Polygenic Score (PGS) ID: PGS000135

Predicted Trait
Reported Trait Schizophrenia
Mapped Trait(s) schizophrenia (MONDO_0005090)
Released in PGS Catalog: March 27, 2020
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Score Details

Score Construction
Development Method
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 MTS = 971,463
Original Genome Build GRCh37
Number of Variants 972,439
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000065
Citation (link to publication) Zheutlin AB et al. Am J Psychiatry (2019)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 94%
East Asian: 6%
87,534 individuals (100%)
PGS Evaluation
European: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST002539
Europe PMC: 25056061
5,219 individuals East Asian NR
GWAS Catalog: GCST002539
Europe PMC: 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)
PGS Sample Set ID
Performance Source Trait PGS Effect Sizes
(per SD change)
Classification Metrics Other Metrics Covariates Included in the Model PGS Performance:
Other Relevant Information
PPM000415 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

Evaluated Samples

PGS Sample Set 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
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 BioMe BioMe Biobank at the Mount Sinai School of Medicine (MSSM)