Targeted sequencing of cancer-related genes in colorectal cancer using next-generation sequencing.
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 perf...
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2013
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oai:doaj.org-article:9e2cb2b8ca8e4bc69b443a777961d5132021-11-18T07:45:06ZTargeted sequencing of cancer-related genes in colorectal cancer using next-generation sequencing.1932-620310.1371/journal.pone.0064271https://doaj.org/article/9e2cb2b8ca8e4bc69b443a777961d5132013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23700467/?tool=EBIhttps://doaj.org/toc/1932-6203Recent 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.Sae-Won HanHwang-Phill KimJong-Yeon ShinEun-Goo JeongWon-Chul LeeKyung-Hun LeeJae-Kyung WonTae-Yong KimDo-Youn OhSeock-Ah ImYung-Jue BangSeung-Yong JeongKyu Joo ParkJae-Gahb ParkGyeong Hoon KangJeong-Sun SeoJong-Il KimTae-You KimPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 5, p e64271 (2013) |
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EN |
| topic |
Medicine R Science Q |
| spellingShingle |
Medicine R Science Q Sae-Won Han Hwang-Phill Kim Jong-Yeon Shin Eun-Goo Jeong Won-Chul Lee Kyung-Hun Lee Jae-Kyung Won Tae-Yong Kim Do-Youn Oh Seock-Ah Im Yung-Jue Bang Seung-Yong Jeong Kyu Joo Park Jae-Gahb Park Gyeong Hoon Kang Jeong-Sun Seo Jong-Il Kim Tae-You Kim Targeted sequencing of cancer-related genes in colorectal cancer using next-generation sequencing. |
| description |
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. |
| format |
article |
| author |
Sae-Won Han Hwang-Phill Kim Jong-Yeon Shin Eun-Goo Jeong Won-Chul Lee Kyung-Hun Lee Jae-Kyung Won Tae-Yong Kim Do-Youn Oh Seock-Ah Im Yung-Jue Bang Seung-Yong Jeong Kyu Joo Park Jae-Gahb Park Gyeong Hoon Kang Jeong-Sun Seo Jong-Il Kim Tae-You Kim |
| author_facet |
Sae-Won Han Hwang-Phill Kim Jong-Yeon Shin Eun-Goo Jeong Won-Chul Lee Kyung-Hun Lee Jae-Kyung Won Tae-Yong Kim Do-Youn Oh Seock-Ah Im Yung-Jue Bang Seung-Yong Jeong Kyu Joo Park Jae-Gahb Park Gyeong Hoon Kang Jeong-Sun Seo Jong-Il Kim Tae-You Kim |
| author_sort |
Sae-Won Han |
| title |
Targeted sequencing of cancer-related genes in colorectal cancer using next-generation sequencing. |
| title_short |
Targeted sequencing of cancer-related genes in colorectal cancer using next-generation sequencing. |
| title_full |
Targeted sequencing of cancer-related genes in colorectal cancer using next-generation sequencing. |
| title_fullStr |
Targeted sequencing of cancer-related genes in colorectal cancer using next-generation sequencing. |
| title_full_unstemmed |
Targeted sequencing of cancer-related genes in colorectal cancer using next-generation sequencing. |
| title_sort |
targeted sequencing of cancer-related genes in colorectal cancer using next-generation sequencing. |
| publisher |
Public Library of Science (PLoS) |
| publishDate |
2013 |
| url |
https://doaj.org/article/9e2cb2b8ca8e4bc69b443a777961d513 |
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