IEEE/ACM Trans Comput Biol Bioinform. 2019 Mar-Apr;16(2):694-699. doi: 10.1109/TCBB.2018.2829698. Epub 2018 Apr 24.
Cancer is known for its heterogeneity and is regarded as an evolutionary process driven by somatic mutations and clonal expansions. This evolutionary process can be modeled by a phylogenetic tree and phylogenetic analysis of multiple subclones of cancer cells can facilitate the study of the tumor variants progression. Copy-number aberration occurs frequently in many types of tumors in terms of segmental amplifications and deletions. In this paper, we developed a distance-based method for reconstructing phylogenies from copy-number profiles of cancer cells. We demonstrate the importance of distance correction from the edit (minimum) distance to the estimated actual number of events. Experimental results show that our approaches provide accurate and scalable results in estimating the actual number of evolutionary events between copy number profiles and in reconstructing phylogenies.
癌症以其异质性而闻名，被认为是由体细胞突变和克隆扩张驱动的进化过程。这个进化过程可以用系统发育树来建模，对癌细胞的多个亚克隆进行系统发育分析可以促进肿瘤变异进展的研究。在许多类型的肿瘤中，拷贝数异常经常发生，表现为片段扩增和缺失。在本文中，我们开发了一种基于距离的方法，从癌细胞的拷贝数谱中重建系统发育树。我们证明了从编辑（最小）距离到估计的实际事件数的距离校正的重要性。实验结果表明，我们的方法在估计拷贝数谱之间的实际进化事件数量和重建系统发育树方面提供了准确和可扩展的结果。
