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.
@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/entities/document/10.4230/LIPIcs.WABI.2022.6}, 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} }
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