Polygenic Score (PGS) ID: PGS000978

Predicted Trait
Reported Trait Bread intake
Mapped Trait(s) carbohydrate intake measurement (EFO_0010811)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI1438
Released in PGS Catalog: Oct. 21, 2021
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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 GBE_INI1438
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 3,483
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%
264,528 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
— 264,528 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
PPM007683 PSS004841|
African Ancestry|
5,979 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Bread intake — — R²: 0.08606 [0.07303, 0.09909]
Incremental R2 (full-covars): -0.00106
PGS R2 (no covariates): 0.00083 [-0.00057, 0.00223]		 age, sex, UKB array type, Genotype PCs —
PPM007684 PSS004842|
East Asian Ancestry|
1,557 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Bread intake — — R²: 0.04803 [0.02826, 0.0678]
Incremental R2 (full-covars): -0.00683
PGS R2 (no covariates): 1e-05 [-0.00021, 0.00022]		 age, sex, UKB array type, Genotype PCs —
PPM007685 PSS004843|
European Ancestry|
24,277 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Bread intake — — R²: 0.09076 [0.08395, 0.09756]
Incremental R2 (full-covars): 0.00266
PGS R2 (no covariates): 0.0026 [0.00134, 0.00386]		 age, sex, UKB array type, Genotype PCs —
PPM007686 PSS004844|
South Asian Ancestry|
7,412 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Bread intake — — R²: 0.05893 [0.04882, 0.06905]
Incremental R2 (full-covars): -0.00378
PGS R2 (no covariates): 0.00041 [-0.00049, 0.0013]		 age, sex, UKB array type, Genotype PCs —
PPM007687 PSS004845|
European Ancestry|
66,112 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Bread intake — — R²: 0.09655 [0.09231, 0.10079]
Incremental R2 (full-covars): 0.00312
PGS R2 (no covariates): 0.0033 [0.00243, 0.00416]		 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
PSS004841 — — 5,979 individuals — African unspecified — UKB —
PSS004842 — — 1,557 individuals — East Asian — UKB —
PSS004843 — — 24,277 individuals — European non-white British ancestry UKB —
PSS004844 — — 7,412 individuals — South Asian — UKB —
PSS004845 — — 66,112 individuals — European white British ancestry UKB Testing cohort (heldout set)