Polygenic Score (PGS) ID: PGS001086

Predicted Trait
Reported Trait Alcohol consumption
Mapped Trait(s) alcohol consumption measurement (EFO_0007878)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/BIN100580
Released in PGS Catalog: Oct. 21, 2021
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Terms and Licenses
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Score Details

Score Construction
PGS Name GBE_BIN100580
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 1,028
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%
116,930 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
—
[
  • 75,021 cases
  • , 41,909 controls
]
 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
PPM008178 PSS003627|
African Ancestry|
2,091 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Alcohol consumed — AUROC: 0.62758 [0.60247, 0.65268] PGS R2 (no covariates): 1e-05
R²: 0.05864
Incremental AUROC (full-covars): -0.00051
PGS AUROC (no covariates): 0.50069 [0.47453, 0.52686]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008179 PSS003628|
East Asian Ancestry|
613 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Alcohol consumed — AUROC: 0.59978 [0.55292, 0.64664] R²: 0.04862
Incremental AUROC (full-covars): -0.00096
PGS R2 (no covariates): 0.0041
PGS AUROC (no covariates): 0.53085 [0.48306, 0.57863]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008180 PSS003629|
European Ancestry|
11,475 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Alcohol consumed — AUROC: 0.57613 [0.56536, 0.58689] R²: 0.02439
Incremental AUROC (full-covars): 0.00362
PGS R2 (no covariates): 0.00374
PGS AUROC (no covariates): 0.52973 [0.51886, 0.54059]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008181 PSS003630|
South Asian Ancestry|
2,331 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Alcohol consumed — AUROC: 0.63584 [0.61091, 0.66076] R²: 0.06374
Incremental AUROC (full-covars): -0.00247
PGS R2 (no covariates): 9e-05
PGS AUROC (no covariates): 0.50765 [0.48217, 0.53314]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008182 PSS003631|
European Ancestry|
29,044 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Alcohol consumed — AUROC: 0.56938 [0.56257, 0.57619] R²: 0.01833
Incremental AUROC (full-covars): 0.00268
PGS R2 (no covariates): 0.00113
PGS AUROC (no covariates): 0.51728 [0.51036, 0.52419]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method

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
PSS003627 — —
[
  • 723 cases
  • , 1,368 controls
]
 — African unspecified — UKB —
PSS003628 — —
[
  • 205 cases
  • , 408 controls
]
 — East Asian — UKB —
PSS003629 — —
[
  • 7,198 cases
  • , 4,277 controls
]
 — European non-white British ancestry UKB —
PSS003630 — —
[
  • 698 cases
  • , 1,633 controls
]
 — South Asian — UKB —
PSS003631 — —
[
  • 18,602 cases
  • , 10,442 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)