Polygenic Score (PGS) ID: PGS001098

Predicted Trait
Reported Trait Hair color, red
Mapped Trait(s) hair colour measurement (EFO_0007822)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/BIN_FC2001747
Released in PGS Catalog: Oct. 21, 2021
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Score Details

Score Construction
PGS Name GBE_BIN_FC2001747
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 1,621
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: 66.7%
African: 33.3%
3 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
—
[
  • 12,353 cases
  • , 256,848 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
PPM008231 PSS003840|
African Ancestry|
6,395 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hair colour (natural, before greying) red — AUROC: 0.66297 [0.41942, 0.90653] R²: 0.03161
Incremental AUROC (full-covars): -0.14372
PGS R2 (no covariates): 0.01304
PGS AUROC (no covariates): 0.33718 [0.05268, 0.62169]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008232 PSS003841|
European Ancestry|
24,865 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hair colour (natural, before greying) red — AUROC: 0.95374 [0.94735, 0.96013] R²: 0.57916
Incremental AUROC (full-covars): 0.27252
PGS R2 (no covariates): 0.58427
PGS AUROC (no covariates): 0.95332 [0.94681, 0.95982]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008233 PSS003843|
European Ancestry|
67,286 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hair colour (natural, before greying) red — AUROC: 0.96093 [0.95755, 0.96431] R²: 0.60335
Incremental AUROC (full-covars): 0.3903
PGS R2 (no covariates): 0.60185
PGS AUROC (no covariates): 0.96068 [0.95728, 0.96408]		 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
PSS003840 — —
[
  • 5 cases
  • , 6,390 controls
]
 — African unspecified — UKB —
PSS003841 — —
[
  • 1,124 cases
  • , 23,741 controls
]
 — European non-white British ancestry UKB —
PSS003843 — —
[
  • 3,058 cases
  • , 64,228 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)