Polygenic Score (PGS) ID: PGS001062

Predicted Trait
Reported Trait Fresh fruit intake
Mapped Trait(s) diet measurement (EFO_0008111)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI1309
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_INI1309
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 4,257
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%
261,191 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
— 261,191 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
PPM008068 PSS004816|
African Ancestry|
6,032 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Fresh fruit intake — — R²: 0.02533 [0.01779, 0.03287]
Incremental R2 (full-covars): 0.00021
PGS R2 (no covariates): 0.00107 [-0.00052, 0.00265]		 age, sex, UKB array type, Genotype PCs —
PPM008069 PSS004817|
East Asian Ancestry|
1,592 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Fresh fruit intake — — R²: 0.01082 [0.00107, 0.02056]
Incremental R2 (full-covars): -0.00286
PGS R2 (no covariates): 4e-05 [-0.00054, 0.00062]		 age, sex, UKB array type, Genotype PCs —
PPM008070 PSS004818|
European Ancestry|
24,138 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Fresh fruit intake — — R²: 0.03809 [0.03342, 0.04275]
Incremental R2 (full-covars): 0.00379
PGS R2 (no covariates): 0.00464 [0.00295, 0.00632]		 age, sex, UKB array type, Genotype PCs —
PPM008071 PSS004819|
South Asian Ancestry|
7,340 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Fresh fruit intake — — R²: 0.01209 [0.00728, 0.0169]
Incremental R2 (full-covars): 0.00017
PGS R2 (no covariates): 0.00092 [-0.00042, 0.00226]		 age, sex, UKB array type, Genotype PCs —
PPM008072 PSS004820|
European Ancestry|
65,281 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Fresh fruit intake — — R²: 0.02519 [0.02286, 0.02753]
Incremental R2 (full-covars): 0.00617
PGS R2 (no covariates): 0.00619 [0.00501, 0.00737]		 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
PSS004816 — — 6,032 individuals — African unspecified — UKB —
PSS004817 — — 1,592 individuals — East Asian — UKB —
PSS004818 — — 24,138 individuals — European non-white British ancestry UKB —
PSS004819 — — 7,340 individuals — South Asian — UKB —
PSS004820 — — 65,281 individuals — European white British ancestry UKB Testing cohort (heldout set)