Polygenic Score (PGS) ID: PGS001897

Predicted Trait
Reported Trait Skin colour
Mapped Trait(s) skin pigmentation (EFO_0003784)
Additional Trait Information physical measures
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-PLR_darker_skin0
Development Method
Name Penalized regression (bigstatsr)
Parameters HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 15,817
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
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
391,124 individuals European UK (+ Ireland) 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
PPM010060 PSS009167|
European Ancestry|
4,029 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Skin colour Partial Correlation (partial-r): 0.3235 [0.2955, 0.3509] sex, age, birth date, deprivation index, 16 PCs
PPM010061 PSS008721|
European Ancestry|
6,521 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Skin colour Partial Correlation (partial-r): 0.326 [0.3041, 0.3476] sex, age, birth date, deprivation index, 16 PCs
PPM010059 PSS009393|
European Ancestry|
19,738 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Skin colour Partial Correlation (partial-r): 0.387 [0.375, 0.3988] sex, age, birth date, deprivation index, 16 PCs
PPM010063 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): 0.1171 [0.0921, 0.1418] sex, age, birth date, deprivation index, 16 PCs
PPM010064 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): 0.0091 [-0.0418, 0.0599] sex, age, birth date, deprivation index, 16 PCs
PPM010065 PSS007837|
African Ancestry|
2,401 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Skin colour Partial Correlation (partial-r): 0.0775 [0.0374, 0.1173] sex, age, birth date, deprivation index, 16 PCs
PPM010066 PSS008941|
African Ancestry|
3,778 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Skin colour Partial Correlation (partial-r): 0.0247 [-0.0073, 0.0567] sex, age, birth date, deprivation index, 16 PCs
PPM010062 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): 0.2918 [0.2352, 0.3465] 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
PSS009167 4,029 individuals European Poland (NE Europe) UKB
PSS008495 1,058 individuals Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB
PSS009393 19,738 individuals European UK (+ Ireland) UKB
PSS008050 1,506 individuals East Asian China (East Asia) UKB
PSS008721 6,521 individuals European Italy (South Europe) UKB
PSS008273 6,068 individuals South Asian India (South Asia) UKB
PSS007837 2,401 individuals African American or Afro-Caribbean Carribean UKB