MSIsensor: microsatellite instability detection using paired tumor-normal sequence data

被引:613
作者
Niu, Beifang [1 ,2 ]
Ye, Kai [1 ,2 ,3 ]
Zhang, Qunyuan [1 ,2 ,3 ]
Lu, Charles [1 ,2 ]
Xie, Mingchao [1 ,2 ]
McLellan, Michael D. [1 ,2 ]
Wendl, Michael C. [1 ,2 ,3 ,4 ,5 ]
Ding, Li [1 ,2 ]
机构
[1] Washington Univ, Genome Inst, Dept Genet, St Louis, MO 63108 USA
[2] Washington Univ, Genome Inst, Dept Math, St Louis, MO 63108 USA
[3] Washington Univ, Div Stat Genom, Dept Genet, St Louis, MO 63108 USA
[4] Washington Univ, Dept Med, St Louis, MO 63108 USA
[5] Washington Univ, Siteman Canc Ctr, St Louis, MO 63108 USA
关键词
D O I
10.1093/bioinformatics/btt755
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
Motivation: 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.
引用
收藏
页码:1015 / 1016
页数:2
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