CNETML: maximum likelihood inference of phylogeny from copy number profiles of multiple samples

Phylogenetic trees based on copy number profiles from multiple samples of a patient are helpful to understand cancer evolution. Here, we develop a new maximum likelihood method, CNETML, to infer phylogenies from such data. CNETML is the first program to jointly infer the tree topology, node ages, an...

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Autores principales: Lu, Bingxin, Curtius, Kit, Graham, Trevor A., Yang, Ziheng, Barnes, Chris P.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2023
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10283241/
https://www.ncbi.nlm.nih.gov/pubmed/37340508
http://dx.doi.org/10.1186/s13059-023-02983-0
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author Lu, Bingxin
Curtius, Kit
Graham, Trevor A.
Yang, Ziheng
Barnes, Chris P.
author_facet Lu, Bingxin
Curtius, Kit
Graham, Trevor A.
Yang, Ziheng
Barnes, Chris P.
author_sort Lu, Bingxin
collection PubMed
description Phylogenetic trees based on copy number profiles from multiple samples of a patient are helpful to understand cancer evolution. Here, we develop a new maximum likelihood method, CNETML, to infer phylogenies from such data. CNETML is the first program to jointly infer the tree topology, node ages, and mutation rates from total copy numbers of longitudinal samples. Our extensive simulations suggest CNETML performs well on copy numbers relative to ploidy and under slight violation of model assumptions. The application of CNETML to real data generates results consistent with previous discoveries and provides novel early copy number events for further investigation. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-023-02983-0.
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spelling pubmed-102832412023-06-22 CNETML: maximum likelihood inference of phylogeny from copy number profiles of multiple samples Lu, Bingxin Curtius, Kit Graham, Trevor A. Yang, Ziheng Barnes, Chris P. Genome Biol Method Phylogenetic trees based on copy number profiles from multiple samples of a patient are helpful to understand cancer evolution. Here, we develop a new maximum likelihood method, CNETML, to infer phylogenies from such data. CNETML is the first program to jointly infer the tree topology, node ages, and mutation rates from total copy numbers of longitudinal samples. Our extensive simulations suggest CNETML performs well on copy numbers relative to ploidy and under slight violation of model assumptions. The application of CNETML to real data generates results consistent with previous discoveries and provides novel early copy number events for further investigation. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-023-02983-0. BioMed Central 2023-06-20 /pmc/articles/PMC10283241/ /pubmed/37340508 http://dx.doi.org/10.1186/s13059-023-02983-0 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Method
Lu, Bingxin
Curtius, Kit
Graham, Trevor A.
Yang, Ziheng
Barnes, Chris P.
CNETML: maximum likelihood inference of phylogeny from copy number profiles of multiple samples
title CNETML: maximum likelihood inference of phylogeny from copy number profiles of multiple samples
title_full CNETML: maximum likelihood inference of phylogeny from copy number profiles of multiple samples
title_fullStr CNETML: maximum likelihood inference of phylogeny from copy number profiles of multiple samples
title_full_unstemmed CNETML: maximum likelihood inference of phylogeny from copy number profiles of multiple samples
title_short CNETML: maximum likelihood inference of phylogeny from copy number profiles of multiple samples
title_sort cnetml: maximum likelihood inference of phylogeny from copy number profiles of multiple samples
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10283241/
https://www.ncbi.nlm.nih.gov/pubmed/37340508
http://dx.doi.org/10.1186/s13059-023-02983-0
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