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This Week in PLOS: Dec 4, 2017

In PLOS Genetics, a Columbia University-led team takes a look at a case-control gene-based collapsing approach for uncovering de novo mutations involved in epileptic encephalopathy. Focusing on very rare variants in protein-coding genes from 488 individuals with epileptic encephalopathy and 12,151 without, the researchers narrowed in on so-called qualifying variants that appeared to have pronounced effects on epileptic encephalopathy. Such alterations were over-represented KCNT1, SCN2A, and STXBP1 — genes known to contribute to the condition. "Our collapsing analysis focused on ultra-rare, highly impactful variants ('qualifying variants') by filtering against large-scale population datasets," the authors explain, "and this approach revealed that most of the standing variation can be filtered out and [de novo mutations] are enriched in 'qualifying variants.'"

Researchers from India report on results from a genomic sequencing analysis of aromatic rice varieties for a paper in PLOS One. The team did whole-genome sequencing on a short-grain aromatic Oryza sativa cultivar known as Seeragasamba, analyzing the sequencing and comparing it with genomes for 76 more aromatic rice varieties. In particular, the analysis highlighted a version of the BADH2 gene that contained an eight base pair insertion in its promoter. That allele, dubbed badh2, was subsequently identified in more than a dozen other indica or japonica rice types. It also turned up in combination with a known BADH2 deletion in another 17 aromatic rice varieties. 

A Mayo Clinic and University of Minnesota team takes a look at the microbes associated with associated with breast cancer using RNA sequence reads generated for the Cancer Genome Atlas project. Using mapped and unmapped reads for 668 breast cancer samples and 72 corresponding, non-cancerous tissue samples, the team searched for microbial operational taxa units and host expression signals, uncovering a rise in Proteobacteria representation and a dip in Actinobacteria in tumor tissue. Other microbes tended to coincide with host expression features in the microenvironment or tumor. Consequently, the authors say, "further unraveling this complicated interplay should enable us to better diagnose and treat breast cancer patients."