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This Week in PNAS: Aug 30, 2016

In the early, online edition of the Proceedings of the National Academy of Sciences, University of Pennsylvania researchers introduce a statistical framework called Canopy, designed to look at tumor evolutionary phylogeny and intra-tumor heterogeneity from SNP and copy number patterns in samples tested by bulk DNA sequencing. In transplantable breast cancer cell lines, breast cancer xenograft samples, and tumor samples from individuals with leukemia or ovarian cancer, the team found that Canopy could pick apart mixed cell lines or intra-tumor sub-clones. "We show that such analyses lead to the identification of potentially useful prognostic/diagnostic biomarkers and successfully recover the tumor's evolutionary history, validated by single-cell sequencing," the study's authors say.

An international team led by investigators at the National Human Genome Research Institute reports on a rare, autoinflammatory condition caused by loss-of-function mutations affecting the linear deubiquitinase enzyme-coding gene OTULIN. The researchers characterized the condition, called otulipenia, in four affected individuals from two Turkish and one Pakistani family. With the help of candidate gene sequencing and exome sequencing in affected and unaffected members of the family, the researchers narrowed in on two missense mutations and one frameshift change to OTULIN in individuals with the newly described disease. Their subsequent cell line experiments began untangling the signaling and inflammatory consequences of such mutations.

Finally, a Mexican team explores network features associated with desiccation tolerance in Arabidopsis thaliana seeds. Using a combination of genomic, bioinformatic, metabolomics, and molecular genetics approaches, the researchers investigated the transcriptional sub-networks and transcription factor regulators behind seed desiccation tolerance. "Understanding the networks that regulate seed [desiccation tolerance] in model plant systems will provide the tools to understand an evolutionary process that played a crucial role in the diversification of flowering plants," the group writes.