Polygenic Score (PGS) ID: PGS001389

Predicted Trait
Reported Trait Dried fruit intake
Mapped Trait(s) diet measurement (EFO_0008111)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI1319
Released in PGS Catalog: Nov. 25, 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_INI1319
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 989
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%
248,701 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
— 248,701 individuals European UKB — — — white British ancestry Training + validation cohort (train_val)

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
PPM005240 PSS004821|
African Ancestry|
5,684 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Dried fruit intake — — R²: 0.00681 [0.00283, 0.0108]
Incremental R2 (full-covars): -0.00044
PGS R2 (no covariates): 1e-05 [-0.00017, 0.0002]		 age, sex, UKB array type, Genotype PCs —
PPM005241 PSS004822|
East Asian Ancestry|
1,402 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Dried fruit intake — — R²: 0.02296 [0.00893, 0.03699]
Incremental R2 (full-covars): 0.00042
PGS R2 (no covariates): 0.00045 [-0.00156, 0.00245]		 age, sex, UKB array type, Genotype PCs —
PPM005242 PSS004823|
European Ancestry|
22,608 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Dried fruit intake — — R²: 0.0347 [0.03024, 0.03917]
Incremental R2 (full-covars): 0.00018
PGS R2 (no covariates): 0.00038 [-0.00011, 0.00086]		 age, sex, UKB array type, Genotype PCs —
PPM005243 PSS004824|
South Asian Ancestry|
6,844 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Dried fruit intake — — R²: 0.01593 [0.01043, 0.02143]
Incremental R2 (full-covars): -1e-05
PGS R2 (no covariates): 4e-05 [-0.00024, 0.00032]		 age, sex, UKB array type, Genotype PCs —
PPM005244 PSS004825|
European Ancestry|
62,203 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Dried fruit intake — — R²: 0.0166 [0.01469, 0.01852]
Incremental R2 (full-covars): 0.00087
PGS R2 (no covariates): 0.00107 [0.00058, 0.00157]		 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
PSS004821 — — 5,684 individuals — African unspecified — UKB —
PSS004822 — — 1,402 individuals — East Asian — UKB —
PSS004823 — — 22,608 individuals — European non-white British ancestry UKB —
PSS004824 — — 6,844 individuals — South Asian — UKB —
PSS004825 — — 62,203 individuals — European white British ancestry UKB Testing cohort (heldout set)