New Lung Cancer Panel for High-Throughput Targeted Resequencing
We present a new next-generation sequencing-based method to identify somatic mutations of lung cancer. It is a comprehensive mutation profiling protocol to detect somatic mutations in 30 genes found frequently in lung adenocarcinoma. The total length of the target regions is 107 kb, and a capture as...
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| Format: | Article |
| Language: | English |
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BioMed Central
2014-06-01
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| Series: | Genomics & Informatics |
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| Online Access: | http://genominfo.org/upload/pdf/gni-12-50.pdf |
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| _version_ | 1832569895459487744 |
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| author | Eun-Hye Kim Sunghoon Lee Jongsun Park Kyusang Lee Jong Bhak Byung Chul Kim |
| author_facet | Eun-Hye Kim Sunghoon Lee Jongsun Park Kyusang Lee Jong Bhak Byung Chul Kim |
| author_sort | Eun-Hye Kim |
| collection | DOAJ |
| description | We present a new next-generation sequencing-based method to identify somatic mutations of lung cancer. It is a comprehensive mutation profiling protocol to detect somatic mutations in 30 genes found frequently in lung adenocarcinoma. The total length of the target regions is 107 kb, and a capture assay was designed to cover 99% of it. This method exhibited about 97% mean coverage at 30× sequencing depth and 42% average specificity when sequencing of more than 3.25 Gb was carried out for the normal sample. We discovered 513 variations from targeted exome sequencing of lung cancer cells, which is 3.9-fold higher than in the normal sample. The variations in cancer cells included previously reported somatic mutations in the COSMIC database, such as variations in TP53, KRAS, and STK11 of sample H-23 and in EGFR of sample H-1650, especially with more than 1,000× coverage. Among the somatic mutations, up to 91% of single nucleotide polymorphisms from the two cancer samples were validated by DNA microarray-based genotyping. Our results demonstrated the feasibility of high-throughput mutation profiling with lung adenocarcinoma samples, and the profiling method can be used as a robust and effective protocol for somatic variant screening. |
| format | Article |
| id | doaj-art-c695a162973541a3b907936fb7f47b1f |
| institution | Kabale University |
| issn | 1598-866X 2234-0742 |
| language | English |
| publishDate | 2014-06-01 |
| publisher | BioMed Central |
| record_format | Article |
| series | Genomics & Informatics |
| spelling | doaj-art-c695a162973541a3b907936fb7f47b1f2025-02-02T19:10:19ZengBioMed CentralGenomics & Informatics1598-866X2234-07422014-06-01122505710.5808/GI.2014.12.2.50125New Lung Cancer Panel for High-Throughput Targeted ResequencingEun-Hye Kim0Sunghoon Lee1Jongsun Park2Kyusang Lee3Jong Bhak4Byung Chul Kim5Theragen Bio Institute, AICT, Suwon 443-270, Korea.Theragen Bio Institute, AICT, Suwon 443-270, Korea.Personal Genomics Institute, Genome Research Foundation, AICT, Suwon 443-270, Korea.Clinomics Inc., Seoul 138-961, Korea.Theragen Bio Institute, AICT, Suwon 443-270, Korea.Personal Genomics Institute, Genome Research Foundation, AICT, Suwon 443-270, Korea.We present a new next-generation sequencing-based method to identify somatic mutations of lung cancer. It is a comprehensive mutation profiling protocol to detect somatic mutations in 30 genes found frequently in lung adenocarcinoma. The total length of the target regions is 107 kb, and a capture assay was designed to cover 99% of it. This method exhibited about 97% mean coverage at 30× sequencing depth and 42% average specificity when sequencing of more than 3.25 Gb was carried out for the normal sample. We discovered 513 variations from targeted exome sequencing of lung cancer cells, which is 3.9-fold higher than in the normal sample. The variations in cancer cells included previously reported somatic mutations in the COSMIC database, such as variations in TP53, KRAS, and STK11 of sample H-23 and in EGFR of sample H-1650, especially with more than 1,000× coverage. Among the somatic mutations, up to 91% of single nucleotide polymorphisms from the two cancer samples were validated by DNA microarray-based genotyping. Our results demonstrated the feasibility of high-throughput mutation profiling with lung adenocarcinoma samples, and the profiling method can be used as a robust and effective protocol for somatic variant screening.http://genominfo.org/upload/pdf/gni-12-50.pdfhigh-throughput nucleotide sequencinglung neoplasmsnext-generation sequencingselector technologysomatic mutation screeningtarget enrichment |
| spellingShingle | Eun-Hye Kim Sunghoon Lee Jongsun Park Kyusang Lee Jong Bhak Byung Chul Kim New Lung Cancer Panel for High-Throughput Targeted Resequencing Genomics & Informatics high-throughput nucleotide sequencing lung neoplasms next-generation sequencing selector technology somatic mutation screening target enrichment |
| title | New Lung Cancer Panel for High-Throughput Targeted Resequencing |
| title_full | New Lung Cancer Panel for High-Throughput Targeted Resequencing |
| title_fullStr | New Lung Cancer Panel for High-Throughput Targeted Resequencing |
| title_full_unstemmed | New Lung Cancer Panel for High-Throughput Targeted Resequencing |
| title_short | New Lung Cancer Panel for High-Throughput Targeted Resequencing |
| title_sort | new lung cancer panel for high throughput targeted resequencing |
| topic | high-throughput nucleotide sequencing lung neoplasms next-generation sequencing selector technology somatic mutation screening target enrichment |
| url | http://genominfo.org/upload/pdf/gni-12-50.pdf |
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