Trait: tea consumption measurement

Experimental Factor Ontology (EFO) Information
Identifier EFO_0010091
Description Quantification of some tea consumption or tea consumption-related behaviour, usually self-reported via a questionnaire.
Trait category
Other measurement
Mapped term PMID:31046077

Associated Polygenic Score(s)

Filter PGS by Participant Ancestry
Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
Display options:
Ancestry legend
Multi-ancestry (including European)
Multi-ancestry (excluding European)
African
East Asian
South Asian
Additional Asian Ancestries
European
Greater Middle Eastern
Hispanic or Latin American
Additional Diverse Ancestries
Not Reported
Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution
GWAS
Dev
Eval
 Scoring File (FTP Link)
PGS000994
(GBE_INI1488)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Tea intake tea consumption measurement 3,119
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000994/ScoringFiles/PGS000994.txt.gz

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) 		Evaluated Score 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 PGS000994
(GBE_INI1488)
 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 PGS000994
(GBE_INI1488)
 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 PGS000994
(GBE_INI1488)
 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 PGS000994
(GBE_INI1488)
 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 PGS000994
(GBE_INI1488)
 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)