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Genome Research Papers on De Novo Mutation Rates, Polyploid Genotyping, Oncogene Epigenomic Translocation

A team from Israel and Ghana measures de novo mutation rates in human hemoglobin subunit beta (HBB) and human hemoglobin subunit delta (HBD) gene region in sperm samples from individuals of African or European ancestry, including an HBB mutation site linked to both sickle cell anemia risk and malaria adaptation. "[W]e have developed a method that enables identifying and counting, with high accuracy, ultra-rare genetic variants of choice in extremely narrow regions of interest (ROIs) within large populations of cells, such as a single target mutant in 100 million genomes," the researchers explain, noting that their analyses pointed to enhanced mutation rates within a small adaptation- and disease-related stretch of the ROI in the HBB gene.

Researchers at the University of Oxford, University of Manchester, and University Medical Center Groningen assess several variant calling methods for genotyping small variants in the germlines of polyploid plants, including their own method called Octopus. Although genotyping errors frequently turned up when searching for small variants in synthetic or real tetraploid or hexaploidy genome sequences, the team noted that such errors were less common in samples profiled with Octopus, prompting additional benchmarking analyses on the autotriploid dwarf Cavendish banana. "Moving forward, there is clearly room for improvement in polyploid genotyping from sequencing," the authors note. "The creation of high-quality validation sets with real polyploid samples would be highly valuable in the development of polyploid-calling algorithms, including Octopus."

Investigators at Newcastle University and elsewhere explore the epigenomic effects of B-cell cancer-related super-enhancer rearrangements involving the immunoglobulin heavy locus (IGH) of B immune cells and the proto-oncogene CCND1. The team's chromatin and DNA breakpoint analyses of B cells from individuals with or without cancer-associated IGH-CCND1 translocations revealed H3K4me3 histone modifications that were typically present in healthy B cells but missing in the translocation-affected cells. In contrast, cells containing IGH-CCND1 translocations were marked by H3K4me3 modifications across CCND1 that appear to have arisen via epigenomic translocation. "Our analysis suggests that H3K4me3-[broad domains (BDs)] can be created by super-enhancers," they write, "and supports the new concept of epigenomic translocation, where the relocation of H3K4me3-BDs from cell identity genes to oncogenes accompanies the translocation of super-enhancers."