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bioRxiv · 10.1101/2022.05.27.493721

Constructing founder sets under allelic and non-allelic homologous recombination

Bonnet, K.·Marschall, T.·Doerr, D.
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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.

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Bonnet, K., Marschall, T., Doerr, D.. 2022-05-29. Constructing founder sets under allelic and non-allelic homologous recombination. https://doi.org/10.1101/2022.05.27.493721

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