Rare and Common Variants Associated with Alcohol Consumption Identify a Conserved Molecular Network

• Published in: bioRxiv
• Main Authors: Leger, Brittany S, Meredith, John J, Ideker, Trey, Sanchez-Roige, Sandra, Palmer, Abraham A
• Format: Journal Article Paper
• Language: English
• Published: United States Cold Spring Harbor Laboratory Press 01.03.2024
• Subjects: Alcohol; Alcohol dehydrogenase; Alcohol use; Comorbidity; Drug use; Equity stake; Gene families; Genes; Genome-wide association studies; Genomes; Statistical analysis; Substance use; Substance use disorder
• ISSN: 2692-8205; 2692-8205
• DOI: 10.1101/2024.02.26.582195

Genome-wide association studies (GWAS) have identified hundreds of common variants associated with alcohol consumption. In contrast, rare variants have only begun to be studied for their role in alcohol consumption. No studies have examined whether common and rare variants implicate the same genes and molecular networks. To address this knowledge gap, we used publicly available alcohol consumption GWAS summary statistics (GSCAN, N=666,978) and whole exome sequencing data (Genebass, N=393,099) to identify a set of common and rare variants for alcohol consumption. Gene-based analysis of each dataset have implicated 294 (common variants) and 35 (rare variants) genes, including ethanol metabolizing genes and which were identified by both analyses, and , , , and , which were identified only by rare variant analysis, but have been associated with related psychiatric traits. We then used a network colocalization procedure to propagate the common and rare gene sets onto a shared molecular network, revealing significant overlap. The shared network identified gene families that function in alcohol metabolism, including , , , and . 74 of the genes in the network were previously implicated in comorbid psychiatric or substance use disorders, but had not previously been identified for alcohol-related behaviors, including , , , and . Differential gene expression analysis showed enrichment in the liver and several brain regions supporting the role of network genes in alcohol consumption. Thus, genes implicated by common and rare variants identify shared functions relevant to alcohol consumption, which also underlie psychiatric traits and substance use disorders that are comorbid with alcohol use.