In PLOS Genetics, researchers from the University of Oxford, the University of Bath, and the Oxford-Suzhou Centre for Advanced Research search for the roots of campylobacteriosis foodborne illness in the genome of Campylobacter jejuni bacteria. With machine learning methods, the team analyzed almost 5,800 C. jejuni and C. coli isolates from infected humans, cattle, sheep, chickens, wildlife, and environmental sources, demonstrating that the genome-based method may boost source prediction compared to conventional multi-locus sequence typing methods. "This approach achieved improvement in accuracy of source attribution by 33 percent over existing methods that use only a subset of genes within the genome," the authors report, "and provided evidence for the relative contribution of different infection sources."
A University of California, San Diego-led team compares genetic factors involved in the risk of inherited retinal dystrophies [IRD] in individuals from Mexican, Pakistani, and European American populations for another PLOS Genetics paper. Using whole genome sequences from 409 individuals with IRD originating in more than 100 IRD-affected families from Mexico, Pakistan, and the US, the researchers narrowed in on causal IRD candidates in dozens of new or IRD-related genes in more than half of the families considered. "This study revealed a spectrum of mutations contributing to IRD in three populations, identifying a large proportion of novel, potentially causative variants that are specific to the corresponding population or not reported in [the gnomAD database]," they write, "and shed light on the genetic architecture of IRD in these diverse global populations."
In PLOS One, investigators at the Wuhan University of Science and Technology and elsewhere describe apparent ties between DYNC1I1 expression and survival in male patients with liver hepatocellular carcinoma. The team initially tracked down almost 1,100 differentially expressed genes by comparing messenger RNA profiles in 371 liver hepatocellular carcinoma tumors and 50 matched normal control samples, subsequently bringing in interaction, functional, and survival data to propose a prognostic role for DYNC1I1. "Abnormal signal pathways a vital role in the occurrence and development of [liver hepatocellular carcinoma] in male patients," the authors note. "We discover that DYNC1I1 can regulate the cell cycle and is related to some transmembrane transportation, which indicates that DYNC1I1 may not only affect the progress of [liver hepatocellular carcinoma] in male patients, but also affect[s] drug transportation."