Case Study

Automating and configuring high performance clinical genomics workflows

Situation
  • One of the most innovative healthcare organizations (1.6m patients per year) aims to advance their personalized medicine efforts, maintaining their status as a center of excellence across treatment areas of rare diseases, cancer care, and transplants
  • This goal requires a robust IT framework with several integrated technologies covering different needs such as genomics, with a supporting interoperable research infrastructure
  • They have invested in new technology (Illumina NovaSeq 6000) to enhance personalized care delivery by focusing on integrating NGS-based genetic testing into clinical workflows, scaling up throughput and automating data processing and interpretation
Challenge
  • Fragmented, highly manual and low output lab process for genetic data production and reporting for clinical use
  • Data management and integration needs have surpassed the capacity of existing internal software, there is a need to upgrade and automate workflows
  • In order to perform comprehensive genetic testing, research panel data is not enough, so the organization needs to scale up and automate processes to support exome/whole genome level studies
  • This is a CLIA accredited lab that requires high level of documentation and quality control for utmost efficiency which can be disrupted and is affected by unreliable manual process
Actions
  • Scalability and Flexibility in Data Processing
    • Achieved how?
      • Elasticity of Cloud
      • Control of GATK pipelines to bioinformaticians
  • Quality Assurance of NGS Data
    • Achieved how?
      • Automated QC using laboratory SOPs
      • Approval tracking
  • Variant Interpretation Per Guidelines
    • Achieved how?
      • Automating guideline based ACMG and ASCO reporting
  • Adherence to Regulatory Requirements
    • Achieved how?
      • ISO standards
      • In Vitro Diagnostic (IVD) Medical Devices Classification
Impact
  • BC Platforms enabled growth, positioning this organization to connect healthcare and research insights for better care
  • Clinicians are able to draw conclusions for patient care improvement, based on high throughput genetic testing that supports risk assessment, accurate diagnosis, and tailored treatment plans for cancer patients
  • Developed a repeatable and scalable process from raw data to seamless reporting, enabling effective preventative medicine as germline sample whole genome analyses can be reused continuously to reveal latest health insights 
  • Latest scientific advancements and experimental data integrated into daily clinical practice, enabling the infinite loop between patient care and research discoveries as data on outcomes flows back into the system to inform drug development