In the early, online edition of the Proceedings of the National Academy of Sciences, the Chinese University of Hong Kong's Dennis Lo and colleagues present an approach for improving blood-based nasopharyngeal carcinoma screening with Epstein-Barr virus (EBV) DNA as a marker. Building on prior proof-of-principle studies, the team used target-capture sequencing to compare the size and abundance of plasma EBV DNA reads in plasma blood samples from 10 individuals with nasopharyngeal cancer and 40 without. The latter group included 20 individuals with persistent EBV infections and 20 transiently positive individuals. In individuals with nasopharyngeal cancer, the investigators saw enhanced EBV levels, along with longer average fragment length. They incorporated those results into a single time point, sequencing-based nasopharyngeal cancer screening test that takes EBV read counts and sequence size into account. "Such an approach is shown to enhance the positive predictive value," they write, "and demonstrate a superior performance for [nasopharyngeal cancer] screening."
For another PNAS paper, Lo's team focuses on cell-free DNA in bloodstream of pregnant women, comparing the size-specific preferred end sites in maternal and fetal DNA fragments. The researchers brought together plasma DNA reads for more than two dozen women pregnant with male fetuses, looking at the prevalence and location of long and short maternal and fetal preferred end sites. Along with a previously described boost in shorter DNA fragments in fetal DNA, the team saw differences in the location of preferred end site cuts — a pattern that held in a subsequent analysis of cell-free DNA reads from 36 trisomy 21 cases and 108 controls. On the other hand, non-pregnant individuals had short and long preferred end profiles that were comparable to those found in maternal DNA, authors report, hinting that "the inter-relationship of preferred DNA ends, chromatin accessibility, and plasma DNA size profile is likely a general one, extending beyond the context of pregnancy."
Researchers from China, the US, and Singapore share a new ray-finned fish phylogeny established using 144 fish genome sequences, more than 150 transcriptomes, and additional exon sequence data for 303 species. Together, the data spans 66 ray-finned fish orders, the team reports, providing an opportunity to retrace phylogenetic relationships, follow whole-genome duplication events, and establish exon markers in the ray-finned fish family tree. "Our time calibrated analysis suggests that most lineages of living fishes were already established in the Mesozoic Period, more than 65 million years ago," the authors write, noting that the newly detected exon marker set "is a promising resource for current sequencing approaches to significantly increase genetic and taxonomic coverage to resolve the tree of life for all fishes."