Genome-wide association study of copy number variations (CNVs) with opioid dependence

Neuropsychopharmacology. 2015 Mar;40(4):1016-26. doi: 10.1038/npp.2014.290. Epub 2014 Sep 27.

Abstract

Single-nucleotide polymorphisms that have been associated with opioid dependence (OD) altogether account for only a small proportion of the known heritability. Most of the genetic risk factors are unknown. Some of the 'missing heritability' might be explained by copy number variations (CNVs) in the human genome. We used Illumina HumanOmni1 arrays to genotype 5152 African-American and European-American OD cases and screened controls and implemented combined CNV calling methods. After quality control measures were applied, a genome-wide association study (GWAS) of CNVs with OD was performed. For common CNVs, two deletions and one duplication were significantly associated with OD genome-wide (eg, P=2 × 10(-8) and OR (95% CI)=0.64 (0.54-0.74) for a chromosome 18q12.3 deletion). Several rare or unique CNVs showed suggestive or marginal significance with large effect sizes. This study is the first GWAS of OD using CNVs. Some identified CNVs harbor genes newly identified here to be of biological importance in addiction, whereas others affect genes previously known to contribute to substance dependence risk. Our findings augment our specific knowledge of the importance of genomic variation in addictive disorders, and provide an addiction CNV pool for further research. These findings require replication.

Publication types

  • Multicenter Study
  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Chromosome Deletion
  • Chromosome Disorders / genetics
  • Chromosomes, Human, Pair 18 / genetics
  • DNA Copy Number Variations / genetics*
  • Female
  • Genetic Predisposition to Disease / genetics*
  • Genome-Wide Association Study
  • Genotype
  • Humans
  • Leukocyte Common Antigens / genetics*
  • Male
  • Meta-Analysis as Topic
  • Opioid-Related Disorders / genetics*
  • Receptor-Like Protein Tyrosine Phosphatases, Class 2 / genetics*
  • alpha Catenin / genetics*

Substances

  • CTNNA3 protein, human
  • alpha Catenin
  • Leukocyte Common Antigens
  • PTPRC protein, human
  • PTPRD protein, human
  • Receptor-Like Protein Tyrosine Phosphatases, Class 2

Supplementary concepts

  • Chromosome 18 deletion syndrome