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Development of an automated coring and nucleic acids extraction platform for FFPE tissue blocks

  • Project Leaders: Aly Karsan, Dirk van Niekerk, Robin Coope
  • Institutions: BC Cancer (Previously BC Cancer Agency (BCCA))
  • Budget: $196949
  • Program/Competition: User Partnership Program
  • Genome Centre(s): Genome British Columbia
  • Fiscal Year: 2016
  • Status: Closed

The Provincial Health Services Authority (PHSA) is expanding clinical genomic testing to strengthen its efforts to be a leader in the use of next generation sequencing in cancer care. This growth creates ever changing pipeline bottlenecks as sample preparation, sequencing and bioinformatics capacities improve. An emerging challenge is scaling the acquisition of cores and extraction of nucleic acids from formalin fixed paraffin embedded (FFPE) tissue blocks while maintaining quality control and sample traceability. Adding quality control steps and expanding manual coring and extraction will not be sustainable as throughput grows. 
To be future ready, Drs. Aly Karsan and Robin Coope at BC Cancer have collaborated with Dr. Dirk Van Niekerk from PHSA to develop an automated platform for: coring blocks at pathologist identified targets, performing nucleic acid extraction, genetic barcode (spike-in) addition and event logging. The platform is comprised of a commercial liquid handler with application-specific hardware and software developed at BC Cancer by Department of Pathology and Laboratory Medicine and the Centre for Clinical Genomics. The coring robot was successfully developed and downstream liquid functions work as expected. The project team is planning for the next level of automation, such as automated tumor identification and automating slide and block alignment. As the robot enters production the team will continue to pursue commercialization with Coastal Genomics or through a new start up.