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| Item Type: | Article |
|---|---|
| Title: | MEDICC2: whole-genome doubling aware copy-number phylogenies for cancer evolution |
| Creators: |
Kaufmann, T.L.  ORCID: https://orcid.org/0000-0003-4374-1338, Petkovic, M. ORCID: https://orcid.org/0000-0003-2875-216X, Watkins, T.B.K. ORCID: https://orcid.org/0000-0001-7414-737X, Colliver, E.C. ORCID: https://orcid.org/0000-0002-1497-0740, Laskina, S., Thapa, N., Minussi, D.C. ORCID: https://orcid.org/0000-0001-8856-4625, Navin, N. ORCID: https://orcid.org/0000-0002-2106-8624, Swanton, C. ORCID: https://orcid.org/0000-0002-4299-3018, Van Loo, P. ORCID: https://orcid.org/0000-0003-0292-1949, Haase, K. ORCID: https://orcid.org/0000-0002-0944-5618, Tarabichi, M. ORCID: https://orcid.org/0000-0002-1635-2348 and Schwarz, R.F. ORCID: https://orcid.org/0000-0001-9155-4268
|
| Abstract: | Aneuploidy, chromosomal instability, somatic copy-number alterations, and whole-genome doubling (WGD) play key roles in cancer evolution and provide information for the complex task of phylogenetic inference. We present MEDICC2, a method for inferring evolutionary trees and WGD using haplotype-specific somatic copy-number alterations from single-cell or bulk data. MEDICC2 eschews simplifications such as the infinite sites assumption, allowing multiple mutations and parallel evolution, and does not treat adjacent loci as independent, allowing overlapping copy-number events. Using simulations and multiple data types from 2780 tumors, we use MEDICC2 to demonstrate accurate inference of phylogenies, clonal and subclonal WGD, and ancestral copy-number states. |
| Keywords: | Somatic Copy-Number Alterations, Chromosomal Instability, Aneuploidy, Whole-Genome Doubling, Intratumor Heterogeneity, Cancer Evolution, Phylogenetic, Reconstruction, Single-Cell Sequencing |
| Source: | Genome Biology |
| ISSN: | 1474-760X |
| Publisher: | BMC |
| Volume: | 23 |
| Number: | 1 |
| Page Range: | 241 |
| Date: | 14 November 2022 |
| Official Publication: | https://doi.org/10.1186/s13059-022-02794-9 |
| PubMed: | View item in PubMed |
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