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This Week in PLoS: Sep 26, 2011

This week, a trio of investigators at the University of Edinburgh reports in PLoS One its generation of thousand-member specific DNA oligonucleotide pools using selective hybridization to complementary DNA microarray "factories."

Over in PLoS Genetics, members of the IBC 50K CAD Consortium report their custom array-based investigation of 49,094 genetic variants in about 2,100 genes of reported cardiovascular relevance in 15,596 coronary artery disease cases and 34,992 controls. The team also describes its study of some perceived "potential mechanisms through which the novel variants could affect CAD [coronary artery disease] risk ... through association tests with vascular risk factors and gene expression." From that, the team reports having "found essentially null results for most previously suggested CAD candidate genes."

Researchers at Johns Hopkins University and at the University of California, Santa Cruz, present a "network of coevolving residues (possible functional interactions), in which nodes are mutant residue positions and links represent two positions found mutated together in the same sequence," for studies on β-lactamase evolution. "Focusing on extended-spectrum resistant sequences," the team sought to identify "triple mutant trajectories of likely special significance for adaptation," it writes, finding that the method "can identify triplets that increase resistance despite the underlying rugged fitness landscape and has the unique ability to make predictions by placing each mutant residue position in its functional context."

And in PLoS Biology, investigators at the University of Zürich and Trinity College Dublin report on their transcriptomic analysis of the Arapidopsis megaspore mother cell, which they say highlights the "important and RNA helicases for plant germline development." The megaspore mother cell, the team writes, "sets the stage for future functional characterization as illustrated by the identification of MEM, a novel gene involved in the restriction of germline fate."

The Scan

Drug Response Variants May Be Distinct in Somatic, Germline Samples

Based on variants from across 21 drug response genes, researchers in The Pharmacogenomics Journal suspect that tumor-only DNA sequences may miss drug response clues found in the germline.

Breast Cancer Risk Gene Candidates Found by Multi-Ancestry Low-Frequency Variant Analysis

Researchers narrowed in on new and known risk gene candidates with variant profiles for almost 83,500 individuals with breast cancer and 59,199 unaffected controls in Genome Medicine.

Health-Related Quality of Life Gets Boost After Microbiome-Based Treatment for Recurrent C. Diff

A secondary analysis of Phase 3 clinical trial data in JAMA Network Open suggests an investigational oral microbiome-based drug may lead to enhanced quality of life measures.

Study Follows Consequences of Early Confirmatory Trials for Accelerated Approval Indications

Time to traditional approval or withdrawal was shorter when confirmatory trials started prior to accelerated approval, though overall regulatory outcomes remained similar, a JAMA study finds.