang J Yang Jian J Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia; School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.
Visscher PM Visscher Peter M PM Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia.
Wray NR Wray Naomi R NR Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia; Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia. Electronic address: naomi.wray@uq.edu.au.
INVESTIGATORS
LASTNAME FORENAME INITIALS AFFILIATION
Ripke Stephan S
Neale Benjamin M BM
Corvin Aiden A
Walters James T R JTR
Farh Kai-How KH
Holmans Peter A PA
Lee Phil P
Bulik-Sullivan Brendan B
Collier David A DA
Huang Hailiang H
Pers Tune H TH
Agartz Ingrid I
Agerbo Esben E
Albus Margot M
Alexander Madeline M
Amin Farooq F
Bacanu Silviu A SA
Begemann Martin M
Belliveau Richard A RA
Bene Judit J
Bergen Sarah E SE
Bevilacqua Elizabeth E
Bigdeli Tim B TB
Black Donald W DW
Bruggeman Richard R
Buccola Nancy G NG
Buckner Randy L RL
Byerley William W
Cahn Wiepke W
Cai Guiqing G
Campion Dominique D
Cantor Rita M RM
Carr Vaughan J VJ
Carrera Noa N
Catts Stanley V SV
Chambert Kimberley D KD
Chan Raymond C K RCK
Chen Ronald Y L RYL
Chen Eric Y H EYH
Cheng Wei W
Cheung Eric F C EFC
Chong Siow Ann SA
Cloninger C Robert CR
Cohen David D
Cohen Nadine N
Cormican Paul P
Craddock Nick N
Crowley James J JJ
Davidson Michael M
Davis Kenneth L KL
Degenhardt Franziska F
Del Favero Jurgen J
Demontis Ditte D
Dikeos Dimitris D
Dinan Timothy T
Djurovic Srdjan S
Donohoe Gary G
Drapeau Elodie E
Duan Jubao J
Dudbridge Frank F
Durmishi Naser N
Eichhammer Peter P
Eriksson Johan J
Escott-Price Valentina V
Essioux Laurent L
Fanous Ayman H AH
Farrell Martilias S MS
Frank Josef J
Franke Lude L
Freedman Robert R
Freimer Nelson B NB
Friedl Marion M
Friedman Joseph I JI
Fromer Menachem M
Genovese Giulio G
Georgieva Lyudmila L
Giegling Ina I
Giusti-Rodríguez Paola P
Godard Stephanie S
Goldstein Jacqueline I JI
Golimbet Vera V
Gopal Srihari S
Gratten Jacob J
de Haan Lieuwe L
Hammer Christian C
Hamshere Marian L ML
Hansen Mark M
Hansen Thomas T
Haroutunian Vahram V
Hartmann Annette M AM
Henskens Frans A FA
Herms Stefan S
Hirschhorn Joel N JN
Hoffmann Per P
Hofman Andrea A
Hollegaard Mads V MV
Hougaard David M DM
Ikeda Masashi M
Joa Inge I
Julià Antonio A
Kahn René S RS
Kalaydjieva Luba L
Karachanak-Yankova Sena S
Karjalainen Juha J
Kavanagh David D
Keller Matthew C MC
Kennedy James L JL
Khrunin Andrey A
Kim Yunjung Y
Klovins Janis J
Knowles James A JA
Konte Bettina B
Kucinskas Vaidutis V
Kucinskiene Zita Ausrele ZA
Kuzelova-Ptackova Hana H
Kähler Anna K AK
Laurent Claudine C
Lee Jimmy J
Lee S Hong SH
Legge Sophie E SE
Lerer Bernard B
Li Miaoxin M
Li Tao T
Liang Kung-Yee KY
Lieberman Jeffrey J
Limborska Svetlana S
Loughland Carmel M CM
Lubinski Jan J
Lönnqvist Jouko J
Macek Milan M
Magnusson Patrik K E PKE
Maher Brion S BS
Maier Wolfgang W
Mallet Jacques J
Marsal Sara S
Mattheisen Manuel M
Mattingsdal Morten M
McCarley Robert W RW
McDonald Colm C
McIntosh Andrew M AM
Meier Sandra S
Meijer Carin J CJ
Melegh Bela B
Melle Ingrid I
Mesholam-Gately Raquelle I RI
Metspalu Andres A
Michie Patricia T PT
Milani Lili L
Milanova Vihra V
Mokrab Younes Y
Morris Derek W DW
Mors Ole O
Murphy Kieran C KC
Murray Robin M RM
Myin-Germeys Inez I
Müller-Myhsok Bertram B
Nelis Mari M
Nenadic Igor I
Nertney Deborah A DA
