https://scholars.lib.ntu.edu.tw/handle/123456789/594618
標題: | MutScape: An analytical toolkit for probing the mutational landscape in cancer genomics | 作者: | Lu C.-H. Wu C.-H. MONG-HSUN TSAI Liang-Chuan Lai ERIC YAO-YU CHUANG |
公開日期: | 2021 | 出版社: | Oxford University Press | 卷: | 3 | 期: | 4 | 起(迄)頁: | lqab099 | 來源出版物: | NAR Genomics and Bioinformatics | 摘要: | Cancer genomics has been evolving rapidly, fueled by the emergence of numerous studies and public databases through next-generation sequencing technologies. However, the downstream programs used to preprocess and analyze data on somatic mutations are scattered in different tools, most of which require specific input formats. Here, we developed a user-friendly Python toolkit, MutScape, which provides a comprehensive pipeline of filtering, combination, transformation, analysis and visualization for researchers, to easily explore the cohort-based mutational characterization for studying cancer genomics when obtaining somatic mutation data. MutScape not only can preprocess millions of mutation records in a few minutes, but also offers various analyses simultaneously, including driver gene detection, mutational signature, large-scale alteration identification and actionable biomarker annotation. Furthermore, MutScape supports somatic variant data in both variant call format and mutation annotation format, and leverages caller combination strategies to quickly eliminate false positives. With only two simple commands, robust results and publication-quality images are generated automatically. Herein, we demonstrate the ability of MutScape to correctly reproduce known results using breast cancer samples from The Cancer Genome Atlas. More significantly, discovery of novel results in cancer genomic studies is enabled through the advanced features in MutScape. MutScape is freely available on GitHub, at https://github.com/anitalu724/MutScape. © 2021 The Author(s) 2021. Published by Oxford University Press on behalf of NAR Genomics and Bioinformatics. |
URI: | https://www.scopus.com/inward/record.uri?eid=2-s2.0-85123225366&doi=10.1093%2fnargab%2flqab099&partnerID=40&md5=3b0c380df1e07feb0a24d458489b7ef2 https://scholars.lib.ntu.edu.tw/handle/123456789/594618 |
ISSN: | 26319268 | DOI: | 10.1093/nargab/lqab099 | SDG/關鍵字: | biological marker; Article; bioinformatics; breast cancer; chromosomal instability; data analysis; false positive result; genetic marker; genetic variation; homologous recombination; human; oncogenomics; open source software; somatic mutation |
顯示於: | 生理學科所 |
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