title: Deep resequencing ofCFTRin 762 F508del homozygotes reveals clusters of non-coding variants associated with cystic fibrosis disease traits.
abstract: 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 surroundingCFTRcontribute to phenotypic variability in cystic fibrosis (CF), we performed deep sequencing ofCFTRin 762 patients homozygous for the common CF-causing variant, F508del. In phase 1, ~200 kb encompassingCFTRand 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 ofCFTR, 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 theCFTRpromoter was associated with variation in both CF traits. Haplotype analysis revealed a single rare recombination event (1.9% frequency) in intron 15 ofCFTRbearing 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 theCFTRlocus suggest a role for non-coding regulatory motifs in trait variation among individuals carrying the common CF allele.
authors.affiliation: McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine , Baltimore, MD, USA.
authors.forename: Briana
authors.initials: B
authors.lastname: Vecchio-Pagán
authors.affiliation: McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Division of Pediatric Endocrinology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
authors.forename: Scott M
authors.identifier: 0000-0002-4532-6421
authors.initials: SM
authors.lastname: Blackman
authors.affiliation: McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine , Baltimore, MD, USA.
authors.forename: Melissa
authors.initials: M
authors.lastname: Lee
authors.affiliation: McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine , Baltimore, MD, USA.
authors.forename: Melis
authors.initials: M
authors.lastname: Atalar
authors.affiliation: McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine , Baltimore, MD, USA.
authors.forename: Matthew J
authors.initials: MJ
authors.lastname: Pellicore
authors.affiliation: Cystic Fibrosis-Pulmonary Research and Treatment Center, University of North Carolina at Chapel Hill , Chapel Hill, NC, USA.
authors.forename: Rhonda G
authors.initials: RG
authors.lastname: Pace
authors.affiliation: McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine , Baltimore, MD, USA.
authors.forename: Arianna L
authors.initials: AL
authors.lastname: Franca
authors.affiliation: McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine , Baltimore, MD, USA.
authors.forename: Karen S
authors.initials: KS
authors.lastname: Raraigh
authors.affiliation: McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine , Baltimore, MD, USA.
authors.forename: Neeraj
authors.initials: N
authors.lastname: Sharma
authors.affiliation: Cystic Fibrosis-Pulmonary Research and Treatment Center, University of North Carolina at Chapel Hill , Chapel Hill, NC, USA.
authors.forename: Michael R
authors.initials: MR
authors.lastname: Knowles
authors.affiliation: McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine , Baltimore, MD, USA.
authors.forename: Garry R
authors.initials: GR
authors.lastname: Cutting