Nestadt Gerald G
Nicodemus Kristin K KK
Nikitina-Zake Liene L
Nisenbaum Laura L
Nordin Annelie A
O'Callaghan Eadbhard E
O'Dushlaine Colm C
O'Neill F Anthony FA
Oh Sang-Yun SY
Olincy Ann A
Olsen Line L
Van Os Jim J
International Consortium Psychosis Endophenotypes PE
Pantelis Christos C
Papadimitriou George N GN
Papiol Sergi S
Parkhomenko Elena E
Pato Michele T MT
Paunio Tiina T
Pejovic-Milovancevic Milica M
Perkins Diana O DO
Pietiläinen Olli O
Pimm Jonathan J
Pocklington Andrew J AJ
Powell John J
Price Alkes A
Pulver Ann E AE
Purcell Shaun M SM
Quested Digby D
Rasmussen Henrik B HB
Reichenberg Abraham A
Reimers Mark A MA
Richards Alexander L AL
Roffman Joshua L JL
Roussos Panos P
Ruderfer Douglas M DM
Salomaa Veikko V
Sanders Alan R AR
Schall Ulrich U
Schubert Christian R CR
Schulze Thomas G TG
Schwab Sibylle G SG
Scolnick Edward M EM
Scott Rodney J RJ
Seidman Larry J LJ
Shi Jianxin J
Sigurdsson Engilbert E
Silagadze Teimuraz T
Silverman Jeremy M JM
Sim Kang K
Slominsky Petr P
Smoller Jordan W JW
So Hon-Cheong HC
Spencer Chris C A CCA
Stahl Eli A EA
Stefansson Hreinn H
Steinberg Stacy S
Stogmann Elisabeth E
Straub Richard E RE
Strengman Eric E
Strohmaier Jana J
Stroup T Scott TS
Subramaniam Mythily M
Suvisaari Jaana J
Svrakic Dragan M DM
Szatkiewicz Jin P JP
Söderman Erik E
Thirumalai Srinivas S
Toncheva Draga D
Tosato Sarah S
Veijola Juha J
Waddington John J
Walsh Dermot D
Wang Dai D
Wang Qiang Q
Webb Bradley T BT
Weiser Mark M
Wildenauer Dieter B DB
Williams Nigel M NM
Williams Stephanie S
Witt Stephanie H SH
Wolen Aaron R AR
Wong Emily H M EHM
Wormley Brandon K BK
Xi Hualin Simon HS
Zai Clement C CC
Zheng Xuebin X
Zimprich Fritz F
Wray Naomi R NR
Stefansson Kari K
Visscher Peter M PM
Case-Control Consortium Wellcome Trust WT
Adolfsson Rolf R
Andreassen Ole A OA
Blackwood Douglas H R DHR
Bramon Elvira E
Buxbaum Joseph D JD
Børglum Anders D AD
Cichon Sven S
Darvasi Ariel A
Domenici Enrico E
Ehrenreich Hannelore H
Esko Tõnu T
Gejman Pablo V PV
Gill Michael M
Gurling Hugh H
Hultman Christina M CM
Iwata Nakao N
Jablensky Assen V AV
Jönsson Erik G EG
Kendler Kenneth S KS
Kirov George G
Knight Jo J
Lencz Todd T
Levinson Douglas F DF
Li Qingqin S QS
Liu Jianjun J
Malhotra Anil K AK
McCarroll Steven A SA
McQuillin Andrew A
Moran Jennifer L JL
Mortensen Preben B PB
Mowry Bryan J BJ
Nöthen Markus M MM
Ophoff Roel A RA
Owen Michael J MJ
Palotie Aarno A
Pato Carlos N CN
Petryshen Tracey L TL
Posthuma Danielle D
Rietschel Marcella M
Riley Brien P BP
Rujescu Dan D
Sham Pak C PC
Sklar Pamela P
St Clair David D
Weinberger Daniel R DR
Wendland Jens R JR
Werge Thomas T
Daly Mark J MJ
Sullivan Patrick F PF
O'Donovan Michael C MC
Wray Naomi R NR
Ripke Stephan S
Mattheisen Manuel M
Trzaskowski Maciej M
Byrne Enda M EM
Abdellaoui Abdel A
Adams Mark J MJ
Agerbo Esben E
Air Tracy M TM
Andlauer Till F M TFM
Bacanu Silviu-Alin SA
Bækvad-Hansen Marie M
Beekman Aartjan T F ATF
Bigdeli Tim B TB
Binder Elisabeth B EB
Bryois Julien J
Buttenschøn Henriette N HN
Bybjerg-Grauholm Jonas J
Cai Na N
Castelao Enrique E
Christensen Jane Hvarregaard JH
Clarke Toni-Kim TK
Coleman Jonathan R I JRI
Colodro-Conde Lucía L
Couvy-Duchesne Baptiste B
Craddock Nick N
Crawford Gregory E GE
Davies Gail G
Deary Ian J IJ
Degenhardt Franziska F
Derks Eske M EM
Direk Nese N
Dolan Conor V CV
