Polygenic Score (PGS) ID: PGS002110

Predicted Trait
Reported Trait Skin color
Mapped Trait(s) skin pigmentation (EFO_0003784)
Additional Trait Information physical measures
Released in PGS Catalog: Jan. 10, 2022
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 portability-ldpred2_darker_skin0
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 275,831
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
PPM011735 PSS009393|
European Ancestry|
19,738 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Skin colour — — Partial Correlation (partial-r): 0.3849 [0.3729, 0.3967] sex, age, birth date, deprivation index, 16 PCs —
PPM011736 PSS009167|
European Ancestry|
4,029 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Skin colour — — Partial Correlation (partial-r): 0.3197 [0.2916, 0.3472] sex, age, birth date, deprivation index, 16 PCs —
PPM011737 PSS008721|
European Ancestry|
6,521 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Skin colour — — Partial Correlation (partial-r): 0.3242 [0.3023, 0.3458] sex, age, birth date, deprivation index, 16 PCs —
PPM011738 PSS008495|
Greater Middle Eastern Ancestry|
1,058 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Skin colour — — Partial Correlation (partial-r): 0.2964 [0.2399, 0.351] sex, age, birth date, deprivation index, 16 PCs —
PPM011739 PSS008273|
South Asian Ancestry|
6,068 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Skin colour — — Partial Correlation (partial-r): 0.1163 [0.0914, 0.1411] sex, age, birth date, deprivation index, 16 PCs —
PPM011740 PSS008050|
East Asian Ancestry|
1,506 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Skin colour — — Partial Correlation (partial-r): 0.0115 [-0.0394, 0.0623] sex, age, birth date, deprivation index, 16 PCs —
PPM011741 PSS007837|
African Ancestry|
2,401 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Skin colour — — Partial Correlation (partial-r): 0.0842 [0.0442, 0.1239] sex, age, birth date, deprivation index, 16 PCs —
PPM011742 PSS008941|
African Ancestry|
3,778 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Skin colour — — Partial Correlation (partial-r): 0.0232 [-0.0088, 0.0551] 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
PSS008941 — — 3,778 individuals — African unspecified Nigeria (West Africa) UKB —
PSS008495 — — 1,058 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS009167 — — 4,029 individuals — European Poland (NE Europe) UKB —
PSS008721 — — 6,521 individuals — European Italy (South Europe) UKB —
PSS009393 — — 19,738 individuals — European UK (+ Ireland) UKB —
PSS008273 — — 6,068 individuals — South Asian India (South Asia) UKB —
PSS008050 — — 1,506 individuals — East Asian China (East Asia) UKB —
PSS007837 — — 2,401 individuals — African American or Afro-Caribbean Carribean UKB —