Trait: longitudinal alcohol consumption measurement

Experimental Factor Ontology (EFO) Information
Identifier EFO_0007645
Description quantification of some aspect of alcohol consumption over a long period of time (typically several years)
Trait category
Other measurement
Mapped term PMID:26081443

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)
PGS001085
(GBE_BIN_FC10001628)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Increased alcohol consumption, versus 10 years ago longitudinal alcohol consumption measurement,
alcohol consumption measurement		 214
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001085/ScoringFiles/PGS001085.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
PPM008173 PGS001085
(GBE_BIN_FC10001628)
 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 PGS001085
(GBE_BIN_FC10001628)
 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 PGS001085
(GBE_BIN_FC10001628)
 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 PGS001085
(GBE_BIN_FC10001628)
 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 PGS001085
(GBE_BIN_FC10001628)
 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)