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This Week in PNAS: Oct 30, 2018

In the early, online version of the Proceedings of the National Academy of Sciences, an international team led by investigators in Belgium and Sweden outlines efforts to bolster genomic resources for plants from the Populus genus with whole genome and population genetic analysis on two aspen species from the Northern Hemisphere. In addition to putting together and annotating de novo genome assemblies for the North American quaking aspen and the Eurasian trembling aspen, the researchers resequenced dozens of P. tremula and P. tremuloides trees, searching for signs of selection through comparisons with new and existing data for the black cottonwood, P. trichocarpa. "The resources we present establish aspens as a powerful study system enabling future studies for understanding the genomic determinants of adaptive evolution," the study's authors note.

Researchers from the Chinese University of Hong Kong and elsewhere describe potential signatures for hepatocellular carcinoma (HCC) tumor DNA circulating through the bloodstream. Using a strategy aimed at identifying all of the somatic mutations present in a given pool of circulating tumor DNA (ctDNA), the team says, it searched for "plasma end coordinates" and somatic alterations associated with cell-free DNA originating in the liver in liver transplant recipients, HCC patients, or individuals with chronic hepatitis B infections. "[W]e showed that there were millions of tumor-associated plasma DNA end coordinates in the genome," investigators report, adding that plasma DNA end coordinates "may therefore serve as hallmarks of ctDNA that could be sampled readily and, hence, may improve the cost-effectiveness of liquid biopsy assessment." GenomeWeb has more on the study, here

An ETH Zurich team takes a look at the proteins found on the surface of various human cell types, including potential drug targets, using a surfaceome predictor, in silico approach called SURFY. After training the machine learning-based method with information on high-confidence surface protein data from the Cell Surface Protein Atlas, the researchers used SURFY to predict nearly 2,900 human surfaceome based on 131 protein domain features. An estimated 1,700 of those appear to be expressed on the surface of embryonic stem cells, they note, while anywhere from 543 to 1,100 appear to dot the surface of cancer cell lines, based on available gene expression data.