PreMSIm: An R package for predicting microsatellite instability from the expression profiling of a gene panel in cancer
PreMSIm: An R package for predicting microsatellite instability from the expression profiling of a gene panel in cancer
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DOI：
10.1016/j.csbj.2020.03.007
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发表时间：
2020-01-01
影响因子：
6
通讯作者：
Wang, Xiaosheng
中科院分区：
文献类型：
--
作者：
Li, Lin;Feng, Qiushi;Wang, Xiaosheng
微卫星不稳定性（MSI）是DNA错配修复缺陷的癌症的基因组特征，是多种癌症类型诊断和治疗的有用标志。特别是，MSI与癌症中的主动免疫检查点阻断治疗反应相关。大多数预测MSI的计算方法是基于DNA测序数据，少数是基于mRNA表达数据。使用来自癌症基因组图谱（TCGA）计划的三个癌症队列（结肠癌、胃癌和子宫内膜癌）的RNA-Seq泛癌症数据集，我们开发了一种算法（PreMSIm），用于从癌症中15个基因组的表达谱预测MSI。我们证明了PreMSIm在大多数情况下使用RNA-Seq和微阵列基因表达数据集预测MSI时具有较高的预测性能。此外，与其他基于DNA或mRNA的方法相比，PreMSlim显示出更优越或相当的性能。上级。我们的结论是，PreMSIM有可能提供一种替代的方法来确定MSI的癌症。(C)2020年，任作家。由Elsevier B. V.代表计算和结构生物技术研究网络出版。
Microsatellite instability (MSI) is a genomic property of the cancers with defective DNA mismatch repair and is a useful marker for cancer diagnosis and treatment in diverse cancer types. In particular, MSI has been associated with the active immune checkpoint blockade therapy response in cancer. Most of computational methods for predicting MSI are based on DNA sequencing data and a few are based on mRNA expression data. Using the RNA-Seq pan-cancer datasets for three cancer cohorts (colon, gastric, and endometrial cancers) from The Cancer Genome Atlas (TCGA) program, we developed an algorithm (PreMSIm) for predicting MSI from the expression profiling of a 15-gene panel in cancer. We demonstrated that PreMSIm had high prediction performance in predicting MSI in most cases using both RNA-Seq and microarray gene expression datasets. Moreover, PreMSIm displayed superior or comparable performance versus other DNA or mRNA-based methods. We conclude that PreMSIm has the potential to provide an alternative approach for identifying MSI in cancer. (C) 2020 The Authors. Published by Elsevier B.V. on behalf of Research Network of Computational and Structural Biotechnology.