Clinical OMICS

JUL-AUG 2019

Healthcare magazine for research scientists, labs, pathologists, hospitals, cancer centers, physicians and biopharma companies providing news articles, expert interviews and videos about molecular diagnostics in precision medicine

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www.clinicalomics.com July/August 2019 Clinical OMICs 9 were doing biologically, and cytokine profiles to determine the women's immune response. The researchers found that African American women had significantly lower levels of Lacto- bacillus crispatus—the main component of the vaginal microbiome—and higher levels of 15 other taxa. They also found that preterm birth associated taxa were correlated with inflammatory cyto- kines. "We can't claim causation, at this point, but there are signatures when we compare these two groups." The study also offers new ways of approaching complex biological prob- lems using Big Data and high-perfor- mance computing. The study required a large multi-disciplinary team of researchers, key people who could work across disciplines to solve novel computational challenges. "The datasets we have generated will stimulate work in those areas," Fettweis said. Microbiome-based diagnostics Fettweis' findings are a starting point for researchers who want to decrease the frequency and disparities in preterm birth. "We're hopeful we developed a proof of principal model that suggests that, using just the microbiome, we can do just about as well as using some of the best clinical mea- sures," Fettweis said. Fettweis also said she can envision a day when a microbiome-based diagnostic test that uses a vaginal swab done during a regular prenatal exam is used to screen women in early pregnancy for preterm birth risk. The U.S. Food and Drug Administration has yet to approve a microbiome-based diagnostic test. That day is coming, said Greg Kuehn, vice president and chief operat- ing officer of Prescient Metabiomics, a joint venture between Metabiomics and Prescient Medicine. Prescient Metabiom- ics is in the preclinical stages of development, preparing to conduct larger and more complex clinical trials as it moves toward FDA clearance of microbiome-based diagnostic tests for colorectal adenoma, colon cancer, and inflammatory bowel disease. Kuehn agreed that Fettweis' work has the potential to be the basis for such a test for preterm pregnancy risk in the future. "For a whole range of diseases there could be tests and therapeutics developed from microbiome diagnostics. It's a new paradigm in human health," he said. Kuehn also pointed to the irony that researchers are basically assessing human health based on microbial populations of micro- environments within the human body, such as the vagina, gut, and colon. These environments depend on the micro- biome to maintain biofilms, maintain the integrity of mucosa, and the suppres- sion of pathogeneic bacte- ria. "It's sort of a regulated environment where there is interaction between the microbiome and the host system." In addition to replicating this study's results, Fett- weis said that researchers in the field need to stan- dardize the way swabs are collected, the primer sets used in analysis, and the number of weeks gestation used to define preterm birth. For example, some studies include women whose labor was induced. Fettweis and her colleagues only included those who gave birth early spontaneously. "We need to harmonize studies moving forward so that we can compare across studies and across populations." Term Birth (N=90) (≥ 37 weeks) sPTB (N=45) (< 37 weeks) TB controls (N=90) (≥ 39 weeks) MOMS-PI Preterm Birth Study MOMS-PI Term Birth Study N=992 N=580 N=236 Phase 1 N=627 Jennifer Fettweis, Ph.D., Virginia Commonwealth University Women in the study were part of the Multi-Omic Microbiome Study-Pregnancy Initiative (MOMS- PI), which included 1572 pregnancies and 12,000 samples.

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