Polygenic Score (PGS) ID: PGS000136

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
PGS Name SCZ_PBK
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 PBK = 833,502
Variants
Original Genome Build GRCh37
Number of Variants 833,502
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%
2 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)		 NR

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
(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 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
PPM000416 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

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
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