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This Week in PLOS: Jun 25, 2018

In PLOS Genetics, researchers from the University of Minnesota and elsewhere consider ties between gut microbiome shifts and mutational patterns in colorectal cancers. Using a combination of 16S ribosomal RNA sequencing-based gut microbiome profiling and whole-exome tumor-matched normal sequencing, the team searched for interactions between gut microbiome members and tumor genetics in 44 individuals with CRC. "We found statistically significant associations between loss-of-function mutations in tumor genes and shifts in the abundances of specific sets of bacterial taxa, suggestive of potential functional interaction," the team reports. Based on this observation, the authors were able to start predicting the presence of loss-of-function tumor mutations using insights from individuals' gut microbe composition.

A team from New Zealand, Japan, the UK, and Australia describe germline or somatic mutations in the transcriptional co-repressor-coding gene TRIM28 that appear to contribute to Wilms tumor development for another PLOS Genetics paper. The researchers performed exome sequencing on matched tumor and normal kidney tissue samples from 18 individuals with the childhood kidney cancer. In a male with Wilms tumor, for example, they saw a germline change to TRIM28 that coincided with loss-of-heterogeneity in the corresponding tumor — a blood-based alterations that was subsequently identified in the patient's affected sister and asymptomatic mother. Still other germline and/or somatic mutations turned up in TRIM28 as well, they report, including inactivating mutations, LOH, and/or epigenetic silencing.

A targeted panel sequencing approach uncovered known or suspected genetic susceptibilities to idiopathic or genetic generalized epilepsy syndromes in affected Koreans, according to research in PLOS One. Researchers from Korea narrowed in on 22 pathogenic or likely pathogenic variants in 16 genes implicated in epilepsy when they used multi-gene panel sequencing to search for risky genetic changes in 51 sporadic epilepsy cases and half a dozen members of epilepsy-affected families. Together, the alterations explained 16 of the 57 cases investigated, leading to 2.8 variants per person, on average, affecting several voltage-gated calcium channel and other genes. "[T]hese data suggest that common familial [genetic generalized epilepsy] syndromes are polygenic disorders with low penetrance and variable expressivity," the authors write.