Polygenic Score (PGS) ID: PGS001149

Predicted Trait
Reported Trait Whole body fat mass
Mapped Trait(s) fat body mass (EFO_0005409)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI23100
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_INI23100
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 27,550
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%
264,738 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
— 264,738 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
PPM008475 PSS005044|
South Asian Ancestry|
7,639 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Whole body fat mass — — R²: 0.17436 [0.1591, 0.18963]
Incremental R2 (full-covars): 0.05377
PGS R2 (no covariates): 0.06028 [0.05006, 0.07049]		 age, sex, UKB array type, Genotype PCs —
PPM008472 PSS005041|
African Ancestry|
6,294 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Whole body fat mass — — R²: 0.22098 [0.20318, 0.23878]
Incremental R2 (full-covars): 0.00715
PGS R2 (no covariates): 0.01342 [0.00786, 0.01897]		 age, sex, UKB array type, Genotype PCs —
PPM008473 PSS005042|
East Asian Ancestry|
1,667 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Whole body fat mass — — R²: 0.10565 [0.0781, 0.1332]
Incremental R2 (full-covars): 0.01419
PGS R2 (no covariates): 0.04325 [0.0244, 0.06211]		 age, sex, UKB array type, Genotype PCs —
PPM008474 PSS005043|
European Ancestry|
24,422 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Whole body fat mass — — R²: 0.1432 [0.13515, 0.15125]
Incremental R2 (full-covars): 0.08949
PGS R2 (no covariates): 0.09358 [0.08669, 0.10047]		 age, sex, UKB array type, Genotype PCs —
PPM008476 PSS005045|
European Ancestry|
66,165 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Whole body fat mass — — R²: 0.16366 [0.15856, 0.16877]
Incremental R2 (full-covars): 0.09847
PGS R2 (no covariates): 0.09893 [0.09465, 0.10321]		 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
PSS005041 — — 6,294 individuals — African unspecified — UKB —
PSS005042 — — 1,667 individuals — East Asian — UKB —
PSS005043 — — 24,422 individuals — European non-white British ancestry UKB —
PSS005044 — — 7,639 individuals — South Asian — UKB —
PSS005045 — — 66,165 individuals — European white British ancestry UKB Testing cohort (heldout set)