title: The evolution of tumour phylogenetics: principles and practice.
abstract: Rapid advances in high-throughput sequencing and a growing realization of the importance of evolutionary theory to cancer genomics have led to a proliferation of phylogenetic studies of tumour progression. These studies have yielded not only new insights but also a plethora of experimental approaches, sometimes reaching conflicting or poorly supported conclusions. Here, we consider this body of work in light of the key computational principles underpinning phylogenetic inference, with the goal of providing practical guidance on the design and analysis of scientifically rigorous tumour phylogeny studies. We survey the range of methods and tools available to the researcher, their key applications, and the various unsolved problems, closing with a perspective on the prospects and broader implications of this field.
authors.affiliation: Department of Biological Sciences and Computational Biology Department, Carnegie Mellon University, Pittsburgh, Pennsylvania 15217, USA.
authors.forename: Russell
authors.initials: R
authors.lastname: Schwartz
authors.affiliation: Computational Biology Branch, National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland 20892, USA.
authors.forename: Alejandro A
authors.initials: AA
authors.lastname: Schäffer
mesh_terms: D000465:Algorithms; D000818:Animals; D005075:Biological Evolution; D023281:Genomics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D009369:Neoplasms / Q000235:genetics*; D010802:Phylogeny