Polygenic Score (PGS) ID: PGS001146

Predicted Trait
Reported Trait Arm fat-free mass (R)
Mapped Trait(s) fat body mass (EFO_0005409)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI23121
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_INI23121
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 29,063
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%
265,102 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
— 265,102 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
PPM008459 PSS005133|
European Ancestry|
24,458 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Arm fat-free mass (R) — — R²: 0.76277 [0.75762, 0.76791]
Incremental R2 (full-covars): 0.03623
PGS R2 (no covariates): 0.03786 [0.03321, 0.04251]		 age, sex, UKB array type, Genotype PCs —
PPM008457 PSS005131|
African Ancestry|
6,302 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Arm fat-free mass (R) — — R²: 0.64816 [0.63439, 0.66193]
Incremental R2 (full-covars): 0.00971
PGS R2 (no covariates): 0.01621 [0.01012, 0.02229]		 age, sex, UKB array type, Genotype PCs —
PPM008458 PSS005132|
East Asian Ancestry|
1,678 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Arm fat-free mass (R) — — R²: 0.75781 [0.73783, 0.77779]
Incremental R2 (full-covars): 0.0021
PGS R2 (no covariates): 0.01403 [0.00296, 0.0251]		 age, sex, UKB array type, Genotype PCs —
PPM008460 PSS005134|
South Asian Ancestry|
7,649 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Arm fat-free mass (R) — — R²: 0.70823 [0.69735, 0.7191]
Incremental R2 (full-covars): 0.02714
PGS R2 (no covariates): 0.018 [0.01216, 0.02383]		 age, sex, UKB array type, Genotype PCs —
PPM008461 PSS005135|
European Ancestry|
66,249 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Arm fat-free mass (R) — — R²: 0.75647 [0.75327, 0.75966]
Incremental R2 (full-covars): 0.0401
PGS R2 (no covariates): 0.04083 [0.03791, 0.04376]		 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
PSS005131 — — 6,302 individuals — African unspecified — UKB —
PSS005132 — — 1,678 individuals — East Asian — UKB —
PSS005133 — — 24,458 individuals — European non-white British ancestry UKB —
PSS005134 — — 7,649 individuals — South Asian — UKB —
PSS005135 — — 66,249 individuals — European white British ancestry UKB Testing cohort (heldout set)