Polygenic Score (PGS) ID: PGS003922

Predicted Trait
Reported Trait Trunk fat mass
Mapped Trait(s) fat body mass (EFO_0005409)
Additional Trait Information http://ipgs.mit.edu/tanigawakellis2023/INI23128
Released in PGS Catalog: Nov. 1, 2023
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Score Details

Score Construction
PGS Name INI23128
Development Method
Name snpnet
Parameters inclusive PGS
Variants
Original Genome Build GRCh37
Number of Variants 34,357
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
319,786 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
— 319,786 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
PPM018929 PSS011127|
European Ancestry|
66,580 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Trunk fat mass — — R²: 0.12779 [0.1231, 0.13249]
PGS R2 (no covariates): 0.11593 [0.1114, 0.12047]
Incremental R2 (full-covars): 0.11466		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
PPM018930 PSS011105|
European Ancestry|
2,837 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Trunk fat mass — — R²: 0.13897 [0.11561, 0.16233]
PGS R2 (no covariates): 0.13241 [0.10944, 0.15539]
Incremental R2 (full-covars): 0.12803		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
PPM018931 PSS011119|
South Asian Ancestry|
1,456 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Trunk fat mass — — R²: 0.12834 [0.09667, 0.16001]
PGS R2 (no covariates): 0.11437 [0.08399, 0.14474]
Incremental R2 (full-covars): 0.1067		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
PPM018932 PSS011157|
African Ancestry|
1,168 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Trunk fat mass — — R²: 0.02303 [0.00639, 0.03967]
PGS R2 (no covariates): 0.01601 [0.00204, 0.02998]
Incremental R2 (full-covars): 0.01465		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
PPM018933 PSS011163|
Multi-ancestry (excluding European)|
7,838 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Trunk fat mass — — R²: 0.14605 [0.13176, 0.16034]
PGS R2 (no covariates): 0.1056 [0.09287, 0.11832]
Incremental R2 (full-covars): 0.08711		 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
PSS011119 — — 1,456 individuals — South Asian — UKB —
PSS011157 — — 1,168 individuals — African unspecified — UKB —
PSS011127 — — 66,580 individuals — European
(white British ancestry)		 — UKB —
PSS011163 — — 7,838 individuals — East Asian, Other admixed ancestry East Asian, Other admixed ancestry UKB —
PSS011105 — — 2,837 individuals — European
(non-white British ancestry)		 — UKB —