Targeted sequencing of cancer-related genes in colorectal cancer using next-generation sequencing

PLoS One. 2013 May 21;8(5):e64271. doi: 10.1371/journal.pone.0064271. Print 2013.

Abstract

Recent advance in sequencing technology has enabled comprehensive profiling of genetic alterations in cancer. We have established a targeted sequencing platform using next-generation sequencing (NGS) technology for clinical use, which can provide mutation and copy number variation data. NGS was performed with paired-end library enriched with exons of 183 cancer-related genes. Normal and tumor tissue pairs of 60 colorectal adenocarcinomas were used to test feasibility. Somatic mutation and copy number alteration were analyzed. A total of 526 somatic non-synonymous sequence variations were found in 113 genes. Among these, 278 single nucleotide variations were 232 different somatic point mutations. 216 SNV were 79 known single nucleotide polymorphisms in the dbSNP. 32 indels were 28 different indel mutations. Median number of mutated gene per tumor was 4 (range 0-23). Copy number gain (>X2 fold) was found in 65 genes in 40 patients, whereas copy number loss (<X0.5 fold) was found in 103 genes in 39 patients. The most frequently altered genes (mutation and/or copy number alteration) were APC in 35 patients (58%), TP53 in 34 (57%), and KRAS in 24 (40%). Altered gene list revealed ErbB signaling pathway as the most commonly involved pathway (25 patients, 42%). Targeted sequencing platform using NGS technology is feasible for clinical use and provides comprehensive genetic alteration data.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adult
  • Aged
  • Aged, 80 and over
  • Colorectal Neoplasms / genetics*
  • Colorectal Neoplasms / metabolism
  • Colorectal Neoplasms / pathology
  • DNA Copy Number Variations
  • Female
  • Genomics
  • High-Throughput Nucleotide Sequencing*
  • Humans
  • INDEL Mutation
  • Male
  • Middle Aged
  • Mutation
  • Neoplasm Staging
  • Oncogenes*
  • Polymorphism, Single Nucleotide
  • Reproducibility of Results
  • Signal Transduction

Grant support

This study was supported by a grant from the Korean Healthcare Technology R&D project, Ministry for Health, Welfare & Family Affairs, Republic of Korea (A091081). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.