In PLOS Genetics, researchers from the University of California, Los Angeles, and the University of North Carolina at Chapel Hill outline a set of tools for uncovering far-flung regulatory variants, or distal expression quantitative trait loci, influencing traits or diseases through transcriptome-wide association studies (TWAS). The team's "multi-omic strategies for TWAS," or MOSTWAS, brings in germline genetic data to find gene expression-related features and biomarkers for teasing out gene-trait associations from TWAS — an approach the authors applied to simulated data and real data on brain tissue or breast tumor samples collected through the Religious Orders Study/Rush Memory and Aging Project and Cancer Genome Atlas effort, respectively. "MOSTWAS enables users to utilize rich reference multi-omic datasets for enhanced gene mapping to better understand the etiology of polygenic traits and diseases with more direct insight into functional follow-up studies," the authors conclude.
A German team takes a closer look at a chromosome 8 region that appears prone to gene amplification in muscle invasive forms of bladder cancer for a paper in PLOS One. With the help of in silico copy number alteration profiles and gene expression data from hundreds of bladder cancer patients profiled for TCGA, the researchers analyzed the amplification-prone 8q22.2 region, ultimately focusing in on a gene called OSR2 that appeared to be found at higher-than-usual levels in tumor samples from muscle invasive bladder cancer (MIBC) patients with poorer outcomes in the original cohort and in another set of tumors tested with RT-qPCR. "Overexpression of the 8q22.2 gene OSR2 predicted shortened [disease-free survival] … and decreased [overall survival]," the authors write, noting that "different levels of the 8q22.2 region are associated with manifestation of different clinical characteristics in MIBC."
For a paper in PLOS Pathogens, investigators in Egypt, the US, and the United Arab Emirates explore COVID-19 transmission patterns, prevalence, and more in hundreds of Egyptian households followed over several months, from April to October of last year. Using blood serum, nasal swab, and oropharyngeal swab samples, including sequential samples from individuals testing positive, the team tested for SARS-CoV-2 infections and blood serum neutralizing antibodies in individuals with respiratory symptoms from households in rural Egypt that were originally enrolled in an influenza surveillance study. Based on data for nearly 1,600 individuals from 290 households, the authors saw a SARS-CoV-2 incidence of 6.9 percent and 34.8 percent seroprevalence, with a secondary attack rate of almost 90 percent within households and neutralizing antibody production within 14 days, in most cases. Together, they say, the point to high rates of asymptomatic or relatively mild infection, along with widespread SARS-CoV-2 transmission within households.