MSIsensor：使用配对的肿瘤-正常序列数据进行微卫星不稳定性检测。
MSIsensor: microsatellite instability detection using paired tumor-normal sequence data.
机构信息
Departments of Genetics and Mathematics, The Genome Institute, Department of Genetics, Division of Statistical Genomics, Department of Medicine and Siteman Cancer Center, Washington University in St. Louis, MO 63108, USA.
出版信息
Bioinformatics. 2014 Apr 1;30(7):1015-6. doi: 10.1093/bioinformatics/btt755. Epub 2013 Dec 25.
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.
AVAILABILITY AND IMPLEMENTATION
动机
微卫星不稳定性（MSI）是基因组不稳定性的一个重要指标，与许多遗传疾病有关，包括林奇综合征。MSI 状态也是多种癌症（如结直肠癌和子宫内膜癌）有利生存的独立预后因素。它还可以指导化疗药物的选择。然而，目前基于 PCR-电泳的检测程序既繁琐又耗时，通常需要进行目视检查来对样本进行分类。我们开发了 MSIsensor，这是一个用于自动检测体细胞微卫星变化的 C++程序。它计算每个微卫星位点在配对肿瘤和正常序列数据中的长度分布，然后使用这些分布在两个样本中进行统计比较。综合测试表明，MSIsensor 是一种从标准肿瘤-正常配对序列数据中得出 MSI 状态的高效、有效的工具。
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