Polygenic Score (PGS) ID: PGS001101

Predicted Trait
Reported Trait Body fat percentage
Mapped Trait(s) body fat percentage (EFO_0007800)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI23099
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_INI23099
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 27,396
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%
265,024 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
— 265,024 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
PPM008244 PSS005036|
African Ancestry|
6,300 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Body fat % — — R²: 0.58609 [0.57069, 0.6015]
Incremental R2 (full-covars): -0.00196
PGS R2 (no covariates): 0.00632 [0.00248, 0.01016]		 age, sex, UKB array type, Genotype PCs —
PPM008245 PSS005037|
East Asian Ancestry|
1,677 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Body fat % — — R²: 0.43955 [0.40434, 0.47477]
Incremental R2 (full-covars): 0.00787
PGS R2 (no covariates): 0.03564 [0.01839, 0.05289]		 age, sex, UKB array type, Genotype PCs —
PPM008246 PSS005038|
European Ancestry|
24,454 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Body fat % — — R²: 0.46731 [0.45827, 0.47636]
Incremental R2 (full-covars): 0.0533
PGS R2 (no covariates): 0.04958 [0.04432, 0.05483]		 age, sex, UKB array type, Genotype PCs —
PPM008247 PSS005039|
South Asian Ancestry|
7,645 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Body fat % — — R²: 0.56822 [0.5538, 0.58263]
Incremental R2 (full-covars): 0.01844
PGS R2 (no covariates): 0.0265 [0.01948, 0.03351]		 age, sex, UKB array type, Genotype PCs —
PPM008248 PSS005040|
European Ancestry|
66,227 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Body fat % — — R²: 0.51245 [0.50718, 0.51771]
Incremental R2 (full-covars): 0.05409
PGS R2 (no covariates): 0.05282 [0.04954, 0.05611]		 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
PSS005036 — — 6,300 individuals — African unspecified — UKB —
PSS005037 — — 1,677 individuals — East Asian — UKB —
PSS005038 — — 24,454 individuals — European non-white British ancestry UKB —
PSS005039 — — 7,645 individuals — South Asian — UKB —
PSS005040 — — 66,227 individuals — European white British ancestry UKB Testing cohort (heldout set)