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Genome Research Studies of WGS-Based mtDNA Profiles, MYC Overexpression, Inbred Scandinavian Wolves

Researchers at the Broad Institute and other centers in the US and Australia dig into mitochondrial DNA variation using whole-genome sequences collected in the Genome Aggregation Database (gnomAD). After developing a pipeline for calling mtDNA variants from the genome sequence data, the team tapped into sequence data for 56,434 individuals of European, African, Latino, or Asian ancestry in version 3.1 of gnomAD, identifying some 10,850 mtDNA variants, related mitochondrial haplotypes, and pathogenic mtDNA variants. "As the first large-scale mtDNA database built from WGS data via a publicly available pipeline, this study has provided both open-source tools and data that will support mtDNA analysis in addition to nuclear variants as part of clinical WGS testing," the authors conclude.

A team at Nanyang Technological University, the National University of Singapore, and the Agency for Science, Technology, and Research characterize the consequences of MYC oncogene overexpression in an osteosarcoma cell line. Using RNA sequencing, chromatin immunoprecipitation sequencing, 4C-seq, and a modified Hi-C chromatin interaction method called "spike-in quantitative Hi-C" (SIQHiC), the investigators tracked chromatin interaction and superenhancer changes in a cell line containing an inducible version of MYC. Along with enhanced MYC binding at superenhancer sites, the authors saw histone acetylation, chromatin contact, promoter-enhancer, and other shifts associated with MYC overexpression. "By elucidating the chromatin landscape of MYC driven cancers, we can potentially target MYC-associated chromatin interactions for cancer therapy," they write.

Finally, investigators in Sweden and Norway document genetic diversity losses in an inbred population of Scandinavian gray wolves. The team used whole-genome re-sequencing to assess 76 representative gray wolves sampled over three decades from a Scandinavian wolf population known to be founded by two males and a single female. "We obtained chromosome-level haplotypes of all three founders and found that [10 to 24 percent] of their diploid genomes had become lost after about 20 years of inbreeding (which approximately corresponds to five generations)," the authors report, noting that the work "provides a novel view of how whole-genome re-sequencing of temporarily stratified samples can be used to visualize and directly quantify the consequences of genetic drift in a small inbred population."

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