Polygenic Score (PGS) ID: PGS001386

Predicted Trait
Reported Trait Degree bothered by pain in arms/legs/joints in the past 3 months
Mapped Trait(s) health-related quality of life measurement (EFO_0011014)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI21049
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_INI21049
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 534
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%
97,888 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
— 97,888 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
PPM005270 PSS004931|
African Ancestry|
1,002 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Degree bothered by pain in arms/legs/joints in the past 3 months — — R²: 0.04832 [0.03815, 0.05849]
Incremental R2 (full-covars): -0.00055
PGS R2 (no covariates): 6e-05 [-0.00033, 0.00046]		 age, sex, UKB array type, Genotype PCs —
PPM005271 PSS004932|
East Asian Ancestry|
396 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Degree bothered by pain in arms/legs/joints in the past 3 months — — R²: 0.04977 [0.02968, 0.06986]
Incremental R2 (full-covars): 0.00065
PGS R2 (no covariates): 0.0014 [-0.00214, 0.00493]		 age, sex, UKB array type, Genotype PCs —
PPM005272 PSS004933|
European Ancestry|
9,141 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Degree bothered by pain in arms/legs/joints in the past 3 months — — R²: 0.01604 [0.01295, 0.01914]
Incremental R2 (full-covars): 0.00043
PGS R2 (no covariates): 0.00057 [-0.00002, 0.00116]		 age, sex, UKB array type, Genotype PCs —
PPM005273 PSS004934|
South Asian Ancestry|
1,195 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Degree bothered by pain in arms/legs/joints in the past 3 months — — R²: 0.02804 [0.02084, 0.03525]
Incremental R2 (full-covars): 0.00067
PGS R2 (no covariates): 0.00053 [-0.00049, 0.00155]		 age, sex, UKB array type, Genotype PCs —
PPM005274 PSS004935|
European Ancestry|
24,448 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Degree bothered by pain in arms/legs/joints in the past 3 months — — R²: 0.01206 [0.01042, 0.0137]
Incremental R2 (full-covars): 0.00085
PGS R2 (no covariates): 0.00086 [0.00042, 0.0013]		 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
PSS004931 — — 1,002 individuals — African unspecified — UKB —
PSS004932 — — 396 individuals — East Asian — UKB —
PSS004933 — — 9,141 individuals — European non-white British ancestry UKB —
PSS004934 — — 1,195 individuals — South Asian — UKB —
PSS004935 — — 24,448 individuals — European white British ancestry UKB Testing cohort (heldout set)