TY - JOUR
T1 - Deep Sequencing of 71 Candidate Genes to Characterize Variation Associated with Alcohol Dependence
AU - Clark, Shaunna L.
AU - McClay, Joseph L.
AU - Adkins, Daniel E.
AU - Kumar, Gaurav
AU - Aberg, Karolina A.
AU - Nerella, Srilaxmi
AU - Xie, Linying
AU - Collins, Ann L.
AU - Crowley, James J.
AU - Quackenbush, Corey R.
AU - Hilliard, Christopher E.
AU - Shabalin, Andrey A.
AU - Vrieze, Scott I
AU - Peterson, Roseann E.
AU - Copeland, William E.
AU - Silberg, Judy L.
AU - Mc Gue, Matt
AU - Maes, Hermine
AU - Iacono, William G
AU - Sullivan, Patrick F.
AU - Costello, Elizabeth J.
AU - van den Oord, Edwin J.
N1 - Funding Information:
This work was supported by the National Institutes of Health (R01 DA024413, R01 MH045268, R01 MH068521, R01 DA036216, R01 DA05147, R01 DA024417, R01 AA09367, R25 DA026119, and K01 AA021266 to SLC). The authors report no conflicts of interest.
Publisher Copyright:
Copyright © 2017 by the Research Society on Alcoholism
PY - 2017
Y1 - 2017
N2 - 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.
AB - 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.
KW - Alcohol Dependence
KW - Aldehyde Dehydrogenase
KW - Genetics
KW - Next-Generation Sequencing
KW - SNP
KW - Serotonin
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U2 - 10.1111/acer.13352
DO - 10.1111/acer.13352
M3 - Article
C2 - 28196272
AN - SCOPUS:85016440106
SN - 0145-6008
VL - 41
SP - 711
EP - 718
JO - Alcoholism: Clinical and Experimental Research
JF - Alcoholism: Clinical and Experimental Research
IS - 4
ER -
