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34 | AUGUST 2014 | GENengnews.com | Genetic Engineering & Biotechnology News TRANSLATIONAL MEDICINE "For a start, we focus our efforts on a panel of 50 genes that could provide actionable in- formation to our clinicians." This panel, notes Dr. Fernandes, poses a practical diffculty. It must be used with an assay sensitive enough to identify a mutation present in less than 5% of a heterogenous population of tumor cells. The most common starting material typi- cally comes from core biopsies embedded in paraffn for preservation. "We were able to successfully use this somewhat compromised material to amplify and analyze multiple genes simultaneously," continues Dr. Fer- nandes. The test that has been validated in the clinical lab is able to use 10 ng of starting DNA to generate sequences covering 2,800 hotspots in the 50-gene panel. The power of this approach was demon- strated in a pilot study aiming to identify se- quence variants in head and neck squamous cell carcinoma (HNSCC) with and without human papilloma virus (HPV). Surprisingly, tumors with increased HPV viral copy num- ber are associated with better response to chemotherapy and prolonged survival. Dr. Fernandes' team utilized NGS to sys- tematically analyze somatic variants in virus- infected and virus-free samples. The data confrmed key differences in signaling path- ways between the two cohorts. Notably, the HPV+ cells retained wild-type p53, which is known to promote cell apoptosis in response to chemotherapy. Several other genes identifed in the study look promising as candidate targets for ther- apy. "In addition to signifcant insights in the pathogenesis of HNSCC we were also able to identify potential diagnostic markers that could become therapeutic targets," asserts Dr. Fernandes. "NGS is rapidly becoming an invaluable tool in translational medicine and oncology." CLIA Certication "I believe that NGS has the potential to become a consolidated platform for multiple genotyping approaches," says Rajyalakshmi Luthra, Ph.D., director of the Molecular Diagnostics Laboratory at the University of Texas MD Anderson Cancer Center. "NGS has capabilities not only to identify substitu- tion mutations and insertions/deletions (in- dels), but also to fnd fusion transcripts and copy number changes." Instead of managing multiple diagnostic platforms, a clinical di- agnostic lab may rely on just one—a next- generation sequencer. Dr. Luthra points out that while the se- quencing technology itself is already capable of detecting indels, variant-calling software packages have not yet reached desired con- sistency. "We continue visual inspection of raw reads until we can be sure that the soft- ware is capable of calling indels with high accuracy," remarks Dr. Luthra. Nevertheless, the Molecular Diagnostics Laboratory has undertaken a concerted ef- fort to validate several NGS platforms using CLIA (Clinical Laboratory Improvement Amendments) standards. For example, the Molecular Diagnostics Laboratory clinically validated the Ion Torrent PGM (Life Tech- nologies) using 10 ng of DNA from 70 par- affn-embedded solid tumor samples. Vari- ants detected by sequencing 740 mutational hotspots in 46 cancer-related genes in the panel were confrmed by orthogonal conven- tional platforms such as Sanger sequencing and pyrosequencing. Overall concordance between NGS and conventional platforms supported routine use of NGS in the CLIA-certifed laboratory. The utility of this approach was elegantly applied to screening mutational hotspots in 54 cancer-related genes using MiSeq, Illu- mina's NGS platform, as a part of diagnostic workup and treatment plan for patients with acute myeloid leukemia. "NGS provides for a single detection plat- form capable of analyzing multiple genes at the same time starting with a fraction of the material required in conventional multigene analysis," notes Dr. Luthra. The laboratory rigorously tested several NGS-based protocols by analyzing and com- paring the archival samples with known mu- tations and samples collected prospectively. NGS platforms showed high level of repro- ducibility and high detection sensitivity. This high sensitivity was useful in detecting the presence of low-level mutations that were missed by less sensitive conventional plat- NGS Continued from page 1 > Natera Launches Carrier Screening Partner- ship with Mount Sinai Genetic Testing Lab Natera and the Mount Sinai Genetic Testing Labora- tory inked a partnership to ofer an expanded Horizon™ genetic carrier screening test for prospective families. Natera will ofer the Horizon test to its OB/GYN custom- ers as part of its women's health business. The Horizon™ multidisease genetic carrier screen pro- vides results for certain genetic disorders, including cystic fbrosis, spinal muscular atrophy (SMA), and Tay-Sachs disease. The test increases detection rates for SMA, refnes risks for Fragile X syndrome, and ofers expanded screen- ing for the Ashkenazi Jewish population. > AutoGenomics, Genomas Ink Partnership to Develop Genetic Tests for Statins Management AutoGenomics and Genomas signed an agreement to jointly develop genetic tests and DNA-guided diag- nostic systems for optimal selection of statins and for improved delivery of statin therapy for the treatment of cardiovascular disease, obesity, and diabetes. By utilizing Genomas SINM PhyzioType® System com- bined with AutoGenomics' INFINITI® multiplexing genet- ic test platform, the collaboration will provide clinicians and physicians with newly developed genetic tests and a decision support system that will allow them to man- age statins, prescribe, and dose these drugs on a DNA- guided, personalized basis. The newly developed DNA-guided statin diagnostic tests are designed to identify individuals who are geneti- cally susceptible to muscle pain while on these statins and who may develop muscular injury while on high-dose statin therapy. > MDxHealth, Miraca Agree to Promote ConfrmMDx for Prostate Cancer MDxHealth entered into an agreement with Miraca Life Sciences to promote MDxHealth's ConfrmMDx® for Pros- tate Cancer testing. MDxHealth is a molecular diagnostic frm that develops and commercializes epigenetic tests. Miraca Life Sciences provides pathology services in the felds of dermatology, hematology, gastroenterology, and urology. Through this strategic partnership, the companies say they can now ofer a validated epigenetic assay that delivers new molecular insights on a patient's risk for un- detected cancer, enabling clients to make more informed decisions about the need for a repeat prostate biopsy. > Transplant Genomics Picks Up Transplant Dx IP Transplant Genomics (TGI) now has an exclusive li- cense to patent rights co-owned by The Scripps Research Institute and Northwestern University that could form the basis for clinical tests to improve management of organ transplant recipients. TGI is planning to use the technol- ogy to develop and commercialize tests that use genomic markers of transplant graft status as part of a program to detect and respond to early signs of graft injury in patients. This licensing agreement gives TGI access to intellec- tual property related to kidney and liver transplant diag- nostics including immune status monitoring and optimi- zation. TGI says its frst test will be used to monitor kid- ney transplant recipients, indicating when treatment or biopsy is required based on analysis of a patient's blood. > Ventana, Merck KGaA to Develop CDx Test for Cancer Treatment Ventana Medical Systems entered into an agreement with Merck KGaA to develop and commercialize a com- panion diagnostic (CDx) for an undisclosed target using Ventana's diagnostic assays. In alignment with Merck KGaA's strategic approach in personalized medicine, the aim is to develop a patient-stratifying diagnostic test that can be used in multiple cancer indications. Merck KGaA will leverage Ventana's global leadership position in cancer diagnostics and expertise in CDx to achieve new levels of diagnostic clarity for the inves- tigated target. As part of the agreement, Ventana will develop and validate the CDx and ensure its readiness, availability, and adherence to FDA and other health au- thority standards for future clinical trials. n The Molecular Diagnostics Laboratory at the MD Anderson Cancer Center has taken steps to validate several NGS platforms, including the Life Technologies Ion Torrent PGM platform and the Illumina MiSeq platform. The laboratory rigorously tested several NGS-based protocols by analyzing and comparing the archival samples with known mutations and samples collected prospectively. News MOLECULAR DIAGNOSTICS See NGS on page 36