Polygenic Score (PGS) ID: PGS001168

Predicted Trait
Reported Trait Trunk fat free mass
Mapped Trait(s) lean body mass (EFO_0004995)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI23129
Released in PGS Catalog: Oct. 21, 2021
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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_INI23129
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 34,749
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%
264,957 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
— 264,957 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
PPM008560 PSS005171|
African Ancestry|
6,298 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Trunk fat-free mass — — R²: 0.59642 [0.58127, 0.61157]
Incremental R2 (full-covars): 0.01057
PGS R2 (no covariates): 0.0178 [0.01143, 0.02418]		 age, sex, UKB array type, Genotype PCs —
PPM008561 PSS005172|
East Asian Ancestry|
1,677 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Trunk fat-free mass — — R²: 0.73696 [0.71556, 0.75835]
Incremental R2 (full-covars): 0.01146
PGS R2 (no covariates): 0.0221 [0.00833, 0.03588]		 age, sex, UKB array type, Genotype PCs —
PPM008562 PSS005173|
European Ancestry|
24,445 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Trunk fat-free mass — — R²: 0.76298 [0.75784, 0.76812]
Incremental R2 (full-covars): 0.04792
PGS R2 (no covariates): 0.04719 [0.04205, 0.05233]		 age, sex, UKB array type, Genotype PCs —
PPM008563 PSS005174|
South Asian Ancestry|
7,645 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Trunk fat-free mass — — R²: 0.69077 [0.67939, 0.70215]
Incremental R2 (full-covars): 0.03748
PGS R2 (no covariates): 0.03123 [0.02365, 0.03881]		 age, sex, UKB array type, Genotype PCs —
PPM008564 PSS005175|
European Ancestry|
66,210 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Trunk fat-free mass — — R²: 0.76832 [0.76525, 0.77138]
Incremental R2 (full-covars): 0.05259
PGS R2 (no covariates): 0.05253 [0.04925, 0.05581]		 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
PSS005171 — — 6,298 individuals — African unspecified — UKB —
PSS005172 — — 1,677 individuals — East Asian — UKB —
PSS005173 — — 24,445 individuals — European non-white British ancestry UKB —
PSS005174 — — 7,645 individuals — South Asian — UKB —
PSS005175 — — 66,210 individuals — European white British ancestry UKB Testing cohort (heldout set)