Polygenic Score (PGS) ID: PGS001160

Predicted Trait
Reported Trait Trunk mass (predicted)
Mapped Trait(s) body composition measurement (EFO_0005106)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI23130
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_INI23130
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 32,685
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%
264,932 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
— 264,932 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
PPM008522 PSS005176|
African Ancestry|
6,298 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Trunk pred. mass — — R²: 0.60813 [0.59327, 0.62298]
Incremental R2 (full-covars): 0.01103
PGS R2 (no covariates): 0.01817 [0.01174, 0.0246]		 age, sex, UKB array type, Genotype PCs —
PPM008523 PSS005177|
East Asian Ancestry|
1,677 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Trunk pred. mass — — R²: 0.74648 [0.72572, 0.76724]
Incremental R2 (full-covars): 0.01277
PGS R2 (no covariates): 0.02185 [0.00815, 0.03555]		 age, sex, UKB array type, Genotype PCs —
PPM008524 PSS005178|
European Ancestry|
24,444 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Trunk pred. mass — — R²: 0.76821 [0.76317, 0.77326]
Incremental R2 (full-covars): 0.04598
PGS R2 (no covariates): 0.04582 [0.04074, 0.05089]		 age, sex, UKB array type, Genotype PCs —
PPM008525 PSS005179|
South Asian Ancestry|
7,642 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Trunk pred. mass — — R²: 0.69886 [0.68771, 0.71]
Incremental R2 (full-covars): 0.03651
PGS R2 (no covariates): 0.03063 [0.02312, 0.03815]		 age, sex, UKB array type, Genotype PCs —
PPM008526 PSS005180|
European Ancestry|
66,204 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Trunk pred. mass — — R²: 0.7731 [0.77009, 0.77611]
Incremental R2 (full-covars): 0.05059
PGS R2 (no covariates): 0.05155 [0.0483, 0.0548]		 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
PSS005180 — — 66,204 individuals — European white British ancestry UKB Testing cohort (heldout set)
PSS005176 — — 6,298 individuals — African unspecified — UKB —
PSS005177 — — 1,677 individuals — East Asian — UKB —
PSS005178 — — 24,444 individuals — European non-white British ancestry UKB —
PSS005179 — — 7,642 individuals — South Asian — UKB —