Introduction

Microsatellite instability (MSI) is an important indicator of larger genome instability and has been linked to many genetic diseases, including Lynch syndrome. MSI status is also an independent prognostic factor for favorable survival in multiple cancer types, such as colorectal and endometrial. It also informs the choice of chemotherapeutic agents. However, the current PCR-electrophoresis-based detection procedure is laborious and time-consuming, often requiring visual inspection to categorize samples. We developed MSIsensor, a C++ program for automatically detecting somatic microsatellite changes. It computes length distributions of microsatellites per site in paired tumor and normal sequence data, subsequently using these to statistically compare observed distributions in both samples. Comprehensive testing indicates MSIsensor is an efficient and effective tool for deriving MSI status from standard tumor-normal paired sequence data.https://github.com/ding-lab/msisensor

Publications

  1. MSIsensor: microsatellite instability detection using paired tumor-normal sequence data.
    Cite this
    Niu B, Ye K, Zhang Q, Lu C, Xie M, McLellan MD, Wendl MC, Ding L, 2014-04-01 - Bioinformatics (Oxford, England)

Credits

  1. Beifang Niu
    Developer

    Departments of Genetics and Mathematics, The Genome Institute, United States of America

  2. Kai Ye
    Developer

  3. Qunyuan Zhang
    Developer

  4. Charles Lu
    Developer

  5. Mingchao Xie
    Developer

  6. Michael D McLellan
    Developer

  7. Michael C Wendl
    Developer

  8. Li Ding
    Investigator

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Summary
AccessionBT003645
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC++
User InterfaceTerminal Command Line
Download Count0
Submitted ByLi Ding