PGS Publication: PGP000065

Publication Information (EuropePMC)
Title Penetrance and Pleiotropy of Polygenic Risk Scores for Schizophrenia in 106,160 Patients Across Four Health Care Systems.
PubMed ID 31416338(Europe PMC)
doi 10.1176/appi.ajp.2019.18091085
Publication Date Aug. 16, 2019
Journal Am J Psychiatry
Author(s) Zheutlin AB, Dennis J, Karlsson Linnér R, Moscati A, Restrepo N, Straub P, Ruderfer D, Castro VM, Chen CY, Ge T, Huckins LM, Charney A, Kirchner HL, Stahl EA, Chabris CF, Davis LK, Smoller JW.
Released in PGS Catalog: March 27, 2020

Associated Polygenic Score(s)

PGS Developed By This Publication

Polygenic Score (PGS) ID PGS Name PGS Publication (PGP) ID Reported Trait Mapped Trait(s) (Ontology) Number of Variants PGS Scoring File (FTP Link)
PGS000136 SCZ_PBK PGP000065 Zheutlin AB et al. Am J Psychiatry (2019) Schizophrenia schizophrenia 833,502 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000136/ScoringFiles/PGS000136.txt.gz
PGS000135 SCZ_MTS PGP000065 Zheutlin AB et al. Am J Psychiatry (2019) Schizophrenia schizophrenia 972,439 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000135/ScoringFiles/PGS000135.txt.gz
PGS000134 SCZ_GHS PGP000065 Zheutlin AB et al. Am J Psychiatry (2019) Schizophrenia schizophrenia 830,589 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000134/ScoringFiles/PGS000134.txt.gz
PGS000133 SCZ_BVU PGP000065 Zheutlin AB et al. Am J Psychiatry (2019) Schizophrenia schizophrenia 604,645 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000133/ScoringFiles/PGS000133.txt.gz

PGS Performance Metrics

Disclaimer: The performance metrics are displayed as reported by the source studies. It is important to note that metrics are not necessarily comparable with each other. For example, metrics depend on the sample characteristics (described by the PGS Catalog Sample Set [PSS] ID), phenotyping, and statistical modelling. Please refer to the source publication for additional guidance on performance.

PGS Performance Metric ID
(PPM ID) 		Evaluated Score PGS Sample Set ID
(PSS ID) 		Performance Source Trait PGS Effect Sizes
(per SD change) 		PGS Classification Metrics Other Metrics Covariates Included in the Model PGS Performance: Other Relevant Information
PPM000420 PGS000136
(SCZ_PBK)
 PSS000244 PGP000065 Zheutlin AB et al. (2019) Reported Trait: Psychosis OR: 1.4768 — — age, sex, 10 PCs of ancestry, genotyping platform, genotyping batch *SNP weights were adjusted for use in this cohort
PPM000418 PGS000134
(SCZ_GHS)
 PSS000240 PGP000065 Zheutlin AB et al. (2019) Reported Trait: Psychosis OR: 1.2224 — — age, sex, 10 PCs of ancestry, genotyping platform, genotyping batch *SNP weights were adjusted for use in this cohort
PPM000417 PGS000133
(SCZ_BVU)
 PSS000238 PGP000065 Zheutlin AB et al. (2019) Reported Trait: Psychosis OR: 1.3755 — — age, sex, 10 PCs of ancestry, genotyping platform, genotyping batch *SNP weights were adjusted for use in this cohort
PPM000416 PGS000136
(SCZ_PBK)
 PSS000243 PGP000065 Zheutlin AB et al. (2019) Reported Trait: Schizophrenia OR: 1.7 AUROC: 0.64 [0.6, 0.69] — age, sex, 10 PCs of ancestry, genotyping platform, genotyping batch *SNP weights were adjusted for use in this cohort
PPM000415 PGS000135
(SCZ_MTS)
 PSS000241 PGP000065 Zheutlin AB et al. (2019) Reported Trait: Schizophrenia — AUROC: 0.74 [0.67, 0.81] — age, sex, 10 PCs of ancestry, genotyping platform, genotyping batch *SNP weights were adjusted for use in this cohort
PPM000414 PGS000134
(SCZ_GHS)
 PSS000239 PGP000065 Zheutlin AB et al. (2019) Reported Trait: Schizophrenia OR: 1.483 AUROC: 0.6 [0.56, 0.64] — age, sex, 10 PCs of ancestry, genotyping platform, genotyping batch *SNP weights were adjusted for use in this cohort
PPM000413 PGS000133
(SCZ_BVU)
 PSS000237 PGP000065 Zheutlin AB et al. (2019) Reported Trait: Schizophrenia OR: 1.691 AUROC: 0.6 [0.55, 0.66] — age, sex, 10 PCs of ancestry, genotyping platform, genotyping batch *SNP weights were adjusted for use in this cohort

Evaluated Samples

PGS Sample Set ID
(PSS ID) 		Phenotype Definitions and Methods Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
PSS000237 Schizophrenia case subjects had two or more ICD codes included in phecode 295.1 —
[
  • 110 cases
  • , 33,584 controls
]
,
46.0 % Male samples
 Mean = 57.9 years
Sd = 20.0 years		 European — BioVu Vanderbilt University Medical Center (VUMC) biobank (BioVU)
PSS000238 Psychosis case subjects were identified with phecode 295 —
[
  • 451 cases
  • , 33,243 controls
]
,
46.0 % Male samples
 Mean = 57.9 years
Sd = 20.0 years		 European — BioVu Vanderbilt University Medical Center (VUMC) biobank (BioVU)
PSS000239 Schizophrenia case subjects had two or more ICD codes included in phecode 295.1 —
[
  • 211 cases
  • , 44,225 controls
]
,
41.0 % Male samples
 Mean = 60.2 years
Sd = 16.9 years		 European — GeHS Geisinger Health System (GHS)
PSS000240 Psychosis case subjects were identified with phecode 295 —
[
  • 499 cases
  • , 43,937 controls
]
,
41.0 % Male samples
 Mean = 60.2 years
Sd = 16.9 years		 European — GeHS Geisinger Health System (GHS)
PSS000241 Schizophrenia case subjects had two or more ICD codes included in phecode 295.1 —
[
  • 53 cases
  • , 9,516 controls
]
,
48.0 % Male samples
 Mean = 57.2 years
Sd = 19.8 years		 European — BMBB, IMP, Mount Sinai BioMe Biobank at the Mount Sinai School of Medicine (MSSM)
PSS000243 Schizophrenia case subjects had two or more ICD codes included in phecode 295.1 —
[
  • 148 cases
  • , 18,313 controls
]
,
46.0 % Male samples
 Mean = 58.5 years
Sd = 16.4 years		 European — PHB Partners HealthCare System (PHS) biobank
PSS000244 Psychosis case subjects were identified with phecode 295 —
[
  • 385 cases
  • , 18,076 controls
]
,
46.0 % Male samples
 Mean = 58.5 years
Sd = 16.4 years		 European — PHB Partners HealthCare System (PHS) biobank