Polygenic Score (PGS) ID: PGS003919

Predicted Trait
Reported Trait Arm fat mass (L)
Mapped Trait(s) fat body mass (EFO_0005409)
Additional Trait Information http://ipgs.mit.edu/tanigawakellis2023/INI23124
Released in PGS Catalog: Nov. 1, 2023
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Score Details

Score Construction
PGS Name INI23124
Development Method
Name snpnet
Parameters inclusive PGS
Variants
Original Genome Build GRCh37
Number of Variants 29,392
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
319,836 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
— 319,836 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
PPM018914 PSS011132|
European Ancestry|
66,594 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Arm fat mass (left) — — R²: 0.14427 [0.13937, 0.14916]
PGS R2 (no covariates): 0.08369 [0.0797, 0.08768]
Incremental R2 (full-covars): 0.08219		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
PPM018915 PSS011105|
European Ancestry|
2,837 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Arm fat mass (left) — — R²: 0.11957 [0.09741, 0.14173]
PGS R2 (no covariates): 0.07793 [0.0592, 0.09667]
Incremental R2 (full-covars): 0.0794		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
PPM018916 PSS011118|
South Asian Ancestry|
1,457 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Arm fat mass (left) — — R²: 0.18653 [0.1509, 0.22216]
PGS R2 (no covariates): 0.0701 [0.04513, 0.09506]
Incremental R2 (full-covars): 0.04734		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
PPM018917 PSS011158|
African Ancestry|
1,169 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Arm fat mass (left) — — R²: 0.12442 [0.08976, 0.15909]
PGS R2 (no covariates): 0.00699 [-0.00233, 0.0163]
Incremental R2 (full-covars): -0.05668		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
PPM018918 PSS011162|
Multi-ancestry (excluding European)|
7,839 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Arm fat mass (left) — — R²: 0.13999 [0.1259, 0.15408]
PGS R2 (no covariates): 0.07732 [0.06609, 0.08856]
Incremental R2 (full-covars): 0.06589		 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 —
PSS011158 — — 1,169 individuals — African unspecified — UKB —
PSS011162 — — 7,839 individuals — East Asian, Other admixed ancestry East Asian, Other admixed ancestry UKB —
PSS011132 — — 66,594 individuals — European
(white British ancestry)		 — UKB —
PSS011105 — — 2,837 individuals — European
(non-white British ancestry)		 — UKB —