Targeted Next-Generation Sequencing Effectively Analyzed the Cystic Fibrosis Transmembrane Conductance Regulator Gene in Pancreatitis

Eriko Nakano, Atsushi Masamune, Tetsuya Niihori, Kiyoshi Kume, Shin Hamada, Yoko Aoki, Yoichi Matsubara, Tooru Shimosegawa

Research output: Contribution to journalArticlepeer-review

12 Citations (Scopus)

Abstract

Background: The cystic fibrosis transmembrane conductance regulator (CFTR) gene, responsible for the development of cystic fibrosis, is known as a pancreatitis susceptibility gene. Direct DNA sequencing of PCR-amplified CFTR gene segments is a first-line method to detect unknown mutations, but it is a tedious and labor-intensive endeavor given the large size of the gene (27 exons, 1,480 amino acids). Next-generation sequencing (NGS) is becoming standardized, reducing the cost of DNA sequencing, and enabling the generation of millions of reads per run. We here report a comprehensive analysis of CFTR variants in Japanese patients with chronic pancreatitis using NGS coupling with target capture. Methods: Exon sequences of the CFTR gene from 193 patients with chronic pancreatitis (121 idiopathic, 46 alcoholic, 17 hereditary, and nine familial) were captured by HaloPlex target enrichment technology, followed by NGS. Results: The sequencing data covered 91.6 % of the coding regions of the CFTR gene by ≥20 reads with a mean read depth of 449. We could identify 12 non-synonymous variants including three novel ones [c.A1231G (p.K411E), c.1753G>T (p.E585X) and c.2869delC (p.L957fs)] and seven synonymous variants including three novel ones in the exonic regions. The frequencies of the c.4056G>C (p.Q1352H) and the c.3468G>T (p.L1156F) variants were higher in patients with chronic pancreatitis than those in controls. Conclusions: Target sequence capture combined with NGS is an effective method for the analysis of pancreatitis susceptibility genes.

Original languageEnglish
Pages (from-to)1297-1307
Number of pages11
JournalDigestive Diseases and Sciences
Volume60
Issue number5
DOIs
Publication statusPublished - 2015 May 1

Keywords

  • Chloride channel
  • HaloPlex
  • In silico analysis
  • MiSeq
  • Target enrichment

ASJC Scopus subject areas

  • Physiology
  • Gastroenterology

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