MEDICC2: whole-genome doubling aware copy-number phylogenies for cancer evolution
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 haplot...
| Main Authors: | , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2022-11-01
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| Series: | Genome Biology |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s13059-022-02794-9 |
| _version_ | 1811309272871469056 |
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| author | Tom L. Kaufmann Marina Petkovic Thomas B. K. Watkins Emma C. Colliver Sofya Laskina Nisha Thapa Darlan C. Minussi Nicholas Navin Charles Swanton Peter Van Loo Kerstin Haase Maxime Tarabichi Roland F. Schwarz |
| author_facet | Tom L. Kaufmann Marina Petkovic Thomas B. K. Watkins Emma C. Colliver Sofya Laskina Nisha Thapa Darlan C. Minussi Nicholas Navin Charles Swanton Peter Van Loo Kerstin Haase Maxime Tarabichi Roland F. Schwarz |
| author_sort | Tom L. Kaufmann |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-13T09:38:19Z |
| format | Article |
| id | doaj.art-e4b330fa56874857bbfdc7ede9300d31 |
| institution | Directory Open Access Journal |
| issn | 1474-760X |
| language | English |
| last_indexed | 2024-04-13T09:38:19Z |
| publishDate | 2022-11-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Biology |
| spelling | doaj.art-e4b330fa56874857bbfdc7ede9300d312022-12-22T02:52:01ZengBMCGenome Biology1474-760X2022-11-0123112710.1186/s13059-022-02794-9MEDICC2: whole-genome doubling aware copy-number phylogenies for cancer evolutionTom L. Kaufmann0Marina Petkovic1Thomas B. K. Watkins2Emma C. Colliver3Sofya Laskina4Nisha Thapa5Darlan C. Minussi6Nicholas Navin7Charles Swanton8Peter Van Loo9Kerstin Haase10Maxime Tarabichi11Roland F. Schwarz12Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC)Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC)The Francis Crick InstituteThe Francis Crick InstituteDepartment of Mathematics and Computer Science, Free University of BerlinUCL Medical School, University College LondonDepartment of Genetics, The University of Texas MD Anderson Cancer CenterDepartment of Genetics, The University of Texas MD Anderson Cancer CenterThe Francis Crick InstituteThe Francis Crick InstituteDivision of Oncology and Hematology, Department of Pediatrics, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu BerlinThe Francis Crick InstituteBerlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC)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.https://doi.org/10.1186/s13059-022-02794-9Somatic copy-number alterationsChromosomal instabilityAneuploidyWhole-genome doublingIntratumor heterogeneityCancer evolution |
| spellingShingle | Tom L. Kaufmann Marina Petkovic Thomas B. K. Watkins Emma C. Colliver Sofya Laskina Nisha Thapa Darlan C. Minussi Nicholas Navin Charles Swanton Peter Van Loo Kerstin Haase Maxime Tarabichi Roland F. Schwarz MEDICC2: whole-genome doubling aware copy-number phylogenies for cancer evolution Genome Biology Somatic copy-number alterations Chromosomal instability Aneuploidy Whole-genome doubling Intratumor heterogeneity Cancer evolution |
| title | MEDICC2: whole-genome doubling aware copy-number phylogenies for cancer evolution |
| title_full | MEDICC2: whole-genome doubling aware copy-number phylogenies for cancer evolution |
| title_fullStr | MEDICC2: whole-genome doubling aware copy-number phylogenies for cancer evolution |
| title_full_unstemmed | MEDICC2: whole-genome doubling aware copy-number phylogenies for cancer evolution |
| title_short | MEDICC2: whole-genome doubling aware copy-number phylogenies for cancer evolution |
| title_sort | medicc2 whole genome doubling aware copy number phylogenies for cancer evolution |
| topic | Somatic copy-number alterations Chromosomal instability Aneuploidy Whole-genome doubling Intratumor heterogeneity Cancer evolution |
| url | https://doi.org/10.1186/s13059-022-02794-9 |
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