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Automation of the Clinical Bioinformatics Pipeline at the Centre for Clinical Genomics

  • Project Leaders: Aly Karsan
  • Institutions: BC Cancer (Previously BC Cancer Agency (BCCA))
  • Budget: $1999999
  • Program/Competition: Health Exemplars
  • Genome Centre(s): Genome British Columbia
  • Fiscal Year: 2016
  • Status: Closed

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. In addition, there are significant information technology barriers when disparate systems across multiple sites, networks, and jurisdictions need to seamlessly and accurately exchange patient information. Compounding to this is the requirement for frequent upgrading and testing of new tools to maximize process efficiencies.


To address these issues by automating the bioinformatics pipeline, the Health Strategy Exemplar Pilot project aims to achieve three goals:

1.    Automate the analytic portion of the clinical bioinformatic pipeline to reducing hands-on bioinformatics time and curation time from 6-8 working days to 1-2 days, thereby lowering turnaround time for somatic cancer and germline testing.

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

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


Overall, the project will create a simple web-based process to receive patient information from clinicians requesting a genomic test, analyse the resulting data in an automated and quality controlled fashion, and then integrate patient demographics and analysis results into an intuitive report accessible via the same web-tool the clinician used to submit the sample. Such an intuitive and accessible interface will transform the BC Healthcare system by providing clinical NGS to the citizens of BC in a sustainable manner.