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BitPhylogeny: a probabilistic framework for reconstructing intra-tumor phylogenies.


Type

Article

Change log

Authors

Yuan, Ke 
Sakoparnig, Thomas 
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

Volume Title

16

Publisher

Springer Science and Business Media LLC
Sponsorship
Cancer Research UK (C14303/A17197)
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.