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This Week in PLOS: Sep 24, 2018

In PLOS Genetics, researchers from Denmark and the UK describe an archaic reference genome-free strategy for picking up archaic introgression in human genomes. By searching for stretches of sequence rife with SNPs that are missing from 'unadmixed outgroup' populations, the team says, the method successfully saw segments of archaic introgression in both simulated and real genome sequence data. Using genome sequences for dozens of Papuans, for example, the authors teased out Neanderthal and Denisovan sequences and used them to estimate archaic introgression times. In that population, they report, the analysis pointed to "more Denisovan admixture than previous studies and … a shift in size distribution of fragments of Neanderthal and Denisovan origin that is compatible with a difference in admixture time."

A team from Canada and the US track immune transcription features in individuals with acute hepatitis C virus (HCV) infections for a paper in PLOS Pathogens. Using RNA sequencing, the researchers assessed longitudinal peripheral blood mononuclear cells from 14 high-risk individuals before, during, and, in some cases, after HCV infection. The group included eight individuals who went on to have chronic HCV infection and half a dozen patients with spontaneous resolution of the virus. The findings "offer a detailed longitudinal description of immune function active during the spontaneous resolution of acute HCV infection," the authors write, "and provide insight into the early events that may contribute to viral clearance."

Researchers from the University of Glasgow and elsewhere explore potential ties between antidepressant treatment response and polygenic risk scores (PRS) previously linked to major depressive disorder (MDD) or neuroticism. The team's meta-analysis, appearing in PLOS One, included more than 700 individuals from three cohorts treated with selective serotonin reuptake inhibitor antidepressants such as citalopram or escitaopram. The authors saw intriguing directional effects, though they did not see significant associations between antidepressant response and the MDD PRS or the neuroticism PRS. Consequently, they suggest "the PRS approach may offer some promise for treatment stratification in MDD and should now be assessed within larger clinical cohorts."