Genetic Engineering & Biotechnology News

MAY15 2018

Genetic Engineering & Biotechnology News (GEN) is the world's most widely read biotech publication. It provides the R&D community with critical information on the tools, technologies, and trends that drive the biotech industry.

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14 | MAY 15, 2018 | | Genetic Engineering & Biotechnology News design portal for validation assays for gene editing experiments. Dr. Patel commented, "dPCR can help you know if your experi- ment worked or not before you invest signifi- cant dollars cloning cells or culturing cells for further use." Oncological Applications Oncology is a key clinical application of dPCR, for both mutation detection and copy number analyses. Bio-Rad has CE (Confor- mité Européene) IVD marks on an automat- ed and a manual dPCR platform, available within Europe and parts of Asia. In addition to CE IVD marking on non-analyte-specific reagents, the company recently received a CE IVD mark on a test for BCR-ABL, the fusion gene driving chronic myeloid leukemia. Dr. Patel said that Bio-Rad is engaged with the FDA on obtaining clearance of the platform and the BCR-ABL test. The BCR- ABL test would be used to monitor patients who are on therapy; the levels of reduction of the BCR-ABL transcript during therapy are used to determine response to therapy. According to Dr. Patel, the sensitivity, ac- curacy, and reproducibility of dPCR in detect- ing BCR-ABL is enabling studies that look at whether therapy can be stopped in patients with very low levels of the transcript. Digital PCR is likely to be used to monitor minimal residual disease in other hematologic malig- nancies and solid tumors. Anthony Magliocco, M.D., a molecular and anatomical pathologist at Moffitt Can- cer Center, described the use of dPCR to detect specific mutations in cell-free DNA in patients to monitor their cancers. The first assay being used clinically at Moffitt detects the EGFR T790M mutation to monitor lung cancer tumor burden and resistance to treat- ment with tyrosine kinase inhibitors. Moffitt is also developing an assay for BRAF V600E in melanoma and thyroid cancer. Moffitt runs its test as a laboratory-devel- oped test (LDT) in accordance with regula- tions described in CLIA (Clinical Laboratory Improvement Amendments). "Our lab pre- fers to run FDA assays if they are available," Dr. Magliocco indicated. For those cancer- related mutations for which there is no FDA- approved test, he said, "we have to create them and launch them as LDTs." EGFR T790M is thought to be a resistance marker that occurs only after treatment of lung cancer with an EGFR inhibitor. Emergence of this mutation indicates the need to change therapy to an agent that can overcome this resistance mutation. "This absolutely guides treatment choice," Dr. Magliocco pointed out. "That's why we created the assay." dPCR can also be used to monitor tumor load using a tumor marker that is not necessarily a thera- peutic target, for example, the p53 protein. Dr. Magliocco said the advantages of dPCR include the small sample size needed and ap- plicability to blood, cerebrospinal fluid, and tissue from fine needle aspiration samples or paraffin sections. "You can monitor changes accurately," he remarked. "It's also very cost effective. It's high throughput. It doesn't need any bioinformatics. "The disadvantages are that you are limited to the number of mutations you can look at. It has no use for screening for mutations unless you are screening for an actionable target. With NGS, you can look at way more mutations, and it can also be quite sensitive. It's costly, however, and it takes a lot of bioinformatics time. It's a complicated assay." Managing Cell-Based Products At Cell and Gene Therapy Catapult, a cen- BRING SMALL CONCENTRATIONS AND LARGE FRAGMENTS INTO FOCUS. Make QC more efficient for the analysis of precious genomic samples with the FEMTO Pulse ® from Advanced Analytical Technologies, Inc. You can quickly evaluate high molecular weight DNA for long read sequencing, and detect low-concentration samples down to the single cell. With incredibly comprehensive QC, you can focus your research in ways you never thought possible. Explore the unprecedented sensitivity and precision of the FEMTO Pulse . FEMTO Pulse ® Automated Pulsed-Field CE Instrument R Digital PCR Continued from page 12 OMICS At the Moffitt Cancer Center's Morsani Molecular Diagnostics Laboratory, liquid biopsies may be processed with droplet digital PCR technology, which can detect and measure trace amounts of circulating DNA shed by tumor cells. This technology may find actionable mutations in liquid biopsy specimens, allowing diagnosis and treatment to proceed even if solid-tissue biopsy specimens are lacking.

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