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This Week in PNAS: Nov 10, 2015

Editor's Note: Some of the articles described below are not yet available at the PNAS site, but they are scheduled to be posted some time this week.

In the early, online edition of the Proceedings of the National Academy of Sciences, an international team led by investigators in Switzerland describe results from a genome-wide association study focused on finding common variants that influence viral load in individuals infected with HIV-1. By comparing genotyping profiles and viral load data for more than 6,300 HIV-infected individuals of European ancestry, the researchers uncovered common variants in the HLA and CCR5 regions that appear to explain some 25 percent of the variability in viral load found between individuals infected with HIV-1. GenomeWeb has more on the study, here.

Researchers from China and the US explore the feasibility of doing non-invasive prenatal testing for fetal sub-chromosomal deletions and duplications using Life Tech's Ion Proton semiconductor sequencing. After trying out semiconductor sequencing on diluted blood samples from 19 newborns with verified deletions or duplications, the team used blood samples from nearly 1,500 pregnant women to come up with strategies for estimating the relative proportion of circulating fetal DNA in maternal blood. Finally, the study's authors demonstrated that they could pick up between 71 percent and nearly 95 percent of array CGH-verified sub-chromosomal changes with semiconductor sequencing — depending on the sequencing depth used — in blood samples from 1,476 pregnant women. When false positive tests turned up, they note, many appeared to coincide with deletions or duplications present in maternal DNA.

A Chinese Academy of Sciences- and University of Chicago-led team describes tumor evolution patterns gleaned from genetic profiles in hundreds of regions in a single hepatocellular carcinoma tumors scrutinized by either exome sequencing or genotyping. Based on the dramatic genetic diversity detected in 286 genotyped samples from the tumor and almost two-dozen regions from the hepatocellular carcinoma that were characterized by exome sequencing, the study's authors argue that the tumor appeared to be subject to non-Darwinian rather than Darwinian selection. "Because the level of genetic diversity will have implications on therapeutic resistance," they write, "non-Darwinian evolution should be heeded in cancer treatments even for microscopic tumors."