Polygenic Score (PGS) ID: PGS001096

Predicted Trait
Reported Trait Hair color, light brown
Mapped Trait(s) hair colour measurement (EFO_0007822)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/BIN_FC3001747
Released in PGS Catalog: Oct. 21, 2021
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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 GBE_BIN_FC3001747
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 2,127
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000244
Citation (link to publication) Tanigawa Y et al. PLoS Genet (2022)
Ancestry Distribution
Score Development/Training
European: 100%
269,201 individuals (100%)
PGS Evaluation
European: 40%
African: 20%
East Asian: 20%
South Asian: 20%
5 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
—
[
  • 112,240 cases
  • , 156,961 controls
]
 European UKB — — — white British ancestry —

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
PPM008221 PSS003894|
African Ancestry|
6,395 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hair colour (natural, before greying) light brown — AUROC: 0.74239 [0.6665, 0.81828] R²: 0.10516
Incremental AUROC (full-covars): 0.00443
PGS R2 (no covariates): 0.03054
PGS AUROC (no covariates): 0.59019 [0.48973, 0.69066]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008222 PSS003895|
East Asian Ancestry|
1,668 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hair colour (natural, before greying) light brown — AUROC: 0.7191 [0.5714, 0.86681] R²: 0.05082
Incremental AUROC (full-covars): 0.01726
PGS R2 (no covariates): 7e-05
PGS AUROC (no covariates): 0.5472 [0.40687, 0.68753]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008223 PSS003896|
European Ancestry|
24,865 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hair colour (natural, before greying) light brown — AUROC: 0.64374 [0.63684, 0.65063] R²: 0.08084
Incremental AUROC (full-covars): 0.08241
PGS R2 (no covariates): 0.08583
PGS AUROC (no covariates): 0.6467 [0.63984, 0.65355]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008224 PSS003897|
South Asian Ancestry|
7,652 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hair colour (natural, before greying) light brown — AUROC: 0.6965 [0.65927, 0.73373] R²: 0.0697
Incremental AUROC (full-covars): 0.04422
PGS R2 (no covariates): 0.04452
PGS AUROC (no covariates): 0.64901 [0.60792, 0.69011]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008225 PSS003898|
European Ancestry|
67,286 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hair colour (natural, before greying) light brown — AUROC: 0.63678 [0.63262, 0.64093] R²: 0.07841
Incremental AUROC (full-covars): 0.10619
PGS R2 (no covariates): 0.0774
PGS AUROC (no covariates): 0.63449 [0.63034, 0.63865]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method

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
PSS003894 — —
[
  • 41 cases
  • , 6,354 controls
]
 — African unspecified — UKB —
PSS003895 — —
[
  • 12 cases
  • , 1,656 controls
]
 — East Asian — UKB —
PSS003896 — —
[
  • 8,887 cases
  • , 15,978 controls
]
 — European non-white British ancestry UKB —
PSS003897 — —
[
  • 201 cases
  • , 7,451 controls
]
 — South Asian — UKB —
PSS003898 — —
[
  • 27,978 cases
  • , 39,308 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)