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Centre for Clinical Genomics (CCG), located at the BC Cancer Agency, pioneers in providing high-throughput next-generation sequencing (NGS) assays for cancer as well as non-malignant conditions to the patients in BC and other provinces. Increasing clinical workload at the CCG has slowed development of new assays and led to a buildup of manual approaches within the clinical bioinformatics pipeline, thereby hindering the development of tracking and analysis tools to improve turnaround times for variant reporting.

To address these issues by automating the bioinformatics pipeline, this Health Strategy Exemplar Pilot project achieved three goals:

1. Automated the analytic portion of the clinical bioinformatic pipeline to reducing hands-on bioinformatics time and curation time from 10-14 working days to less than one day, thereby lowering turnaround time for somatic cancer and germline testing.

2. Developed a web-based client interface for clinical specimens, reporting and report delivery.

3. Automated continuous quality improvement activities to reduce hands-on time spent on quality assurance activities, as well as number of process deviations and nonconformances in the CCG pipeline.

These optimizations have allowed for the development of additional cancer-testing assays with expanded gene sets. Novel assays are in development based on the foundational work implemented in this project.  The streamlining of the bioinformatic pipeline has significantly reduced turnaround time and increased patient sample throughput to improve accessibility to clinical genomics by BC patients.