MSIsensor-RNA:Microsatellite Instability Detection for Bulk and Single-cell Gene Expression Data  

作　　者：Peng Jia Xuanhao Yang Xiaofei Yang Tingjie Wang Yu Xu Kai Ye 

机构地区：[1]Department of Gynecology and Obstetrics,Center for Mathematical Medical,The First Affiliated Hospital of Xi’an Jiaotong University,Xi’an 710061,China [2]MOE Key Lab for Intelligent Networks&Networks Security,Faculty of Electronic and Information Engineering,Xi’an Jiaotong University,Xi’an 710049,China [3]School of Automation Science and Engineering,Faculty of Electronic and Information Engineering,Xi’an Jiaotong University,Xi’an 710049,China [4]School of Computer Science and Technology,Faculty of Electronic and Information Engineering,Xi’an Jiaotong University,Xi’an 710049,China [5]Genome Institute,The First Affiliated Hospital of Xi’an Jiaotong University,Xi’an 710061,China [6]School of Life Science and Technology,Xi’an Jiaotong University,Xi’an 710049,China

出　　处：《Genomics, Proteomics & Bioinformatics》2024年第3期85-90,共6页基因组蛋白质组与生物信息学报（英文版）

基　　金：supported by the National Natural Science Foundation of China(Grant Nos.32070663,32125009,and 62172325);the National Key R&D Program of China(Grant No.2022YFC3400300);the Fundamental Research Funds for the Central Universities,China(Grant No.xzy012020012);the Natural Science Basic Research Program of Shaanxi,China(Grant No.2021GXLH-Z-098)to Kai Ye and Xaiofei Yang.

摘　　要：Microsatellite instability(MSI)is an indispensable biomarker in cancer immunotherapy.Currently,MSI scoring methods by high-throughput omics methods have gained popularity and demonstrated better performance than the gold standard method for MSI detection.However,the MSI detection method on expression data,especially single-cell expression data,is still lacking,limiting the scope of clinical application and prohibiting the investigation of MSI at a single-cell level.Herein,we developed MSIsensor-RNA,an accurate,robust,adaptable,and standalone software to detect MSI status based on expression values of MSI-associated genes.We demonstrated the favorable performance and promise of MSIsensor-RNA in both bulk and single-cell gene expression data in multiplatform technologies including RNA sequencing(RNA-seq),microarray,and single-cell RNA-seq.MSIsensor-RNA is a versatile,efficient,and robust method for MSI status detection from both bulk and single-cell gene expression data in clinical studies and applications.MSIsensor-RNA is available at https://github.com/xjtu-omics/msisensor-rna.

关 键 词：Microsatellite instability Gene expression Single-cell RNA-seq RNA-SEQ MICROARRAY 

分 类 号：Q811.4[生物学—生物工程]