Complete ascertainment of intragenic copy number mutations (CNMs) in the CFTR gene and its implications for CNM formation at other autosomal loci

Abstract

Over the last 20 years since the discovery of the cystic fibrosis transmembrane conductance regulator (CFTR) gene, more than 1,600 different putatively pathological CFTR mutations have been identified. Until now, however, copy number mutations (CNMs) involving the CFTR gene have not been methodically analyzed, resulting almost certainly in the underascertainment of CFTR gene duplications compared with deletions. Here, high-resolution array comparative genomic hybridization (averaging one interrogating probe every 95 bp) was used to analyze the entire length of the CFTR gene (189 kb) in 233 cystic fibrosis chromosomes lacking conventional mutations. We succeeded in identifying five duplication CNMs that would otherwise have been refractory to analysis. Based upon findings from this and other studies, we propose that deletion and duplication CNMs in the human autosomal genome are likely to be generated in the proportion of approximately 2-3:1. We further postulate that intragenic gene duplication CNMs in other disease loci may have been routinely underascertained. Finally, our analysis of +/-20 bp flanking each of the 40 CFTR breakpoints characterized at the DNA sequence level provide support for the emerging concept that non-B DNA conformations in combination with specific sequence motifs predispose to both recurring and nonrecurring genomic rearrangements.

Figure 1

Overview of cystic fibrosis-causing CNMs reported in this study. Upper panel: Genomic structure of the CFTR gene (scaled). Vertical bars represent the 27 exons. Lower panel: black horizontal lines indicate intragenic deletions whereas gray horizontal lines indicate intragenic duplications. Breakpoint ends not yet fully characterized are indicated by dots. The CNMs are arranged in the same order as in Table 1.

Figure 2

Examples of CFTR CNMs identified by array-CGH. Green plots indicate deletions, red plots duplications. CNM numbers are in accord with those described in Table 1 and Figure 1. Note that in A, the carrier is a compound heterozygote of CNMs 7 and 11.