Polygenic Score (PGS) ID: PGS001096

Predicted Trait
Reported Trait Hair color, light brown
Mapped Trait(s) strand of hair color (OBA_0002313)
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
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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
]
EuropeanUKB———white British ancestry—
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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.

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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
PPM008221PSS003894|
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 PCsFull Model & PGS R2 is estimated using Nagelkerke's method
PPM008222PSS003895|
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 PCsFull Model & PGS R2 is estimated using Nagelkerke's method
PPM008223PSS003896|
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 PCsFull Model & PGS R2 is estimated using Nagelkerke's method
PPM008224PSS003897|
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 PCsFull Model & PGS R2 is estimated using Nagelkerke's method
PPM008225PSS003898|
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 PCsFull Model & PGS R2 is estimated using Nagelkerke's method
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Evaluated Samples

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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
]
—Europeannon-white British ancestryUKB—
PSS003897——
[
  • 201 cases
  • , 7,451 controls
]
—South Asian—UKB—
PSS003898——
[
  • 27,978 cases
  • , 39,308 controls
]
—Europeanwhite British ancestryUKBTesting cohort (heldout set)
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