Polygenic Score (PGS) ID: PGS003912

Predicted Trait
Reported Trait Leg fat percentage (L)
Mapped Trait(s) body fat percentage (EFO_0007800)
Additional Trait Information http://ipgs.mit.edu/tanigawakellis2023/INI23115
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 INI23115
Development Method
Name snpnet
Parameters inclusive PGS
Variants
Original Genome Build GRCh37
Number of Variants 33,293
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
319,934 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
— 319,934 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
PPM018879 PSS011123|
European Ancestry|
66,609 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Leg fat percentage (left) — — R²: 0.78716 [0.78432, 0.79001]
PGS R2 (no covariates): 0.02265 [0.02044, 0.02487]
Incremental R2 (full-covars): 0.02424		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
PPM018880 PSS011105|
European Ancestry|
2,837 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Leg fat percentage (left) — — R²: 0.77429 [0.75983, 0.78874]
PGS R2 (no covariates): 0.01845 [0.00874, 0.02815]
Incremental R2 (full-covars): 0.02867		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
PPM018881 PSS011118|
South Asian Ancestry|
1,457 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Leg fat percentage (left) — — R²: 0.83462 [0.81929, 0.84994]
PGS R2 (no covariates): 0.01713 [0.00409, 0.03018]
Incremental R2 (full-covars): 0.01262		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
PPM018882 PSS011158|
African Ancestry|
1,169 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Leg fat percentage (left) — — R²: 0.81111 [0.79202, 0.8302]
PGS R2 (no covariates): 0.00463 [-0.00297, 0.01223]
Incremental R2 (full-covars): -0.0031		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
PPM018883 PSS011177|
Multi-ancestry (excluding European)|
7,841 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Leg fat percentage (left) — — R²: 0.76995 [0.76111, 0.77879]
PGS R2 (no covariates): 0.0179 [0.01214, 0.02365]
Incremental R2 (full-covars): 0.01686		 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
PSS011177 — — 7,841 individuals — East Asian, Other admixed ancestry East Asian, Other admixed ancestry UKB —
PSS011118 — — 1,457 individuals — South Asian — UKB —
PSS011123 — — 66,609 individuals — European
(white British ancestry)		 — UKB —
PSS011158 — — 1,169 individuals — African unspecified — UKB —
PSS011105 — — 2,837 individuals — European
(non-white British ancestry)		 — UKB —