Reconstructing cancer phylogenies using Pairtree, a clone tree reconstruction algorithm
Ethan Kulman, Jeff Wintersinger, Quaid Morris
Abstract
Pairtree is a clone tree reconstruction algorithm that uses somatic point mutations to build clone trees describing the evolutionary history of individual cancers. Using the Pairtree software package, we describe steps to preprocess somatic mutation data, cluster mutations into subclones, search for clone trees, and visualize clone trees. Pairtree builds clone trees using up to 100 samples from a single cancer with at least 30 subclonal populations. For complete details on the use and execution of this protocol, please refer to Wintersinger et al. (2022).
Topics & Concepts
clone (Java method)Tree (set theory)BiologyMutationComputational biologyComputer scienceAlgorithmGeneticsGeneMathematicsCombinatoricsCancer Genomics and DiagnosticsGenetic factors in colorectal cancerGenomics and Phylogenetic Studies