Polygenic Score (PGS) ID: PGS001065

Predicted Trait
Reported Trait Never eat wheat
Mapped Trait(s) diet measurement (EFO_0008111)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/BIN_FC3006144
Released in PGS Catalog: Oct. 21, 2021
Download Score FTP directory
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_BIN_FC3006144
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 5
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%
269,092 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
—
[
  • 7,799 cases
  • , 261,293 controls
]
 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
PPM008083 PSS003909|
African Ancestry|
6,368 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Never eat wheat — AUROC: 0.55785 [0.52697, 0.58872] R²: 0.0067
Incremental AUROC (full-covars): -0.00998
PGS R2 (no covariates): 1e-05
PGS AUROC (no covariates): 0.49224 [0.4594, 0.52508]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008084 PSS003910|
East Asian Ancestry|
1,653 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Never eat wheat — AUROC: 0.64888 [0.57732, 0.72044] R²: 0.04019
Incremental AUROC (full-covars): 0.00386
PGS R2 (no covariates): 0.00453
PGS AUROC (no covariates): 0.56299 [0.49269, 0.63329]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008085 PSS003911|
European Ancestry|
24,800 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Never eat wheat — AUROC: 0.62411 [0.60564, 0.64259] R²: 0.02456
Incremental AUROC (full-covars): 0.02182
PGS R2 (no covariates): 0.01049
PGS AUROC (no covariates): 0.56561 [0.54517, 0.58606]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008086 PSS003912|
South Asian Ancestry|
7,539 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Never eat wheat — AUROC: 0.59764 [0.56396, 0.63132] R²: 0.01641
Incremental AUROC (full-covars): 0.00593
PGS R2 (no covariates): 0.00163
PGS AUROC (no covariates): 0.53668 [0.50324, 0.57012]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008087 PSS003913|
European Ancestry|
67,271 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Never eat wheat — AUROC: 0.58236 [0.56955, 0.59518] R²: 0.0117
Incremental AUROC (full-covars): 0.01856
PGS R2 (no covariates): 0.00607
PGS AUROC (no covariates): 0.55077 [0.53718, 0.56437]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method

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
PSS003909 — —
[
  • 327 cases
  • , 6,041 controls
]
 — African unspecified — UKB —
PSS003910 — —
[
  • 55 cases
  • , 1,598 controls
]
 — East Asian — UKB —
PSS003911 — —
[
  • 865 cases
  • , 23,935 controls
]
 — European non-white British ancestry UKB —
PSS003912 — —
[
  • 287 cases
  • , 7,252 controls
]
 — South Asian — UKB —
PSS003913 — —
[
  • 1,955 cases
  • , 65,316 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)