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This Week in PNAS: Dec 10, 2013

In the early, online edition of the Proceedings of the National Academy of Sciences, a team from China and the US describes the looping-based amplification and exome sequencing approaches it used to see recurrent copy number variations in individual tumor cells nabbed from the blood stream of individuals with lung cancer. Through exome sequencing on two dozen circulating tumor cells from four individuals with lung adenocarcinoma, the researchers uncovered CNVs that reliably turned up in matched metastatic tumors from the each individuals and, in some cases, in tumors from other patients with the same lung cancer subtype. "Our findings suggest that CNVs at certain genomic loci are selected for the metastasis of cancer," they write. "The reproducibility of cancer-specific CNVs offers potential for [circulating tumor cell]-based cancer diagnostics.

Adaptive evolution by epidemic strains of Pseudomonas aeruginosa that cause chronic infections in cystic fibrosis patients appears to involve non-clonal populations of the pathogen, according to another PNAS study. Investigators at the University of Ottawa and the University of Calgary performed genome sequencing on P. aeruginosa strains in sputum samples from 24 Canadian cystic fibrosis patients, defining core and accessory genome sequences that appear to contribute to adaptation. Diversity present in the isolates, together with existing P. aeruginosa sequence data, pointed to a non-clonal epidemic population structure as well as genetic ties between at least one strain causing infections at cystic fibrosis centers in North America and the UK.

Researchers from the US, Israel, and Canada used high-coverage whole-genome sequencing to track down genomic differentiation between fruit fly populations from the distinct microclimates found on opposite slopes of Mount Carmel in Israel. Fruit fly sequence data from these locales — part of the so-called Evolution Canyon — indicated that nearly 600 Drosophila genes show different allele frequencies in the divergent fruit fly populations from the two mountain slopes. The analysis picked up other potential signs of adaptation, too, study authors say, including possible selective sweeps, chromosomal island and recombination events.