MutationalPatterns2: The one stop shop for the analysis of mutational processes: DNA repair deletions

We developed MutationalPatterns2, a package for the analysis of mutational processes. To show how the package can be used to generate novel biological insights, we applied it on genome mutation data of cell lines in which we deleted specific DNA repair processes. We generated HPRT-only knockout lines as well as the combination of HPRT with MSH2, UNG and XPC. Whole genome sequencing was performed on generated clones and subclones. By subtracting variants present in the clones from those in the subclones, the somatic mutations, that accumulated in between the clonal steps, were determined.EGA study EGAS00001004789

我们开发了MutationalPatterns2——一款用于突变过程分析的专用工具包。为阐明该工具包在挖掘全新生物学发现方面的应用价值，我们将其应用于经特定DNA修复过程（DNA repair processes）敲除的细胞系基因组突变数据。本研究构建了仅敲除HPRT的细胞系，以及同时敲除HPRT与MSH2、UNG、XPC的细胞系组合。对所获得的克隆及亚克隆开展全基因组测序（whole genome sequencing）。通过将亚克隆中的变异与对应克隆的变异相减，我们得以确定克隆传代过程中累积的体细胞突变（somatic mutations）。本数据集关联EGA研究EGAS00001004789。