Polygenic Score (PGS) ID: PGS001123

Predicted Trait
Reported Trait Coffee consumption
Mapped Trait(s) coffee consumption measurement (EFO_0006781)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/BIN100240
Released in PGS Catalog: Oct. 21, 2021
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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_BIN100240
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 48
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%
116,930 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
—
[
  • 91,145 cases
  • , 25,785 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
PPM008343 PSS003607|
African Ancestry|
2,091 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Coffee consumed — AUROC: 0.56543 [0.54078, 0.59007] R²: 0.02152
Incremental AUROC (full-covars): 0.00175
PGS R2 (no covariates): 0.00286
PGS AUROC (no covariates): 0.52506 [0.50028, 0.54984]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008344 PSS003608|
East Asian Ancestry|
613 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Coffee consumed — AUROC: 0.60702 [0.56152, 0.65252] PGS R2 (no covariates): 0.00015
R²: 0.06384
Incremental AUROC (full-covars): 0.00101
PGS AUROC (no covariates): 0.50685 [0.46035, 0.55335]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008345 PSS003609|
European Ancestry|
11,475 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Coffee consumed — AUROC: 0.60041 [0.58833, 0.61249] R²: 0.03144
Incremental AUROC (full-covars): 0.00304
PGS R2 (no covariates): 0.00129
PGS AUROC (no covariates): 0.51901 [0.50649, 0.53153]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008346 PSS003610|
South Asian Ancestry|
2,331 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Coffee consumed — AUROC: 0.61704 [0.5943, 0.63978] R²: 0.05335
Incremental AUROC (full-covars): 0.00112
PGS R2 (no covariates): 0.0008
PGS AUROC (no covariates): 0.51646 [0.49302, 0.53991]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008347 PSS003611|
European Ancestry|
29,044 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Coffee consumed — AUROC: 0.57876 [0.57089, 0.58662] R²: 0.01993
Incremental AUROC (full-covars): 0.00268
PGS R2 (no covariates): 0.00154
PGS AUROC (no covariates): 0.52002 [0.51203, 0.52801]		 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
PSS003607 — —
[
  • 962 cases
  • , 1,129 controls
]
 — African unspecified — UKB —
PSS003608 — —
[
  • 370 cases
  • , 243 controls
]
 — East Asian — UKB —
PSS003609 — —
[
  • 8,832 cases
  • , 2,643 controls
]
 — European non-white British ancestry UKB —
PSS003610 — —
[
  • 1,099 cases
  • , 1,232 controls
]
 — South Asian — UKB —
PSS003611 — —
[
  • 22,541 cases
  • , 6,503 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)