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PLOS Papers on Population Selection Detection, Canine Lymphoma, EBV-Associated Gastric Cancer

In PLOS Genetics, researchers from Pennsylvania State University and Florida Atlantic University present a computational tool known as "Sweep inference using regularized FDA [functional data analysis] with wavelets," or SURFDAWave, which is designed for modeling genetic diversity and using those patterns to pick up signs of selection. The method "translates measures of genetic diversity calculated in genomic windows to functional data," they write. "By transforming our discrete data points to be outputs of continuous functions defined over genomic space, we are able to learn the features of these functions that signify selection." In proof-of-principle analyses presented in the paper, the team applied SURFDAWave to human population data, uncovering known selective sweeps, along with signs of adaptive introgression in and around a potential skin color-related gene called BNC2 in European individuals.

For a paper in PLOS One, an Ontario Veterinary College team presents findings from a whole-genome sequencing-based analysis of canine lymphoma, focusing on samples from half a dozen chemotherapy-treated dogs with multicentric B-cell lymphoma. With the help of genome sequence data for paired tumor and normal mononuclear blood samples from the animals, the researchers searched for alterations that appeared to track with better or worse response to the treatment over time — a search that highlighted variants in a pair of genes with potential ties to good response and alterations in another seven genes that appeared to correspond with poorer treatment outcomes. "As knowledge continues to expand regarding [canine lymphoma] genetics, the goals are to improve the prognosis of affected dogs and to potentially apply findings to humans," the authors note, though they caution that the current [canine lymphoma] subtypes do not yet correspond directly with those used to classify [non-Hodgkin lymphoma] cases in humans.

Investigators at Ohio State University and the University of California, San Francisco, consider host expression and epigenetic responses to Epstein-Barr virus (EBV)-associated gastric cancers in a PLOS Pathogens paper. Using available RNA sequencing and array-based methylation profiles for gastric cancer tumors with or without EBV, the team picked up a subset of human genes that appear prone to excess DNA methylation and lower-than-usual expression in the EBV-positive gastric cancer cases, including immune-related genes with antiviral activity. "Collectively, our results demonstrated that epigenetic silencing of [immune-related genes] is a viral strategy to escape immune surveillance and promote viral propagation," they say, "which is overall beneficial to viral oncogenesis of human gamma-herpesviruses (EBV and [Kaposi's sarcoma-associated herpesvirus, another gamma-herpesvirus]), considering that these [immune-related genes] possess antiviral activities against these oncoviruses."