Polygenic Score (PGS) ID: PGS001227

Predicted Trait
Reported Trait Waist circumference
Mapped Trait(s) waist circumference (EFO_0004342)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI48
Released in PGS Catalog: Oct. 21, 2021
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Terms and Licenses
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 GBE_INI48
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 25,538
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000244
Citation (link to publication) Tanigawa Y et al. PLoS Genet (2022)
Ancestry Distribution
Score Development/Training
European: 100%
269,260 individuals (100%)
PGS Evaluation
European: 40%
African: 20%
East Asian: 20%
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
— 269,260 individuals European UKB — — — white British 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
PPM008649 PSS007356|
African Ancestry|
6,418 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Waist circumference — — R²: 0.04902 [0.03878, 0.05925]
Incremental R2 (full-covars): 0.01275
PGS R2 (no covariates): 0.01765 [0.01131, 0.024]		 age, sex, UKB array type, Genotype PCs —
PPM008650 PSS007357|
East Asian Ancestry|
1,698 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Waist circumference — — R²: 0.31538 [0.27895, 0.35182]
Incremental R2 (full-covars): 0.00143
PGS R2 (no covariates): 0.02593 [0.01107, 0.0408]		 age, sex, UKB array type, Genotype PCs —
PPM008651 PSS007358|
European Ancestry|
24,833 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Waist circumference — — R²: 0.30589 [0.29635, 0.31542]
Incremental R2 (full-covars): 0.05708
PGS R2 (no covariates): 0.0673 [0.06129, 0.07331]		 age, sex, UKB array type, Genotype PCs —
PPM008652 PSS007359|
South Asian Ancestry|
7,756 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Waist circumference — — R²: 0.19567 [0.17992, 0.21142]
Incremental R2 (full-covars): 0.03363
PGS R2 (no covariates): 0.03558 [0.02753, 0.04364]		 age, sex, UKB array type, Genotype PCs —
PPM008653 PSS007360|
European Ancestry|
67,330 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Waist circumference — — R²: 0.29142 [0.28565, 0.2972]
Incremental R2 (full-covars): 0.06556
PGS R2 (no covariates): 0.0665 [0.06287, 0.07013]		 age, sex, UKB array type, Genotype PCs —

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
PSS007356 — — 6,418 individuals — African unspecified — UKB —
PSS007357 — — 1,698 individuals — East Asian — UKB —
PSS007358 — — 24,833 individuals — European non-white British ancestry UKB —
PSS007359 — — 7,756 individuals — South Asian — UKB —
PSS007360 — — 67,330 individuals — European white British ancestry UKB Testing cohort (heldout set)