Polygenic Score (PGS) ID: PGS001061

Predicted Trait
Reported Trait Cooked vegetable consumption
Mapped Trait(s) diet measurement (EFO_0008111)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI1289
Released in PGS Catalog: Oct. 21, 2021
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Score Details

Score Construction
PGS Name GBE_INI1289
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 1,085
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%
262,541 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
— 262,541 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
PPM008064 PSS004812|
East Asian Ancestry|
1,578 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Cooked vegetable intake — — R²: 0.0129 [0.00227, 0.02352]
Incremental R2 (full-covars): -0.00036
PGS R2 (no covariates): 0.00013 [-0.00096, 0.00123]		 age, sex, UKB array type, Genotype PCs —
PPM008065 PSS004813|
European Ancestry|
24,087 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Cooked vegetable intake — — Incremental R2 (full-covars): 0.00028
R²: 0.01788 [0.01462, 0.02114]
PGS R2 (no covariates): 0.00042 [-0.00009, 0.00093]		 age, sex, UKB array type, Genotype PCs —
PPM008066 PSS004814|
South Asian Ancestry|
7,034 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Cooked vegetable intake — — R²: 0.02023 [0.01406, 0.0264]
Incremental R2 (full-covars): -0.00028
PGS R2 (no covariates): 0.0 [-0.00004, 0.00004]		 age, sex, UKB array type, Genotype PCs —
PPM008063 PSS004811|
African Ancestry|
5,840 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Cooked vegetable intake — — R²: 0.01567 [0.00968, 0.02166]
Incremental R2 (full-covars): 0.00017
PGS R2 (no covariates): 0.00022 [-0.0005, 0.00094]		 age, sex, UKB array type, Genotype PCs —
PPM008067 PSS004815|
European Ancestry|
65,598 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Cooked vegetable intake — — R²: 0.01065 [0.00911, 0.01219]
Incremental R2 (full-covars): 0.0009
PGS R2 (no covariates): 0.00097 [0.0005, 0.00145]		 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
PSS004811 — — 5,840 individuals — African unspecified — UKB —
PSS004812 — — 1,578 individuals — East Asian — UKB —
PSS004813 — — 24,087 individuals — European non-white British ancestry UKB —
PSS004814 — — 7,034 individuals — South Asian — UKB —
PSS004815 — — 65,598 individuals — European white British ancestry UKB Testing cohort (heldout set)