Analysis of variation in the protein kinase C-epsilon gene in the COGA study

The Collaborative study on the Genetics of Alcoholism (COGA) has previously reported evidence of linkage between alcohol dependence and microsatellite markers on the long arm of chromosome 2. Follow-up studies have also shown linkage in the same region of chromosome 2 for habitual smoking. Indeed the strongest evidence for linkage in this region of chromosome 2 is with the combined phenotype of alcohol dependence and habitual smoking. This analysis generated a lod score of 4.21 close to marker D2S379. Here we report analysis of a candidate gene, protein kinase C-epsilon (PRKCE) that maps within this region of linkage. PRKCE null mutant mice have an altered sensitivity to ethanol, leading to decreased self-administration of alcohol and super-sensitivity to the behavioral effects of ethanol, such as ethanol withdrawal-associated seizure and painful alcoholic neuropathy. Sequence analysis of the PRKCE gene in ten COGA alcohol dependent probands from families showing evidence of linkage to chromosome 2 led to the identification of four novel single nucleotide polymorphisms (SNPs), including a rare missense mutation. In addition, 36 putative SNPs were identified from the public databases that map within genomic DNA clones containing the PRKCE gene. Thirteen of these putative SNPs were verified by DNA sequencing of pooled DNA. To determine whether variation in the PRKCE gene alters risk for alcohol dependence, we have genotyped ten of these SNPs spaced throughout the gene in trios (two parents and one offspring) from 142 COGA families. In each trio the offspring meets diagnostic criteria for COGA alcohol dependence. The TDT is being used to test the SNP data for evidence of linkage disequilibrium between specific alleles of the SNP and alcohol dependence or alcohol dependence and habitual smoking. Our initial studies with a SNP that is 1.5 kb upstream from exon 1 of PRKCE showed a significant P value of 0.00876 with alcohol dependence. We will present single SNP and haplotype results for the novel SNPs in PRKCE.