title: Targeted sequencing of cancer-related genes in colorectal cancer using next-generation sequencing.
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.
authors.affiliation: Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea.
authors.forename: Sae-Won
authors.initials: SW
authors.lastname: Han
authors.forename: Hwang-Phill
authors.initials: HP
authors.lastname: Kim
authors.forename: Jong-Yeon
authors.initials: JY
authors.lastname: Shin
authors.forename: Eun-Goo
authors.initials: EG
authors.lastname: Jeong
authors.forename: Won-Chul
authors.initials: WC
authors.lastname: Lee
authors.forename: Kyung-Hun
authors.initials: KH
authors.lastname: Lee
authors.forename: Jae-Kyung
authors.initials: JK
authors.lastname: Won
authors.forename: Tae-Yong
authors.initials: TY
authors.lastname: Kim
authors.forename: Do-Youn
authors.initials: DY
authors.lastname: Oh
authors.forename: Seock-Ah
authors.initials: SA
authors.lastname: Im
authors.forename: Yung-Jue
authors.initials: YJ
authors.lastname: Bang
authors.forename: Seung-Yong
authors.initials: SY
authors.lastname: Jeong
authors.forename: Kyu Joo
authors.initials: KJ
authors.lastname: Park
authors.forename: Jae-Gahb
authors.initials: JG
authors.lastname: Park
authors.forename: Gyeong Hoon
authors.initials: GH
authors.lastname: Kang
authors.forename: Jeong-Sun
authors.initials: JS
authors.lastname: Seo
authors.forename: Jong-Il
authors.initials: JI
authors.lastname: Kim
authors.forename: Tae-You
authors.initials: TY
authors.lastname: Kim
mesh_terms: D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D015179:Colorectal Neoplasms / Q000235:genetics* / Q000378:metabolism / Q000473:pathology; D056915:DNA Copy Number Variations; D005260:Female; D023281:Genomics; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D054643:INDEL Mutation; D008297:Male; D008875:Middle Aged; D009154:Mutation; D009367:Neoplasm Staging; D009857:Oncogenes; D020641:Polymorphism, Single Nucleotide; D015203:Reproducibility of Results; D015398:Signal Transduction