title: Tree inference for single-cell data.
abstract: Understanding the mutational heterogeneity within tumors is a keystone for the development of efficient cancer therapies. Here, we present SCITE, a stochastic search algorithm to identify the evolutionary history of a tumor from noisy and incomplete mutation profiles of single cells. SCITE comprises a flexible Markov chain Monte Carlo sampling scheme that allows the user to compute the maximum-likelihood mutation history, to sample from the posterior probability distribution, and to estimate the error rates of the underlying sequencing experiments. Evaluation on real cancer data and on simulation studies shows the scalability of SCITE to present-day single-cell sequencing data and improved reconstruction accuracy compared to existing approaches.
authors.affiliation: Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.|SIB, Swiss Institute of Bioinformatics, Basel, Switzerland.
authors.forename: Katharina
authors.initials: K
authors.lastname: Jahn
authors.affiliation: Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.|SIB, Swiss Institute of Bioinformatics, Basel, Switzerland.
authors.forename: Jack
authors.initials: J
authors.lastname: Kuipers
authors.affiliation: Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland. niko.beerenwinkel@bsse.ethz.ch.|SIB, Swiss Institute of Bioinformatics, Basel, Switzerland. niko.beerenwinkel@bsse.ethz.ch.
authors.forename: Niko
authors.initials: N
authors.lastname: Beerenwinkel
mesh_terms: D060965:Clonal Evolution; D004273:DNA, Neoplasm / Q000737:chemistry / Q000235:genetics*; D018740:Genetic Heterogeneity; D006801:Humans; D009154:Mutation; D009369:Neoplasms / Q000235:genetics*; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA / Q000379:methods* / Q000592:standards; D059010:Single-Cell Analysis / Q000379:methods* / Q000592:standards; D012984:Software
chemical_list: D004273:DNA, Neoplasm