Polygenic Score (PGS) ID: PGS001087

Predicted Trait
Reported Trait Alcohol intake frequency
Mapped Trait(s) alcohol consumption measurement (EFO_0007878)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/QT_FC1001558
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_QT_FC1001558
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 8,353
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%
269,521 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
— 269,521 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
PPM008184 PSS007567|
East Asian Ancestry|
1,666 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Alcohol intake frequency. — — R²: 0.06423 [0.04175, 0.0867]
Incremental R2 (full-covars): 0.00344
PGS R2 (no covariates): 0.00917 [0.00018, 0.01817]		 age, sex, UKB array type, Genotype PCs —
PPM008183 PSS007566|
African Ancestry|
6,405 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Alcohol intake frequency. — — R²: 0.08212 [0.06934, 0.09491]
Incremental R2 (full-covars): -0.00402
PGS R2 (no covariates): 0.00011 [-0.0004, 0.00062]		 age, sex, UKB array type, Genotype PCs —
PPM008185 PSS007568|
European Ancestry|
24,881 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Alcohol intake frequency. — — R²: 0.05667 [0.05109, 0.06224]
Incremental R2 (full-covars): 0.01563
PGS R2 (no covariates): 0.01863 [0.0153, 0.02196]		 age, sex, UKB array type, Genotype PCs —
PPM008186 PSS007569|
South Asian Ancestry|
7,655 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Alcohol intake frequency. — — R²: 0.12724 [0.11346, 0.14103]
Incremental R2 (full-covars): 0.00158
PGS R2 (no covariates): 0.00484 [0.00177, 0.0079]		 age, sex, UKB array type, Genotype PCs —
PPM008187 PSS007570|
European Ancestry|
67,383 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Alcohol intake frequency. — — R²: 0.05002 [0.04681, 0.05323]
Incremental R2 (full-covars): 0.01708
PGS R2 (no covariates): 0.01731 [0.01536, 0.01926]		 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
PSS007566 — — 6,405 individuals — African unspecified — UKB —
PSS007567 — — 1,666 individuals — East Asian — UKB —
PSS007568 — — 24,881 individuals — European non-white British ancestry UKB —
PSS007569 — — 7,655 individuals — South Asian — UKB —
PSS007570 — — 67,383 individuals — European white British ancestry UKB Testing cohort (heldout set)