Polygenic Score (PGS) ID: PGS001385

Predicted Trait
Reported Trait Degree bothered by headaches in the last 3 months
Mapped Trait(s) health-related quality of life measurement (EFO_0011014)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI21051
Released in PGS Catalog: Nov. 25, 2021
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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_INI21051
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 9
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%
97,917 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
— 97,917 individuals European UKB — — — white British ancestry Training + validation cohort (train_val)

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
PPM005277 PSS004938|
European Ancestry|
9,142 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Degree bothered by headaches in the last 3 months — — R²: 0.05819 [0.05255, 0.06383]
Incremental R2 (full-covars): 0.00083
PGS R2 (no covariates): 0.00259 [0.00133, 0.00385]		 age, sex, UKB array type, Genotype PCs —
PPM005275 PSS004936|
African Ancestry|
1,001 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Degree bothered by headaches in the last 3 months — — R²: 0.07897 [0.06639, 0.09155]
Incremental R2 (full-covars): -0.00025
PGS R2 (no covariates): 1e-05 [-0.00011, 0.00012]		 age, sex, UKB array type, Genotype PCs —
PPM005276 PSS004937|
East Asian Ancestry|
396 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Degree bothered by headaches in the last 3 months — — R²: 0.06474 [0.04219, 0.0873]
Incremental R2 (full-covars): 0.00012
PGS R2 (no covariates): 0.00041 [-0.00151, 0.00232]		 age, sex, UKB array type, Genotype PCs —
PPM005278 PSS004939|
South Asian Ancestry|
1,195 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Degree bothered by headaches in the last 3 months — — R²: 0.09268 [0.08045, 0.10491]
Incremental R2 (full-covars): 0.00089
PGS R2 (no covariates): 0.00183 [-0.00006, 0.00371]		 age, sex, UKB array type, Genotype PCs —
PPM005279 PSS004940|
European Ancestry|
24,455 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Degree bothered by headaches in the last 3 months — — R²: 0.06122 [0.05772, 0.06473]
Incremental R2 (full-covars): 0.00053
PGS R2 (no covariates): 0.00089 [0.00044, 0.00134]		 age, sex, UKB array type, Genotype PCs —

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
PSS004936 — — 1,001 individuals — African unspecified — UKB —
PSS004937 — — 396 individuals — East Asian — UKB —
PSS004938 — — 9,142 individuals — European non-white British ancestry UKB —
PSS004939 — — 1,195 individuals — South Asian — UKB —
PSS004940 — — 24,455 individuals — European white British ancestry UKB Testing cohort (heldout set)