An innovative single‐base extension method for synchronous detection of point mutations and MSI status in colorectal cancer
Abstract Background An accurate genotyping analysis is one of the critical prerequisites for patients with colorectal cancer receiving matched therapies. Conventional genotyping analysis is currently used to detect either gene mutations or MSI status, delaying the detection of critical tumor biomark...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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Wiley
2023-04-01
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| Series: | Cancer Medicine |
| Subjects: | |
| Online Access: | https://doi.org/10.1002/cam4.5557 |
| _version_ | 1797838388439547904 |
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| author | Li Liang Xin Li Lin Nong Weijing Cai Jixin Zhang Ping Liu Ting Li |
| author_facet | Li Liang Xin Li Lin Nong Weijing Cai Jixin Zhang Ping Liu Ting Li |
| author_sort | Li Liang |
| collection | DOAJ |
| description | Abstract Background An accurate genotyping analysis is one of the critical prerequisites for patients with colorectal cancer receiving matched therapies. Conventional genotyping analysis is currently used to detect either gene mutations or MSI status, delaying the detection of critical tumor biomarkers and thus the optimal time for treatment. An assay that analyzes both biomarkers in a streamlined process is eagerly needed. Methods We developed an assay combining Multiplex PCR Amplification, Single‐base Extension and capillary electrophoresis (CE) analysis (MASE‐CE) for synchronous detection of KRAS/NRAS/BRAF mutations and MSI status. In a 190 colorectal cancer cohort, we identified seven somatic mutations in KRAS, NRAS and BRAF as well as five MSI loci (D2S123/D5S346/D17S250/BAT‐25/BAT‐26) simultaneously. KRAS/NRAS/BRAF mutations were detected by NGS and MASE‐CE, and MSI status were detected by PCR‐CE and MASE‐CE methods. Results The MASE‐CE method showed high consistency with NGS for mutation detection (Kappa value ≥0.8) and PCR‐CE (Kappa value = 0.79). In addition, the limits of detection (LOD) of MASE‐CE assay for MSI and somatic mutation were 5% and 2%, respectively. Conclusions In somatic mutation detection and MSI detection, the LOD of MASE‐CE assay was superior to that of qPCR and NGS. MASE‐CE assay is a highly sensitive, time‐saving and specimen‐saving method, which can greatly avoid the cumbersome testing process and provide clinical decision for doctors in time. |
| first_indexed | 2024-04-09T15:41:02Z |
| format | Article |
| id | doaj.art-a371370838444350ab96e824c4e24165 |
| institution | Directory Open Access Journal |
| issn | 2045-7634 |
| language | English |
| last_indexed | 2024-04-09T15:41:02Z |
| publishDate | 2023-04-01 |
| publisher | Wiley |
| record_format | Article |
| series | Cancer Medicine |
| spelling | doaj.art-a371370838444350ab96e824c4e241652023-04-27T10:12:43ZengWileyCancer Medicine2045-76342023-04-011278367837710.1002/cam4.5557An innovative single‐base extension method for synchronous detection of point mutations and MSI status in colorectal cancerLi Liang0Xin Li1Lin Nong2Weijing Cai3Jixin Zhang4Ping Liu5Ting Li6Peking University First Hospital Beijing ChinaPeking University First Hospital Beijing ChinaPeking University First Hospital Beijing ChinaShanghai Tongshu Biotechnology Co., Ltd Shanghai ChinaPeking University First Hospital Beijing ChinaPeking University First Hospital Beijing ChinaPeking University First Hospital Beijing ChinaAbstract Background An accurate genotyping analysis is one of the critical prerequisites for patients with colorectal cancer receiving matched therapies. Conventional genotyping analysis is currently used to detect either gene mutations or MSI status, delaying the detection of critical tumor biomarkers and thus the optimal time for treatment. An assay that analyzes both biomarkers in a streamlined process is eagerly needed. Methods We developed an assay combining Multiplex PCR Amplification, Single‐base Extension and capillary electrophoresis (CE) analysis (MASE‐CE) for synchronous detection of KRAS/NRAS/BRAF mutations and MSI status. In a 190 colorectal cancer cohort, we identified seven somatic mutations in KRAS, NRAS and BRAF as well as five MSI loci (D2S123/D5S346/D17S250/BAT‐25/BAT‐26) simultaneously. KRAS/NRAS/BRAF mutations were detected by NGS and MASE‐CE, and MSI status were detected by PCR‐CE and MASE‐CE methods. Results The MASE‐CE method showed high consistency with NGS for mutation detection (Kappa value ≥0.8) and PCR‐CE (Kappa value = 0.79). In addition, the limits of detection (LOD) of MASE‐CE assay for MSI and somatic mutation were 5% and 2%, respectively. Conclusions In somatic mutation detection and MSI detection, the LOD of MASE‐CE assay was superior to that of qPCR and NGS. MASE‐CE assay is a highly sensitive, time‐saving and specimen‐saving method, which can greatly avoid the cumbersome testing process and provide clinical decision for doctors in time.https://doi.org/10.1002/cam4.5557colorectal cancerMASE‐CEMSIsingle‐base extensiontimesaver |
| spellingShingle | Li Liang Xin Li Lin Nong Weijing Cai Jixin Zhang Ping Liu Ting Li An innovative single‐base extension method for synchronous detection of point mutations and MSI status in colorectal cancer Cancer Medicine colorectal cancer MASE‐CE MSI single‐base extension timesaver |
| title | An innovative single‐base extension method for synchronous detection of point mutations and MSI status in colorectal cancer |
| title_full | An innovative single‐base extension method for synchronous detection of point mutations and MSI status in colorectal cancer |
| title_fullStr | An innovative single‐base extension method for synchronous detection of point mutations and MSI status in colorectal cancer |
| title_full_unstemmed | An innovative single‐base extension method for synchronous detection of point mutations and MSI status in colorectal cancer |
| title_short | An innovative single‐base extension method for synchronous detection of point mutations and MSI status in colorectal cancer |
| title_sort | innovative single base extension method for synchronous detection of point mutations and msi status in colorectal cancer |
| topic | colorectal cancer MASE‐CE MSI single‐base extension timesaver |
| url | https://doi.org/10.1002/cam4.5557 |
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