Association and interaction analysis of variants in CHRNA5/CHRNA3/CHRNB4 gene cluster with nicotine dependence in African and European Americans

Abstract

Several previous genome-wide and targeted association studies revealed that variants in the CHRNA5-CHRNA3-CHRNB4 (CHRNA5/A3/B4) gene cluster on chromosome 15 that encode the alpha5, alpha3, and beta4 subunits of the nicotinic acetylcholine receptors (nAChRs) are associated with nicotine dependence (ND) in European Americans (EAs) or others of European origin. Considering the distinct linkage disequilibrium patterns in European and other ethnic populations such as African Americans (AAs), it would be interesting to determine whether such associations exist in other ethnic populations. We performed a comprehensive association and interaction analysis of the CHRNA5/A3/B4 cluster in two ethnic samples to investigate the role of variants in the risk for ND, which was assessed by Smoking Quantity, Heaviness Smoking Index, and Fagerström test for ND. Using a family-based association test, we found a nominal association of single nucleotide polymorphisms (SNPs) rs1317286 and rs8040868 in CHRNA3 with ND in the AA and combined AA and EA samples. Furthermore, we found that several haplotypes in CHRNA5 and CHRNA3 are nominally associated with ND in AA, EA, and pooled samples. However, none of these associations remained significant after correction for multiple testing. In addition, we performed interaction analysis of SNPs within the CHRNA5/A3/B4 cluster using the pedigree-based generalized multifactor dimensionality reduction method and found significant interactions within CHRNA3 and among the three subunit genes in the AA and pooled samples. Together, these results indicate that variants within CHRNA3 and among CHRNA5, CHRNA3, and CHRNB4 contribute significantly to the etiology of ND through gene-gene interactions, although the association of each subunit gene with ND is weak in both the AA and EA samples.

Figure 1

Haploview-generated LD patterns for 22 SNPs within the CHRNA5/A3/B4 cluster in the pooled (A), AA (B), and EA (C) samples. Pair-wise LD between all SNPs was evaluated using the Haploview program (Barrett and others 2005) with the option of determining haplotype blocks according to the criteria defined by Gabriel et al. (2002). The number in each box represents the D’ value for each SNP pair.

Figure 1

Haploview-generated LD patterns for 22 SNPs within the CHRNA5/A3/B4 cluster in the pooled (A), AA (B), and EA (C) samples. Pair-wise LD between all SNPs was evaluated using the Haploview program (Barrett and others 2005) with the option of determining haplotype blocks according to the criteria defined by Gabriel et al. (2002). The number in each box represents the D’ value for each SNP pair.

Figure 1

Haploview-generated LD patterns for 22 SNPs within the CHRNA5/A3/B4 cluster in the pooled (A), AA (B), and EA (C) samples. Pair-wise LD between all SNPs was evaluated using the Haploview program (Barrett and others 2005) with the option of determining haplotype blocks according to the criteria defined by Gabriel et al. (2002). The number in each box represents the D’ value for each SNP pair.