Polygenic Score (PGS) ID: PGS001124

Predicted Trait
Reported Trait Coffee consumption (ground coffee)
Mapped Trait(s) coffee consumption measurement (EFO_0006781)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/BIN_FC30001508
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_FC30001508
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 9,694
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%
215,128 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
—
[
  • 51,589 cases
  • , 163,539 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
PPM008348 PSS003874|
African Ancestry|
3,487 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Coffee type: Ground coffee (include espresso, filter etc) — AUROC: 0.60248 [0.57445, 0.6305] R²: 0.02526
Incremental AUROC (full-covars): -0.00838
PGS R2 (no covariates): 0.00112
PGS AUROC (no covariates): 0.51847 [0.48874, 0.54821]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008349 PSS003875|
East Asian Ancestry|
1,059 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Coffee type: Ground coffee (include espresso, filter etc) — AUROC: 0.62271 [0.58544, 0.65999] R²: 0.06183
Incremental AUROC (full-covars): -0.00244
PGS R2 (no covariates): 0.00176
PGS AUROC (no covariates): 0.52394 [0.48401, 0.56387]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008350 PSS003876|
European Ancestry|
19,513 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Coffee type: Ground coffee (include espresso, filter etc) — AUROC: 0.6398 [0.632, 0.64761] R²: 0.07694
Incremental AUROC (full-covars): 2e-05
PGS R2 (no covariates): 0.01506
PGS AUROC (no covariates): 0.55973 [0.55158, 0.56789]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008351 PSS003877|
South Asian Ancestry|
3,748 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Coffee type: Ground coffee (include espresso, filter etc) — AUROC: 0.57148 [0.54785, 0.59512] R²: 0.01345
Incremental AUROC (full-covars): -0.00658
PGS R2 (no covariates): 0.00195
PGS AUROC (no covariates): 0.52707 [0.50259, 0.55154]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008352 PSS003878|
European Ancestry|
53,524 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Coffee type: Ground coffee (include espresso, filter etc) — AUROC: 0.584 [0.57837, 0.58964] R²: 0.02384
Incremental AUROC (full-covars): 0.02525
PGS R2 (no covariates): 0.01318
PGS AUROC (no covariates): 0.56269 [0.55703, 0.56835]		 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
PSS003874 — —
[
  • 417 cases
  • , 3,070 controls
]
 — African unspecified — UKB —
PSS003875 — —
[
  • 275 cases
  • , 784 controls
]
 — East Asian — UKB —
PSS003876 — —
[
  • 8,000 cases
  • , 11,513 controls
]
 — European non-white British ancestry UKB —
PSS003877 — —
[
  • 606 cases
  • , 3,142 controls
]
 — South Asian — UKB —
PSS003878 — —
[
  • 12,738 cases
  • , 40,786 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)