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This Week in PNAS: Oct 15, 2014

Characteristic mutations to the tumor suppressor gene TP53 do not seem to dial up copy-number changes in individuals with the cancer predisposition condition Li-Fraumeni syndrome, according to a study in the early, online edition of the Proceedings of the National Academies of Sciences. A team from the US, Malaysia, France, and Brazil did whole-genome sequencing on 13 individuals from two generations of a family affected by Li-Fraumeni syndrome. The researchers did not see shifts in copy number variants over time or across generations. Rather, their follow-up analyses of hundreds more Li-Fraumeni syndrome pedigrees pointed to a more complex "genetic regression" model that may explain heterogeneity in the condition within families.

Researchers from Switzerland, Brazil, and the US used genome sequencing to characterize Mitosporidium daphniae, a microsporidia intracellular parasite that lives in the Daphnia crustacean gut. A phylogenomic look at the data indicated that M. daphniae is an early branching member of the microsporidia — a group that itself falls on an early diverging fungal tree branch. Meanwhile, the team's comparative genomic analyses uncovered several streamlined functions by the parasite, including a dip in energy metabolism and a decline in DNA recombination and repair, gene expression, and cell cycle control genes.

In an effort to understand human papillomavirus contributions to head and neck cancer, a Massachusetts-led team that included members of the Cancer Genome Atlas Network used RNA sequencing and DNA sequencing to assess almost 300 primary head and neck squamous cell carcinomas. Thirty-five of the tumors — more than 12 percent — contained sequences stemming from HPV types considered risky, such as HPV 16, 33, or 35. In 25 of the 35 cases, the researchers saw signs of HPV sequences that had inserted themselves at one or more sites in the host human genome, with integrations turning up especially often in protein-coding parts of the genome. "Integrations had a marked impact on the human genome," they write, "and were associated with alterations in DNA copy number, [messenger RNA] transcript abundance and splicing, and both inter- and intrachromosomal rearrangements."