Polygenic Score (PGS) ID: PGS001106

Predicted Trait
Reported Trait Arm fat percentage (R)
Mapped Trait(s) body fat percentage (EFO_0007800)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI23119
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_INI23119
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 23,943
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%
265,125 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
— 265,125 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
PPM008269 PSS005121|
African Ancestry|
6,302 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Arm fat % (R) — — R²: 0.61876 [0.60418, 0.63333]
Incremental R2 (full-covars): 0.0012
PGS R2 (no covariates): 0.00365 [0.00072, 0.00657]		 age, sex, UKB array type, Genotype PCs —
PPM008270 PSS005122|
East Asian Ancestry|
1,678 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Arm fat % (R) — — R²: 0.46296 [0.42833, 0.49759]
Incremental R2 (full-covars): 0.00917
PGS R2 (no covariates): 0.03415 [0.01724, 0.05107]		 age, sex, UKB array type, Genotype PCs —
PPM008271 PSS005123|
European Ancestry|
24,458 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Arm fat % (R) — — R²: 0.45741 [0.4483, 0.46653]
Incremental R2 (full-covars): 0.04769
PGS R2 (no covariates): 0.04324 [0.03829, 0.04818]		 age, sex, UKB array type, Genotype PCs —
PPM008272 PSS005124|
South Asian Ancestry|
7,649 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Arm fat % (R) — — R²: 0.62976 [0.61675, 0.64277]
Incremental R2 (full-covars): 0.0194
PGS R2 (no covariates): 0.02347 [0.01685, 0.0301]		 age, sex, UKB array type, Genotype PCs —
PPM008273 PSS005125|
European Ancestry|
66,253 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Arm fat % (R) — — R²: 0.5084 [0.50311, 0.51369]
Incremental R2 (full-covars): 0.04751
PGS R2 (no covariates): 0.04648 [0.04338, 0.04959]		 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
PSS005121 — — 6,302 individuals — African unspecified — UKB —
PSS005122 — — 1,678 individuals — East Asian — UKB —
PSS005123 — — 24,458 individuals — European non-white British ancestry UKB —
PSS005124 — — 7,649 individuals — South Asian — UKB —
PSS005125 — — 66,253 individuals — European white British ancestry UKB Testing cohort (heldout set)