Polygenic Score (PGS) ID: PGS003900

Predicted Trait
Reported Trait Whole body fat mass
Mapped Trait(s) fat body mass (EFO_0005409)
Additional Trait Information http://ipgs.mit.edu/tanigawakellis2023/INI23100
Released in PGS Catalog: Nov. 1, 2023
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Score Details

Score Construction
PGS Name INI23100
Development Method
Name snpnet
Parameters inclusive PGS
Variants
Original Genome Build GRCh37
Number of Variants 33,555
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
319,441 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
— 319,441 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
PPM018819 PSS011125|
European Ancestry|
66,530 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Whole body fat mass — — R²: 0.17244 [0.16727, 0.17762]
PGS R2 (no covariates): 0.1047 [0.10033, 0.10906]
Incremental R2 (full-covars): 0.10407		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
PPM018820 PSS011107|
European Ancestry|
2,833 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Whole body fat mass — — R²: 0.15896 [0.13456, 0.18336]
PGS R2 (no covariates): 0.11465 [0.09283, 0.13646]
Incremental R2 (full-covars): 0.1146		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
PPM018821 PSS011115|
South Asian Ancestry|
1,452 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Whole body fat mass — — R²: 0.21253 [0.17571, 0.24935]
PGS R2 (no covariates): 0.09752 [0.06894, 0.1261]
Incremental R2 (full-covars): 0.07719		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
PPM018823 PSS011164|
Multi-ancestry (excluding European)|
7,824 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Whole body fat mass — — R²: 0.17428 [0.15919, 0.18938]
PGS R2 (no covariates): 0.10059 [0.0881, 0.11308]
Incremental R2 (full-covars): 0.08234		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
PPM018822 PSS011156|
African Ancestry|
1,166 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Whole body fat mass — — R²: 0.15685 [0.11937, 0.19432]
PGS R2 (no covariates): 0.01295 [0.00035, 0.02556]
Incremental R2 (full-covars): -0.04775		 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
PSS011115 — — 1,452 individuals — South Asian — UKB —
PSS011156 — — 1,166 individuals — African unspecified — UKB —
PSS011125 — — 66,530 individuals — European
(white British ancestry)		 — UKB —
PSS011164 — — 7,824 individuals — East Asian, Other admixed ancestry East Asian, Other admixed ancestry UKB —
PSS011107 — — 2,833 individuals — European
(non-white British ancestry)		 — UKB —