Kaufmann, Tom L., Petkovic, Marina ORCID: 0000-0003-2875-216X, Watkins, Thomas B. K., Colliver, Emma C., Laskina, Sofya, Thapa, Nisha, Minussi, Darlan C., Navin, Nicholas, Swanton, Charles, Van Loo, Peter ORCID: 0000-0003-0292-1949, Haase, Kerstin, Tarabichi, Maxime ORCID: 0000-0002-1635-2348 and Schwarz, Roland F. (2022). MEDICC2: whole-genome doubling aware copy-number phylogenies for cancer evolution. Genome Biol., 23 (1). LONDON: BMC. ISSN 1474-760X

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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.

Item Type: Journal Article
Creators:
CreatorsEmailORCIDORCID Put Code
Kaufmann, Tom L.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Petkovic, MarinaUNSPECIFIEDorcid.org/0000-0003-2875-216XUNSPECIFIED
Watkins, Thomas B. K.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Colliver, Emma C.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Laskina, SofyaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Thapa, NishaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Minussi, Darlan C.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Navin, NicholasUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Swanton, CharlesUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Van Loo, PeterUNSPECIFIEDorcid.org/0000-0003-0292-1949UNSPECIFIED
Haase, KerstinUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Tarabichi, MaximeUNSPECIFIEDorcid.org/0000-0002-1635-2348UNSPECIFIED
Schwarz, Roland F.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
URN: urn:nbn:de:hbz:38-694235
DOI: 10.1186/s13059-022-02794-9
Journal or Publication Title: Genome Biol.
Volume: 23
Number: 1
Date: 2022
Publisher: BMC
Place of Publication: LONDON
ISSN: 1474-760X
Language: English
Faculty: Unspecified
Divisions: Unspecified
Subjects: no entry
Uncontrolled Keywords:
KeywordsLanguage
CHROMOSOMAL INSTABILITY; TUMOR HETEROGENEITY; NEAR-TETRAPLOIDY; RECONSTRUCTION; ANEUPLOIDY; PATTERNS; MUTATIONMultiple languages
Biotechnology & Applied Microbiology; Genetics & HeredityMultiple languages
URI: http://kups.ub.uni-koeln.de/id/eprint/69423

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