Polygenic Score (PGS) ID: PGS001058

Predicted Trait
Reported Trait Cereal consumption (biscuit cereal)
Mapped Trait(s) diet measurement (EFO_0008111)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/BIN_FC20001468
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_FC20001468
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 146
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%
227,069 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
—
[
  • 42,789 cases
  • , 184,280 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
PPM008048 PSS003810|
African Ancestry|
4,766 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Cereal type: Biscuit cereal (e.g. Weetabix) — AUROC: 0.53868 [0.51659, 0.56077] PGS R2 (no covariates): 0.00013
R²: 0.00503
Incremental AUROC (full-covars): 0.00148
PGS AUROC (no covariates): 0.50487 [0.48225, 0.52748]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008049 PSS003811|
East Asian Ancestry|
988 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Cereal type: Biscuit cereal (e.g. Weetabix) — AUROC: 0.56685 [0.51503, 0.61867] R²: 0.02055
Incremental AUROC (full-covars): 0.00316
PGS R2 (no covariates): 0.00024
PGS AUROC (no covariates): 0.50224 [0.44501, 0.55946]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008050 PSS003812|
European Ancestry|
18,951 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Cereal type: Biscuit cereal (e.g. Weetabix) — AUROC: 0.58711 [0.57552, 0.5987] R²: 0.01991
Incremental AUROC (full-covars): 0.00031
PGS R2 (no covariates): 4e-05
PGS AUROC (no covariates): 0.50281 [0.49093, 0.51469]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008051 PSS003813|
South Asian Ancestry|
5,759 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Cereal type: Biscuit cereal (e.g. Weetabix) — AUROC: 0.56331 [0.54576, 0.58087] R²: 0.01354
Incremental AUROC (full-covars): -0.00093
PGS R2 (no covariates): 2e-05
PGS AUROC (no covariates): 0.49754 [0.47927, 0.5158]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008052 PSS003814|
European Ancestry|
56,841 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Cereal type: Biscuit cereal (e.g. Weetabix) — AUROC: 0.55057 [0.54462, 0.55652] R²: 0.00808
Incremental AUROC (full-covars): 0.00209
PGS R2 (no covariates): 0.00069
PGS AUROC (no covariates): 0.51496 [0.50892, 0.521]		 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
PSS003810 — —
[
  • 785 cases
  • , 3,981 controls
]
 — African unspecified — UKB —
PSS003811 — —
[
  • 115 cases
  • , 873 controls
]
 — East Asian — UKB —
PSS003812 — —
[
  • 2,595 cases
  • , 16,356 controls
]
 — European non-white British ancestry UKB —
PSS003813 — —
[
  • 1,252 cases
  • , 4,507 controls
]
 — South Asian — UKB —
PSS003814 — —
[
  • 10,762 cases
  • , 46,079 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)