Polygenic Score (PGS) ID: PGS000193

Predicted Trait
Reported Trait Major depression
Mapped Trait(s) major depressive disorder (MONDO_0002009)
Released in PGS Catalog: June 3, 2020
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Score Details

Disclaimer: The original published polygenic score is unavailable. The authors have provided an alternative polygenic for the Catalog. Please note some details and performance metrics may differ from the publication.
Score Construction
PGS Name MDD_0.001_Coleman_2020
Development Method
Name PRSice
Parameters PRSice 2.1.0.beta; pThreshold = 0.001;--clump-kb 250;--clump-p 1; --clump-r2 0.1;--info-base INFO,0.9;--model add;--stat OR; Effect allele is A1
Variants
Original Genome Build hg19
Number of Variants 1,138
Effect Weight Type log(OR)
PGS Source
PGS Catalog Publication (PGP) ID PGS000080
Citation (link to publication) Coleman JRI et al. Mol Psychiatry (2020)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
431,394 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: 29700475
[
  • 116,404 cases
  • , 314,990 controls
]
 European PGC

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
PPM000564 PSS000294|
European Ancestry|
92,957 individuals
 PGS000080 |
Coleman JRI et al. Mol Psychiatry (2020)
 Reported Trait: Major depressive disorder OR: 1.179 — R²: 0.01485
Nagelkerke pseudo-R2 (increase when adding PRS to null model of covariates): 0.00785		 batch, centre, genomic prinicipal components (x6) —

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
PSS000294 Participants completed an online follow-up questionnaire assessing common mental health disorders, including MDD symptoms. Phenotypes were derived from this questionnaire. Individuals with probable MDD met lifetime criteria based on their responses to questions derived from the Composite International Diagnostic Interview. We excluded cases if they self-reported diagnoses of schizophrenia, other psychoses, or bipolar disorder. Controls were excluded if they self-reported any mental illness, taking any drug with an antidepressant indication, or had been hospitalised with a mood disorder or met previously-defined criteria for a mood disorder. —
[
  • 29,475 cases
  • , 63,482 controls
]
,
45.0 % Male samples
 Range = [46.0, 80.0] years European — UKB —