Deep Sequencing of 71 Candidate Genes to Characterize Variation Associated with Alcohol Dependence.
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AuthorClark, Shaunna L
McClay, Joseph L
Adkins, Daniel E
Aberg, Karolina A
Collins, Ann L
Crowley, James J
Quackenbush, Corey R
Hilliard, Christopher E
Shabalin, Andrey A
Vrieze, Scott I
Peterson, Roseann E
Copeland, William E
Silberg, Judy L
Iacono, William G
Sullivan, Patrick F
Costello, Elizabeth J
van den Oord, Edwin J
Journal titleAlcoholism, clinical and experimental research
Publication Begin page711
Publication End page718
MetadataShow full item record
AbstractPrevious genomewide association studies (GWASs) have identified a number of putative risk loci for alcohol dependence (AD). However, only a few loci have replicated and these replicated variants only explain a small proportion of AD risk. Using an innovative approach, the goal of this study was to generate hypotheses about potentially causal variants for AD that can be explored further through functional studies.
We employed targeted capture of 71 candidate loci and flanking regions followed by next-generation deep sequencing (mean coverage 78X) in 806 European Americans. Regions included in our targeted capture library were genes identified through published GWAS of alcohol, all human alcohol and aldehyde dehydrogenases, reward system genes including dopaminergic and opioid receptors, prioritized candidate genes based on previous associations, and genes involved in the absorption, distribution, metabolism, and excretion of drugs. We performed single-locus tests to determine if any single variant was associated with AD symptom count. Sets of variants that overlapped with biologically meaningful annotations were tested for association in aggregate.
No single, common variant was significantly associated with AD in our study. We did, however, find evidence for association with several variant sets. Two variant sets were significant at the q-value <0.10 level: a genic enhancer for ADHFE1 (p = 1.47 × 10 ; q = 0.019), an alcohol dehydrogenase, and ADORA1 (p = 5.29 × 10 ; q = 0.035), an adenosine receptor that belongs to a G-protein-coupled receptor gene family.
To our knowledge, this is the first sequencing study of AD to examine variants in entire genes, including flanking and regulatory regions. We found that in addition to protein coding variant sets, regulatory variant sets may play a role in AD. From these findings, we have generated initial functional hypotheses about how these sets may influence AD.
CitationClark SL, McClay JL, Adkins DE, Kumar G, Aberg KA, Nerella S, Xie L, Collins AL, Crowley JJ, Quackenbush CR, Hilliard CE, Shabalin AA, Vrieze SI, Peterson RE, Copeland WE, Silberg JL, McGue M, Maes H, Iacono WG, Sullivan PF, Costello EJ, van den Oord EJ. Deep Sequencing of 71 Candidate Genes to Characterize Variation Associated with Alcohol Dependence. Alcohol Clin Exp Res. 2017 Apr;41(4):711-718. doi: 10.1111/acer.13352. Epub 2017 Mar 24. PMID: 28196272; PMCID: PMC5378639.
The following license files are associated with this item:
- Creative Commons
Except where otherwise noted, this item's license is described as Copyright © 2017 by the Research Society on Alcoholism.
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