Haplotypic variants in DRD2, ANKK1, TTC12, and NCAM1 are associated with comorbid alcohol and drug dependence

Abstract

Background: Each gene in the chromosome 11q23 cluster of NCAM1, TTC12, ANKK1, and DRD2 is functionally linked to dopamine in brain. Many association studies of DRD2 and substance dependence (SD), including alcohol dependence (AD) and drug dependence (DD), have been reported; the results have been inconsistent. Recent association studies have considered this cluster more comprehensively, examining the association of SD with several risk variants mapped to the other genes in the cluster. Because comorbid AD with DD (AD+DD) is common, we hypothesized that heterogeneity of the SD diagnoses studied might have contributed to the inconsistency of prior results.

Methods: We conducted 2 separate association studies of AD+DD and AD without DD (AD-only) in 1,090 European-Americans using family-based and case-control designs and 43 single nucleotide polymorphisms mapped to this cluster. We used a generalized linear model and haplotype score tests for the case-control sample, and the family-based association test for the family sample.

Results: For AD+DD, the risk regions centered on TTC12 exon 3 [optimal individual haplotype simulated p (p(oihs)) = 0.000015], and another extended from ANKK1 exon 8 to DRD2;C957T (p(oihs) = 0.0028), in both samples. NCAM1 exon 12 markers showed global significance in both designs, but were significant for specific haplotypes (p(oihs) = 0.0029) only for the family sample. For AD-only, NCAM1 intron 14 to 18 and the junction of ANKK1 and DRD2 were associated globally. Population stratification was excluded as the basis for these results. Linkage disequilibrium contrast tests supported selection at TTC12 exon 3 and ANKK1 exon 2.

Conclusions: We conclude that variants in TTC12 exon 3, NCAM1 exon 12, and the two 3'-ends of ANKK1 and DRD2 co-regulate risk for comorbid AD and DD.

Figure 1

Map of the NCAM1, TTC12, ANKK1 and DRD2 gene region. (A) Relative gene locations, and the distribution of 43 SNPs studied. (B) Associated regions identified in analyzing phenotypes of AD-all, AD+DD, AD-only and ND-all. Solid black or grey indicates a finding in the case-control (“c”) sample, black or grey with white stripes indicates a finding in the family (“f”). A finding in black color indicates significance both in global and individual specific haplotypic association; a finding in grey color indicates significance in global haplotypic association only. Each diamond above the block indicates the position of the corresponding SNP in the associated haplotype. The number underneath each block is annotated for the corresponding genetic region.

Figure 2

Results of single SNP and haplotype association analyses for the case-control samples of AD+DD and AD-only, and AD+DD of family samples. Global simulated p-values are shown. For haplotype analyses, the value at each SNP location represents the haplotype with SNPs starting from the current location downward from the NCAM1 direction to DRD2. The horizontal dashed lines correspond to type I error rate of 0.05. The three vertical lines from left to right indicate the positions of SNPs N19, T10 and A7, respectively.

Figure 3

Ellipse plots for the results of the LD contrast tests. For each ellipse plot, the pairwise LD matrices are displayed for the contrast of cases and controls, respectively, above and below the diagonal line. The shape of an ellipse indicates the magnitude of LD and the direction shows the sign of the disequilibrium. The more circular shape of an ellipse reflects a low degree of LD, and 45o-oriented ellipses suggest a positive value of LD.