Polygenic Score (PGS) ID: PGS000134

Predicted Trait
Reported Trait Schizophrenia
Mapped Trait(s) schizophrenia (EFO_0000692)
Released in PGS: March 27, 2020

Score Details

Score Construction
PGS Name SCZ_GHS
Variants
Original Genome Build GRCh37
Number of Variants 830,589
Development Method
Name PRS-CS
Parameters Bayesian polygenic prediction method, with continuous shrinkage. Parameters: b = 0.5, phi = 1, LD-reference panel = 1000 Genomes Project European samples, # of available SNPs in GHS = 833,502
PGS Source
PGS Catalog Publication (PGP) ID PGP000065
Citation (link to publication) Zheutlin AB et al. Am J Psychiatry (2019)

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST002539
EuropePMC: 25056061
5,219 individuals East Asian
GWAS Catalog: GCST002539
EuropePMC: 25056061
82,315 individuals European
(Portugal, U.K., Republic of Ireland, Denmark)

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)
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
PPM000414 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
PPM000418 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

Evaluated Samples

PGS Sample Set ID
(PSS ID)
Detailed Phenotype Description Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
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)