Polygenic Score (PGS) ID: PGS001059

Predicted Trait
Reported Trait Cereal consumption (other)
Mapped Trait(s) diet measurement (EFO_0008111)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/BIN_FC50001468
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_FC50001468
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 1,286
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
[
  • 45,742 cases
  • , 181,327 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
PPM008053 PSS003959|
African Ancestry|
4,766 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Cereal type: Other (e.g. Cornflakes, Frosties) AUROC: 0.61741 [0.59849, 0.63633] : 0.04438
Incremental AUROC (full-covars): -0.00159
PGS R2 (no covariates): 0.0
PGS AUROC (no covariates): 0.49817 [0.47857, 0.51776]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008054 PSS003960|
East Asian Ancestry|
988 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Cereal type: Other (e.g. Cornflakes, Frosties) AUROC: 0.64303 [0.60109, 0.68497] : 0.07487
Incremental AUROC (full-covars): -0.00286
PGS R2 (no covariates): 0.00017
PGS AUROC (no covariates): 0.5106 [0.46867, 0.55253]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008055 PSS003961|
European Ancestry|
18,951 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Cereal type: Other (e.g. Cornflakes, Frosties) AUROC: 0.60408 [0.59345, 0.6147] : 0.03191
Incremental AUROC (full-covars): 0.00341
PGS R2 (no covariates): 0.00282
PGS AUROC (no covariates): 0.53042 [0.51944, 0.54141]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008056 PSS003962|
South Asian Ancestry|
5,759 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Cereal type: Other (e.g. Cornflakes, Frosties) AUROC: 0.59996 [0.58323, 0.61669] : 0.03365
Incremental AUROC (full-covars): 0.00229
PGS R2 (no covariates): 0.0016
PGS AUROC (no covariates): 0.52513 [0.50821, 0.54206]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008057 PSS003963|
European Ancestry|
56,841 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Cereal type: Other (e.g. Cornflakes, Frosties) AUROC: 0.58769 [0.58186, 0.59353] : 0.02328
Incremental AUROC (full-covars): 0.00502
PGS R2 (no covariates): 0.00268
PGS AUROC (no covariates): 0.52828 [0.52234, 0.53422]
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
PSS003959
[
  • 1,053 cases
  • , 3,713 controls
]
African unspecified UKB
PSS003960
[
  • 218 cases
  • , 770 controls
]
East Asian UKB
PSS003961
[
  • 3,166 cases
  • , 15,785 controls
]
European non-white British ancestry UKB
PSS003962
[
  • 1,476 cases
  • , 4,283 controls
]
South Asian UKB
PSS003963
[
  • 11,307 cases
  • , 45,534 controls
]
European white British ancestry UKB Testing cohort (heldout set)