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Rapid Evolution of a clinical high-throughput DNA sequencing pipeline to next-generation sequencing

  • Project Leaders: Aly Karsan
  • Institutions: BC Cancer (Previously BC Cancer Agency (BCCA))
  • Budget: $400000
  • Program/Competition: Strategic Opportunities Fund
  • Genome Centre(s): Genome British Columbia
  • Status: Closed

Recent developments in DNA sequencing technologies have changed the way scientists collect and interpret genomic data as these “next-generation sequencers” can generate at least 1000x the throughput of older machines and are more than 300x more cost effective. These projects have been capitalizing on the capacity of next-generation sequencing devices and develop applications that will be of significance to a broad spectrum of biological and medical studies. For instance, the Centre for Clinical Diagnostic Genomics (CDG) at the PHSA is the first clinically accredited laboratory in Canada to use these next-generation sequencing devices for the routine clinical testing of the BRCA1 and BRCA2 breast cancer genes.  The technology delivers results faster, which means therapy decisions are made more quickly. Following on that success another project aimed at establishing a process to screen the entire 14-gene panel that covers the repertoire of genes examined by the Hereditary Cancer Program (HCP) at the BCCA. The Raindance Sheared design, as validated for clinical use through this project, was chosen for immediate clinical implementation at the BCCA due to excellent clinical performance metrics. This methodology achieves a near identical cost point to that of the current BRCA1/2 assay for the target clinical batch size of 24 samples, while interrogating an additional 12 genes. The avoidance of serial testing and costs associated with that process will result in net savings to the system, while offering enhanced patient care – the key to sustainable clinical service in the face of increasing demand. This is the first group in Canada to offer this type of testing, further establishing their role as a centre of excellence in clinical genetic and genomic testing.  Note that commercial entities offering similar products have relatively higher price points.  The Raindance DirectSeq design shows promise as a near-future implementation to provide faster turnaround time and potentially lower cost and will continue to be investigated.