title: Estimation of rearrangement phylogeny for cancer genomes.
abstract: 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.
authors: Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom. C.Greenman@uea.ac.uk
authors: Chris D
authors: CD
authors: Greenman
authors: Erin D
authors: ED
authors: Pleasance
authors: Scott
authors: S
authors: Newman
authors: Fengtang
authors: F
authors: Yang
authors: Beiyuan
authors: B
authors: Fu
authors: Serena
authors: S
authors: Nik-Zainal
authors: David
authors: D
authors: Jones
authors: King Wai
authors: KW
authors: Lau
authors: Nigel
authors: N
authors: Carter
authors: Paul A W
authors: PA
authors: Edwards
authors: P Andrew
authors: PA
authors: Futreal
authors: Michael R
authors: MR
authors: Stratton
authors: Peter J
authors: PJ
authors: Campbell
mesh_terms: D019295:Computational Biology / Q000379:methods; D056915:DNA Copy Number Variations; D019143:Evolution, Molecular; D015894:Genome, Human; D006801:Humans; D008957:Models, Genetic; D009154:Mutation; D009369:Neoplasms / Q000235:genetics*; D010802:Phylogeny; D014178:Translocation, Genetic