Polygenic Score (PGS) ID: PGS000994

Predicted Trait
Reported Trait Tea intake
Mapped Trait(s) tea consumption measurement (EFO_0010091)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI1488
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_INI1488
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 3,119
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%
262,083 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
— 262,083 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
PPM007733 PSS004851|
African Ancestry|
6,099 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Tea intake — — R²: 0.01841 [0.01194, 0.02489]
Incremental R2 (full-covars): -5e-05
PGS R2 (no covariates): 0.00125 [-0.00047, 0.00296]		 age, sex, UKB array type, Genotype PCs —
PPM007734 PSS004852|
East Asian Ancestry|
1,584 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Tea intake — — R²: 0.01758 [0.00524, 0.02993]
Incremental R2 (full-covars): 0.00231
PGS R2 (no covariates): 0.00318 [-0.00215, 0.00851]		 age, sex, UKB array type, Genotype PCs —
PPM007735 PSS004853|
European Ancestry|
23,719 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Tea intake — — R²: 0.04822 [0.04303, 0.05341]
Incremental R2 (full-covars): 0.00374
PGS R2 (no covariates): 0.00925 [0.00688, 0.01162]		 age, sex, UKB array type, Genotype PCs —
PPM007736 PSS004854|
South Asian Ancestry|
7,565 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Tea intake — — R²: 0.02074 [0.0145, 0.02699]
Incremental R2 (full-covars): 0.00223
PGS R2 (no covariates): 0.00377 [0.00106, 0.00648]		 age, sex, UKB array type, Genotype PCs —
PPM007737 PSS004855|
European Ancestry|
65,544 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Tea intake — — R²: 0.0109 [0.00934, 0.01246]
Incremental R2 (full-covars): 0.0069
PGS R2 (no covariates): 0.00698 [0.00572, 0.00823]		 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
PSS004851 — — 6,099 individuals — African unspecified — UKB —
PSS004852 — — 1,584 individuals — East Asian — UKB —
PSS004853 — — 23,719 individuals — European non-white British ancestry UKB —
PSS004854 — — 7,565 individuals — South Asian — UKB —
PSS004855 — — 65,544 individuals — European white British ancestry UKB Testing cohort (heldout set)