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

ABSTRACT: 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.

SUBMITTER: Markowska M

PROVIDER: S-EPMC9185904 | biostudies-literature | 2022 Jun

REPOSITORIES: biostudies-literature

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

Markowska Magda M Cąkała Tomasz T Miasojedow BłaŻej B Aybey Bogac B Juraeva Dilafruz D Mazur Johanna J Ross Edith E Staub Eike E Szczurek Ewa E

Genome biology 20220609 1

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 penaltie ...[more]

PMID: 35681161

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