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

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

Gross genomic rearrangements involving deletions in the CFTR gene: characterization of six new events from a large cohort of hitherto unidentified cystic fibrosis chromosomes and meta-analysis of the underlying mechanisms

Novel complex mutations in the CFTR gene were characterized. All events were caused by non-homologous recombination. Deletion breakpoints were localized to regions of low sequence complexity. Recombination promoting motifs were in the vicinity. Some simple deletions were explicable by replication slippage. Complex deletions appear to have risen by multiple mechanisms. Large genomic rearrangements in the CFTR gene were compared with other genes

Gross genomic rearrangements involving deletions in the CFTR gene: characterization of six new events from a large cohort of hitherto unidentified cystic fibrosis chromosomes and meta-analysis of the underlying mechanisms

Novel complex mutations in the CFTR gene were characterized. All events were caused by non-homologous recombination. Deletion breakpoints were localized to regions of low sequence complexity. Recombination promoting motifs were in the vicinity. Some simple deletions were explicable by replication slippage. Complex deletions appear to have risen by multiple mechanisms. Large genomic rearrangements in the CFTR gene were compared with other genes

Is CFTR 621+3 A > G a cystic fibrosis causing mutation?

The 621+3 A>G variant of the CFTR gene was initially detected in four Greek patients with a severe form of cystic fibrosis, and it is reported to impair CFTR mRNA splicing. We present three lines of evidence that argue against the pathogenicity of this variant. First, its allelic frequency in the Italian population was 0.4%. Even considering the lowest value in the confidence interval we would expect 10% of Italian CF patients to be heterozygotes for this variant, whereas it has been reported only in one patient (0.04% of Italian CF patients). Second, expression of the 621+3 A>G variant in HeLa cells using a hybrid minigene showed that 39.5+/-1.1% of transcripts were correctly spliced, indicating that its effects on mRNA splicing are similar to those of the CFTR intron 8 5T variant, associated with congenital bilateral absence of vas deferens (CBAVD), but not with CF. Third, we have identified an asymptomatic individual who harbored the 621+3 A>G variant in trans with the Q552X mutation. Because 621+3 A>G is often included in population-screening programs, this information is critical to provide adequate counseling to patients. Further work should be aimed at investigating whether this variant may have a role in CBAVD or atypical CF

Cystic fibrosis on the African continent

Cystic fibrosis (CF; OMIM 219700) is a life-shortening and costly autosomal recessive disease that has been most extensively studied in individuals of Caucasian descent. There is ample evidence, however, that it also affects other ethnicities. In Africa there have been several reports of CF, but there has been no concerted effort toward establishing the molecular epidemiology of this disease on the continent, which is the first step toward outlining a public health strategy to effectively address the needs of these patients. A literature search revealed reports from only 12 of the 54 African states on the molecular analysis of the mutations present in suspected CF patients, resulting in the identification of 79 mutations. Based on previous functional investigations, 39 of these cause CF, 10 are of varying clinical consequence, 4 have no associated evidence regarding whether they cause CF, 4 are synonymous, 5 are novel, and 21 are unique to Africa. We propose that CF be more thoroughly investigated on the continent to ensure that the public health needs of African CF patients—both those in Africa and those of African descent living elsewhere—are met.The University of Pretoria Vice-Chancellor’s Post-doctoral Research Programme, the Institute for Cellular and Molecular Medicine at the University of Pretoria and the Genomics Research Institute (a University of Pretoria Institutional Research Theme).2017-01-31hb2016Immunolog