License: Creative Commons Attribution 4.0 International license (CC BY 4.0)
When quoting this document, please refer to the following
DOI: 10.4230/LIPIcs.WABI.2022.6
URN: urn:nbn:de:0030-drops-170403
URL: http://dagstuhl.sunsite.rwth-aachen.de/volltexte/2022/17040/
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Bonnet, Konstantinn ; Marschall, Tobias ; Doerr¹, Daniel

Constructing Founder Sets Under Allelic and Non-Allelic Homologous Recombination

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Abstract

Homologous recombination between the maternal and paternal copies of a chromosome is a key mechanism for human inheritance and shapes population genetic properties of our species. However, a similar mechanism can also act between different copies of the same sequence, then called non-allelic homologous recombination (NAHR). This process can result in genomic rearrangements - including deletion, duplication, and inversion - and is underlying many genomic disorders. Despite its importance for genome evolution and disease, there is a lack of computational models to study genomic loci prone to NAHR.
In this work, we propose such a computational model, providing a unified framework for both (allelic) homologous recombination and NAHR. Our model represents a set of genomes as a graph, where human haplotypes correspond to walks through this graph. We formulate two founder set problems under our recombination model, provide flow-based algorithms for their solution, and demonstrate scalability to problem instances arising in practice.

BibTeX - Entry

@InProceedings{bonnet_et_al:LIPIcs.WABI.2022.6,
  author =	{Bonnet, Konstantinn and Marschall, Tobias and Doerr¹, Daniel},
  title =	{{Constructing Founder Sets Under Allelic and Non-Allelic Homologous Recombination}},
  booktitle =	{22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)},
  pages =	{6:1--6:23},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-243-3},
  ISSN =	{1868-8969},
  year =	{2022},
  volume =	{242},
  editor =	{Boucher, Christina and Rahmann, Sven},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/opus/volltexte/2022/17040},
  URN =		{urn:nbn:de:0030-drops-170403},
  doi =		{10.4230/LIPIcs.WABI.2022.6},
  annote =	{Keywords: founder set reconstruction, variation graph, pangenomics, NAHR, homologous recombination}
}

Keywords: founder set reconstruction, variation graph, pangenomics, NAHR, homologous recombination
Collection: 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)
Issue Date: 2022
Date of publication: 26.08.2022
Supplementary Material: Software (Source Code): https://github.com/marschall-lab/hrfs archived at: https://archive.softwareheritage.org/swh:1:dir:32151e14f3faef777e58b7e1af01942431deec26

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