Complete ascertainment of intragenic copy number mutations (CNMs) in the CFTR gene and its implications for CNM formation at other autosomal loci
Quemener, Sylvia × Chen, Jian-Min Chuzhanova, Nadia Bénech, Caroline Casals, Teresa Macek, Milan Bienvenu, Thierry McDevitt, Trudi Farrell, Philip M Loumi, Ourida Messaoud, Taieb Cuppens, Harry Cutting, Garry R Stenson, Peter D Giteau, Karine Audrézet, Marie-Pierre Cooper, David N Férec, Claude #
John Wiley & Sons, Inc.
Human Mutation vol:31 issue:4 pages:421-428
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 under-ascertainment of CFTR gene duplications as 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 which 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 under-ascertained. Finally, our analysis of +/-20 bp flanking each of the 40 CFTR breakpoints characterized at the DNA sequence level provide support to the emerging concept that non-B DNA conformations in combination with specific sequence motifs predispose to both recurring and non-recurring genomic rearrangements. (c) 2009 Wiley-Liss, Inc.