Polygenic Score (PGS) ID: PGS001085

Predicted Trait
Reported Trait Increased alcohol consumption, versus 10 years ago
Mapped Trait(s)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/BIN_FC10001628
Released in PGS Catalog: Oct. 21, 2021
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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_BIN_FC10001628
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 214
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%
250,957 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
—
[
  • 43,777 cases
  • , 207,180 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
PPM008173 PSS003701|
African Ancestry|
4,734 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Alcohol intake versus 10 years previously (More nowadays) — AUROC: 0.61924 [0.59643, 0.64206] R²: 0.03617
Incremental AUROC (full-covars): -0.00135
PGS R2 (no covariates): 0.00063
PGS AUROC (no covariates): 0.48029 [0.45567, 0.50491]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008174 PSS003702|
East Asian Ancestry|
1,152 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Alcohol intake versus 10 years previously (More nowadays) — AUROC: 0.59668 [0.5559, 0.63746] R²: 0.03361
Incremental AUROC (full-covars): -7e-05
PGS R2 (no covariates): 0.00016
PGS AUROC (no covariates): 0.49533 [0.45262, 0.53804]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008175 PSS003703|
European Ancestry|
22,711 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Alcohol intake versus 10 years previously (More nowadays) — AUROC: 0.57487 [0.56499, 0.58474] R²: 0.01586
Incremental AUROC (full-covars): 0.00294
PGS R2 (no covariates): 0.00217
PGS AUROC (no covariates): 0.52723 [0.51724, 0.53721]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008176 PSS003704|
South Asian Ancestry|
3,896 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Alcohol intake versus 10 years previously (More nowadays) — AUROC: 0.62832 [0.60431, 0.65233] R²: 0.04483
Incremental AUROC (full-covars): 0.00126
PGS R2 (no covariates): 0.00102
PGS AUROC (no covariates): 0.51677 [0.49198, 0.54156]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008177 PSS003705|
European Ancestry|
62,689 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Alcohol intake versus 10 years previously (More nowadays) — AUROC: 0.57771 [0.57181, 0.58362] R²: 0.01714
Incremental AUROC (full-covars): 0.00186
PGS R2 (no covariates): 0.00101
PGS AUROC (no covariates): 0.51871 [0.51274, 0.52468]		 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
PSS003701 — —
[
  • 616 cases
  • , 4,118 controls
]
 — African unspecified — UKB —
PSS003702 — —
[
  • 227 cases
  • , 925 controls
]
 — East Asian — UKB —
PSS003703 — —
[
  • 3,856 cases
  • , 18,855 controls
]
 — European non-white British ancestry UKB —
PSS003704 — —
[
  • 605 cases
  • , 3,291 controls
]
 — South Asian — UKB —
PSS003705 — —
[
  • 10,844 cases
  • , 51,845 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)