De Sano Luca, Caravagna Giulio, Ramazzotti Daniele, Graudenzi Alex, Mauri Giancarlo, Mishra Bud, Antoniotti Marco
Department of Informatics, Systems and Communication, University of Milano-Bicocca.
Department of Informatics, Systems and Communication, University of Milano-Bicocca, School of Informatics, University of Edinburgh, Edinburgh, UK.
Bioinformatics. 2016 Jun 15;32(12):1911-3. doi: 10.1093/bioinformatics/btw035. Epub 2016 Feb 9.
We introduce TRanslational ONCOlogy (TRONCO), an open-source R package that implements the state-of-the-art algorithms for the inference of cancer progression models from (epi)genomic mutational profiles. TRONCO can be used to extract population-level models describing the trends of accumulation of alterations in a cohort of cross-sectional samples, e.g. retrieved from publicly available databases, and individual-level models that reveal the clonal evolutionary history in single cancer patients, when multiple samples, e.g. multiple biopsies or single-cell sequencing data, are available. The resulting models can provide key hints for uncovering the evolutionary trajectories of cancer, especially for precision medicine or personalized therapy.
TRONCO is released under the GPL license, is hosted at http://bimib.disco.unimib.it/ (Software section) and archived also at bioconductor.org.
Supplementary data are available at Bioinformatics online.
我们推出了转化肿瘤学(TRONCO),这是一个开源的R软件包,它实现了用于从(表观)基因组突变谱推断癌症进展模型的最新算法。TRONCO可用于提取描述横断面样本队列中改变积累趋势的群体水平模型,例如从公开可用数据库中检索到的样本,以及当有多个样本(例如多次活检或单细胞测序数据)时揭示单个癌症患者克隆进化历史的个体水平模型。所得模型可为揭示癌症的进化轨迹提供关键线索,特别是对于精准医学或个性化治疗。
TRONCO根据GPL许可发布,托管在http://bimib.disco.unimib.it/(软件部分),也存档于bioconductor.org。
补充数据可在《生物信息学》在线获取。