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This Week in PLOS: Nov 5, 2018

In PLOS Genetics, a Fred Hutchinson Cancer Research Center-led team shares a statistical approach for finding somatic mutation-based associations. In addition to taking uncertainty around somatic mutation calling into consideration, they say, the so-called "Somatic mutation association test with measurement errors," or SAME, approach reveals associations involving specific mutations or oft-mutated genes. When they applied SAME to data for a dozen cancer types profiled through the Cancer Genome Atlas Project, for example, the authors found that "some somatic mutations affect gene expression in several cancer types."

Researchers from the Feinstein Institute for Medical Research and the Donald and Barbara Zucker School of Medicine at Hofstra/Northwell report on findings from a cell population study of serous epithelial ovarian cancer in PLOS One. Using single-cell RNA sequencing, the team profiled 14 samples from nine individuals with high-grade, low-grade, or benign ovarian tumors, uncovering 16 malignant or benign cell types. Among them: a handful of main malignant cell types and specific sub-populations that appeared to coincide with serous ovarian cancer grade.

A team from the US Department of Agriculture's National Animal Disease Center document genomic and methylomic patterns in virulent and non-virulent serotypes of the bacterial species Haemophilus parasuis, a potential swine respiratory pathogen for another PLOS One paper. Along with their genome sequencing, annotation, and analyses of a virulent, "Nagasaki" strain of H. parasuis and the non-virulent D74 strain, the researchers profiled methylation patterns and compared potential virulence contributors in the bugs. "Our hope is that the assembly and annotation of these genomes, coupled with the comparative genomic analyses reported … will aid in the identification of genetic elements that underlie and influence phenotypic differences between the isolates," the authors explain, adding that such insights "can support future research and the development of vaccines with improved efficacy towards H.s parasuis in swine."