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.

微卫星不稳定性（MSI）是DNA错配修复缺陷的癌症的基因组特性，并且是多种癌症类型的癌症诊断和治疗的有用标记。特别是，MSI已与癌症中的主动免疫检查点封锁疗法反应相关。预测MSI的大多数计算方法都是基于DNA测序数据，而少数是基于mRNA表达数据。使用来自癌症基因组图谱（TCGA）程序的三个癌症队列（结肠癌，胃癌和子宫内膜癌）的RNA-Seq泛癌数据集，我们开发了一种算法（PreMSIm），可根据15-癌症中的基因组。我们证明，在大多数情况下，使用RNA-Seq和微阵列基因表达数据集，PreMSIm在预测MSI方面具有较高的预测性能。此外，PreMSIm显示出优于其他基于DNA或mRNA的方法的性能。我们得出的结论是，PreMSIm有潜力为鉴定癌症中的MSI提供另一种方法。