2026-07-23T04:54:15Z https://drops.dagstuhl.de/oai

oai:drops-oai.dagstuhl.de:17040 2024-03-06T10:58:35Z ddc:004 open_access

Constructing Founder Sets Under Allelic and Non-Allelic Homologous Recombination Bonnet, Konstantinn Marschall, Tobias Doerr¹, Daniel founder set reconstruction variation graph pangenomics NAHR homologous recombination 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. Schloss Dagstuhl – Leibniz-Zentrum für Informatik Konstantinn Bonnet and Tobias Marschall and Daniel Doerr¹ 2022 Is Part Of LIPIcs, Volume 242, 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022) InProceedings Text doc-type:ResearchArticle publishedVersion application/pdf doi:10.4230/LIPIcs.WABI.2022.6 urn:nbn:de:0030-drops-170403 https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2022.6 eng https://creativecommons.org/licenses/by/4.0/legalcode