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This Week in PLOS: Jan 28, 2019

In PLOS Genetics, researchers from the University of Chicago and Loyola University describe a statistical approach called MultiXcan for integrating expression quantitative trait locus (eQTL) and genome-wide association study insights across tissue types. The approach "tests the joint effects of gene expression variation from different tissues," the authors explain, while a related approach known as Summary-MultiXcan provides similar insights based on GWAS summary statistics. The team used MultiXcan to analyze more than 200 real and simulated complex traits in UK Biobank participants, along with 109 traits reported from prior GWAS, comparing it with other approaches for prioritizing genes with significant effects on such traits. 

For a PLOS Pathogens paper, a University of Queensland-led team presents results from a genome sequencing analysis of Schistosoma bovis, a parasitic flatworm known for causing schistosomiasis intestinal infections in cattle, sheep, goats, and humans in Africa and parts of the Middle East. Using DNA from S. bovis flukes grown in the lab with eggs from an infected Tanzanian cow liver, the researchers generated short- and long-read sequences that were assembled into a 374 million base genome containing an estimated 11,631 protein-coding genes. Comparing S. bovis genome to sequences from the human parasite S. haematobium, they saw that the two species contain 98 percent of the same genes and up to 100 percent sequence identity across some parts of the genome — similarities that may stem from inter-species hybridization between the parasites. 

Italian researchers reporting in PLOS One propose a 46-microRNA signature that appears to distinguish malignant from benign salivary gland tumors. The team used a Nanostring nCounter assay to profile the expression of 798 miRNAs in tumor samples from 14 individuals with low- or high-grade malignant and 10 individuals with benign salivary gland tumors. With the help of analyses of the pathways potentially affected by such miRNAs, the authors focused in on 46 miRNAs that were differentially expressed in the malignant and benign forms of the disease. Based on their findings, they suggest the signature "could improve diagnosis and allow better clinical decision-making with more appropriate treatment of [salivary gland tumors]."