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This Week in Genome Research: Oct 15, 2014

A Singapore-led team used genome sequencing to look at population diversity and other patterns in the pathogen Burkholderia pseudomallei, which can cause an infectious condition called melioidosis. By sequencing 106 Asian isolates of B. pseudomallei that had been collected in clinics, from environmental sources, or from animal sources in Singapore and Malaysia, the researchers identified B. pseudomallei clades that tended to coincide with previously described multi-locus sequence types. The sequence data pointed to rampant recombination that's shuffling hundreds of regions from the pathogen's core genome, study authors say, though sequence swaps between different clades appeared relatively uncommon.

Age-related stochastic changes in methylation in cytosine- and guanine-rich parts of the genome may be largely reined in by both genetic and environmental factors, according to a study by investigators in Australia and the UK. The team used arrays to track genome-wide CpG methylation profiles in blood samples from 478 individuals enrolled in Scottish birth cohorts established in 1921 and 1936. With the help of data from a past Australian study examining the heritability of cytosine methylation in more than 100 families, the team saw signs that highly heritable sites tended to be immune to methylation changes over time, as were sex- and smoking-associated CpG sites.

Researchers from the University of California, Santa Cruz, and other sites around the world outline the rationale and results of a competition called the Alignathon, a multiple sequence alignment competition that centered on three datasets. The organizers received submissions from 10 teams who turned to various iterations of a dozen alignment pipelines to tackle the datasets: simulated primate and mammalian sequences and a third dataset comprised of 20 authentic Drosophila genomes. "We provide all datasets, submissions, and assessment programs for further study," authors of the paper note, "and provide, as a resource for future benchmarking, a convenient repository of code and data for reproducing the simulation assessments."

The Scan

RNA Editing in Octopuses Seems to Help Acclimation to Shifts in Water Temperature

A paper in Cell reports that octopuses use RNA editing to help them adjust to different water temperatures.

Topical Compound to Block EGFR Inhibitors May Ease Skin Toxicities, Study Finds

A topical treatment described in Science Translational Medicine may limit skin toxicities seen with EGFR inhibitor therapy.

Dozen Genetic Loci Linked to Preeclampsia Risk in New GWAS

An analysis of genome-wide association study data in JAMA Cardiology finds genetic loci linked to preeclampsia that have ties to blood pressure.

Cancer Survival Linked to Mutational Burden in Pan-Cancer Analysis

A pan-cancer paper appearing in JCO Precision Oncology suggests tumor mutation patterns provide clues for predicting cancer survival that are independent of other prognostic factors.