TY - JOUR T1 - Constructing founder sets under allelic and non-allelic homologous recombination JF - bioRxiv DO - 10.1101/2022.05.27.493721 SP - 2022.05.27.493721 AU - Konstantinn Bonnet AU - Tobias Marschall AU - Daniel Doerr Y1 - 2022/01/01 UR - http://biorxiv.org/content/early/2022/08/01/2022.05.27.493721.abstract N2 - 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.Competing Interest StatementThis work was supported in part by the National Institutes of Health grant 1U01HG010973 to T.M., by the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 956229, and by the BMBF-funded de.NBI Cloud within the German Network for Bioinformatics Infrastructure (de.NBI) (031A532B, 031A533A, 031A533B, 031A534A, 031A535A, 031A537A, 031A537B, 031A537C, 031A537D, 031A538A). ER -