Polygenic Score (PGS) ID: PGS001147

Predicted Trait
Reported Trait Leg fat mass (R)
Mapped Trait(s) fat body mass (EFO_0005409)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI23112
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_INI23112
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 23,565
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%
265,162 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
— 265,162 individuals 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
PPM008462 PSS005091|
African Ancestry|
6,305 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Leg fat mass (R) — — R²: 0.43888 [0.42081, 0.45695]
Incremental R2 (full-covars): 0.00478
PGS R2 (no covariates): 0.00647 [0.00258, 0.01035]		 age, sex, UKB array type, Genotype PCs —
PPM008463 PSS005092|
East Asian Ancestry|
1,680 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Leg fat mass (R) — — R²: 0.46789 [0.43339, 0.50238]
Incremental R2 (full-covars): -0.00071
PGS R2 (no covariates): 0.03169 [0.01535, 0.04803]		 age, sex, UKB array type, Genotype PCs —
PPM008464 PSS005093|
European Ancestry|
24,463 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Leg fat mass (R) — — R²: 0.34025 [0.33069, 0.34981]
Incremental R2 (full-covars): 0.05666
PGS R2 (no covariates): 0.05548 [0.04995, 0.061]		 age, sex, UKB array type, Genotype PCs —
PPM008465 PSS005094|
South Asian Ancestry|
7,649 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Leg fat mass (R) — — R²: 0.44907 [0.43273, 0.46542]
Incremental R2 (full-covars): 0.02496
PGS R2 (no covariates): 0.03286 [0.0251, 0.04063]		 age, sex, UKB array type, Genotype PCs —
PPM008466 PSS005095|
European Ancestry|
66,259 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Leg fat mass (R) — — R²: 0.37892 [0.37315, 0.38469]
Incremental R2 (full-covars): 0.06155
PGS R2 (no covariates): 0.0616 [0.05808, 0.06511]		 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
PSS005091 — — 6,305 individuals — African unspecified — UKB —
PSS005092 — — 1,680 individuals — East Asian — UKB —
PSS005093 — — 24,463 individuals — European non-white British ancestry UKB —
PSS005094 — — 7,649 individuals — South Asian — UKB —
PSS005095 — — 66,259 individuals — European white British ancestry UKB Testing cohort (heldout set)