Dunn Erin C EC
Eley Thalia C TC
Escott-Price Valentina V
Hassan Kiadeh Farnush Farhadi FF
Finucane Hilary K HK
Foo Jerome C JC
Forstner Andreas J AJ
Frank Josef J
Gaspar Héléna A HA
Gill Michael M
Goes Fernando S FS
Gordon Scott D SD
Grove Jakob J
Hall Lynsey S LS
Hansen Christine Søholm CS
Hansen Thomas F TF
Herms Stefan S
Hickie Ian B IB
Hoffmann Per P
Homuth Georg G
Horn Carsten C
Hottenga Jouke-Jan JJ
Hougaard David M DM
Howard David M DM
Ising Marcus M
Jansen Rick R
Jones Ian I
Jones Lisa A LA
Jorgenson Eric E
Knowles James A JA
Kohane Isaac S IS
Kraft Julia J
Kretzschmar Warren W WW
Kutalik Zoltán Z
Li Yihan Y
Lind Penelope A PA
MacIntyre Donald J DJ
MacKinnon Dean F DF
Maier Robert M RM
Maier Wolfgang W
Marchini Jonathan J
Mbarek Hamdi H
McGrath Patrick P
McGuffin Peter P
Medland Sarah E SE
Mehta Divya D
Middeldorp Christel M CM
Mihailov Evelin E
Milaneschi Yuri Y
Milani Lili L
Mondimore Francis M FM
Montgomery Grant W GW
Mostafavi Sara S
Mullins Niamh N
Nauck Matthias M
Ng Bernard B
Nivard Michel G MG
Nyholt Dale R DR
O'Reilly Paul F PF
Oskarsson Hogni H
Owen Michael J MJ
Painter Jodie N JN
Pedersen Carsten Bøcker CB
Pedersen Marianne Giørtz MG
Peterson Roseann E RE
Peyrot Wouter J WJ
Pistis Giorgio G
Posthuma Danielle D
Quiroz Jorge A JA
Qvist Per P
Rice John P JP
Riley Brien P BP
Rivera Margarita M
Mirza Saira Saeed SS
Schoevers Robert R
Schulte Eva C EC
Shen Ling L
Shi Jianxin J
Shyn Stanley I SI
Sigurdsson Engilbert E
Sinnamon Grant C B GCB
Smit Johannes H JH
Smith Daniel J DJ
Stefansson Hreinn H
Steinberg Stacy S
Streit Fabian F
Strohmaier Jana J
Tansey Katherine E KE
Teismann Henning H
Teumer Alexander A
Thompson Wesley W
Thomson Pippa A PA
Thorgeirsson Thorgeir E TE
Traylor Matthew M
Treutlein Jens J
Trubetskoy Vassily V
Uitterlinden André G AG
Umbricht Daniel D
Van der Auwera Sandra S
van Hemert Albert M AM
Viktorin Alexander A
Visscher Peter M PM
Wang Yunpeng Y
Webb Bradley T BT
Weinsheimer Shantel Marie SM
Wellmann Jürgen J
Willemsen Gonneke G
Witt Stephanie H SH
Wu Yang Y
Xi Hualin S HS
Yang Jian J
Zhang Futao F
Arolt Volker V
Baune Bernhard T BT
Berger Klaus K
Boomsma Dorret I DI
Cichon Sven S
Dannlowski Udo U
de Geus E J C EJC
DePaulo J Raymond JR
Domenici Enrico E
Domschke Katharina K
Esko Tõnu T
Grabe Hans J HJ
Hamilton Steven P SP
Hayward Caroline C
Heath Andrew C AC
Kendler Kenneth S KS
Kloiber Stefan S
Lewis Glyn G
Li Qingqin S QS
Lucae Susanne S
Madden Pamela A F PAF
Magnusson Patrik K PK
Martin Nicholas G NG
McIntosh Andrew M AM
Metspalu Andres A
Mors Ole O
Mortensen Preben Bo PB
Müller-Myhsok Bertram B
Nordentoft Merete M
Nöthen Markus M MM
O'Donovan Michael C MC
Paciga Sara A SA
Pedersen Nancy L NL
JOURNAL
VOLUME:
ISSUE:
TITLE: Biological psychiatry
ISOABBREVIATION: Biol Psychiatry
YEAR: 2021
MONTH: May
DAY: 04
MEDLINEDATE:
SEASON:
CITEDMEDIUM: Internet
ISSN: 1873-2402
ISSNTYPE: Electronic
MEDLINE JOURNAL
MEDLINETA: Biol Psychiatry
COUNTRY: United States
ISSNLINKING: 0006-3223
NLMUNIQUEID: 0213264
PUBLICATION TYPE
PUBLICATIONTYPE TEXT
Journal Article
COMMENTS AND CORRECTIONS
GRANTS
GENERAL NOTE
KEYWORDS
KEYWORD
LDpred2
Lassosum
Major depressive disorder
MegaPRS
PRS-CS
Polygenic scores
Psychiatric disorders
Risk prediction
SBayesR
Schizophrenia
MESH HEADINGS
SUPPLEMENTARY MESH
GENE SYMBOLS
CHEMICALS
OTHER ID's