Deep Sequencing of 71 Candidate Genes to Characterize Variation Associated with Alcohol Dependence
Shaunna L Clark, Daniel E Adkins, Karolina A Aberg, Gaurav Kumar, Sri Nerella, Linying Xie, Ann L Collins, James J
Crowley, Corey R Quakenbush, Christopher E Hillard, Guimin Gao, Andrey A Shabalin,
Roseann E Peterson, William E Copeland, Judy L Silberg, Hermine Maes, Patrick F Sullivan,
Elizabeth J Costello, Edwin J van den Oord. (2017). “Deep sequencing of 71 candidate
genes to characterize variation associated with alcohol dependence.” Alcoholism: Clinical
and Experimental Research, 41 (4): 711-718.
https://doi.org/10.1111/acer.13352
BACKGROUND:
Previous 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.
METHODS:
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.
RESULTS:
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 × 10-5 ;
q = 0.019), an alcohol dehydrogenase, and ADORA1 (p = 5.29 × 10-5 ; q = 0.035), an
adenosine receptor that belongs to a G-protein-coupled receptor gene family.
CONCLUSIONS:
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