Polygenic Score (PGS) ID: PGS003899

Predicted Trait
Reported Trait Body fat percentage
Mapped Trait(s) body fat percentage (EFO_0007800)
Additional Trait Information http://ipgs.mit.edu/tanigawakellis2023/INI23099
Released in PGS Catalog: Nov. 1, 2023
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PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name INI23099
Development Method
Name snpnet
Parameters inclusive PGS
Variants
Original Genome Build GRCh37
Number of Variants 34,374
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
319,798 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
— 319,798 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
PPM018814 PSS011129|
European Ancestry|
66,584 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Body fat percentage — — R²: 0.51746 [0.51223, 0.52269]
PGS R2 (no covariates): 0.05601 [0.05265, 0.05938]
Incremental R2 (full-covars): 0.05783		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
PPM018815 PSS011106|
European Ancestry|
2,836 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Body fat percentage — — R²: 0.49108 [0.46513, 0.51704]
PGS R2 (no covariates): 0.06034 [0.04354, 0.07714]
Incremental R2 (full-covars): 0.06709		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
PPM018816 PSS011116|
South Asian Ancestry|
1,455 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Body fat percentage — — R²: 0.60374 [0.57251, 0.63497]
PGS R2 (no covariates): 0.04598 [0.02523, 0.06673]
Incremental R2 (full-covars): 0.03132		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
PPM018817 PSS011157|
African Ancestry|
1,168 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Body fat percentage — — R²: 0.5945 [0.55941, 0.62959]
PGS R2 (no covariates): 0.00973 [-0.00123, 0.02069]
Incremental R2 (full-covars): -0.01506		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
PPM018818 PSS011165|
Multi-ancestry (excluding European)|
7,837 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Body fat percentage — — R²: 0.47607 [0.46025, 0.4919]
PGS R2 (no covariates): 0.05911 [0.0491, 0.06913]
Incremental R2 (full-covars): 0.04525		 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
PSS011116 — — 1,455 individuals — South Asian — UKB —
PSS011157 — — 1,168 individuals — African unspecified — UKB —
PSS011129 — — 66,584 individuals — European
(white British ancestry)		 — UKB —
PSS011165 — — 7,837 individuals — East Asian, Other admixed ancestry East Asian, Other admixed ancestry UKB —
PSS011106 — — 2,836 individuals — European
(non-white British ancestry)		 — UKB —