Estimation of rearrangement phylogeny for cancer genomes

Greenman, Chris D., Pleasance, Erin D., Newman, Scott, Yang, Fengtang, Fu, Beiyuan, Nik-Zainal, Serena, Jones, David, Lau, King Wai, Carter, Nigel, Edwards, Paul A. W., Futreal, P. Andrew, Stratton, Michael R. and Campbell, Peter J. (2012) Estimation of rearrangement phylogeny for cancer genomes. Genome Research, 22 (2). pp. 346-361. ISSN 1088-9051

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Cancer genomes are complex, carrying thousands of somatic mutations including base substitutions, insertions and deletions, rearrangements, and copy number changes that have been acquired over decades. Recently, technologies have been introduced that allow generation of high-resolution, comprehensive catalogs of somatic alterations in cancer genomes. However, analyses of these data sets generally do not indicate the order in which mutations have occurred, or the resulting karyotype. Here, we introduce a mathematical framework that begins to address this problem. By using samples with accurate data sets, we can reconstruct relatively complex temporal sequences of rearrangements and provide an assembly of genomic segments into digital karyotypes. For cancer genes mutated in rearranged regions, this information can provide a chronological examination of the selective events that have taken place.

Item Type: Article
Uncontrolled Keywords: sdg 3 - good health and well-being ,/dk/atira/pure/sustainabledevelopmentgoals/good_health_and_well_being
Faculty \ School: Faculty of Science > School of Computing Sciences
Depositing User: Pure Connector
Date Deposited: 04 Jul 2014 12:39
Last Modified: 11 Oct 2022 23:51
DOI: 10.1101/gr.118414.110

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