Microsatellite instability (MSI) is a key biomarker for cancer therapy and prognosis. Traditional experimental assays are laborious and time-consuming, and next-generation sequencing-based computational methods do not work on leukemia samples, paraffin-embedded samples, or patient-derived xenografts/organoids, due to the requirement of matched normal samples. Herein, we developed MSIsensor-pro, an open-source single sample MSI scoring method for research and clinical applications. MSIsensor-pro introduces a multinomial distribution model to quantify polymerase slippages for each tumor sample and a discriminative site selection method to enable MSI detection without matched normal samples. We demonstrate that MSIsensor-pro is an ultrafast, accurate, and robust MSI calling method. Using samples with various sequencing depths and tumor purities, MSIsensor-pro significantly outperformed the current leading methods in both accuracy and computational cost. MSIsensor-pro is available at https://github.com/xjtu-omics/msisensor-pro and free for non-commercial use, while a commercial license is provided upon request.
微卫星不稳定性（Microsatellite instability, MSI）是由恶性肿瘤DNA错配修复系统受损导致，在基因组微卫星区域发生超突变的一种分子表型，多发于结直肠癌、胃癌、和子宫内膜癌。MSI与肿瘤的发生、发展及预后密切相关，更是免疫治疗疗效预测的分子标记物。当前，临床上使用的两种MSI的金标准检测方法分别是MSI-PCR和MSI-IHC，但都费时费力且成本较高。近年来，随着高通量测序的发展，基于NGS的MSI检测方法开始显露头角，在检测结果与两种临床金标准保持高度一致的情况下，极大的缩减了检测时间并减少了检测成本，大幅提高了推广MSI检测的可行性。2014年，叶凯教授及其团队基于NGS开发的MSIsensor，作为全世界首个泛肿瘤检测方案MSK-IMPACT的MSI计算方法，通过了美国FDA的严格测试并获得批准。美国纪念斯隆凯特琳癌症中心（MSKCC）的测试表明，MSIsensor与金标准的一致性可达99.4%。然而，包括MSIsensor在内的基于NGS的MSI检测算法大都在低肿瘤纯度、低测序深度情况下表现较差。特别是，由于这些算法要求输入与肿瘤样本匹配的对照样本，限制了MSI的应用场景，尤其难以应用于血癌标本、福尔马林包埋标本、PDX/PDO等不易获得正常对照的样本。基于此，本研究综合MSI发生机理，采用多项分布描述基因组微卫星区域的复制过程，并对DNA聚合酶在该区域的滑动情况进行定量模拟。基于微卫星区域DNA聚合酶滑动的数学模型，叶凯团队于2019年成功开发了MSIsensor-pro，实现了对无正常对照样本的单个肿瘤样本进行MSI评估，解决了当前基于NGS的MSI检测工具所存在的技术难题。





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