In a study slated to appear in the early, online edition of the Proceedings of the National Academy of Sciences this week, researchers from Stanford and Yale Universities explore the extent to which somatic genetic variation occurs in tissues from the same individual. Using high-resolution array comparative genomic hybridization, the researchers tested for CNVs in multiple tissue types from six individuals, post-mortem. From analyses of three to 11 tissue types per person, the researchers saw signs that regularly dividing tissues — such as liver or pancreatic tissue — are more prone to somatic copy number shifts than those that undergo little to no division. "Our results have important consequences for understanding normal genetic and phenotypic variation within individuals," the study's authors say, "and they have significant implications for both the etiology of genetic diseases such as cancer and for immortalized cell lines that might be used in research and therapeutics."
Gene transfer patterns between microbes can provide a means of estimating the timing of microbial evolution, according to French and American researchers reporting in PNAS. They came up with a probabilistic model for studying genome evolution that takes into account lateral gene transfer, gene duplication, gene loss, and other events that lead to differences between gene family- and species-level phylogenies. After testing the method with genomic data representing bacteria and archaea from 10 phyla, the researchers went on use the same strategy to accurately order speciation events and determine phylogenetic relationships for cyanobacteria, using data from three-dozen cyanobacterial genomes. "Our results demonstrate that lateral gene transfers, detected by probabilistic models of genome evolution, can be used as a source of information on the timing of evolution," senior author Vincent Daubin, with the French National Center for Scientific Research, and his colleagues write, "providing a valuable complement to the limited prokaryotic fossil record."
An international team led by investigators at the University of Cologne and the University of California, San Francisco, describe its efforts to uncover genomic features in small cell lung cancer that could potentially serve as new treatment targets. For the study, also set to appear online in PNAS, the team screened dozens of small cell lung cancer lines for sensitivity to more than 250 compounds, looking at how copy number profiles in the lines corresponded to pharmacological activity. For instance, it reports, compounds that interfere with the Aurora B kinase seemed to staunch the growth of small cell lung cancer lines containing MYC amplifications, suggesting that these inhibitors could be useful against a subset of small cell lung cancer cases.