PGS Catalog - PGS003920 / Arm fat-free mass (L) (Polygenic Score)

Polygenic Score (PGS) ID: PGS003920

Predicted Trait
Reported Trait	Arm fat-free mass (L)
Mapped Trait(s)	lean body mass (EFO_0004995)
Additional Trait Information	http://ipgs.mit.edu/tanigawakellis2023/INI23125

Released in PGS Catalog: Nov. 1, 2023

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Score Details

Score Construction
PGS Name	INI23125
Development Method
Name	snpnet
Parameters	inclusive PGS
Variants
Original Genome Build	GRCh37
Number of Variants	39,276
Effect Weight Type	beta

PGS Source
PGS Catalog Publication (PGP) ID	PGP000502
Citation (link to publication)	Tanigawa Y et al. AJHG (2023)

Ancestry Distribution
Score Development/Training	Multi-ancestry (including European): 100% European South Asian African Additional Diverse Ancestries 319,831 individuals (100%)
PGS Evaluation	European: 40% African: 20% Multi-ancestry (excluding European): 20% East Asian Additional Diverse Ancestries 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
—	319,831 individuals	European, South Asian, African unspecified, Other admixed ancestry	UKB	—	—	—	European, South Asian, African unspecified, Other admixed 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
PPM018919	PSS011130\| European Ancestry\| 66,591 individuals	PGP000502 \| Tanigawa Y et al. AJHG (2023)	Reported Trait: Arm fat-free mass (left)	—	—	R²: 0.73845 [0.73506, 0.74183] PGS R2 (no covariates): 0.0462 [0.04311, 0.04928] Incremental R2 (full-covars): 0.04641	age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18)	—
PPM018920	PSS011105\| European Ancestry\| 2,837 individuals	PGP000502 \| Tanigawa Y et al. AJHG (2023)	Reported Trait: Arm fat-free mass (left)	—	—	R²: 0.74029 [0.72403, 0.75655] PGS R2 (no covariates): 0.0595 [0.0428, 0.07619] Incremental R2 (full-covars): 0.0506	age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18)	—
PPM018921	PSS011118\| South Asian Ancestry\| 1,457 individuals	PGP000502 \| Tanigawa Y et al. AJHG (2023)	Reported Trait: Arm fat-free mass (left)	—	—	R²: 0.67307 [0.64587, 0.70027] PGS R2 (no covariates): 0.03556 [0.01712, 0.05401] Incremental R2 (full-covars): 0.0433	age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18)	—
PPM018922	PSS011157\| African Ancestry\| 1,168 individuals	PGP000502 \| Tanigawa Y et al. AJHG (2023)	Reported Trait: Arm fat-free mass (left)	—	—	R²: 0.58307 [0.54734, 0.6188] PGS R2 (no covariates): 0.00737 [-0.00219, 0.01694] Incremental R2 (full-covars): 0.00113	age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18)	—
PPM018923	PSS011162\| Multi-ancestry (excluding European)\| 7,839 individuals	PGP000502 \| Tanigawa Y et al. AJHG (2023)	Reported Trait: Arm fat-free mass (left)	—	—	R²: 0.73548 [0.72554, 0.74541] PGS R2 (no covariates): 0.03563 [0.02766, 0.0436] Incremental R2 (full-covars): 0.03443	age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18)	—

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
PSS011118	—	—	1,457 individuals	—	South Asian	—	UKB	—
PSS011157	—	—	1,168 individuals	—	African unspecified	—	UKB	—
PSS011130	—	—	66,591 individuals	—	European (white British ancestry)	—	UKB	—
PSS011162	—	—	7,839 individuals	—	East Asian, Other admixed ancestry	East Asian, Other admixed ancestry	UKB	—
PSS011105	—	—	2,837 individuals	—	European (non-white British ancestry)	—	UKB	—