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VarStack: a web tool for data retrieval to interpret somatic variants in cancer
Database: The Journal of Biological Databases and Curation ( IF 3.4 ) Pub Date : 2020-11-28 , DOI: 10.1093/database/baaa092
Morgan Howard 1 , Bruce Kane 2 , Mary Lepry 2 , Paul Stey 3 , Ashok Ragavendran 3, 4 , Ece D Gamsiz Uzun 1, 5, 6
Affiliation  

Advances in tumor genome sequencing created an urgent need for bioinformatics tools to support the interpretation of the clinical significance of the variants detected. VarStack is a web tool which is a base to retrieve somatic variant data relating to cancer from existing databases. VarStack incorporates data from several publicly available databases and presents them with an easy-to-navigate user interface. It currently supports data from the Catalogue of Somatic Mutations in Cancer, gnomAD, cBioPortal, ClinVar, OncoKB, CiViC and UCSC Genome Browser. It retrieves the data from these databases and returns them back to the user in a fraction of the time it would take to manually navigate each site independently. Users submit a variant with a gene symbol, peptide change and coding sequence change. They may select a variety of tumor-specific studies in cBioPortal to search through in addition to their original query. The results from the databases are presented in tabs. Users can export the results as an Excel file. VarStack also has the batch search feature in which the user can submit a list of variants and download an Excel file with the data from the databases. With the batch search and data download options, users can easily incorporate VarStack into their workflow or tools. VarStack saves time by providing somatic variant information to the user from multiple databases in an easy-to-export and interpretable format. VarStack is freely available under https://varstack.brown.edu.

中文翻译:

VarStack:一种用于数据检索的网络工具,用于解释癌症中的体细胞变异

肿瘤基因组测序的进步迫切需要生物信息学工具来支持对检测到的变异的临床意义的解释。VarStack 是一个网络工具,它是从现有数据库中检索与癌症相关的体细胞变异数据的基础。VarStack 整合了来自多个公开可用数据库的数据,并以易于导航的用户界面呈现它们。它目前支持来自癌症体细胞突变目录、gnomAD、cBioPortal、ClinVar、OncoKB、CiViC 和 UCSC Genome Browser 的数据。它从这些数据库中检索数据并将它们返回给用户,而时间比手动独立导航每个站点所需的时间短。用户提交带有基因符号、肽段变化和编码序列变化的变体。除了原始查询之外,他们还可以在 cBioPortal 中选择各种肿瘤特异性研究进行搜索。来自数据库的结果显示在选项卡中。用户可以将结果导出为 Excel 文件。VarStack 还具有批量搜索功能,用户可以在其中提交变体列表并下载带有数据库数据的 Excel 文件。借助批量搜索和数据下载选项,用户可以轻松地将 VarStack 整合到他们的工作流程或工具中。VarStack 通过以易于导出和可解释的格式从多个数据库向用户提供体细胞变异信息来节省时间。VarStack 可在 https://varstack.brown.edu 下免费获得。用户可以将结果导出为 Excel 文件。VarStack 还具有批量搜索功能,用户可以在其中提交变体列表并下载带有数据库数据的 Excel 文件。借助批量搜索和数据下载选项,用户可以轻松地将 VarStack 整合到他们的工作流程或工具中。VarStack 通过以易于导出和可解释的格式从多个数据库向用户提供体细胞变异信息来节省时间。VarStack 可在 https://varstack.brown.edu 下免费获得。用户可以将结果导出为 Excel 文件。VarStack 还具有批量搜索功能,用户可以在其中提交变体列表并下载带有数据库数据的 Excel 文件。借助批量搜索和数据下载选项,用户可以轻松地将 VarStack 整合到他们的工作流程或工具中。VarStack 通过以易于导出和可解释的格式从多个数据库向用户提供体细胞变异信息来节省时间。VarStack 可在 https://varstack.brown.edu 下免费获得。VarStack 通过以易于导出和可解释的格式从多个数据库向用户提供体细胞变异信息来节省时间。VarStack 可在 https://varstack.brown.edu 下免费获得。VarStack 通过以易于导出和可解释的格式从多个数据库向用户提供体细胞变异信息来节省时间。VarStack 可在 https://varstack.brown.edu 下免费获得。
更新日期:2020-12-01
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