Polygenic Score (PGS) ID: PGS001169

Predicted Trait
Reported Trait Whole body fat free mass
Mapped Trait(s) lean body mass (EFO_0004995)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI23101
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_INI23101
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 34,486
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%
265,157 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
— 265,157 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
PPM008565 PSS005046|
African Ancestry|
6,304 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Whole body fat-free mass — — R²: 0.60157 [0.58655, 0.61659]
Incremental R2 (full-covars): 0.01013
PGS R2 (no covariates): 0.01873 [0.0122, 0.02526]		 age, sex, UKB array type, Genotype PCs —
PPM008566 PSS005047|
East Asian Ancestry|
1,680 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Whole body fat-free mass — — R²: 0.75252 [0.73217, 0.77286]
Incremental R2 (full-covars): 0.00794
PGS R2 (no covariates): 0.01884 [0.00608, 0.03161]		 age, sex, UKB array type, Genotype PCs —
PPM008567 PSS005048|
European Ancestry|
24,463 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Whole body fat-free mass — — R²: 0.75918 [0.75397, 0.76439]
Incremental R2 (full-covars): 0.04637
PGS R2 (no covariates): 0.04707 [0.04193, 0.0522]		 age, sex, UKB array type, Genotype PCs —
PPM008568 PSS005049|
South Asian Ancestry|
7,649 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Whole body fat-free mass — — R²: 0.69559 [0.68435, 0.70683]
Incremental R2 (full-covars): 0.03597
PGS R2 (no covariates): 0.02818 [0.02096, 0.03541]		 age, sex, UKB array type, Genotype PCs —
PPM008569 PSS005050|
European Ancestry|
66,262 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Whole body fat-free mass — — R²: 0.76094 [0.75779, 0.76409]
Incremental R2 (full-covars): 0.05193
PGS R2 (no covariates): 0.05222 [0.04895, 0.05548]		 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
PSS005046 — — 6,304 individuals — African unspecified — UKB —
PSS005047 — — 1,680 individuals — East Asian — UKB —
PSS005048 — — 24,463 individuals — European non-white British ancestry UKB —
PSS005049 — — 7,649 individuals — South Asian — UKB —
PSS005050 — — 66,262 individuals — European white British ancestry UKB Testing cohort (heldout set)