Polygenic Score (PGS) ID: PGS001094

Predicted Trait
Reported Trait Hair color, brown
Mapped Trait(s) hair colour measurement (EFO_0007822)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/BIN_FC7001747
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_FC7001747
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 4,024
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
—
[
  • 211,969 cases
  • , 57,232 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
PPM008211 PSS004004|
African Ancestry|
6,395 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hair colour (natural, before greying) brown — AUROC: 0.71768 [0.69956, 0.7358] R²: 0.12623
Incremental AUROC (full-covars): -0.03583
PGS R2 (no covariates): 0.03239
PGS AUROC (no covariates): 0.39864 [0.37618, 0.42109]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008212 PSS004005|
East Asian Ancestry|
1,668 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hair colour (natural, before greying) brown — AUROC: 0.65007 [0.61813, 0.68201] R²: 0.07693
Incremental AUROC (full-covars): -0.01602
PGS R2 (no covariates): 0.00012
PGS AUROC (no covariates): 0.49459 [0.45931, 0.52988]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008213 PSS004006|
European Ancestry|
24,865 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hair colour (natural, before greying) brown — AUROC: 0.63987 [0.63123, 0.64851] R²: 0.07778
Incremental AUROC (full-covars): 0.06751
PGS R2 (no covariates): 0.06909
PGS AUROC (no covariates): 0.62444 [0.61553, 0.63335]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008214 PSS004007|
South Asian Ancestry|
7,652 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hair colour (natural, before greying) brown — AUROC: 0.71561 [0.70281, 0.7284] R²: 0.16063
Incremental AUROC (full-covars): -0.03646
PGS R2 (no covariates): 0.02063
PGS AUROC (no covariates): 0.42996 [0.41544, 0.44447]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008215 PSS004008|
European Ancestry|
67,286 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hair colour (natural, before greying) brown — AUROC: 0.69817 [0.69293, 0.70341] R²: 0.14719
Incremental AUROC (full-covars): 0.16012
PGS R2 (no covariates): 0.14428
PGS AUROC (no covariates): 0.69511 [0.68976, 0.70046]		 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
PSS004004 — —
[
  • 753 cases
  • , 5,642 controls
]
 — African unspecified — UKB —
PSS004005 — —
[
  • 307 cases
  • , 1,361 controls
]
 — East Asian — UKB —
PSS004006 — —
[
  • 18,755 cases
  • , 6,110 controls
]
 — European non-white British ancestry UKB —
PSS004007 — —
[
  • 2,087 cases
  • , 5,565 controls
]
 — South Asian — UKB —
PSS004008 — —
[
  • 52,905 cases
  • , 14,381 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)