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This Week in PLOS: Jan 4, 2016

A team from the Icahn School of Medicine at Mount Sinai searches for circulating tumor DNA patterns associated with treatment response and survival in women being treated for gynecologic cancers such as high-grade serous ovarian and endometrial cancer in PLOS One. After identifying tumor-specific mutations in samples from 44 women with ovarian cancer, uterine cancer, peritoneal cancer, and/or fallopian tube cancer using whole-exome and targeted sequencing, the researchers searched for and quantified ctDNA in patient blood samples with the help of droplet digital PCR. Indeed, they were able to track down ctDNA in nearly 94 percent of the 32 patients with targetable tumor mutations at levels that coincided with tumor imaging results and serum levels of the cancer antigen marker CA-125.

In PLOS Genetics, researchers from Spain and the Netherlands delve into the source of de novo gene emergence in human and chimp genes. Through deep transcriptome sequencing on samples from human, chimpanzee, macaque, and mouse — and comparisons with several other mammalian species — the team uncovered more than 5,000 transcripts containing multiple exons that were present in human and chimpanzee alone. By delving into the sequences surrounding the apparent de novo genes coding for such transcripts, the study's authors identified new regulatory motifs surrounding them. "Taken together," they write, "the data support a model in which frequently-occurring new transcriptional events in the genome provide the raw material for the evolution of new proteins."

A paper appearing in PLOS Neglected Tropical Diseases by researchers in the US and Colombia describes genetic diversity patterns detected in a handful of malaria-causing Plasmodium vivax isolates from Colombia. The team sequenced the genomes of eight P. vivax isolates collected from patients in the Cordóba region of Colombia between 2011 and 2013. When they scrutinized these sequences and compared them to P. vivax isolates characterized in the past, the investigators identified a set of polymorphisms in Colombia that seemed to point to relative genetic diversity in the Colombia isolates compared to P. vivax in other parts of the Americas. GenomeWeb has more on the study, here.