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MEDICC2: whole-genome doubling aware copy-number phylogenies for cancer evolution.
Kaufmann, Tom L; Petkovic, Marina; Watkins, Thomas B K; Colliver, Emma C; Laskina, Sofya; Thapa, Nisha; Minussi, Darlan C; Navin, Nicholas; Swanton, Charles; Van Loo, Peter; Haase, Kerstin; Tarabichi, Maxime; Schwarz, Roland F.
Afiliación
  • Kaufmann TL; Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, 13125, Berlin, Germany. tom.kaufmann@mdc-berlin.de.
  • Petkovic M; Department of Electrical Engineering & Computer Science, Technische Universität Berlin, Marchstr. 23, 10587, Berlin, Germany. tom.kaufmann@mdc-berlin.de.
  • Watkins TBK; BIFOLD, Berlin Institute for the Foundations of Learning and Data, Berlin, Germany. tom.kaufmann@mdc-berlin.de.
  • Colliver EC; Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, 13125, Berlin, Germany.
  • Laskina S; Department of Biology, Humboldt University of Berlin, Unter den Linden 6, 10099, Berlin, Germany.
  • Thapa N; Division of Oncology and Hematology, Department of Pediatrics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Augustenburger Platz 1, 13353, Berlin, Germany.
  • Minussi DC; The Francis Crick Institute, London, UK.
  • Navin N; The Francis Crick Institute, London, UK.
  • Swanton C; Department of Mathematics and Computer Science, Free University of Berlin, Berlin, Germany.
  • Van Loo P; UCL Medical School, University College London, London, UK.
  • Haase K; Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
  • Tarabichi M; Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
  • Schwarz RF; The Francis Crick Institute, London, UK.
Genome Biol ; 23(1): 241, 2022 11 14.
Article en En | MEDLINE | ID: mdl-36376909
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.
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Texto completo: 1 Colección: 01-internacional Banco de datos: MEDLINE Asunto principal: Neoplasias Límite: Humans Idioma: En Revista: Genome Biol Asunto de la revista: BIOLOGIA MOLECULAR / GENETICA Año: 2022 Tipo del documento: Article País de afiliación: Alemania
Texto completo
Imprimir
XML
PubMed Links
Buscar en Google

Texto completo: 1 Colección: 01-internacional Banco de datos: MEDLINE Asunto principal: Neoplasias Límite: Humans Idioma: En Revista: Genome Biol Asunto de la revista: BIOLOGIA MOLECULAR / GENETICA Año: 2022 Tipo del documento: Article País de afiliación: Alemania