Polygenic Score (PGS) ID: PGS001125

Predicted Trait
Reported Trait Coffee consumption (instant coffee)
Mapped Trait(s) coffee consumption measurement (EFO_0006781)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/BIN_FC20001508
Released in PGS Catalog: Oct. 21, 2021
Download Score FTP directory
Terms and Licenses
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Score Details

Score Construction
PGS Name GBE_BIN_FC20001508
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 432
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
—
[
  • 122,962 cases
  • , 92,166 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
PPM008353 PSS003815|
African Ancestry|
3,487 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Coffee type: Instant coffee — AUROC: 0.56676 [0.54763, 0.58589] R²: 0.01807
Incremental AUROC (full-covars): 0.00096
PGS R2 (no covariates): 0.00043
PGS AUROC (no covariates): 0.50852 [0.48917, 0.52787]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008354 PSS003816|
East Asian Ancestry|
1,059 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Coffee type: Instant coffee — AUROC: 0.58603 [0.55141, 0.62065] R²: 0.04389
Incremental AUROC (full-covars): -0.00701
PGS R2 (no covariates): 0.00663
PGS AUROC (no covariates): 0.46336 [0.42819, 0.49853]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008355 PSS003817|
European Ancestry|
19,513 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Coffee type: Instant coffee — AUROC: 0.62091 [0.61307, 0.62875] R²: 0.05743
Incremental AUROC (full-covars): 0.00079
PGS R2 (no covariates): 0.00216
PGS AUROC (no covariates): 0.52276 [0.51464, 0.53088]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008356 PSS003818|
South Asian Ancestry|
3,748 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Coffee type: Instant coffee — AUROC: 0.56461 [0.54534, 0.58388] R²: 0.01489
Incremental AUROC (full-covars): 0.00295
PGS R2 (no covariates): 0.00158
PGS AUROC (no covariates): 0.52329 [0.50344, 0.54314]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008357 PSS003819|
European Ancestry|
53,524 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Coffee type: Instant coffee — AUROC: 0.55986 [0.55497, 0.56475] R²: 0.01438
Incremental AUROC (full-covars): 0.00115
PGS R2 (no covariates): 0.00071
PGS AUROC (no covariates): 0.51308 [0.50814, 0.51802]		 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
PSS003815 — —
[
  • 1,999 cases
  • , 1,488 controls
]
 — African unspecified — UKB —
PSS003816 — —
[
  • 619 cases
  • , 440 controls
]
 — East Asian — UKB —
PSS003817 — —
[
  • 8,877 cases
  • , 10,636 controls
]
 — European non-white British ancestry UKB —
PSS003818 — —
[
  • 2,481 cases
  • , 1,267 controls
]
 — South Asian — UKB —
PSS003819 — —
[
  • 30,561 cases
  • , 22,963 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)