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

Genome Biology

Bogac Aybey¹  Edith Ross¹  Eike Staub¹  Johanna Mazur¹  Dilafruz Juraeva¹  Magda Markowska²  Tomasz Cąkała²  Ewa Szczurek²  BłaŻej Miasojedow² 

[1] Merck Healthcare KGaA, Translational Medicine, Oncology Bioinformatics;University of Warsaw, Faculty of Mathematics, Informatics and Mechanics;

关键词: Copy number alterations;    Tumor evolution;    Single-cell sequencing;    Probabilistic model;    MCMC sampling;   

DOI  :  10.1186/s13059-022-02693-z

来源: DOAJ

【 摘 要 】

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.

【 授权许可】

Unknown