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)

Filter PGS by Participant Ancestry
Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
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Multi-ancestry (including European)
Multi-ancestry (excluding European)
African
East Asian
South Asian
Additional Asian Ancestries
European
Greater Middle Eastern
Hispanic or Latin American
Additional Diverse Ancestries
Not Reported

PGS Developed By This Publication

Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution PGS Scoring File (FTP Link)
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
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
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
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

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)
Evaluated Score PGS Sample Set ID
(PSS)
Performance Source Trait PGS Effect Sizes
(per SD change)
Classification Metrics Other Metrics Covariates Included in the Model PGS Performance:
Other Relevant Information
PPM000420 PGS000136
(SCZ_PBK)
PSS000244|
European Ancestry|
18,461 individuals
PGP000065 |
Zheutlin AB et al. Am J Psychiatry (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|
European Ancestry|
44,436 individuals
PGP000065 |
Zheutlin AB et al. Am J Psychiatry (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|
European Ancestry|
33,694 individuals
PGP000065 |
Zheutlin AB et al. Am J Psychiatry (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|
European Ancestry|
18,461 individuals
PGP000065 |
Zheutlin AB et al. Am J Psychiatry (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|
European Ancestry|
9,569 individuals
PGP000065 |
Zheutlin AB et al. Am J Psychiatry (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|
European Ancestry|
44,436 individuals
PGP000065 |
Zheutlin AB et al. Am J Psychiatry (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|
European Ancestry|
33,694 individuals
PGP000065 |
Zheutlin AB et al. Am J Psychiatry (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)
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