Clinical OMICS

JUL-AUG 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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Page 25 of 51

24 Clinical OMICs July/August 2019 conclusion was that "careful selection of the algorithms for each type and size range of SVs is required for accurate calling of SVs." The first author of that paper is Shunichi Kosugi of the RIKEN Center. But most of these analysis tools are not easy to use. "Most physicians cannot do this on their own," Rehm says. "A lot of expertise is needed to go from the sequence data to interpreting and validating your results." That requires bio- informaticians and geneticists with specialized knowledge. "The folks who help us do the analysis are called clinical genomic analysts," said Shimul Chowdhury, clinical labo- ratory director at Rady Children's. "They pass the analysis to the laboratory directors who are board certified genet- icists. We also have multiple genetic counselors on our team." Each case is handled by two-to-three people before it reaches the treating physician. They will comb the literature to learn about implicated variants, and then create a report that is "digestible" to non-specialists, as Chowdhury says. Another helpful advance has been cloud-based platforms, which allow companies to increase the amount of data they are working with and securely collaborate with anyone. DNAnexus offers an end-to-end genome informatics solu- tion with access to tools and datasets for clients to build and run their own analysis workflows. Researchers can stream NGS data from their instruments to the cloud and work securely there with collaborators around the globe. "We built the infrastructure to take the data from the sequencer, process and analyze it, and get it through tertiary analysis," said Richard Daly, CEO of DNAnexus. A wide range of tools, including commercial products and home-grown solutions, can operate in this cloud environ- ment, which becomes increasingly important as the amount of data being generated increases. "The unit volume is cur- rently highest in prenatal testing," Daly said. But as NGS becomes more common place, platforms like DNAnexus' will come into wider use. The company is currently work- ing with more than 30 organizations, many of whom, Daly reports, are using thousands of servers to process tens of thousands of samples per year. Other companies have invested in building knowledge- bases that can inform the process of reaching a diagnosis. Fabric, as mentioned above, has a database of more than 50,000 genes to train its algorithms. And at QIAGEN, the company has been building for more than 20 years what Scott describes as "the industry's largest knowledge base (continued from page 22) Sean P. Scott, VP business development, QIAGEN (continued on page 26) LeoWolfert / iStock / Getty Images

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