BitPhylogeny: a probabilistic framework for reconstructing intra-tumor phylogenies.
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Authors
Yuan, Ke
Sakoparnig, Thomas
Markowetz, Florian https://orcid.org/0000-0002-2784-5308
Beerenwinkel, Niko
Abstract
Cancer has long been understood as a somatic evolutionary process, but many details of tumor progression remain elusive. Here, we present BitPhylogenyBitPhylogeny, a probabilistic framework to reconstruct intra-tumor evolutionary pathways. Using a full Bayesian approach, we jointly estimate the number and composition of clones in the sample as well as the most likely tree connecting them. We validate our approach in the controlled setting of a simulation study and compare it against several competing methods. In two case studies, we demonstrate how BitPhylogeny BitPhylogeny reconstructs tumor phylogenies from methylation patterns in colon cancer and from single-cell exomes in myeloproliferative neoplasm.
Description
Keywords
Bayes Theorem, Clonal Evolution, Colonic Neoplasms, DNA Methylation, Exome, Humans, Myeloproliferative Disorders, Phylogeny, Single-Cell Analysis
Journal Title
Genome Biol
Conference Name
Journal ISSN
1474-7596
1474-760X
1474-760X
Volume Title
16
Publisher
Springer Science and Business Media LLC
Publisher DOI
Sponsorship
Cancer Research UK (C14303/A17197)
Cancer Research UK (CB4320)
Cancer Research UK (CB4320)
KY and FM would like to acknowledge the support of the University of Cambridge, Cancer Research UK and Hutchison Whampoa Limited.