Polygenic Score (PGS) ID: PGS002739

Predicted Trait
Reported Trait Alcohol use disorder
Mapped Trait(s) alcohol dependence (MONDO_0007079)
Released in PGS Catalog: Aug. 3, 2022
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Score Details

Score Construction
PGS Name PRS_gene
Development Method
Name PRS-CSx (gene-based)
Parameters Concordant variants located within gene boundaries (defined as within the region containing the gene plus 1 kb upstream of the transcription start site and 1kb downstream of the transcription end site; annotated using ANNOVAR based on NCBI RefSeq GRCh37) were used
Variants
Original Genome Build GRCh37
Number of Variants 858
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000346
Citation (link to publication) Lai D et al. Transl Psychiatry (2022)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 88.5%
African: 11.5%
492,211 individuals (100%)
PGS Evaluation
African: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST008259
Europe PMC: 30940813
 56,648 individuals African American or Afro-Caribbean MVP
GWAS Catalog: GCST010546
Europe PMC: 32451486
 435,563 individuals European MVP, PGC, UKB

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
PPM014842 PSS009912|
African Ancestry|
6,315 individuals
 PGP000346 |
Lai D et al. Transl Psychiatry (2022)
 Reported Trait: Alcohol use disorder β: 0.17 (0.03) — Odds Ratio (OR top 10% vs rest): 1.76 [1.32, 2.34] — —

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
PSS009912 — —
[
  • 2,786 cases
  • , 3,529 controls
]
 — African American or Afro-Caribbean — COGA, SAGE, Yale-Penn —