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
Issue link: https://clinicalomics.epubxp.com/i/853204
22 Clinical OMICs July/August 2017 www.clinicalomics.com cally, is innovative ways to enrich or isolate the fetal DNA from maternal circulation and then perform sequencing," commented Dr. Abou Tayoun. Currently, cfDNA sequencing has to be performed at a much higher depth than sequencing performed on CVS or amniocentesis samples, he explained. Yet, despite the higher depth of sequencing, the chance of missing a variant is still quite high compared with standard diagnostic testing samples. Quest for Single-Cell Analysis Clinician and molecular diagnostics expert Arthur Beau- det, M.D., Baylor College of Medicine, has been working to develop cell-based prenatal screening for many years and has recently had success with cell-based testing in a research setting. He published two papers last year, one with U.S.- based single-cell analysis company Rarecyte, and a second with Danish firm Arcedi Biotech, both of which demon- strated the feasibility of a screening technique targeting fetal trophoblast cells. He explained that Rarecyte uses a technique that micro- scopically scans all the nucleated cells in the sample and identifies ones that stain positively for a protein called cyto- keratin, whereas Arcedi has taken a different approach of trying to identify antibodies that will bind specifically to the fetal cells and then use magnetic bead try to pull out fetal cells from the maternal cells. In his current work, Dr. Beaudet and his team are using antibodies to enrich for the fetal cells and then picking indi- vidual cells after cytokeratin staining. "The downstream part, to take the cell and analyze its DNA, is done quite a lot in preimplantation genetic screen- ing and preimplantation genetic diagnosis. So the techniques for the downstream part are relatively well established, but it's getting hold of the cells that is the challenge," said Dr. Beaudet. He added that finding ways to accurately scale up the cell- based testing methods are needed. "I would love to be able to launch a test even at low volume very, very soon, but I just don't know. It's tricky to make guesses," he commented. Ripudaman Singh, Ph.D., chief technical officer at Arcedi Biotech, highlighted why analyzing whole fetal cells is so advantageous. "Because cell-based non-invasive prenatal diagnosis technologies offer intact fetal cells with access to the complete fetal genome, uncontaminated with maternal DNA, the possibilities of even detecting small changes (eg., copy number variations) in the fetal genome are immense." In addition to the three most common aneuplodies, Arcedi Biotech has detected subchromosal abnormalities, such as a 31–Mb translocation between chromosomes 4 and 8 and a 12.2–Mb duplication on chromosome 21, with their test. These results were confirmed using CVS. (continued from previous page) Recent research suggests that cfDNA tests are more accurate than standard noninvasive prenatal screening, at least for the main aneuploidies. They have a lower rates of false positives and a higher positive predictive value (PPV ). The PPV, or likelihood that a positive result on a test is a true positive, is an important measure for genetic tests. It is signifi- cantly affected by the prevalence of a disease in a population. This means that in a low-risk population, a greater number of positive test results will be false positives. For example, the chance of a true positive result for Down syn- drome in a 40-year-old woman undergoing prenatal screening is higher than the chance of a true positive result in a 20-year- old woman. The low population prevalence of the deletion syndromes such as DiGeorge means that, at present, most of the cfDNA tests that cover them have very low PPV (~5%) and are very unlikely to produce a true positive result. Neeta Vora, M.D., an OB-GYN from the University of North Carolina at Chapel Hill School of Medicine, has been working to improve the knowledge of both patients and providers about PPV and calculation of risk from cfDNA test results for a number of years. "What we found for many providers was that there was a Predicting the Positive Alyssa LaFaro (continued on page 24) Neeta Vora, M.D., an OB-GYN from the University of North Carolina at Chapel Hill School of Medicine.