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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26 Clinical OMICs January/February 2019 www.clinicalomics.com lel research arm to leverage the data for use by academic and commercial entities. The data and associated dis- coveries will allow NHS to continu- ally improve its service to patients. It was the focus on both research and clinical care and how the two disciplines feed off of each other, and depend on one another that drew Tom Fowler to Genomics England. "I was working as a regional epide- miologist investigating infectious dis- ease outbreaks. When the opportunity came up to work at Genomics England and the 100,000 Genomes Project, it was about being able to influence healthcare transformation," said Fowler, deputy chief scientist and one of the organi- zation's key liaisons with NHS for the project. "I'm a firm believer that a lot of healthcare transformation is bringing research and clinical practice closer together and embed- ding the two together." At launch, the intention was to split rare disease and can- cer sequences roughly 50-50. But soon after starting sam- ple collection in cancer, Fowler and his team noticed that what worked for most research settings was not going to fly for the clinic, namely relying on FFPE tissue samples. Long used by clinicians and researchers alike, the FFPE samples provide advan- tages for storing human tissue and often aid in com- paring samples taken at different times to track the progression of the disease. But sequencing of these samples was often pan- el-based for a small hand- ful of genes, activities that are often not affected by the known degradation and fragmentation of DNA that results from the tissue fixing process. At the beginning of the pilot, Fowler said they experi- mented a bit with tumor sample types—both FFPE and fresh frozen—in the hopes they could use FFPE since it is easier to store and transport. "It would have made our lives a lot eas- ier if we had been able to use FFPE samples," Fowler noted. "Although we found ways to optimize the FFPE process— to mean we got better results—the comparison to the fresh frozen made it clear the only viable option was to get fresh frozen working" as the samples to use for cancer patients. The decision to ditch FFPE blocks shut down cancer patient recruitment for the project for about a year and is what led to the a split of roughly 60 percent rare disease genomes and 40 percent cancer genomes in the final tally. The development of new sample collection and handling pathways largely fell to NHS workers in the field within each of the 13 regional recruitment areas for the project, which required new equipment, sample collection protocol and a revamped consent protocol due to the significant dif- ferences of managing and handling fresh frozen samples. "I pay tribute to the frontline NHS workers because on top of all their normal activity, they did a lot to figure out how this should work," said Fowler. Over the course of a few months, Fowler witnessed a progression of each region's ability to provide viable samples for sequencing. Parallel to solving the logistical questions for nationwide collection of the relatively fragile samples, Genomics England research- ers were experimenting with different methods of freezing them to determine whether it impacted sequencing quality, as well as how long samples would maintain their integrity using different shipping methods. "I'm not sure what the exact number is officially but we are now at a point where we are getting 400 fresh frozen samples coming through per week, and we never imagined we'd get to those numbers," Fowler said. While each of the 13 regional centers solved sample col- lection individually to get sample flowing again for the pilot, best practices have since been distilled to a system- atized method that can work across the entire NHS. Education and Training Central to delivering an effective program of genomic (continued from previous page) (continued on page 29) Gemma Chandratillake, East England training lead, NHS

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