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J Mol Diagn. 2018 Mar;20(2):225-231. doi: 10.1016/j.jmoldx.2017.11.007. Epub 2017 Dec 19.

A Novel and Reliable Method to Detect Microsatellite Instability in Colorectal Cancer by Next-Generation Sequencing.

Author information

1
Department of Medical Oncology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China; Cancer Institute Key Laboratory of Cancer Prevention and Intervention, Chinese National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China.
2
Cancer Institute Key Laboratory of Cancer Prevention and Intervention, Chinese National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China.
3
Department of Bioinformatics, Burning Rock Biotech, Guangzhou, China.
4
Department of Research and Development, Burning Rock Biotech, Guangzhou, China.
5
Department of Pathology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China.
6
Department of Surgical Oncology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China.
7
Department of Medical Oncology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China; Cancer Institute Key Laboratory of Cancer Prevention and Intervention, Chinese National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China. Electronic address: yuanying1999@zju.edu.cn.

Abstract

Two types of molecular tests have been established to assess the deficiency of the DNA mismatch repair (MMR) system: microsatellite instability (MSI) and immunohistochemical (IHC) analysis. We have developed a reliable method to analyze the MSI status by next-generation sequencing (NGS) based on read-count distribution. A total of 91 patients with primary colorectal cancer were recruited. These patients included 54 cases with loss of expression of any MMR protein in IHC, suggesting deficient MMR (dMMR), and 37 cases of colorectal cancer with staining of all four MMR proteins in IHC, suggesting proficient MMR in the sample after surgery. DNA was extracted from paired tumor-normal tissue for MSI detection by both the ColonCore NGS panel and PCR. The sequencing data from the NGS panel was processed using various MSI detection pipelines for a comparison with the ColonCore panel. Using the MSI-PCR test as the gold standard, MSI-ColonCore achieved 97.9% sensitivity (47 of 48) and 100% specificity (37 of 37) for the detection of MSI status. MSI-ColonCore also showed more efficient and robust performance compared with other NGS-based MSI detection algorithms. The concordance rate was 92.3% between MSI-ColonCore and IHC testing, and 93.4% between MSI-PCR and IHC testing. These results suggest that MSI-ColonCore is a reliable and robust method for MSI status detection by NGS based on read-count distribution.

PMID:
29277635
DOI:
10.1016/j.jmoldx.2017.11.007
[Indexed for MEDLINE]

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