The complexity of genome rearrangement combinatorics under the infinite sites model

Christopher Greenman; Taoyang Wu; Luca Penso Dolfin

doi:10.1016/j.jtbi.2020.110335

The complexity of genome rearrangement combinatorics under the infinite sites model

Christopher Greenman (Lead Author), Taoyang Wu, Luca Penso Dolfin

Research output: Contribution to journal › Article › peer-review

3 Citations (Scopus)

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Abstract

Rearrangements are discrete processes whereby discrete segments of DNA are deleted, replicated and inserted into novel positions. A sequence of such configurations, termed a rearrangement evolution, results in jumbled DNA arrangements, frequently observed in cancer genomes. We introduce a method that allows us to precisely count these different evolutions for a range of processes including breakage-fusion-bridge-cycles, tandem-duplications, inverted-duplications, reversals, transpositions and deletions, showing that the space of rearrangement evolution is superexponential in size. These counts assume the infinite sites model of unique breakpoint usage.

Original language	English
Article number	110335
Number of pages	14
Journal	Journal of Theoretical Biology
Volume	501
Early online date	22 May 2020
DOIs	https://doi.org/10.1016/j.jtbi.2020.110335
Publication status	Published - 21 Sept 2020

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10.1016/j.jtbi.2020.110335

Manuscript3Accepted author manuscript, 1.91 MBLicence: CC BY-NC-ND

Christopher Greenman
- C.Greenmanuea.acuk
- School of Computing Sciences - Lecturer
- Centre for Photonics and Quantum Science - Member
- Computational Biology - Member
- Statistics - Member
Person: Research Group Member, Academic, Teaching and Research
Taoyang Wu
- Taoyang.Wuuea.acuk
- School of Computing Sciences - Associate Professor in Computing Sciences
- Centre for Ecology, Evolution and Conservation - Member
- Computational Biology - Member
- Data Science and AI - Member
Person: Research Group Member, Research Centre Member, Academic, Teaching and Research

Cite this

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abstract = "Rearrangements are discrete processes whereby discrete segments of DNA are deleted, replicated and inserted into novel positions. A sequence of such configurations, termed a rearrangement evolution, results in jumbled DNA arrangements, frequently observed in cancer genomes. We introduce a method that allows us to precisely count these different evolutions for a range of processes including breakage-fusion-bridge-cycles, tandem-duplications, inverted-duplications, reversals, transpositions and deletions, showing that the space of rearrangement evolution is superexponential in size. These counts assume the infinite sites model of unique breakpoint usage.",

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The complexity of genome rearrangement combinatorics under the infinite sites model

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Christopher Greenman

Taoyang Wu

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