The complexity of genome rearrangement combinatorics under the infinite sites model

•Combinations of rearrangement processes produce distinct jumbled DNA configurations.•Such processes are implicated in many diseases including cancer.•The reported methods allow the number of configurations to be precisely calculated for a range of processes in combination.•The number of configurati...

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Bibliographic Details
Published inJournal of theoretical biology Vol. 501; p. 110335
Main Authors Greenman, Chris D., Penso-Dolfin, Luca, Wu, Taoyang
Format Journal Article
LanguageEnglish
Published England Elsevier Ltd 21.09.2020
Subjects
Cancer
Combinatorics
Complexity
Rearrangements
Combinatorics
Rearrangements
Complexity
Cancer
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Summary:•Combinations of rearrangement processes produce distinct jumbled DNA configurations.•Such processes are implicated in many diseases including cancer.•The reported methods allow the number of configurations to be precisely calculated for a range of processes in combination.•The number of configurations grows at a super-exponential rate. 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 super-exponential in size. These counts assume the infinite sites model of unique breakpoint usage.
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ISSN:0022-5193
1095-8541
DOI:10.1016/j.jtbi.2020.110335