title: Array-based profiling of DNA methylation changes associated with alcohol dependence.
abstract: BACKGROUND
  Epigenetic regulation through DNA methylation may influence vulnerability to numerous disorders, including alcohol dependence (AD).
  
  
  METHODS
  Peripheral blood DNA methylation levels of 384 CpGs in the promoter regions of 82 candidate genes were examined in 285 African Americans (AAs; 141 AD cases and 144 controls) and 249 European Americans (EAs; 144 AD cases and 105 controls) using Illumina GoldenGate Methylation Array assays. Association of AD and DNA methylation changes was analyzed using multivariate analyses of covariance with frequency of intoxication, sex, age, and ancestry proportion as covariates. CpGs showing significant methylation alterations in AD cases were further examined in a replication sample (49 EA cases and 32 EA controls) using Sequenom's MassARRAY EpiTYPER technology.
  
  
  RESULTS
  In AAs, 2 CpGs in 2 genes (GABRB3 and POMC) were hypermethylated in AD cases compared with controls (p ≤ 0.001). In EAs, 6 CpGs in 6 genes (HTR3A, NCAM1, DRD4, MBD3, HTR2B, and GRIN1) were hypermethylated in AD cases compared with controls (p ≤ 0.001); CpG cg08989585 in the HTR3A promoter region showed a significantly higher methylation level in EA cases than in EA controls after Bonferroni correction (p = 0.00007). Additionally, methylation levels of 6 CpGs (including cg08989585) in the HTR3A promoter region were analyzed in the replication sample. Although the 6 HTR3A promoter CpGs did not show significant methylation differences between EA cases and EA controls (p = 0.067 to 0.877), the methylation level of CpG cg08989585 was nonsignificantly higher in EA cases (26.9%) than in EA controls (18.6%; p = 0.139).
  
  
  CONCLUSIONS
  The findings from this study suggest that DNA methylation profile appears to be associated with AD in a population-specific way and the predisposition to AD may result from a complex interplay of genetic variation and epigenetic modifications.
authors.affiliation: Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut 06516, USA. huiping.zhang@yale.edu
authors.forename: Huiping
authors.initials: H
authors.lastname: Zhang
authors.forename: Aryeh I
authors.initials: AI
authors.lastname: Herman
authors.forename: Henry R
authors.initials: HR
authors.lastname: Kranzler
authors.forename: Raymond F
authors.initials: RF
authors.lastname: Anton
authors.forename: Hongyu
authors.initials: H
authors.lastname: Zhao
authors.forename: Wei
authors.initials: W
authors.lastname: Zheng
authors.forename: Joel
authors.initials: J
authors.lastname: Gelernter
mesh_terms: D001741:Black or African American / Q000208:ethnology / Q000235:genetics*; D000437:Alcoholism / Q000208:ethnology / Q000235:genetics*; D019175:DNA Methylation / Q000235:genetics*; D005260:Female; D056726:Genetic Association Studies / Q000379:methods; D006801:Humans; D008297:Male; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D044465:White People / Q000208:ethnology / Q000235:genetics*