PGS Catalog - PGS000133 / Schizophrenia (Polygenic Score)

Polygenic Score (PGS) ID: PGS000133

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_BVU
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 BVU = 604,645
Variants
Original Genome Build	GRCh37
Number of Variants	604,645
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
PPM000417	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
PPM000413	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	—	33,694 individuals [ 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	—	33,694 individuals [ 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)