Estimation of rearrangement phylogeny for cancer genomes

Chris D. Greenman, Erin D. Pleasance, Scott Newman, Fengtang Yang, Beiyuan Fu, Serena Nik-Zainal, David Jones, King Wai Lau, Nigel Carter, Paul A. W. Edwards, P. Andrew Futreal, Michael R. Stratton, Peter J. Campbell

Research output: Contribution to journalArticlepeer-review


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.
Original languageEnglish
Pages (from-to)346-361
Number of pages16
JournalGenome Research
Issue number2
Publication statusPublished - 1 Feb 2012

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