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Markowska M, Cąkała T, Miasojedow B, Aybey B, Juraeva D, Mazur J, Ross E, Staub E, Szczurek E. CONET: copy number event tree model of evolutionary tumor history for single-cell data. Genome Biol 2022; 23:128. [PMID: 35681161 PMCID: PMC9185904 DOI: 10.1186/s13059-022-02693-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 05/23/2022] [Indexed: 11/10/2022] Open
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.
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Affiliation(s)
- Magda Markowska
- University of Warsaw, Faculty of Mathematics, Informatics and Mechanics, Banacha 2, Warsaw, Poland.,Medical University of Warsaw, Postgraduate School of Molecular Medicine, Ks. Trojdena 2a Street, Warsaw, Poland
| | - Tomasz Cąkała
- University of Warsaw, Faculty of Mathematics, Informatics and Mechanics, Banacha 2, Warsaw, Poland
| | - BłaŻej Miasojedow
- University of Warsaw, Faculty of Mathematics, Informatics and Mechanics, Banacha 2, Warsaw, Poland
| | - Bogac Aybey
- Merck Healthcare KGaA, Translational Medicine, Oncology Bioinformatics, Frankfurter Str. 250, Darmstadt, 64293, Germany
| | - Dilafruz Juraeva
- Merck Healthcare KGaA, Translational Medicine, Oncology Bioinformatics, Frankfurter Str. 250, Darmstadt, 64293, Germany
| | - Johanna Mazur
- Merck Healthcare KGaA, Translational Medicine, Oncology Bioinformatics, Frankfurter Str. 250, Darmstadt, 64293, Germany
| | - Edith Ross
- Merck Healthcare KGaA, Translational Medicine, Oncology Bioinformatics, Frankfurter Str. 250, Darmstadt, 64293, Germany
| | - Eike Staub
- Merck Healthcare KGaA, Translational Medicine, Oncology Bioinformatics, Frankfurter Str. 250, Darmstadt, 64293, Germany
| | - Ewa Szczurek
- University of Warsaw, Faculty of Mathematics, Informatics and Mechanics, Banacha 2, Warsaw, Poland.
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