Polygenic Score (PGS) ID: PGS003897

Predicted Trait
Reported Trait Body mass index (BMI)
Mapped Trait(s) body mass index (EFO_0004340)
Additional Trait Information http://ipgs.mit.edu/tanigawakellis2023/INI21001
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 INI21001
Development Method
Name snpnet
Parameters inclusive PGS
Variants
Original Genome Build GRCh37
Number of Variants 35,941
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
324,009 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
— 324,009 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
PPM018804 PSS011131|
European Ancestry|
67,538 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Body mass index (BMI) — — R²: 0.13408 [0.1293, 0.13885]
PGS R2 (no covariates): 0.11906 [0.11448, 0.12364]
Incremental R2 (full-covars): 0.11579		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
PPM018805 PSS011104|
European Ancestry|
2,877 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Body mass index (BMI) — — R²: 0.1241 [0.10164, 0.14656]
PGS R2 (no covariates): 0.11155 [0.08996, 0.13315]
Incremental R2 (full-covars): 0.10512		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
PPM018806 PSS011114|
South Asian Ancestry|
1,448 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Body mass index (BMI) — — R²: 0.0829 [0.05612, 0.10967]
PGS R2 (no covariates): 0.08942 [0.0618, 0.11703]
Incremental R2 (full-covars): 0.08059		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
PPM018807 PSS011159|
African Ancestry|
1,191 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Body mass index (BMI) — — R²: 0.00924 [-0.00145, 0.01994]
PGS R2 (no covariates): 0.01761 [0.00298, 0.03223]
Incremental R2 (full-covars): 0.00743		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
PPM018808 PSS011161|
Multi-ancestry (excluding European)|
7,959 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Body mass index (BMI) — — R²: 0.13658 [0.12261, 0.15055]
PGS R2 (no covariates): 0.10283 [0.09023, 0.11543]
Incremental R2 (full-covars): 0.08683		 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
PSS011114 — — 1,448 individuals — South Asian — UKB —
PSS011159 — — 1,191 individuals — African unspecified — UKB —
PSS011161 — — 7,959 individuals — East Asian, Other admixed ancestry East Asian, Other admixed ancestry UKB —
PSS011131 — — 67,538 individuals — European
(white British ancestry)		 — UKB —
PSS011104 — — 2,877 individuals — European
(non-white British ancestry)		 — UKB —