Computer Network Information Center, Chinese Academy of Sciences, Beijing 100190, China.
University of the Chinese Academy of Sciences, Beijing 100190, China.
Brief Bioinform. 2021 Sep 2;22(5). doi: 10.1093/bib/bbaa402.
Microsatellite instability (MSI) is a promising biomarker for cancer prognosis and chemosensitivity. Techniques are rapidly evolving for the detection of MSI from tumor-normal paired or tumor-only sequencing data. However, tumor tissues are often insufficient, unavailable, or otherwise difficult to procure. Increasing clinical evidence indicates the enormous potential of plasma circulating cell-free DNA (cfNDA) technology as a noninvasive MSI detection approach.
We developed MSIsensor-ct, a bioinformatics tool based on a machine learning protocol, dedicated to detecting MSI status using cfDNA sequencing data with a potential stable MSIscore threshold of 20%. Evaluation of MSIsensor-ct on independent testing datasets with various levels of circulating tumor DNA (ctDNA) and sequencing depth showed 100% accuracy within the limit of detection (LOD) of 0.05% ctDNA content. MSIsensor-ct requires only BAM files as input, rendering it user-friendly and readily integrated into next generation sequencing (NGS) analysis pipelines.
MSIsensor-ct is freely available at https://github.com/niu-lab/MSIsensor-ct.
Supplementary data are available at Briefings in Bioinformatics online.
微卫星不稳定性 (MSI) 是一种有前途的癌症预后和化疗敏感性生物标志物。从肿瘤-正常配对或仅肿瘤测序数据中检测 MSI 的技术正在迅速发展。然而，肿瘤组织通常不足、无法获得或难以获取。越来越多的临床证据表明，血浆循环无细胞 DNA (cfNDA) 技术作为一种非侵入性 MSI 检测方法具有巨大的潜力。
我们开发了 MSIsensor-ct，这是一种基于机器学习协议的生物信息学工具，专门用于使用 cfDNA 测序数据检测 MSI 状态，潜在的稳定 MSIscore 阈值为 20%。在具有不同循环肿瘤 DNA (ctDNA) 和测序深度的独立测试数据集上评估 MSIsensor-ct 表明，在检测限 (LOD) 为 0.05% ctDNA 含量的范围内，准确率为 100%。MSIsensor-ct 仅需要 BAM 文件作为输入，使其易于使用，并可轻松集成到下一代测序 (NGS) 分析管道中。
MSIsensor-ct 可在 https://github.com/niu-lab/MSIsensor-ct 上免费获得。
补充数据可在Briefings in Bioinformatics 在线获得。
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