title: Deep Sequencing of 71 Candidate Genes to Characterize Variation Associated with Alcohol Dependence.
abstract: 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.
  
  
  
  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 × 10-5; 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.
  
  
  
  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.
authors.affiliation: Center for Biomarker Research and Precision Medicine , School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia.
authors.forename: Shaunna L
authors.initials: SL
authors.lastname: Clark
authors.affiliation: Center for Biomarker Research and Precision Medicine , School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia.
authors.forename: Joseph L
authors.initials: JL
authors.lastname: McClay
authors.affiliation: Center for Biomarker Research and Precision Medicine , School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia.
authors.forename: Daniel E
authors.initials: DE
authors.lastname: Adkins
authors.affiliation: Center for Biomarker Research and Precision Medicine , School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia.
authors.forename: Gaurav
authors.initials: G
authors.lastname: Kumar
authors.affiliation: Center for Biomarker Research and Precision Medicine , School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia.
authors.forename: Karolina A
authors.initials: KA
authors.lastname: Aberg
authors.affiliation: Center for Biomarker Research and Precision Medicine , School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia.
authors.forename: Srilaxmi
authors.initials: S
authors.lastname: Nerella
authors.affiliation: Center for Biomarker Research and Precision Medicine , School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia.
authors.forename: Linying
authors.initials: L
authors.lastname: Xie
authors.affiliation: Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.
authors.forename: Ann L
authors.initials: AL
authors.lastname: Collins
authors.affiliation: Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.
authors.forename: James J
authors.initials: JJ
authors.lastname: Crowley
authors.affiliation: Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.
authors.forename: Corey R
authors.initials: CR
authors.lastname: Quackenbush
authors.affiliation: Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.
authors.forename: Christopher E
authors.initials: CE
authors.lastname: Hilliard
authors.affiliation: Center for Biomarker Research and Precision Medicine , School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia.
authors.forename: Andrey A
authors.initials: AA
authors.lastname: Shabalin
authors.affiliation: Department of Psychology and Neuroscience, Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, Colorado.|Department of Psychology, University of Minnesota, Minneapolis, Minnesota.
authors.forename: Scott I
authors.initials: SI
authors.lastname: Vrieze
authors.affiliation: Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, Virginia.
authors.forename: Roseann E
authors.initials: RE
authors.lastname: Peterson
authors.affiliation: Department of Psychiatry and Behavioral Sciences, Duke University Medical Center, Durham, North Carolina.
authors.forename: William E
authors.initials: WE
authors.lastname: Copeland
authors.affiliation: Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, Virginia.
authors.forename: Judy L
authors.initials: JL
authors.lastname: Silberg
authors.affiliation: Department of Psychology, University of Minnesota, Minneapolis, Minnesota.
authors.forename: Matt
authors.initials: M
authors.lastname: McGue
authors.affiliation: Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, Virginia.
authors.forename: Hermine
authors.initials: H
authors.lastname: Maes
authors.affiliation: Department of Psychology, University of Minnesota, Minneapolis, Minnesota.
authors.forename: William G
authors.initials: WG
authors.lastname: Iacono
authors.affiliation: Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.|Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.
authors.forename: Patrick F
authors.initials: PF
authors.lastname: Sullivan
authors.affiliation: Department of Psychiatry and Behavioral Sciences, Duke University Medical Center, Durham, North Carolina.
authors.forename: Elizabeth J
authors.initials: EJ
authors.lastname: Costello
authors.affiliation: Center for Biomarker Research and Precision Medicine , School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia.
authors.forename: Edwin J
authors.initials: EJ
authors.lastname: van den Oord
mesh_terms: D000328:Adult; D000437:Alcoholism / Q000175:diagnosis* / Q000453:epidemiology / Q000235:genetics*; D005260:Female; D056726:Genetic Association Studies / Q000379:methods*; D014644:Genetic Variation / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D008297:Male; D017422:Sequence Analysis, DNA / Q000379:methods*; D055815:Young Adult
keywords: 
  SNP
  ; Alcohol Dependence; Aldehyde Dehydrogenase; Genetics; Next-Generation Sequencing; Serotonin