Polygenic Score (PGS) ID: PGS002667

Predicted Trait
Reported Trait Tanning
Mapped Trait(s) suntan (EFO_0004279)
Released in PGS Catalog: June 9, 2022
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Score Details

Score Construction
PGS Name pigment_TANNING.PolyFun-pred
Development Method
Name PolyFun-pred
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 123,613
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000332
Citation (link to publication) Weissbrod O et al. Nat Genet (2022)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
330,738 individuals (100%)
PGS Evaluation
African: 25%
East Asian: 25%
European: 25%
South Asian: 25%
4 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
— 330,738 individuals 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
PPM014530 PSS009846|
South Asian Ancestry|
6,976 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: Tanning — — Incremental R2 (full model when combined with BOLT-LMM vs. covariates alone): 0.0001 age, sex, age*sex, assessment center, genotyping array, 10 PCs See pigment_TANNING.mixweights file at http://data.broadinstitute.org/alkesgroup/polypred_results for combination weights
PPM014383 PSS009843|
African Ancestry|
4,649 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: Tanning — — Incremental R2 (full model when combined with BOLT-LMM vs. covariates alone): 0.0 age, sex, age*sex, assessment center, genotyping array, 10 PCs See pigment_TANNING.mixweights file at http://data.broadinstitute.org/alkesgroup/polypred_results for combination weights
PPM014432 PSS009844|
East Asian Ancestry|
864 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: Tanning — — Incremental R2 (full model when combined with BOLT-LMM vs. covariates alone): 0.0015 age, sex, age*sex, assessment center, genotyping array, 10 PCs See pigment_TANNING.mixweights file at http://data.broadinstitute.org/alkesgroup/polypred_results for combination weights
PPM014481 PSS009845|
European Ancestry|
42,556 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: Tanning — — Incremental R2 (full model when combined with BOLT-LMM vs. covariates alone): 0.1326 age, sex, age*sex, assessment center, genotyping array, 10 PCs See pigment_TANNING.mixweights file at http://data.broadinstitute.org/alkesgroup/polypred_results for combination weights

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
PSS009844 — — 864 individuals — East Asian — UKB —
PSS009845 — — 42,556 individuals — European Non-British European UKB —
PSS009846 — — 6,976 individuals — South Asian — UKB —
PSS009843 — — 4,649 individuals — African unspecified — UKB —