McDonnell Genome Institute’s CAP-accredited, CLIA-licensed environment provides clinical sequencing services.

Through work with large-scale projects such as The Cancer Genome Atlas (TCGA), MGI developed a validated assay that may provide clinicians with better tools for the treatment of acute myeloid leukemia (AML). Current trials with Siteman Cancer Center are ongoing, with plans to expand with Washington University clinicians.

Assays

MGI offers the following assays:

NGv3+RMG-1

Custom exome sequencing with tumor/normal variant detection and known variant analysis in a patient-matched follow-up sample, as well as a limited germline analysis for incidental findings.

Targeted cancer panel (CCGSv3.2)

Targeted hybridization capture of tumor-derived genomic DNA coupled with next-generation sequencing (NGS). This approach enables deep, comprehensive coverage of all coding exons and key introns of ordered genes, and allows assessment of the molecular complexity of each DNA specimen, minimizing sampling bias even in cases of low DNA mass or quality.

Variations detected:

  • Single nucleotide variants (SNVs)
  • Small insertions and deletions (indels)
  • Selected larger indels
  • Structural rearrangements involving selected genes

For solid tumors, this test is routinely performed using FFPE tissues and is able to detect SNVs under 10% allelic fraction in the sequenced tissue.

MyeloSeq

A targeted sequencing assay for 40 genes and gene hotspots that are recurrently mutated in acute myeloid leukemia and myelodysplastic syndrome using UMI-based targeted sequencing with the Agilent HaloplexHS.

IDT Exome

Exome sequencing of a tumor/normal sample pair with automated tumor-associated SNV and small coding indel variant detection.

Additional resources

Dedicated laboratory space, equipment and personnel

  • Laboratory supervisor and four clinical laboratory technologists

  • Automated DNA extraction, library preparation and target enrichment

  • Illumina sequencers: Two HiSeq 2500s, MiniSeq, NovaSeq

Fully compliant with CLIA regulations and CAP accreditation requirements

  • Extensive documentation infrastructure
  • Electronic quality control management plan for laboratory and informatics
  • Regular internal and external inspections to ensure compliance

Workflows in place for assay validation to establish performance

  • Coverage requirements, sensitivity, specificity, positive predictive value
  • Analysis pipeline development
  • Assay quality control and management
  • Creation of test protocols for all relevant specimen types