Polygenic Score (PGS) ID: PGS003898

Predicted Trait
Reported Trait Weight
Mapped Trait(s) body weight (EFO_0004338)
Additional Trait Information http://ipgs.mit.edu/tanigawakellis2023/INI21002
Released in PGS Catalog: Nov. 1, 2023
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Score Details

Score Construction
PGS Name INI21002
Development Method
Name snpnet
Parameters inclusive PGS
Variants
Original Genome Build GRCh37
Number of Variants 38,592
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
324,213 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
— 324,213 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
PPM018809 PSS011142|
European Ancestry|
67,561 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Weight — — R²: 0.32755 [0.32176, 0.33335]
PGS R2 (no covariates): 0.11144 [0.10697, 0.1159]
Incremental R2 (full-covars): 0.10907		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
PPM018810 PSS011101|
European Ancestry|
2,878 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Weight — — R²: 0.34564 [0.31765, 0.37364]
PGS R2 (no covariates): 0.12035 [0.09814, 0.14255]
Incremental R2 (full-covars): 0.11103		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
PPM018812 PSS011160|
African Ancestry|
1,195 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Weight — — R²: 0.04318 [0.02087, 0.0655]
PGS R2 (no covariates): 0.01871 [0.00365, 0.03378]
Incremental R2 (full-covars): 0.01737		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
PPM018813 PSS011171|
Multi-ancestry (excluding European)|
7,964 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Weight — — R²: 0.34315 [0.3263, 0.36]
PGS R2 (no covariates): 0.1022 [0.08963, 0.11476]
Incremental R2 (full-covars): 0.0801		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
PPM018811 PSS011117|
South Asian Ancestry|
1,473 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Weight — — R²: 0.25281 [0.21471, 0.29091]
PGS R2 (no covariates): 0.096 [0.0676, 0.12441]
Incremental R2 (full-covars): 0.09952		 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
PSS011142 — — 67,561 individuals — European
(white British ancestry)		 — UKB —
PSS011117 — — 1,473 individuals — South Asian — UKB —
PSS011160 — — 1,195 individuals — African unspecified — UKB —
PSS011101 — — 2,878 individuals — European
(non-white British ancestry)		 — UKB —
PSS011171 — — 7,964 individuals — East Asian, Other admixed ancestry East Asian, Other admixed ancestry UKB —