Topological data analysis captures recombination from large genomic samples
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Population-based recombination maps capture the recombination history of populations using genomic data and are a valuable tool in the study of human recombination. We have developed fast statistical estimators of the recombination rate based on topological summaries. Compared to standard linkage-based estimators, topology-based estimators can deal with a larger number of segregating sites and genomes without incurring excessive computational costs. Applying these estimators to phased genotype data of 647 human individuals, we have produced high-resolution, genome-wide maps of human recombination, which have uncovered several novel associations. Specific transcription factor binding sites are frequently associated with recombination. These include binding sites of MLL complexes, which play prominent regulatory roles in germ cell development and early embryogenesis. Additionally, some repeat-derived loci, coding families of transposable elements that are expressed during embryogenesis, are also enriched for recombination.
“Topological Data Analysis Generates High-Resolution, Genome-wide Maps of Human Recombination”
AUTHORS: Pablo G. Camara, Daniel I.S. Rosenbloom, Kevin J. Emmett, Arnold J. Levine, Raul Rabadan.
LINK TO PUBLICATION:
Cell Systems 2016 June. doi: 10.1016/j.cels.2016.05.008.