Clinical OMICS

JAN-FEB 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 January/February 2019 Clinical OMICs 21 example, a test for SNPRN methyla- tion is used to diagnose Prader-Willi and Angelman syndromes—inher- ited disorders of the chromosome in neurological, behavioral, and devel- opmental symptoms. In cancer, the FDA-approved Epi proColon and Cologuard tests are used in colorec- tal cancer screening. Epi proColon detects a hypermethylated promoter region of the SEPT9 gene in cell-free DNA (cfDNA) and Cologuard mea- sures aberrantly methylated BMP3 and NDRG4 promoter regions in a stool sample. But, there are many more markers being studied for future use in the clinic, either alone or in combination with other tests. Cancer Salhia's lab is focused on developing a test for breast cancer recurrence. Currently, the approach for classify- ing women as high-risk or low-risk of recurrence is based on relatively crude factors and relies on tissue at the sin- gle time point of diagnosis. Once ther- apy is complete, many women will be cured, but some will not be and will end up developing recurrence up to 30 years past their initial diagnosis. "Their risk of recurrence at diagno- sis could have either been inaccurate or changed after therapy. Either way, you just don't know whether you are one of the ones cured or not cured and you just have to let time tell you," Salhia explained. Over 90 percent of deaths due to breast cancer are the result of metastasis, which kills more than 40,000 women in the U.S. every year. Salhia's lab is developing a cell-free DNA methylation test to be used in early stage breast cancer set- tings. "We believe that we can have the sensitivity to detect the 'needle in the haystack' and serve as a prognos- tic test for recurrence. Meaning, we want to detect residual disease at the completion of therapy, which would indicate metastasis in the future." In time, Salhia said she hopes this test would be predictive and lead to prescription of additional thera- pies that would help deter recur- rence. Salhia and her colleagues published a feasibility study in (continued on next page) Dennis Grayson, Ph.D. University of Illinois at Chicago A New Tool for Assessing Epigenetic Differences In early 2019, Bio-Rad will begin shipping a new single-cell ATAC-Seq solution for epigenetics research. The product, now in early access, improves upon existing ATAC- Seq technology (Assay for Transposes Ac- cessible Chromatin with high-throughput sequencing), which allows researchers to measure gene regulation by determining what parts of the chromatin are open and available for transcription. ATAC-Seq was invented in 2015 by a group at Stanford University. One of the inventors, Jason Buenrostro, Ph.D., is now a fellow at the Broad Institute of MIT and Harvard. In a video he produced with Bio-Rad, he explains that ATAC-seq finds different parts of the genome that are controlling the expression of genes. "A simple measurement of gene expression is to measure how open the genome is," Buenrostro stated in the video. It uses Bio-Rad's Single-Cell Isolator to encapsulate thousands of cell nuclei into nanoliter-sized droplets, in which library preparation for next generation sequenc- ing occurs. Currently, ATAQ-seq is a mostly manual process, allowing for only tens to hundreds of cells to be studied at once. The product allows for thousands of cells to be studied at once with increased sensitivity. "Epigenetics researchers will now be able to ask deeper questions about cell fate, identify the cell types present in heterogeneous tissues, and validate sin- gle-cell gene expression data," said Caro- lyn Reifsnyder, director of life science mar- keting, digital biology group at Bio-Rad. Instead of averages, researchers will get profiles based on data from single cells. —Camille Mojica Rey n Westend6 / Getty Images

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