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This Week in PLoS: May 18, 2009

In PLoS Computational Biology this week, scientists at UCSD have used a systems biology approach to identify a protein-binding network associated with adverse drug reactions to the CETP inhibitor, Torcetrapib, which can cause hypertension. Their "novel computational strategy" can be used to identify protein-ligand binding profiles on a genome-wide scale of cholesteryl ester transfer protein inhibitors, and their findings show that the side effects of CETP inhibitors are "modulated through the combinatorial control of multiple interconnected pathways."

Researchers looked at 11 yeast species to reconstruct the content and structure of the genome of an ancestral yeast that existed 100 million years ago. In going from this species to the current S. cerevisiae, they found 73 inversions, 66 reciprocal translocations, and five translocations involving telomeres. They also identified 124 relatively new genes and in some places, there seemed to be fragile sites in the genome that have been "broken repeatedly during evolution." Their paper was published in PLoS Genetics this week.

Also in PLoS Genetics, University of Oxford scientists have designed a method for simulating large genome-wide association samples that accounts for the complex correlations between SNPs due to linkage disequilibrium, they say in the author summary, and they used this method to compare the power of current genotyping chips. A main conclusion, they say, is that "differences in genome coverage may not translate into appreciable differences in power and that, when taking budgetary considerations into account, the most powerful design may not always correspond to the chip with the highest coverage."

In PLoS One this week, Tokyo Medical University researchers have found a possible strong candidate for a leukemia plasma biomarker. Using a miRNA microarray on the plasma of a leukemia patient, they found that miR-638 is stable in human plasmas and miR-92a is dramatically decreased in the plasmas of acute leukemia patients. Especially, the ratio of miR-92a to miR-638 in plasma was "very useful for distinguishing leukemia patients" from healthy people, they write.

The Scan

Study Finds Sorghum Genetic Loci Influencing Composition, Function of Human Gut Microbes

Focusing on microbes found in the human gut microbiome, researchers in Nature Communications identified 10 sorghum loci that appear to influence the microbial taxa or microbial metabolite features.

Treatment Costs May Not Coincide With R&D Investment, Study Suggests

Researchers in JAMA Network Open did not find an association between ultimate treatment costs and investments in a drug when they analyzed available data on 60 approved drugs.

Sleep-Related Variants Show Low Penetrance in Large Population Analysis

A limited number of variants had documented sleep effects in an investigation in PLOS Genetics of 10 genes with reported sleep ties in nearly 192,000 participants in four population studies.

Researchers Develop Polygenic Risk Scores for Dozens of Disease-Related Exposures

With genetic data from two large population cohorts and summary statistics from prior genome-wide association studies, researchers came up with 27 exposure polygenic risk scores in the American Journal of Human Genetics.