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CONET: copy number event tree model of evolutionary tumor history for single-cell data

Copy number alterations constitute important phenomena in tumor evolution. Whole genome single-cell sequencing gives insight into copy number profiles of individual cells, but is highly noisy. Here, we propose CONET, a probabilistic model for joint inference of the evolutionary tree on copy number e...

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Autores principales: Markowska, Magda, Cąkała, Tomasz, Miasojedow, BłaŻej, Aybey, Bogac, Juraeva, Dilafruz, Mazur, Johanna, Ross, Edith, Staub, Eike, Szczurek, Ewa
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9185904/
https://www.ncbi.nlm.nih.gov/pubmed/35681161
http://dx.doi.org/10.1186/s13059-022-02693-z
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author Markowska, Magda
Cąkała, Tomasz
Miasojedow, BłaŻej
Aybey, Bogac
Juraeva, Dilafruz
Mazur, Johanna
Ross, Edith
Staub, Eike
Szczurek, Ewa
author_facet Markowska, Magda
Cąkała, Tomasz
Miasojedow, BłaŻej
Aybey, Bogac
Juraeva, Dilafruz
Mazur, Johanna
Ross, Edith
Staub, Eike
Szczurek, Ewa
author_sort Markowska, Magda
collection PubMed
description Copy number alterations constitute important phenomena in tumor evolution. Whole genome single-cell sequencing gives insight into copy number profiles of individual cells, but is highly noisy. Here, we propose CONET, a probabilistic model for joint inference of the evolutionary tree on copy number events and copy number calling. CONET employs an efficient, regularized MCMC procedure to search the space of possible model structures and parameters. We introduce a range of model priors and penalties for efficient regularization. CONET reveals copy number evolution in two breast cancer samples, and outperforms other methods in tree reconstruction, breakpoint identification and copy number calling. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at (10.1186/s13059-022-02693-z).
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spelling pubmed-91859042022-06-11 CONET: copy number event tree model of evolutionary tumor history for single-cell data Markowska, Magda Cąkała, Tomasz Miasojedow, BłaŻej Aybey, Bogac Juraeva, Dilafruz Mazur, Johanna Ross, Edith Staub, Eike Szczurek, Ewa Genome Biol Method Copy number alterations constitute important phenomena in tumor evolution. Whole genome single-cell sequencing gives insight into copy number profiles of individual cells, but is highly noisy. Here, we propose CONET, a probabilistic model for joint inference of the evolutionary tree on copy number events and copy number calling. CONET employs an efficient, regularized MCMC procedure to search the space of possible model structures and parameters. We introduce a range of model priors and penalties for efficient regularization. CONET reveals copy number evolution in two breast cancer samples, and outperforms other methods in tree reconstruction, breakpoint identification and copy number calling. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at (10.1186/s13059-022-02693-z). BioMed Central 2022-06-09 /pmc/articles/PMC9185904/ /pubmed/35681161 http://dx.doi.org/10.1186/s13059-022-02693-z Text en © The Author(s) 2022 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
Markowska, Magda
Cąkała, Tomasz
Miasojedow, BłaŻej
Aybey, Bogac
Juraeva, Dilafruz
Mazur, Johanna
Ross, Edith
Staub, Eike
Szczurek, Ewa
CONET: copy number event tree model of evolutionary tumor history for single-cell data
title CONET: copy number event tree model of evolutionary tumor history for single-cell data
title_full CONET: copy number event tree model of evolutionary tumor history for single-cell data
title_fullStr CONET: copy number event tree model of evolutionary tumor history for single-cell data
title_full_unstemmed CONET: copy number event tree model of evolutionary tumor history for single-cell data
title_short CONET: copy number event tree model of evolutionary tumor history for single-cell data
title_sort conet: copy number event tree model of evolutionary tumor history for single-cell data
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9185904/
https://www.ncbi.nlm.nih.gov/pubmed/35681161
http://dx.doi.org/10.1186/s13059-022-02693-z
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