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Issue link: https://clinicalomics.epubxp.com/i/827649
16 Clinical OMICs May/June 2017 www.clinicalomics.com Diagnostics Next-Gen Diagnostics Thermo Fisher Scientific, University Hospital Basel Partner to Develop, Validate NGS Cancer Diagnostics Alex Philippidis, Senior News Editor A partnership launched by Thermo Fisher Scientific with the Insti- tute of Medical Genetics and Pathol- ogy at University Hospital Basel aims to accelerate clinical research into oncology and immuno-oncology by developing and validating next-gener- ation sequencing (NGS)-based cancer diagnostics. The Institute is the first partner in Thermo Fisher Scientific's Next Gen- eration Sequencing Companion Dx Center of Excellence Program. The Institute will serve as one of the pro- gram's global sites focused on devel- oping and refining Thermo Fisher Scientific's NGS-based research assays from its Oncomine oncology portfolio, with the goal of eventually introduc- ing them into clinical use as compan- ion diagnostics. Both organizations are cooperating in forming global alliances and strate- gic partnerships with hospitals, test- ing facilities, and biopharma groups. "The partnership with Thermo Fisher will further enhance our poten- tial by increasing our throughput capacity up to several thousand sam- ples per year, thus allowing us to be able to satisfy the typical needs of large international multicenter trials," Markus Tolnay, M.D., manager of the Institute, told Clinical OMICs. "Even- tually, new gene panels tested within the context of a clinical trial could expedite the routine molecular diag- nostic setting." The partnership envisions intro- ducing new solu- tions for routine genomic analy- ses, such as gene panels in sarcoma and CNS tumors, as well as improv- ing current bioinformatic pipelines for complex variant calling. "We intend to increase both sensitivity and specificity of currently used kits and increase the quality of data produced by Thermo Fisher instruments," Dr. Tolnay added. He said the Institute's contributions will include its experience in human Formalin-Fixed Paraffin Embedded (FFPE) tissue handling and its Insti- tute BioBank of tissues, consisting of about 3.2 million FFPE blocks and some 35,000 fresh frozen samples from a variety of pathological and normal tissues. The Center of Excellence builds on previous collaborations by the Insti- tute and Thermo Fisher Scientific. About three years ago, the Institute concluded Thermo Fisher 's Ion Tor- rent sequencing system could best address testing limited material from FFPE tissue. The Institute was among the first in Europe to switch from Sanger sequencing to NGS for routine genomic profiling of cancer patients. That transaction led to other efforts, from working to improve commercial- ized NGS-related solutions, such as the company's Ion Reporter software, to participating in early access cus- tomer programs involving Oncomine. A year ago, the Institute began using Oncomine's liquid biopsy panels and immune response panels in immuno- therapy applications. The Institute is one of 11 institutions within a network of researchers organized by Thermo Fisher Scientific, called the OncoNet- work Consortium. Initial promising results from that collaboration were presented in April at the Associa- tion for Molecular Pathology (AMP) Global Congress on Molecular Pathol- ogy in Berlin. "The Institute has served as an early access opinion leader, and has been approached by many other groups outside of Switzerland to receive clin- ical training on their technology. They also worked with other hospitals who hadn't yet had access to the technol- ogy, to help patient decision-making," said Mark Stevenson, president of life "We intend to increase both sensitivity and specificity of currently used kits and increase the quality of data produced." — Markus Tolnay, M.D.