Polygenic Score (PGS) ID: PGS001095

Predicted Trait
Reported Trait Hair color, dark brown
Mapped Trait(s) hair colour measurement (EFO_0007822)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/BIN_FC4001747
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_FC4001747
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 5,662
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
—
[
  • 101,313 cases
  • , 167,888 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
PPM008216 PSS003934|
African Ancestry|
6,395 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hair colour (natural, before greying) dark brown — AUROC: 0.65156 [0.63203, 0.67109] R²: 0.05774
Incremental AUROC (full-covars): -0.10551
PGS R2 (no covariates): 0.06147
PGS AUROC (no covariates): 0.36004 [0.33679, 0.38329]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008217 PSS003935|
East Asian Ancestry|
1,668 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hair colour (natural, before greying) dark brown — AUROC: 0.61634 [0.58316, 0.64951] R²: 0.04892
Incremental AUROC (full-covars): -0.04911
PGS R2 (no covariates): 0.00247
PGS AUROC (no covariates): 0.46704 [0.43121, 0.50287]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008218 PSS003936|
European Ancestry|
24,865 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hair colour (natural, before greying) dark brown — AUROC: 0.73384 [0.7277, 0.73998] R²: 0.17609
Incremental AUROC (full-covars): 0.13518
PGS R2 (no covariates): 0.18215
PGS AUROC (no covariates): 0.73591 [0.72979, 0.74203]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008219 PSS003937|
South Asian Ancestry|
7,652 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hair colour (natural, before greying) dark brown — AUROC: 0.6651 [0.65094, 0.67927] R²: 0.08302
Incremental AUROC (full-covars): -0.08617
PGS R2 (no covariates): 0.02576
PGS AUROC (no covariates): 0.41252 [0.3978, 0.42725]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008220 PSS003938|
European Ancestry|
67,286 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hair colour (natural, before greying) dark brown — AUROC: 0.77552 [0.77202, 0.77902] R²: 0.26416
Incremental AUROC (full-covars): 0.24306
PGS R2 (no covariates): 0.26448
PGS AUROC (no covariates): 0.77588 [0.77238, 0.77938]		 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
PSS003934 — —
[
  • 712 cases
  • , 5,683 controls
]
 — African unspecified — UKB —
PSS003935 — —
[
  • 295 cases
  • , 1,373 controls
]
 — East Asian — UKB —
PSS003936 — —
[
  • 9,961 cases
  • , 14,904 controls
]
 — European non-white British ancestry UKB —
PSS003937 — —
[
  • 1,887 cases
  • , 5,765 controls
]
 — South Asian — UKB —
PSS003938 — —
[
  • 25,313 cases
  • , 41,973 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)