The Diagnostic Laboratory Services Enhances Variant Analysis & Streamlines Patient Treatment Matching with GenomOncology
As an affiliate of the Queen's Health Systems, the Diagnostic Laboratory Services, Inc. (DLS) is the largest, locally-owned clinical laboratory in Hawaii. To further advance the cancer care available in Hawaii, DLS established an enterprise-level multidisciplinary project to create a testing service in support of Queen’s innovative precision medicine program. This precision medicine program provides cancer patients access to more targeted and relevant cancer treatment options in order to ultimately improve their patient care.
In early 2021, DLS implemented the GenomOncology (GO) Pathology Workbench to streamline variant analysis, validation, and overall support for the TruSight Oncology 500 assay, performed on the Illumina NextSeq 550, in an effort to enhance the Queen’s Medical Center’s precision medicine program. The GO Pathology Workbench is an end-to-end software solution that integrates directly with lab sequencers in order to annotate detected variants, match potential clinical trials and therapies, and create a comprehensive summary report that can be integrated directly back into a patient’s record for further review.
During implementation, the GenomOncology team customized the GO Pathology Workbench to pull in and prioritize institutional trials in order to ensure an effective analysis workflow. Due to these customizations, the DLS team is able to make informed variant interpretations, as well as gain insight into institutional and geolocated clinical trial availability. Understanding what treatment options are available within their network is essential to ensuring their patient population has access to the best cancer care within their community.
The GO Pathology Workbench Improves Patient Cancer Care
Since implementation, the GO Pathology Workbench has proven successful for the DLS team, specifically in the recent case of a patient who had been diagnosed with metastatic liposarcoma. When this patient got sick, the clinicians had her tumor sequenced so they could further examine her diagnosis. Once sequenced, the DLS team ran the sample results through the GO Pathology Workbench for analysis and validation, and the solution picked up a single nucleotide mutation with high variant allele frequency and a CDK6 amplification. The GO Pathology Workbench was customized to specifically search within the Queen's Health System's affiliated clinical trial network. With these two mutations identified, the GO Pathology Workbench was able to automatically match the patient to two targeted clinical trials within the institution’s clinical trials portfolio.
The variants were also then reviewed by the clinical trial's Molecular Tumor Board for further review. In their Molecular Tumor Board meeting, the clinicians examined the two matched clinical trial options that output from the GO Pathology Workbench, and selected one of the clinical trials for the patient to enroll in based on the evidence provided and their overall expertise and knowledge. Today, this patient is currently enrolled in the selected institutional clinical trial.
The GO Pathology Workbench system’s auto-classification of the variants, based on both the ACMG classification system and the somatic tiering system from AMP/ASCO/CAP, simplified the reporting and prioritization for the DLS team. Also, the included annotations and insights provided the DLS team all the information necessary for variant interpretation right at the click of button, ultimately reducing the overall time for analysis and treatment identification.
“The GO Team was meticulous in tailoring the Pathology Workbench to our needs and interests. This is a living process. The monthly GO update meetings allow us to continually improve the Pathology Workbench as the field and targets change. This is extremely helpful as we adopt homologous recombination deficiency reporting. The Pathology Workbench gives us the flexibility and knowledge necessary to make informed treatment decisions.
In this case, without the GO Pathology Workbench, the two targetable variants may not have been identified, reducing the chances of the patient ever knowing about the matched clinical trial. The solution not only provides insight into what variants are identified and why, it also automatically matches these patients to relevant, open clinical trials available within our network, which will ultimately improve overall patient cancer care within our community,” said Dr. Christopher Lum, Medical Director for Molecular Diagnostics, DLS.
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