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This Week in PNAS: Dec 23, 2014

Researchers led by Johns Hopkins University School of Medicine's Bert Vogelstein estimate that only three driver mutations are needed for lung and colorectal cancer to develop, not the six or seven mutations that previous models suggested. As they report this week in the Proceedings of that National Academy of Sciences, Vogelstein and his colleagues drew on both genome-wide sequencing data and epidemiological studies to compare incidence data to somatic mutation rates for different patient groups. This, the researchers say, has implications for future cancer genome sequencing efforts.

A trio of researchers from Sweden used a phylogenetic approach to analyze retroviruses that have inserted themselves into vertebrate genomes. They found more than 36,000 endogenous retroviruses across the 65 vertebrate genomes they analyzed, finding that retroviruses are host generalists and that there are likely many more unknown retroviruses. GenomeWeb has more on these findings here.

Also in PNAS, researchers from the UK and elsewhere present their study of host specialization using subspecies of Salmonella enterica — a lineage with generalist species as well as ones adapted just to birds or cattle, for instance. They sequenced the genomes of some 60 isolates, and by analyzing them, the researchers were able to follow pseudogene formation and how that led to host-adapted pathogens. They further note that specialist subspecies like S. Gallinarum and S. Pullorum lost some metabolic capabilities. "[S]hedding light on how human and animal pathogens arose in the past [could allow] us to predict how emerging pathogens will evolve in the future," the researchers say.