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This Week in Genome Research: Oct 14, 2009

Using a technique called TraDIS, for transposon directed insertion-site sequencing, scientists at the Wellcome Trust Sanger Institute led work that mapped 370,000 unique transposon insertion sites to the Salmonella enterica serovar Typhi chromosome. The density and resolution -- "an average of one every 13 base pairs," they say -- has allowed them to assay genome-wide for "essential genes" and create a list of candidates.

Another abstract has an update on the Human Microbiome Project, including its history and implementation. This NIH program is attempting to characterize the human microbiome in five body sites from healthy volunteers and determine the relationship to disease. "The ultimate objective of the HMP," says author Jane Peterson, "is to create opportunities to improve human health through monitoring or manipulation of the human microbiome."

Scientists performed metagenomic analysis on organic matter collected from a moving vehicle's windshield to "design and test a comprehensive pipeline for phylogenetic profiling" of bugs, plants, and other living organisms. The work, says a related story at our sister publication, GenomeWeb Daily News, was done by Members of the Galaxy, a collaborative project funded by NSF, Pennsylvania State University, and the Huck Institutes of the Life Sciences.

Gonçalo Pereira of Unicamp in São Paulo, Brazil, is senior author on a paper that analyzed the genomes of a strain of Saccharomyces cerevisia that's widely used in the production of bioethanol, PE-2 derived diploid JAY270 and a haploid derivative, JAY291. The JAY270 genome has several chromosomal rearrangements, but these are only in peripheral regions of the chromosomes, with breakpoints within repetitive sequences. "This observation is consistent with a model in which the peripheral regions of chromosomes represent plastic domains of the genome that are free to recombine ectopically and experiment with alternative structures," they say.

The Scan

Study Finds Few FDA Post-Market Regulatory Actions Backed by Research, Public Assessments

A Yale University-led team examines in The BMJ safety signals from the US FDA Adverse Event Reporting System and whether they led to regulatory action.

Duke University Team Develops Programmable RNA Tool for Cell Editing

Researchers have developed an RNA-based editing tool that can target specific cells, as they describe in Nature.

Novel Gene Editing Approach for Treating Cystic Fibrosis

Researchers in Science Advances report on their development of a non-nuclease-based gene editing approach they hope to apply to treat cystic fibrosis.

Study Tracks Responses in Patients Pursuing Polygenic Risk Score Profiling

Using interviews, researchers in the European Journal of Human Genetics qualitatively assess individuals' motivations for, and experiences with, direct-to-consumer polygenic risk score testing.