Polygenic Score (PGS) ID: PGS003893

Predicted Trait
Reported Trait Waist circumference
Mapped Trait(s) waist circumference (EFO_0004342)
Additional Trait Information http://ipgs.mit.edu/tanigawakellis2023/INI48
Released in PGS Catalog: Nov. 1, 2023
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Score Details

Score Construction
PGS Name INI48
Development Method
Name snpnet
Parameters inclusive PGS
Variants
Original Genome Build GRCh37
Number of Variants 31,406
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
324,605 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
— 324,605 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
PPM018786 PSS011117|
South Asian Ancestry|
1,473 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Waist circumference — — R²: 0.21134 [0.17457, 0.24811]
PGS R2 (no covariates): 0.06699 [0.0425, 0.09148]
Incremental R2 (full-covars): 0.06504		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
PPM018787 PSS011160|
African Ancestry|
1,195 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Waist circumference — — R²: 0.03112 [0.01194, 0.0503]
PGS R2 (no covariates): 0.01643 [0.00228, 0.03058]
Incremental R2 (full-covars): 0.01312		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
PPM018788 PSS011175|
Multi-ancestry (excluding European)|
7,973 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Waist circumference — — R²: 0.28891 [0.27218, 0.30565]
PGS R2 (no covariates): 0.05072 [0.04135, 0.06008]
Incremental R2 (full-covars): 0.04529		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
PPM018784 PSS011149|
European Ancestry|
67,635 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Waist circumference — — R²: 0.29939 [0.29361, 0.30516]
PGS R2 (no covariates): 0.07085 [0.06712, 0.07457]
Incremental R2 (full-covars): 0.0682		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
PPM018785 PSS011098|
European Ancestry|
2,886 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Waist circumference — — R²: 0.29851 [0.27062, 0.3264]
PGS R2 (no covariates): 0.07361 [0.05532, 0.0919]
Incremental R2 (full-covars): 0.06239		 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
PSS011175 — — 7,973 individuals — East Asian, Other admixed ancestry East Asian, Other admixed ancestry UKB —
PSS011117 — — 1,473 individuals — South Asian — UKB —
PSS011149 — — 67,635 individuals — European
(white British ancestry)		 — UKB —
PSS011160 — — 1,195 individuals — African unspecified — UKB —
PSS011098 — — 2,886 individuals — European
(non-white British ancestry)		 — UKB —