Polygenic Score (PGS) ID: PGS001394

Predicted Trait
Reported Trait Freq. of drinking alcohol
Mapped Trait(s) alcohol consumption measurement (EFO_0007878)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI20414
Released in PGS Catalog: Nov. 25, 2021
Download Score FTP directory
Terms and Licenses
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_INI20414
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 860
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%
88,182 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
— 88,182 individuals European UKB — — — white British ancestry Training + validation cohort (train_val)

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
PPM005250 PSS004901|
African Ancestry|
916 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Freq. of drinking alcohol — — R²: 0.06812 [0.0563, 0.07994]
Incremental R2 (full-covars): -0.00597
PGS R2 (no covariates): 0.00346 [0.00061, 0.0063]		 age, sex, UKB array type, Genotype PCs —
PPM005251 PSS004902|
East Asian Ancestry|
362 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Freq. of drinking alcohol — — R²: 0.0612 [0.03919, 0.08321]
Incremental R2 (full-covars): 0.00664
PGS R2 (no covariates): 0.00812 [-0.00035, 0.01659]		 age, sex, UKB array type, Genotype PCs —
PPM005252 PSS004903|
European Ancestry|
8,143 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Freq. of drinking alcohol — — R²: 0.03774 [0.03309, 0.04238]
Incremental R2 (full-covars): 0.00221
PGS R2 (no covariates): 0.00497 [0.00323, 0.00671]		 age, sex, UKB array type, Genotype PCs —
PPM005253 PSS004904|
South Asian Ancestry|
1,046 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Freq. of drinking alcohol — — R²: 0.08608 [0.0742, 0.09795]
Incremental R2 (full-covars): 0.00166
PGS R2 (no covariates): 0.00099 [-0.0004, 0.00239]		 age, sex, UKB array type, Genotype PCs —
PPM005254 PSS004905|
European Ancestry|
22,013 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Freq. of drinking alcohol — — R²: 0.03531 [0.03257, 0.03804]
Incremental R2 (full-covars): 0.00358
PGS R2 (no covariates): 0.00342 [0.00254, 0.0043]		 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
PSS004901 — — 916 individuals — African unspecified — UKB —
PSS004902 — — 362 individuals — East Asian — UKB —
PSS004903 — — 8,143 individuals — European non-white British ancestry UKB —
PSS004904 — — 1,046 individuals — South Asian — UKB —
PSS004905 — — 22,013 individuals — European white British ancestry UKB Testing cohort (heldout set)