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This Week in PLOS: Sep 11, 2017

In PLOS One, a team from Taiwan and Singapore explores the effectiveness of an 18-gene classifier for predicting distant metastasis in individuals with breast cancer. The researchers applied the algorithm — initially established to predict local progression or regional recurrence — to fresh-frozen primary breast tumor samples from 683 individuals with breast cancer, including 101 individuals who experienced metastasis and 583 who were metastases-free. More than 96 percent of 146 individuals classified as low risk by the 18-gene classifier remained free from distant metastasis over five years, they report, while just under 81 percent of the high-risk group avoided metastasis in that time frame. The authors subsequently validated the algorithm in two more datasets.

For a PLOS Neglected Tropical Diseases paper, investigators from the Czech Republic and the Netherlands present findings from a genome sequencing study of two Treponema pallidum strains, focusing on the pertenue subspecies implicated in yaws. The team put together de novo genome assemblies for two T. pallidum strains subsp. pertenue isolates obtained from infected children in Ghana nearly a decade apart, in 1980 and 1988. Although a handful of heterogeneous sites turned up in the genome, the overall genome sequences were largely identical, spurring additional analyses of the strains and clinical data associated with them. "Taken together, the data … are consistent with the relatively slow evolution rate of yaws treponemes and suggest that the appearance of the most recent common ancestor of syphilis and yaws treponemes took a very long time, perhaps even a length of time comparable to the evolution of modern humans," the authors write.

Finally, in a commentary paper appearing in PLOS Pathogens, a team from Belgium, Colombia, and Portugal calls for more standardized and consistently curated Zika virus (ZIKV) reference sequences to improve studies of the virus and its effects. "[M]ost human ZIKV genomes available to date originate from the ongoing outbreak," they write. "While this proliferation of genomic data offers new opportunities for comparative and evolutionary genomics of ZIKV, we demonstrate that the rapid advance in ZIKV genomics has resulted in inconsistencies that complicate the interpretation, reproducibility, and comparison of findings from and across studies, particularly due to the lack of consensus on a standardized and representative reference genome annotation."