CoMutPlotter: a web tool for visual summary of mutations in cancer cohorts
CoMutPlotter: a web tool for visual summary of mutations in cancer cohorts
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DOI：
10.1186/s12920-019-0510-y
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发表时间：
2019-07-11
影响因子：
2.7
通讯作者：
Tsai, Pei-Chien
中科院分区：
文献类型：
--
作者：
Huang, Po-Jung;Lin, Hou-Hsien;Tsai, Pei-Chien
BackgroundCoMut 图广泛用于癌症研究出版物中，作为癌症队列中突变景观的可视化总结。该汇总图可以检查基因突变率和样本突变负担及其相关临床细节，这是分析样本间基因突变的复发和共现的常见第一步。 cBioPortal 和 iCoMut 是两个基于网络的工具，允许用户从预加载的 TCGA 和 ICGC 数据创建复杂的可视化。对于定制数据分析，目前仅提供有限的命令行包，这使得 CoMut 图的生成难以实现，特别是对于没有高级生物信息学技能的研究人员而言。为了满足自定义数据和 TCGA/ICGC 数据比较的需求，我们创建了 CoMutPlotter，这是一个基于网络的工具，用于以易于使用和自动的方式生成出版质量的图表。结果我们引入了一个名为 CoMutPlotter 的基于网络的工具，以降低复杂癌症基因组数据和研究人员之间的障碍，提供对来自 TCGA/ICGC 项目以及自定义队列研究的突变谱的直观访问。 CoMutPlotter 支持多种文件格式，可将癌症突变谱转化为生物学见解和临床应用，其中包括突变注释格式 (MAF)、制表符分隔值 (TSV) 和变体调用格式 (VCF) 文件。 结论 总之，CoMutPlotter 是同类中第一个支持 VCF 文件（最广泛使用的文件格式）作为其输入材料的工具。 CoMutPlotter 还提供了最需要的功能，用于比较自定义队列和 TCGA/ICGC 项目之间的突变模式。单个样本中 COSMIC 突变特征的贡献也包含在摘要图中，这是我们工具的独特功能。CoMutPlotter 可在 http://tardis.cgu.edu.tw/comutplotter 上免费获取。
BackgroundCoMut plot is widely used in cancer research publications as a visual summary of mutational landscapes in cancer cohorts. This summary plot can inspect gene mutation rate and sample mutation burden with their relevant clinical details, which is a common first step for analyzing the recurrence and co-occurrence of gene mutations across samples. The cBioPortal and iCoMut are two web-based tools that allow users to create intricate visualizations from pre-loaded TCGA and ICGC data. For custom data analysis, only limited command-line packages are available now, making the production of CoMut plots difficult to achieve, especially for researchers without advanced bioinformatics skills. To address the needs for custom data and TCGA/ICGC data comparison, we have created CoMutPlotter, a web-based tool for the production of publication-quality graphs in an easy-of-use and automatic manner.ResultsWe introduce a web-based tool named CoMutPlotter to lower the barriers between complex cancer genomic data and researchers, providing intuitive access to mutational profiles from TCGA/ICGC projects as well as custom cohort studies. A wide variety of file formats are supported by CoMutPlotter to translate cancer mutation profiles into biological insights and clinical applications, which include Mutation Annotation Format (MAF), Tab-separated values (TSV) and Variant Call Format (VCF) files.ConclusionsIn summary, CoMutPlotter is the first tool of its kind that supports VCF file, the most widely used file format, as its input material. CoMutPlotter also provides the most-wanted function for comparing mutation patterns between custom cohort and TCGA/ICGC project. Contributions of COSMIC mutational signatures in individual samples are also included in the summary plot, which is a unique feature of our tool.CoMutPlotter is freely available at http://tardis.cgu.edu.tw/comutplotter.