Deep resequencing of CFTR in 762 F508del homozygotes reveals clusters of non-coding variants associated with cystic fibrosis disease traits

Extensive phenotypic variability is commonly observed in individuals with Mendelian disorders, even among those with identical genotypes in the disease-causing gene. To determine whether variants within and surrounding CFTR contribute to phenotypic variability in cystic fibrosis (CF), we performed deep sequencing of CFTR in 762 patients homozygous for the common CF-causing variant, F508del. In phase 1, ~200 kb encompassing CFTR and extending 10 kb 5′ and 5 kb 3′ of the gene was sequenced in 486 F508del homozygotes selected from the extremes of sweat chloride concentration. In phase 2, a 510 kb region, which included the entire topologically associated domain of CFTR, was sequenced in 276 F508del homozygotes drawn from extremes of lung function. An additional 163 individuals who carried F508del and a different CF-causing variant were sequenced to inform haplotype construction. Region-based burden testing of both common and rare variants revealed seven regions of significance (α=0.01), five of which overlapped known regulatory elements or chromatin interactions. Notably, the −80 kb locus known to interact with the CFTR promoter was associated with variation in both CF traits. Haplotype analysis revealed a single rare recombination event (1.9% frequency) in intron 15 of CFTR bearing the F508del variant. Otherwise, the majority of F508del chromosomes were markedly similar, consistent with a single origin of the F508del allele. Together, these high-resolution variant analyses of the CFTR locus suggest a role for non-coding regulatory motifs in trait variation among individuals carrying the common CF allele. Researchers in the USA offer an explanation for differences in cystic fibrosis symptom severity among patients with the same mutation. Cystic fibrosis (CF) most frequently results from mutation of the CFTR gene. A team led by Garry Cutting at the Johns Hopkins University School of Medicine sequenced CFTR and the surrounding region in 762 CF patients carrying the mutated version. They identified new genetic variants which altered the gene, but none were associated with the variation in CF symptoms. However, genetic variants in seven known or suspected regulatory regions surrounding the gene were linked with CF symptom variability. This natural variation in the regulation of CFTR may modulate the severity of symptoms when the gene becomes mutated. These findings offer a new understanding of the link between CFTR and CF.