Polygenic Score (PGS) ID: PGS002152

Predicted Trait
Reported Trait Alcohol intake frequency
Mapped Trait(s) alcohol consumption quality (OBA_1000840)
Additional Trait Information lifestyle and environment
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-ldpred2_less_alcohol
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 946,965
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000263
Citation (link to publication) Privé F et al. Am J Hum Genet (2022)
Ancestry Distribution
Score Development/Training
European: 100%
391,124 individuals (100%)
PGS Evaluation
European: 37.5%
African: 25%
East Asian: 12.5%
Greater Middle Eastern: 12.5%
South Asian: 12.5%
8 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
— 391,124 individuals European UKB — — — UK (+ Ireland) —

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
PPM012064 PSS009195|
European Ancestry|
4,117 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Alcohol intake frequency — — Partial Correlation (partial-r): 0.1643 [0.1343, 0.1939] sex, age, birth date, deprivation index, 16 PCs —
PPM012063 PSS009421|
European Ancestry|
19,981 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Alcohol intake frequency — — Partial Correlation (partial-r): 0.1645 [0.1509, 0.1779] sex, age, birth date, deprivation index, 16 PCs —
PPM012065 PSS008749|
European Ancestry|
6,635 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Alcohol intake frequency — — Partial Correlation (partial-r): 0.176 [0.1526, 0.1993] sex, age, birth date, deprivation index, 16 PCs —
PPM012066 PSS008523|
Greater Middle Eastern Ancestry|
1,161 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Alcohol intake frequency — — Partial Correlation (partial-r): 0.0596 [0.0016, 0.1173] sex, age, birth date, deprivation index, 16 PCs —
PPM012067 PSS008301|
South Asian Ancestry|
6,209 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Alcohol intake frequency — — Partial Correlation (partial-r): 0.0571 [0.0322, 0.0819] sex, age, birth date, deprivation index, 16 PCs —
PPM012068 PSS008078|
East Asian Ancestry|
1,789 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Alcohol intake frequency — — Partial Correlation (partial-r): 0.1084 [0.0621, 0.1542] sex, age, birth date, deprivation index, 16 PCs —
PPM012069 PSS007865|
African Ancestry|
2,460 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Alcohol intake frequency — — Partial Correlation (partial-r): 0.0391 sex, age, birth date, deprivation index, 16 PCs —
PPM012070 PSS008969|
African Ancestry|
3,855 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Alcohol intake frequency — — Partial Correlation (partial-r): 0.0299 [-0.0017, 0.0615] sex, age, birth date, deprivation index, 16 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
PSS008969 — — 3,855 individuals — African unspecified Nigeria (West Africa) UKB —
PSS008523 — — 1,161 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS009195 — — 4,117 individuals — European Poland (NE Europe) UKB —
PSS009421 — — 19,981 individuals — European UK (+ Ireland) UKB —
PSS008749 — — 6,635 individuals — European Italy (South Europe) UKB —
PSS008301 — — 6,209 individuals — South Asian India (South Asia) UKB —
PSS008078 — — 1,789 individuals — East Asian China (East Asia) UKB —
PSS007865 — — 2,460 individuals — African American or Afro-Caribbean Carribean UKB —