A Maximum Parsimony Principle for Multichromosomal Complex Genome Rearrangements

Pijus Simonaitis, Benjamin J. Raphael

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Motivation. Complex genome rearrangements, such as chromothripsis and chromoplexy, are common in cancer and have also been reported in individuals with various developmental and neurological disorders. These mutations are proposed to involve simultaneous breakage of the genome at many loci and rejoining of these breaks that produce highly rearranged genomes. Since genome sequencing measures only the novel adjacencies present at the time of sequencing, determining whether a collection of novel adjacencies resulted from a complex rearrangement is a complicated and ill-posed problem. Current heuristics for this problem often result in the inference of complex rearrangements that affect many chromosomes. Results. We introduce a model for complex rearrangements that builds upon the methods developed for analyzing simple genome rearrangements such as inversions and translocations. While nearly all of these existing methods use a maximum parsimony assumption of minimizing the number of rearrangements, we propose an alternative maximum parsimony principle based on minimizing the number of chromosomes involved in a rearrangement scenario. We show that our model leads to inference of more plausible sequences of rearrangements that better explain a complex congenital rearrangement in a human genome and chromothripsis events in 22 cancer genomes.

Original languageEnglish (US)
Title of host publication22nd International Workshop on Algorithms in Bioinformatics, WABI 2022
EditorsChristina Boucher, Sven Rahmann
PublisherSchloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing
ISBN (Electronic)9783959772433
DOIs
StatePublished - Sep 1 2022
Event22nd International Workshop on Algorithms in Bioinformatics, WABI 2022 - Potsdam, Germany
Duration: Sep 5 2022Sep 7 2022

Publication series

NameLeibniz International Proceedings in Informatics, LIPIcs
Volume242
ISSN (Print)1868-8969

Conference

Conference22nd International Workshop on Algorithms in Bioinformatics, WABI 2022
Country/TerritoryGermany
CityPotsdam
Period9/5/229/7/22

All Science Journal Classification (ASJC) codes

  • Software

Keywords

  • Genome rearrangements
  • affected chromosomes
  • cancer evolution
  • chromothripsis
  • maximum parsimony
  • structural variation

Fingerprint

Dive into the research topics of 'A Maximum Parsimony Principle for Multichromosomal Complex Genome Rearrangements'. Together they form a unique fingerprint.

Cite this