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This Week in PNAS: Aug 18, 2015

Metabolomics could be a key tool for personalized medicine, say researchers from Metabolon in the Proceedings of the National Academy of Sciences. They conducted a metabolomics analysis of plasma samples from a cohort of 80 healthy volunteers, profiling some 600 metabolites and covering 72 biochemical pathways. By folding this metabolomics data in with whole-exome sequencing data from the same cohort, they were able to identify metabolic abnormalities linked with potential disease conditions as well as find gene mutations based on observed abnormal metabolic phenotypes. "The results of our study demonstrate that metabolomics can effectively enhance the interpretation of NGS data and improve the overall disease diagnosis and risk assessment for patient care," the researchers say.

An altered vaginal microbiome is associated with preterm birth, according to a Stanford University School of Medicine study also appearing in PNAS this week. Stanford's David Relman and colleagues collected vagina, distal gut, saliva, and tooth/gum samples from 49 pregnant women weekly during pregnancy and monthly after delivery. From this, they found that women with a Lactobacillus-poor vaginal community state type and elevated levels of Gardnerella or Ureaplasma were at higher risk for pre-term birth, a finding they validated in a further set of samples from nine women. This, the researchers add, has "important implications for predicting premature labor."

Finally, Johns Hopkins University researchers report that L1 retrotransposition is active in esophageal adenocarcinoma and in Barrett's esophagus, a condition that is often a precursor to esophageal cancer. By performing L1-seq and follow-up PCR on five patients with benign Barrett's esophagus, five patients with Barrett's esophagus and concomitant EAC, and 10 additional patients with esophageal adenocarcinoma, the researchers found and confirmed 118 somatic insertions in half of those patients. Further, these insertions were clonally expanded in Barrett's esophagus and esophageal adenocarcinoma, "indicating that somatic L1 insertions are not only potential mutagens in the development of EAC, but also useful markers of tumor clones as well."