Validation of Customized Cancer Panel for Detecting Somatic Mutations and Copy Number Alterations
Accurate detection of genomic alterations, especially druggable hotspot mutations in tumors, has become an essential part of precision medicine. With targeted sequencing, we can obtain deeper coverage of reads and handle data more easily with a relatively lower cost and less time than whole-exome or...
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| Language: | English |
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BioMed Central
2017-12-01
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| Series: | Genomics & Informatics |
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| Online Access: | http://genominfo.org/upload/pdf/gi-2017-15-4-136.pdf |
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| author | Su-Hye Choi Seung-Hyun Jung Yeun-Jun Chung |
| author_facet | Su-Hye Choi Seung-Hyun Jung Yeun-Jun Chung |
| author_sort | Su-Hye Choi |
| collection | DOAJ |
| description | Accurate detection of genomic alterations, especially druggable hotspot mutations in tumors, has become an essential part of precision medicine. With targeted sequencing, we can obtain deeper coverage of reads and handle data more easily with a relatively lower cost and less time than whole-exome or whole-genome sequencing. Recently, we designed a customized gene panel for targeted sequencing of major solid cancers. In this study, we aimed to validate its performance. The cancer panel targets 95 cancer-related genes. In terms of the limit of detection, more than 86% of target mutations with a mutant allele frequency (MAF) <1% can be identified, and any mutation with >3% MAF can be detected. When we applied this system for the analysis of Acrometrix Oncology Hotspot Control DNA, which contains more than 500 COSMIC mutations across 53 genes, 99% of the expected mutations were robustly detected. We also confirmed the high reproducibility of the detection of mutations in multiple independent analyses. When we explored copy number alterations (CNAs), the expected CNAs were successfully detected, and this result was confirmed by target-specific genomic quantitative polymerase chain reaction. Taken together, these results support the reliability and accuracy of our cancer panel in detecting mutations. This panel could be useful for key mutation profiling research in solid tumors and clinical translation. |
| format | Article |
| id | doaj-art-36bfe7c33f4843afa024a155c2f1fc02 |
| institution | Kabale University |
| issn | 2234-0742 |
| language | English |
| publishDate | 2017-12-01 |
| publisher | BioMed Central |
| record_format | Article |
| series | Genomics & Informatics |
| spelling | doaj-art-36bfe7c33f4843afa024a155c2f1fc022025-02-02T15:50:44ZengBioMed CentralGenomics & Informatics2234-07422017-12-0115413614110.5808/GI.2017.15.4.136496Validation of Customized Cancer Panel for Detecting Somatic Mutations and Copy Number AlterationsSu-Hye Choi0Seung-Hyun Jung1Yeun-Jun Chung2 Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea Integrated Research Center for Genome Polymorphism, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul 06591, KoreaAccurate detection of genomic alterations, especially druggable hotspot mutations in tumors, has become an essential part of precision medicine. With targeted sequencing, we can obtain deeper coverage of reads and handle data more easily with a relatively lower cost and less time than whole-exome or whole-genome sequencing. Recently, we designed a customized gene panel for targeted sequencing of major solid cancers. In this study, we aimed to validate its performance. The cancer panel targets 95 cancer-related genes. In terms of the limit of detection, more than 86% of target mutations with a mutant allele frequency (MAF) <1% can be identified, and any mutation with >3% MAF can be detected. When we applied this system for the analysis of Acrometrix Oncology Hotspot Control DNA, which contains more than 500 COSMIC mutations across 53 genes, 99% of the expected mutations were robustly detected. We also confirmed the high reproducibility of the detection of mutations in multiple independent analyses. When we explored copy number alterations (CNAs), the expected CNAs were successfully detected, and this result was confirmed by target-specific genomic quantitative polymerase chain reaction. Taken together, these results support the reliability and accuracy of our cancer panel in detecting mutations. This panel could be useful for key mutation profiling research in solid tumors and clinical translation.http://genominfo.org/upload/pdf/gi-2017-15-4-136.pdfcancer panelhigh-throughput DNA sequencingnext-generation sequencingprecision medicine |
| spellingShingle | Su-Hye Choi Seung-Hyun Jung Yeun-Jun Chung Validation of Customized Cancer Panel for Detecting Somatic Mutations and Copy Number Alterations Genomics & Informatics cancer panel high-throughput DNA sequencing next-generation sequencing precision medicine |
| title | Validation of Customized Cancer Panel for Detecting Somatic Mutations and Copy Number Alterations |
| title_full | Validation of Customized Cancer Panel for Detecting Somatic Mutations and Copy Number Alterations |
| title_fullStr | Validation of Customized Cancer Panel for Detecting Somatic Mutations and Copy Number Alterations |
| title_full_unstemmed | Validation of Customized Cancer Panel for Detecting Somatic Mutations and Copy Number Alterations |
| title_short | Validation of Customized Cancer Panel for Detecting Somatic Mutations and Copy Number Alterations |
| title_sort | validation of customized cancer panel for detecting somatic mutations and copy number alterations |
| topic | cancer panel high-throughput DNA sequencing next-generation sequencing precision medicine |
| url | http://genominfo.org/upload/pdf/gi-2017-15-4-136.pdf |
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