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This Week in PLOS: Mar 18, 2019

In PLOS Genetics, researchers from the US and Canada describe a computational strategy for improving gene set analysis testing in genome-wide association studies. The team's "Generalized Berk-Jones" (GBJ) statistic-based tests "that possess both rigorous statistical motivation and excellent performance in application," the authors say, to replace prior methods that include ad hoc steps or other potential confounders. The investigators applied the approach to data from previous breast cancer, height, and schizophrenia GWAS to demonstrate the GBJ approach could increase the power for finding suspicious genes. They note that "pathways significantly associated with human height are much more likely to contain signals spread throughout an entire gene set," for example, "while pathways associated with breast cancer are more likely to see their signals localized to a few genes."

A team from Spain present findings from an analysis of circulating blood microRNAs in individuals with or without obstructive sleep apnea for a PLOS One study. Starting with Taqman array-based miRNA profiles in blood plasma samples from 30 individuals with obstructive sleep apnea and 10 individuals without, the researchers searched for potential miRNA markers for the common upper airway condition, narrowing in on eight candidate endogenous control miRNA markers that were subsequently validated in another 40 obstructive sleep apnea cases and 20 unaffected controls. "The results of this study identified a set of miRNAs that could be used as [endogenous controls] for standard normalization of miRNA profiling in [obstructive sleep apnea]," the authors say.

Researchers from the National Institutes of Health, the Simons Foundation, and elsewhere report on expression patterns at a chromosome 22 region linked to the neurodevelopmental, intellectual disability, and language delay condition Phelan-McDermid syndrome for another PLOS One paper. Using RNA sequence data on post-mortem brain samples on 41 donors ranging from eight weeks post-conception to 40 years into adulthood, the team tracked expression dynamics for dozens of genes at 22q13.3, a region previously implicated in the rare genetic condition. "This work begins to show how the PMS region is involved in normal neurodevelopment, and specifically how dynamic temporal and spatial expression profiles may hint at gene function and mechanisms of disease," the authors conclude, and "may be used to guide future functional studies."