Polygenic Score (PGS) ID: PGS000991

Predicted Trait
Reported Trait Never eat sugar
Mapped Trait(s) sugar consumption measurement (EFO_0010158)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/BIN_FC4006144
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_FC4006144
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 2,816
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000244
Citation (link to publication) Tanigawa Y et al. medRxiv (2021) Preprint
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
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
[
  • 54,275 cases
  • , 214,817 controls
]
European white British ancestry UKB

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
PPM007727 PSS003948|
European Ancestry|
67,271 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Never eat sugar AUROC: 0.61373 [0.60865, 0.61881] : 0.04147
Incremental AUROC (full-covars): 0.00834
PGS R2 (no covariates): 0.00519
PGS AUROC (no covariates): 0.54069 [0.5353, 0.54607]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007723 PSS003944|
African Ancestry|
6,368 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Never eat sugar AUROC: 0.6377 [0.61811, 0.6573] : 0.05071
Incremental AUROC (full-covars): -4e-05
PGS R2 (no covariates): 0.00087
PGS AUROC (no covariates): 0.51667 [0.49625, 0.5371]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007724 PSS003945|
East Asian Ancestry|
1,653 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Never eat sugar AUROC: 0.64533 [0.60258, 0.68809] : 0.05896
Incremental AUROC (full-covars): 0.0007
PGS R2 (no covariates): 0.0005
PGS AUROC (no covariates): 0.51881 [0.47535, 0.56226]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007725 PSS003946|
European Ancestry|
24,800 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Never eat sugar AUROC: 0.62033 [0.61189, 0.62878] : 0.04489
Incremental AUROC (full-covars): 0.00242
PGS R2 (no covariates): 0.00208
PGS AUROC (no covariates): 0.5258 [0.51682, 0.53477]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007726 PSS003947|
South Asian Ancestry|
7,539 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Never eat sugar AUROC: 0.6355 [0.61763, 0.65337] : 0.04896
Incremental AUROC (full-covars): 0.00252
PGS R2 (no covariates): 0.00172
PGS AUROC (no covariates): 0.52933 [0.51032, 0.54833]
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
PSS003944
[
  • 916 cases
  • , 5,452 controls
]
African unspecified UKB
PSS003945
[
  • 190 cases
  • , 1,463 controls
]
East Asian UKB
PSS003946
[
  • 4,945 cases
  • , 19,855 controls
]
European non-white British ancestry UKB
PSS003947
[
  • 1,046 cases
  • , 6,493 controls
]
South Asian UKB
PSS003948
[
  • 13,687 cases
  • , 53,584 controls
]
European white British ancestry UKB Testing cohort (heldout set)