Polygenic Score (PGS) ID: PGS001105

Predicted Trait
Reported Trait Body fat percentage (trunk fat)
Mapped Trait(s) body fat percentage (EFO_0007800)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI23127
Released in PGS Catalog: Oct. 21, 2021
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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_INI23127
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 25,651
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%
265,023 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
— 265,023 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
PPM008264 PSS005161|
African Ancestry|
6,299 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Trunk fat % — — R²: 0.33345 [0.31474, 0.35216]
Incremental R2 (full-covars): -0.0012
PGS R2 (no covariates): 0.01046 [0.00554, 0.01538]		 age, sex, UKB array type, Genotype PCs —
PPM008265 PSS005162|
East Asian Ancestry|
1,678 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Trunk fat % — — R²: 0.13249 [0.10257, 0.16242]
Incremental R2 (full-covars): 0.02072
PGS R2 (no covariates): 0.03925 [0.02121, 0.05729]		 age, sex, UKB array type, Genotype PCs —
PPM008266 PSS005163|
European Ancestry|
24,452 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Trunk fat % — — R²: 0.23391 [0.22471, 0.24311]
Incremental R2 (full-covars): 0.07149
PGS R2 (no covariates): 0.07404 [0.06778, 0.0803]		 age, sex, UKB array type, Genotype PCs —
PPM008267 PSS005164|
South Asian Ancestry|
7,646 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Trunk fat % — — R²: 0.26434 [0.2476, 0.28109]
Incremental R2 (full-covars): 0.03313
PGS R2 (no covariates): 0.04146 [0.03282, 0.05011]		 age, sex, UKB array type, Genotype PCs —
PPM008268 PSS005165|
European Ancestry|
66,224 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Trunk fat % — — R²: 0.26796 [0.26224, 0.27368]
Incremental R2 (full-covars): 0.07557
PGS R2 (no covariates): 0.07501 [0.07118, 0.07883]		 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
PSS005161 — — 6,299 individuals — African unspecified — UKB —
PSS005162 — — 1,678 individuals — East Asian — UKB —
PSS005163 — — 24,452 individuals — European non-white British ancestry UKB —
PSS005164 — — 7,646 individuals — South Asian — UKB —
PSS005165 — — 66,224 individuals — European white British ancestry UKB Testing cohort (heldout set)