Polygenic Score (PGS) ID: PGS002036

Predicted Trait
Reported Trait Depression
Mapped Trait(s) depressive disorder (MONDO_0002050)
Additional Trait Information psychiatric disorders
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-ldpred2_296.2
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 807,338
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000263
Citation (link to publication) Privé F et al. Am J Hum Genet (2022)
Ancestry Distribution
Score Development/Training
European: 100%
391,124 individuals (100%)
PGS Evaluation
European: 37.5%
African: 25%
East Asian: 12.5%
Greater Middle Eastern: 12.5%
South Asian: 12.5%
8 Sample Sets

Development Samples

Score Development/Training
Study Identifiers Sample Numbers Sample Ancestry Cohort(s) Phenotype Definitions & Methods Age of Study Participants Participant Follow-up Time Additional Ancestry Description Additional Sample/Cohort Information
— 391,124 individuals European UKB — — — UK (+ Ireland) —

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
PPM011155 PSS009299|
European Ancestry|
17,764 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Depression — — Partial Correlation (partial-r): 0.0556 [0.041, 0.0703] sex, age, birth date, deprivation index, 16 PCs —
PPM011156 PSS009073|
European Ancestry|
3,729 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Depression — — Partial Correlation (partial-r): 0.0583 [0.0261, 0.0903] sex, age, birth date, deprivation index, 16 PCs —
PPM011158 PSS008401|
Greater Middle Eastern Ancestry|
1,055 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Depression — — Partial Correlation (partial-r): 0.0239 [-0.0371, 0.0847] sex, age, birth date, deprivation index, 16 PCs —
PPM011159 PSS008181|
South Asian Ancestry|
5,870 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Depression — — Partial Correlation (partial-r): 0.0224 [-0.0033, 0.048] sex, age, birth date, deprivation index, 16 PCs —
PPM011160 PSS007966|
East Asian Ancestry|
1,742 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Depression — — Partial Correlation (partial-r): 0.0549 [0.0077, 0.1019] sex, age, birth date, deprivation index, 16 PCs —
PPM011161 PSS007747|
African Ancestry|
2,272 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Depression — — Partial Correlation (partial-r): 0.0029 [-0.0384, 0.0442] sex, age, birth date, deprivation index, 16 PCs —
PPM011162 PSS008851|
African Ancestry|
3,678 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Depression — — Partial Correlation (partial-r): 0.0178 [-0.0147, 0.0501] sex, age, birth date, deprivation index, 16 PCs —
PPM011157 PSS008627|
European Ancestry|
5,989 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Depression — — Partial Correlation (partial-r): 0.0415 [0.0162, 0.0668] sex, age, birth date, deprivation index, 16 PCs —

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
PSS008401 — — 1,055 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS009073 — — 3,729 individuals — European Poland (NE Europe) UKB —
PSS009299 — — 17,764 individuals — European UK (+ Ireland) UKB —
PSS008851 — — 3,678 individuals — African unspecified Nigeria (West Africa) UKB —
PSS008181 — — 5,870 individuals — South Asian India (South Asia) UKB —
PSS008627 — — 5,989 individuals — European Italy (South Europe) UKB —
PSS007966 — — 1,742 individuals — East Asian China (East Asia) UKB —
PSS007747 — — 2,272 individuals — African American or Afro-Caribbean Carribean UKB —