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PreMSIm: An R package for predicting microsatellite instability from the expression profiling of a gene panel in cancer.

Abstract：

: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.

journal_name

Comput Struct Biotechnol J

journal_title

Computational and structural biotechnology journal

authors

Li L,Feng Q,Wang X

doi

10.1016/j.csbj.2020.03.007

subject

Has Abstract

pub_date

2020-03-19 00:00:00

pages

668-675

issn

2001-0370

pii

S2001-0370(19)30544-6

journal_volume

18

pub_type

杂志文章

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