PGS Catalog - PGS000135 / Schizophrenia (Polygenic Score)

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
PGS Name	SCZ_MTS
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 MTS = 971,463
Variants
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)	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
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 (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
PSS000241	Schizophrenia case subjects had two or more ICD codes included in phecode 295.1	—	9,569 individuals [ 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)