SUMMARY Clinical genomics is a rapidly evolving field focused on the use of genome sequencing information to guide patient diagnosis and treatment. Whole genome sequencing has been dubbed “the test to replace all genetic tests”, since one sequencing run can identify all genetic variants present in a patient's genome. Implementing clinical-grade, whole genome sequencing across large patient cohorts represents a substantial big data challenge. We will present our “Sabretooth” plan for scaling operations in our centre from an estimated 800 to 18,000 genomes per year.
Liviu Constantinescu completed his PhD in computer science at the University of Sydney as part of the Biomedical and Multimedia Information Technology Research Group, specialising in software development and multimedia technologies. His research focuses on improving the practice of healthcare through state-ofthe-art networking and software development methods. the SeqWare working group at the Ontario Institute for Cancer Research (OICR). We’ve developed an in-house adaptation of their SeqWare framework, a set of infrastructure tools designed to guarantee the correctness of sequence analysis pipelines and deploy new versions on-the-fly. This framework supports a full hierarchy of functional, scientific and regression tests; retains history and metrics for every run; and incorporates a powerful query engine for interrogating our growing corpus of genome datasets8.
Finally, a suite of agile process management and documentation tools centred around Atlassian’s JIRA3 augments our pipeline via automatic collection of business intelligence data regarding every stage of the process, guaranteeing end-to-end auditability and allowing clinical, analytical and management teams to tap into continuously updated information that traditional paper-based reporting cannot capture4. This information integrates release management, continuous integration and issue tracking, so the scope of every software and analytics change can be constantly monitored in terms of its impact on business and clinical outcomes.