Year: 2023
Type: article
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 haplotypes correspond to walks through this graph. We formulate two founder set problems under our recombination model, provide flow-based algorithms for their solution, describe exact methods to characterize the number of recombinations, and demonstrate scalability to problem instances arising in practice.
Source: Algorithms for Molecular Biology
Institution: Heinrich Heine University Düsseldorf
Language: English
Subfield: Genetics
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $1,901
Funders: European Commission, Bundesministerium für Bildung und Forschung, Ministerium für Kultur und Wissenschaft des Landes Nordrhein-Westfalen, German Network for Bioinformatics Infrastructure, National Institutes of Health, Horizon 2020 Framework Programme, National Human Genome Research Institute
Awards: G1147967356, G1159569226, G1254183670, G1408866189, G1511448630, de.NBI - Etablierungsphase - Heidelberg Center for Human Bioinformatics - HD-HuB, G2082019117, de.NBI - Etablierungsphase - Leistungszentrum - BiGi - Bioinformatisches Resourcenzentrum für mikrobielle Genomforschung in Biotechnologie und Medizin, G2813928278, G434337789, G4459715584, de.NBI - Etablierungsphase - Leistungszentrum CiBi - Zentrum für integrative Bioinformatik, Representing structural haplotypes and complex genetic variation in pan-genome graphs, G5121333388, G5139259834, de.NBI - Etablierungsphase - Heidelberg Center for Human Bioinformatics - HD-HuB - Humane Genetik und Genomik, Humane Mikrobiomik, systematische Phänotypisierung humaner Zellen, G5576285491, de.NBI - Etablierungsphase - Leistungszentrum: RBC - RNA Bioinformatic, G586762481, de.NBI - Etablierungsphase - Heidelberg Center for Human Bioinformatics - HD-HuB - Humane Genetik und Genomik, Humane Metagenomik, systematische Phänotypisierung humaner Zellen, Epigenetik und de.NBI Cloud Standort Heidelberg/Berlin, G6253329826, de.NBI - Etablierungsphase - Leistungszentrum - BioInfra.Prot - Bioinformatik der Proteomik, ALgorithms for PAngenome Computational Analysis, de.NBI - Etablierungsphase - Koordinierungs- und Administrationseinheit - CAU - Geschäftsstelle, G838540276, de.NBI - Etablierungsphase - Leistungszentrum - BiGi - Bioinformatisches Resourcenzentrum für mikrobielle Genomforschung in Biotechnologie und Medizin, de.NBI - Etablierungsphase-European Molecular Biology Laboratory-HD-HUB
OpenAlex ID: W4387163927