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Discovery of potential causative mutations in human coding and noncoding genome with the interactive software BasePlayer.
Nature Protocols ( IF 14.8 ) Pub Date : 2018-Nov-01 , DOI: 10.1038/s41596-018-0052-3
Riku Katainen , Iikki Donner , Tatiana Cajuso , Eevi Kaasinen , Kimmo Palin , Veli Mäkinen , Lauri A. Aaltonen , Esa Pitkänen

Next-generation sequencing (NGS) is routinely applied in life sciences and clinical practice, but interpretation of the massive quantities of genomic data produced has become a critical challenge. The genome-wide mutation analyses enabled by NGS have had a revolutionary impact in revealing the predisposing and driving DNA alterations behind a multitude of disorders. The workflow to identify causative mutations from NGS data, for example in cancer and rare diseases, commonly involves phases such as quality filtering, case-control comparison, genome annotation, and visual validation, which require multiple processing steps and usage of various tools and scripts. To this end, we have introduced an interactive and user-friendly multi-platform-compatible software, BasePlayer, which allows scientists, regardless of bioinformatics training, to carry out variant analysis in disease genetics settings. A genome-wide scan of regulatory regions for mutation clusters can be carried out with a desktop computer in ~10 min with a dataset of 3 million somatic variants in 200 whole-genome-sequenced (WGS) cancers.

中文翻译:

使用交互式软件BasePlayer发现人类编码和非编码基因组中潜在的致病突变。

下一代测序(NGS)通常在生命科学和临床实践中应用,但是对产生的大量基因组数据的解释已成为一项严峻的挑战。NGS支持的全基因组突变分析对揭示多种疾病背后的诱因和驱动DNA改变具有革命性的影响。从NGS数据中识别出致病突变的工作流程,例如在癌症和罕见病中,通常涉及多个阶段,例如质量过滤,病例对照比较,基因组注释和视觉验证,这需要多个处理步骤以及各种工具和脚本的使用。为此,我们推出了一种交互式且用户友好的多平台兼容软件BasePlayer,无论生物信息学培训如何,该软件都可以让科学家进行研究,在疾病遗传学环境中进行变异分析。可以使用台式计算机在大约10分钟内对200个全基因组测序(WGS)癌症中的300万个体细胞变异的数据集进行台式计算机,对突变簇的调节区域进行全基因组扫描。
更新日期:2018-10-16
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