Polygenic Score (PGS) ID: PGS001126

Predicted Trait
Reported Trait Coffee intake
Mapped Trait(s) coffee consumption measurement (EFO_0006781)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI1498
Released in PGS Catalog: Oct. 21, 2021
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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_INI1498
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 3,154
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%
252,192 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
— 252,192 individuals 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
PPM008358 PSS004856|
African Ancestry|
5,753 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Coffee intake — — R²: 0.02026 [0.01348, 0.02704]
Incremental R2 (full-covars): -0.00015
PGS R2 (no covariates): 0.00245 [0.00005, 0.00484]		 age, sex, UKB array type, Genotype PCs —
PPM008359 PSS004857|
East Asian Ancestry|
1,455 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Coffee intake — — R²: 0.05298 [0.03232, 0.07363]
Incremental R2 (full-covars): 0.00443
PGS R2 (no covariates): 0.00591 [-0.00133, 0.01315]		 age, sex, UKB array type, Genotype PCs —
PPM008360 PSS004858|
European Ancestry|
23,191 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Coffee intake — — R²: 0.02284 [0.01917, 0.02651]
Incremental R2 (full-covars): 0.00663
PGS R2 (no covariates): 0.00615 [0.00421, 0.00809]		 age, sex, UKB array type, Genotype PCs —
PPM008361 PSS004859|
South Asian Ancestry|
6,844 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Coffee intake — — R²: 0.02847 [0.02121, 0.03573]
Incremental R2 (full-covars): -0.00336
PGS R2 (no covariates): 0.00187 [-0.00004, 0.00379]		 age, sex, UKB array type, Genotype PCs —
PPM008362 PSS004860|
European Ancestry|
62,965 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Coffee intake — — R²: 0.01573 [0.01387, 0.01759]
Incremental R2 (full-covars): 0.00848
PGS R2 (no covariates): 0.00833 [0.00697, 0.0097]		 age, sex, UKB array type, Genotype PCs —

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
PSS004860 — — 62,965 individuals — European white British ancestry UKB Testing cohort (heldout set)
PSS004856 — — 5,753 individuals — African unspecified — UKB —
PSS004857 — — 1,455 individuals — East Asian — UKB —
PSS004858 — — 23,191 individuals — European non-white British ancestry UKB —
PSS004859 — — 6,844 individuals — South Asian — UKB —