PGS Catalog - PGS000140 / Broad Depression (seen a General Practitioner for nerves, anxiety, tension or depression) (Polygenic Score)

Polygenic Score (PGS) ID: PGS000140

Predicted Trait
Reported Trait	Broad Depression (seen a General Practitioner for nerves, anxiety, tension or depression)
Mapped Trait(s)	seeing a general practitioner for nerves, anxiety, tension or depression, self-reported (EFO_0009820) depressive disorder (MONDO_0002050)

Released in PGS Catalog: April 29, 2020

Download Score FTP directory

Terms and Licenses

PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name	GPpsy
Development Method
Name	LD-clumping and p-value thresholding (Ricopilli)
Parameters	Clumping r2 < 0.1. Scores provided at a p-value threshold = 0.1 (LD-clumped summary statistics require to calculate the score at other threshold are linked in GWAS sample descriptions)
Variants
Original Genome Build	NR
Number of Variants	24,665
Effect Weight Type	NR

PGS Source
PGS Catalog Publication (PGP) ID	PGP000068
Citation (link to publication)	Cai N et al. Nat Genet (2020)

Ancestry Distribution
Source of Variant Associations (GWAS)	European: 100% 332,622 individuals (100%)
PGS Evaluation	European: 100% 1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)

Study Identifiers	Sample Numbers	Sample Ancestry	Cohort(s)
Europe PMC: 32231276	332,622 individuals [ 113,262 cases , 219,360 controls ]	European	UKB

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
PPM000432	PSS000250\| European Ancestry\| 36,709 individuals	PGP000068 \| Cai N et al. Nat Genet (2020)	Reported Trait: Major Depressive Disorder status	—	AUROC: 0.53193	R²: 0.00481	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
PSS000250	—	—	36,709 individuals [ 14,696 cases , 22,013 controls ]	—	European	—	15 cohorts BOMA ,CoLaus ,Edinburgh ,GenPOD ,GenRED ,MARS ,MPIP ,NESDA ,QIMR ,RADIANT ,RS ,SHIP ,STAR*D ,TwinGene ,i2b2	Part of PGC29 (PMID: 29700475)