BitPhylogeny: A probabilistic framework for reconstructing intra-tumor phylogenies
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Yuan, K., Sakoparnig, T., Markowetz, F., & Beerenwinkel, N. (2015). BitPhylogeny: A probabilistic framework for reconstructing intra-tumor phylogenies. GENOME BIOLOGY, 16 https://doi.org/10.1186/s13059-015-0592-6
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.
KY and FM would like to acknowledge the support of the University of Cambridge, Cancer Research UK and Hutchison Whampoa Limited.
Cancer Research UK (C14303_do not transfer)
Cancer Research UK (CB4320)
External DOI: https://doi.org/10.1186/s13059-015-0592-6
This record's URL: https://www.repository.cam.ac.uk/handle/1810/247261
Attribution 2.0 UK: England & Wales
Licence URL: http://creativecommons.org/licenses/by/2.0/uk/
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