Yuan, K. , Sakoparnig, T., Markowetz, F. and Beerenwinkel, N. (2015) BitPhylogeny: a probabilistic framework for reconstructing intra-tumor phylogenies. Genome Biology, 16(1), p. 36. (doi: 10.1186/s13059-015-0592-6) (PMID:25786108) (PMCID:PMC4359483)
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Abstract
Cancer has long been understood as a somatic evolutionary process, but many details of tumor progression remain elusive. Here, we present BitPhylogeny, 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 reconstructs tumor phylogenies from methylation patterns in colon cancer and from single-cell exomes in myeloproliferative neoplasm.
| Item Type: | Articles |
|---|---|
| Status: | Published |
| Refereed: | Yes |
| Glasgow Author(s) Enlighten ID: | Yuan, Dr Ke |
| Authors: | Yuan, K., Sakoparnig, T., Markowetz, F., and Beerenwinkel, N. |
| College/School: | College of Science and Engineering > School of Computing Science |
| Journal Name: | Genome Biology |
| Publisher: | BioMed Central |
| ISSN: | 1465-6906 |
| ISSN (Online): | 1474-760X |
| Published Online: | 13 February 2015 |
| Copyright Holders: | Copyright © 2015 Yuan et al. |
| First Published: | First published in Genome Biology 16:36 |
| Publisher Policy: | Reproduced under a creative commons license |
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