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This Week in PNAS: May 6, 2014

Researchers from China and the US report on efforts to sequence fetal DNA circulating in maternal blood samples using Ion Proton semiconductor sequencing. The team used the semiconductor sequencing approach to do retrospective karyotyping on samples from 515 pregnant women, identifying known cases of fetal trisomies 21, 18, and 13 with sensitivities and specificities of more than 99 percent. Likewise, prospective testing on samples from another 1,760 pregnant women using the same approach picked up those trisomies, along with aneuploidies involving the sex chromosomes. "To our knowledge, this is the first large-scale clinical study to systematically identify chromosomal aneuploidies based on cell-free DNA using the [semiconductor sequencing platform]," the study's authors write, "and provides an effective strategy for large-scale non-invasive screening for chromosomal aneuploidies in a clinical setting."

Stanford University's Stephen Quake led a team using microarrays and high-throughput RNA sequencing to track tissue-specific gene expression in blood samples from healthy adults and pregnant women — an approach that they say has promise for tracking diseases such as Alzheimer's and for following events during pregnancy and after pregnancy. "By focusing on tissue-specific genes, we were able to identify the relative contributions of these tissues to circulating RNA and monitor changes during tissue development and neurodegenerative disease states," Quake and colleagues argue. Our sister publication GenomeWeb Daily News has more on the study, here.

A Duke University team reporting in the early, online edition of the Proceedings of the National Academy of Sciences used microarray-based recombination and rearrangement mapping took a look at the distribution of fragile chromosome sites across the genomes of Saccharomyces cerevisiae, including strains with lower than usual DNA polymerase levels. The diminished polymerase levels appeared to prompt a jump in aneuploidy and in deletion and duplication events, the researchers report, though the patterns were somewhat different in cells with or without typical polymerase levels. Their experiments also highlighted several sequence or structure patterns in the yeast genome that tend to correspond with recombination events such as those apparently stemming from DNA replication fork pauses.