Phylogenetic Tree Inference: A Top-Down Approach to Track Tumor Evolution

doi:10.3389/fgene.2019.01371

	Phylogenetic Tree Inference: A Top-Down Approach to Track Tumor Evolution
	Wu, Pin1,2 ; Hou, Linjun1,2 ; Zhang, Yingdong3 ; Zhang, Liye1
	2020-02-07
发表期刊	FRONTIERS IN GENETICS (IF:2.8[JCR-2023],3.3[5-Year])
EISSN	1664-8021
卷号	10
发表状态	已发表
DOI	10.3389/fgene.2019.01371
摘要	Recently, an increasing number of studies sequence multiple biopsies of primary tumors, and even paired metastatic tumors to understand heterogeneity and the evolutionary trajectory of cancer progression. Although several algorithms are available to infer the phylogeny, most tools rely on accurate measurements of mutation allele frequencies from deep sequencing, which is often hard to achieve for clinical samples (especially FFPE samples). In this study, we present a novel and easy-to-use method, PTI (Phylogenetic Tree Inference), which use an iterative top-down approach to infer the phylogenetic tree structure of multiple tumor biopsies from same patient using just the presence or absence of somatic mutations without their allele frequencies. Therefore PTI can be used in a wide range of cases even when allele frequency data is not available. Comparison with existing state-of-the-art methods, such as LICHeE, Treeomics, and BAMSE, shows that PTI achieves similar or slightly better performance within a short run time. Moreover, this method is generally applicable to infer phylogeny for any other data sets (such as epigenetics) with a similar zero and one feature-by-sample matrix.
关键词	phylogenetics tumor evolution multi-region sequencing lineage tracing allele frequency
收录类别	SCI ; SCIE
语种	英语
资助项目	National Natural Science Foundation of China[NSF 31871332]
WOS研究方向	Genetics & Heredity
WOS类目	Genetics & Heredity
WOS记录号	WOS:000517289600001
出版者	FRONTIERS MEDIA SA
WOS关键词	CANCER ; HETEROGENEITY ; MUTATION ; ORIGINS
原始文献类型	Article
引用统计	正在获取...
文献类型	期刊论文
条目标识符	https://kms.shanghaitech.edu.cn/handle/2MSLDSTB/114841
专题	生命科学与技术学院_硕士生生命科学与技术学院_PI研究组_张力烨组图书信息中心
通讯作者	Zhang, Liye
作者单位	1.ShanghaiTech Univ, Sch Life Sci & Technol, Shanghai, Peoples R China 2.Univ Chinese Acad Sci, Beijing, Peoples R China 3.ShanghaiTech Univ, Lib & Informat Ctr, Shanghai, Peoples R China
第一作者单位	生命科学与技术学院
通讯作者单位	生命科学与技术学院
第一作者的第一单位	生命科学与技术学院
推荐引用方式 GB/T 7714	Wu, Pin,Hou, Linjun,Zhang, Yingdong,et al. Phylogenetic Tree Inference: A Top-Down Approach to Track Tumor Evolution[J]. FRONTIERS IN GENETICS,2020,10.
APA	Wu, Pin,Hou, Linjun,Zhang, Yingdong,&Zhang, Liye.(2020).Phylogenetic Tree Inference: A Top-Down Approach to Track Tumor Evolution.FRONTIERS IN GENETICS,10.
MLA	Wu, Pin,et al."Phylogenetic Tree Inference: A Top-Down Approach to Track Tumor Evolution".FRONTIERS IN GENETICS 10(2020).