CARD15 genetic variation in a Quebec population: prevalence, genotype-phenotype relationship, and haplotype structure

Abstract

The caspase recruitment domain gene (CARD15) was recently identified as the underlying gene associated with the IBD1 locus that confers susceptibility to Crohn disease (CD). CARD15 is related to the NOD1/Apaf-1 family of apoptosis regulators, and three sequence variants (Arg702Trp, Gly908Arg, and Leu1007fsinsC) in the gene were demonstrated to be associated with CD. We collected a cohort of 231 patients with CD and 71 healthy control individuals from the Canadian province of Quebec, to determine the prevalence of these sequence variants in an independent population. Clinical records of all patients were systematically reviewed, and detailed phenotypic information was obtained. All patient DNA samples were genotyped for the three variants, thus enabling an analysis of genotype-phenotype correlations. In this cohort, 45.0% of patients with CD carried at least one variant in the CARD15 gene, compared with 9.0% of control individuals (P<10-7). Allele frequencies of Arg702Trp, Gly908Arg, and Leu1007fsinsC were 12.9%, 5.2%, and 10.3% in patients with CD, compared with 4.2%, 0.7%, and 0.7% in control individuals, respectively. Importantly, CARD15 mutants were seen with equal frequency in patients with familial and sporadic CD. Analysis of the relationship between genotype and phenotype convincingly demonstrates that CARD15 variants are significantly associated with ileal disease involvement, as opposed to strictly colonic disease (P<.001). Moreover, we were able to determine the haplotype structure surrounding this disease gene by genotyping 45 single-nucleotide polymorphisms (SNPs) in a 177-kb region that contained the CARD15 gene. This structure helps clarify the history of these causal mutations. Finally, this analysis shows that CARD15 involvement with CD is detectable by use of publicly available SNPs alone.

Figure 1

Blocklike haplotype structure of the CARD15 gene. A, Common haplotype patterns in the four blocks of low diversity encompassing the CARD15 gene. Dashed lines indicate locations where >5% of all chromosomes were observed to connect one common haplotype to another. Alleles at each SNP are indicated as numbers (1 = A, 2 = C, 3 = G, and 4 = T). All SNPs included in the haplotype structure have an MAF >5%. The CARD15 gene (topmost purple box) represents the location of the gene in relation to the blocks. The gray vertical bars represent intervals of historical recombination between the blocks. Distances between Blocks 1 and 2, 2 and 3, and 3 and 4 are 33 kb, 14 kb, and 3 kb, respectively. B, Percentage of each of the common patterns among all observed chromosomes (transmitted and untransmitted). C, Haplotype structure of the wild-type haplotype C (C_wt), which contains no risk alleles, and the three subvariants of haplotype C (C₁, C₂, C₃), which confer risk of CD. For the three subvariants, blocks 2, 3, and 4 are in tight LD; therefore, all three blocks are displayed. Greater recombination is seen between blocks 2, 3, and 4 for the wild-type haplotype C, so only block 3 is displayed. SNPs that confer risk of CD are highlighted in red and boxed. D, Frequencies and transmitted:untransmitted ratios of the specified allele calculated for each individual SNP. The SNPs that confer risk of CD are highlighted in red and boxed. E, Overall frequencies and frequency among transmitted (F_T) and untransmitted (F_U) chromosomes for the common block 3 haplotypes (A, B, and C [top]) and for the C_wt and C subvariant block 3 haplotypes (C₁, C₂, and C₃) (bottom).