Polygenic Score (PGS) ID: PGS001097

Predicted Trait
Reported Trait Hair color, other
Mapped Trait(s) hair colour measurement (EFO_0007822)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/BIN_FC6001747
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_FC6001747
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 21
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
—
[
  • 3,472 cases
  • , 265,729 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
PPM008226 PSS003984|
African Ancestry|
6,395 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hair colour (natural, before greying) other — AUROC: 0.68416 [0.60178, 0.76653] R²: 0.04963
Incremental AUROC (full-covars): 0.00247
PGS R2 (no covariates): 0.00135
PGS AUROC (no covariates): 0.53686 [0.45932, 0.6144]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008227 PSS003985|
East Asian Ancestry|
1,668 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hair colour (natural, before greying) other — AUROC: 0.85339 [0.78314, 0.92364] R²: 0.12305
Incremental AUROC (full-covars): -0.00248
PGS R2 (no covariates): 0.00835
PGS AUROC (no covariates): 0.40595 [0.19292, 0.61897]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008228 PSS003986|
European Ancestry|
24,865 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hair colour (natural, before greying) other — AUROC: 0.65979 [0.63012, 0.68946] R²: 0.03266
Incremental AUROC (full-covars): 0.01921
PGS R2 (no covariates): 0.0114
PGS AUROC (no covariates): 0.59367 [0.56236, 0.62499]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008229 PSS003987|
South Asian Ancestry|
7,652 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hair colour (natural, before greying) other — AUROC: 0.77253 [0.71966, 0.82541] R²: 0.09785
Incremental AUROC (full-covars): 0.00187
PGS R2 (no covariates): 0.00125
PGS AUROC (no covariates): 0.52534 [0.46064, 0.59004]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008230 PSS003988|
European Ancestry|
67,286 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hair colour (natural, before greying) other — AUROC: 0.66009 [0.64226, 0.67793] R²: 0.03193
Incremental AUROC (full-covars): 0.02994
PGS R2 (no covariates): 0.01286
PGS AUROC (no covariates): 0.59773 [0.57827, 0.61719]		 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
PSS003984 — —
[
  • 55 cases
  • , 6,340 controls
]
 — African unspecified — UKB —
PSS003985 — —
[
  • 8 cases
  • , 1,660 controls
]
 — East Asian — UKB —
PSS003986 — —
[
  • 314 cases
  • , 24,551 controls
]
 — European non-white British ancestry UKB —
PSS003987 — —
[
  • 76 cases
  • , 7,576 controls
]
 — South Asian — UKB —
PSS003988 — —
[
  • 856 cases
  • , 66,430 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)