→ Poster doi:10.7490/f1000research.1112591.1
John H. Letaw, Carol Beadling, Julja Burchard, Charles Scott Dahl, Andrew Hadd, Douglas King, William Moore, Mandy Terrill, Jane Thanner, Richard Press, Sue Richards, Christopher L. Corless, Oscar BarneyAbstract
Clinical laboratories have begun to offer a range of next-generation sequencing services to bring precision medicine to patients. Delivering secure, cost-effective, timely, clinically informative results from precision-medicine assays requires an end-to end integrated system. At Oregon Health and Science University, we have designed such a system and reduced it to practice. We describe here the system, the steps of its implementation, and selected use cases spanning from the sequencing of a patient sample to the creation of a report that is handed off to the physician. The first step in the process is properly validating a single invocation of a clinical sequencing analysis workflow against known results. Second, these sequencing analyses are documented and certified, in accordance with CLIA (Clinical Laboratory Improvement Amendments) and CAP (College of American Pathologists) regulations. Third, we engineered a robust process to encapsulate the certified analyses using the Galaxy platform as a workflow engine. Fourth, a team from our ITG (Information Technology Group) team built a Clinical Genomics Database (CGD) that allows us to collect, annotate, and report from automated, Galaxy-managed, CLIA/CAP certified pipelines to clinicians, in a convenient and organized manner. The CGD also collects and disseminates all current and relevant clinical genomics knowledge to provide decision support to our physicians and geneticists. The CGD has been successful in streamlining sequence data analysis, partnered with the Galaxy platform. We illustrate benefits of our system to patients, clinicians, and researchers.