Clinical cancer trials are a key element of cancer research at Huntsman Cancer Institute (HCI), and they increasingly require newly discovered molecular diagnostics testing not yet available as Clinical Laboratory Improvement Amendments (CLIA) certified tests. CLIA certification is a complex process requiring an average of a year or more per assay, which is too long for clinical trials attempting rapid deployment of new discoveries for cancer patients. The Biorepository and Molecular Pathology Shared Resource was developed to enable pre-CLIA certified patient molecular testing to support clinical research at HCI.
Once a patient is consented on a clinical trial, the Biorepository and Research Histology sections of the BMP Core facilitate rapid specimen procurement of either fresh, frozen, or FFPE tissue. A staff pathologist verifies the diagnosis and identifies the specimen or tumor area for molecular testing. Information about the patient and specimen are entered into itBioPath, a biospecimen tracking database, and a request for testing is submitted through GNomEx, a LIMS and data repository system. After receiving the specimen, the Molecular Diagnostics Laboratory isolates DNA and performs the genetic testing. A staff scientist analyzes the data and generates an easy-to-read report for the clinical research coordinator to provide to the requesting clinician. Both the molecular testing report and results are uploaded to GNomEx, which enables future queries of the genetic data that is linked to the patient via itBioPath.
The Molecular Diagnostics Laboratory is currently performing genetic testing of consented patient specimens for several investigator-initiated clinical trials at HCI utilizing the Sequenom MassArray and Illumina MiSeq.
Sequenom Clinical Research
The Molecular Diagnostics Laboratory utilizes the Sequenom MassArray for SNP genotyping and somatic mutation profiling of clinical trial specimens. A pipeline has been developed to obtain specimens from consented patients, isolate DNA, perform sequencing, and generate a report within 1-2 weeks.
The Molecular Diagnostics staff will work with clinical researchers to develop custom SNP genotyping or Somatic Mutation panels utilizing the Sequenom MassArray. The main advantage of this technology is the ability to go from DNA to data in one day, which makes it well suited for clinical research. After a new panel has been developed, initial validation studies are performed to determine the sensitivity, reproducibility, and lower level of detection of the assay. Upon completion of the initial validation studies, the Molecular Diagnostics laboratory will perform analysis of clinical trial specimens in real time.
If you are interested in utilizing the Sequenom MassArray in your clinical trial, please contact us.
Illumina MiSeq Clinical Research
The Molecular Diagnostics Laboratory has access to an Illumina MiSeq for targeted next-generation sequencing of clinical trial specimens. A pipeline has been developed to obtain specimens from consented patients, isolate DNA, perform sequencing, and generate a report within 2-4 weeks. The rapid turnaround time enables real time analysis of specimens from consented patients enrolled in prospective clinical trials.
The Molecular Diagnostics staff will work with clinical researchers to develop custom enrichment panels for sequencing specific regions of interest using the Illumina MiSeq. The MiSeq is a benchtop sequencer capable of generating upwards of 15 Gb of output in approximately 24 hours, making it ideally suited for rapid turnaround of clinical research specimens. Once the custom design process is complete, initial validation studies are performed to ensure efficient target area enrichment and identify optimal sample multiplexing levels to achieve adequate coverage. In addition, a robust bioinformatics data analysis pipeline is developed to facilitate generation of a sequencing report. Upon completion of the initial validation studies, the Molecular Diagnostics Laboratory will perform analysis of clinical trial specimens in real time.
If you are interested in utilizing next-generation sequencing in your clinical trial, please contact us. For sequencing of research specimens using the Illumina MiSeq, please submit a request to the High-Throughput Genomics Core Facility at HCI.
Any data generated by the Molecular Diagnostics Laboratory are for research purposes only. The results are Not CLIA certified and cannot be used for standard-of-care treatment decisions.