title: A comprehensive assay for CFTR mutational analysis using next-generation sequencing.
abstract: BACKGROUND
  Cystic fibrosis is a life-threatening genetic disorder that has been associated with mutations in the CFTR [cystic fibrosis transmembrane conductance regulator (ATP-binding cassette sub-family C, member 7)] gene. Hundreds of CFTR mutations have been detected to date. Current CFTR genotyping assays target a subset of these mutations, particularly a mutation panel recommended by the American College of Medical Genetics for carrier screening of the general population. Fast sequencing of the entire coding sequence in a scalable manner could expand the detection of CFTR mutations and facilitate management of costs and turnaround times in the clinical laboratory.
  
  
  METHODS
  We describe a proof-of-concept CFTR assay that uses PCR target enrichment and next-generation sequencing on the Ion Torrent Personal Genome Machine™ (PGM™) platform.
  
  
  RESULTS
  The scalability of the assay was demonstrated, with an average mean depth of coverage ranging from 500× to 3500×, depending on the number of multiplexed patient samples and the Ion Torrent chip used. In a blinded study of 79 previously genotyped patient DNA samples and cell lines, our assay detected most of the mutations, including single-nucleotide variants, small insertions and deletions, and large copy-number variants. The reproducibility was 100% for detecting mutations in independent runs. Our assay demonstrated high specificity, with only 2 false-positive calls (at 2184delA) found in 2 samples caused by a sequencing error in a homopolymer stretch of sequence. The detection rate for variants of unknown significance was very low in the targeted region.
  
  
  CONCLUSIONS
  With continued optimization and system refinements, PGM sequencing promises to be a powerful, rapid, and scalable means of clinical diagnostic sequencing.
authors.affiliation: Department of Pathology, Geisel School of Medicine at Dartmouth, Hanover, NH, and Dartmouth-Hitchcock Medical Center and Norris Cotton Cancer Center, Lebanon, NH;
authors.forename: Ahmad N
authors.initials: AN
authors.lastname: Abou Tayoun
authors.forename: Christopher D
authors.initials: CD
authors.lastname: Tunkey
authors.forename: Trevor J
authors.initials: TJ
authors.lastname: Pugh
authors.forename: Tristen
authors.initials: T
authors.lastname: Ross
authors.forename: Minita
authors.initials: M
authors.lastname: Shah
authors.forename: Clarence C
authors.initials: CC
authors.lastname: Lee
authors.forename: Timothy T
authors.initials: TT
authors.lastname: Harkins
authors.forename: Wendy A
authors.initials: WA
authors.lastname: Wells
authors.forename: Laura J
authors.initials: LJ
authors.lastname: Tafe
authors.forename: Christopher I
authors.initials: CI
authors.lastname: Amos
authors.forename: Gregory J
authors.initials: GJ
authors.lastname: Tsongalis
mesh_terms: D002460:Cell Line; D019005:Cystic Fibrosis Transmembrane Conductance Regulator / Q000097:blood / Q000235:genetics*; D018628:Gene Dosage; D006801:Humans; D009154:Mutation; D016133:Polymerase Chain Reaction / Q000379:methods; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA
chemical_list: C505032:CFTR protein, human; D019005:Cystic Fibrosis Transmembrane Conductance Regulator