Polygenic Score (PGS) ID: PGS001092

Predicted Trait
Reported Trait Hair color, black
Mapped Trait(s) hair colour measurement (EFO_0007822)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/BIN_FC5001747
Released in PGS Catalog: Oct. 21, 2021
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 GBE_BIN_FC5001747
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 1,649
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
—
[
  • 11,543 cases
  • , 257,658 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
PPM008203 PSS003969|
African Ancestry|
6,395 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hair colour (natural, before greying) black — AUROC: 0.73806 [0.72041, 0.75572] R²: 0.15759
Incremental AUROC (full-covars): -0.00158
PGS R2 (no covariates): 0.06773
PGS AUROC (no covariates): 0.64443 [0.62282, 0.66604]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008204 PSS003970|
East Asian Ancestry|
1,668 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hair colour (natural, before greying) black — AUROC: 0.64698 [0.61512, 0.67883] R²: 0.06317
Incremental AUROC (full-covars): -0.01356
PGS R2 (no covariates): 0.00159
PGS AUROC (no covariates): 0.51653 [0.48088, 0.55219]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008205 PSS003971|
European Ancestry|
24,865 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hair colour (natural, before greying) black — AUROC: 0.86644 [0.85917, 0.87371] R²: 0.31811
Incremental AUROC (full-covars): 0.10937
PGS R2 (no covariates): 0.25773
PGS AUROC (no covariates): 0.83509 [0.82689, 0.84329]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008206 PSS003972|
South Asian Ancestry|
7,652 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hair colour (natural, before greying) black — AUROC: 0.73447 [0.7223, 0.74664] R²: 0.19134
Incremental AUROC (full-covars): -0.00772
PGS R2 (no covariates): 0.03493
PGS AUROC (no covariates): 0.59358 [0.57931, 0.60784]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008207 PSS003973|
European Ancestry|
67,286 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hair colour (natural, before greying) black — AUROC: 0.88391 [0.87857, 0.88926] R²: 0.30488
Incremental AUROC (full-covars): 0.14967
PGS R2 (no covariates): 0.21551
PGS AUROC (no covariates): 0.83054 [0.82335, 0.83772]		 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
PSS003969 — —
[
  • 5,590 cases
  • , 805 controls
]
 — African unspecified — UKB —
PSS003970 — —
[
  • 1,360 cases
  • , 308 controls
]
 — East Asian — UKB —
PSS003971 — —
[
  • 1,986 cases
  • , 22,879 controls
]
 — European non-white British ancestry UKB —
PSS003972 — —
[
  • 5,499 cases
  • , 2,153 controls
]
 — South Asian — UKB —
PSS003973 — —
[
  • 2,842 cases
  • , 64,444 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)