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.
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.
J Mol Diagn. 2018 Mar;20(2):225-231. doi: 10.1016/j.jmoldx.2017.11.007. Epub 2017 Dec 19.
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.
已经建立了两种类型的分子测试来评估 DNA 错配修复（MMR）系统的缺陷：微卫星不稳定性（MSI）和免疫组织化学（IHC）分析。我们已经开发了一种基于读长分布的可靠方法，通过下一代测序（NGS）来分析 MSI 状态。共招募了 91 名原发性结直肠癌患者。这些患者包括 54 例 IHC 中任何 MMR 蛋白表达缺失的病例，提示 MMR 缺陷（dMMR），以及 37 例 IHC 中所有 4 种 MMR 蛋白染色的结直肠癌病例，提示手术后样本中 MMR 功能正常。从配对的肿瘤-正常组织中提取 DNA，用于通过 ColonCore NGS 面板和 PCR 进行 MSI 检测。使用各种 MSI 检测管道处理 NGS 面板的测序数据，与 ColonCore 面板进行比较。使用 MSI-PCR 测试作为金标准，MSI-ColonCore 对 MSI 状态的检测具有 97.9%的灵敏度（48 例中的 47 例）和 100%的特异性（37 例中的 37 例）。与其他基于 NGS 的 MSI 检测算法相比，MSI-ColonCore 还显示出更高效和稳健的性能。MSI-ColonCore 与 IHC 检测之间的一致性率为 92.3%，MSI-PCR 与 IHC 检测之间的一致性率为 93.4%。这些结果表明，MSI-ColonCore 是一种基于读长分布的可靠且稳健的 NGS 方法，用于检测 MSI 状态。
