OnkoSightTM Technical Process
OnkoSightTM is a completely custom built assay and bioinformatics pipeline, unlike most off-the-shelf kits on the market today. OnkoSightTM is designed to be more sensitive, cost-effective, and actionable than competing products.
Click on any step in the OnkoSightTM technical process below to learn more
TISSUE PROCUREMENT
- Each bone marrow collection kit will have a dedicated EDTA tube for specimen collection. This tube is labeled in bright green with GENOMICS TESTING to assist with proper specimen routing.
- For solid tumors, GenPath’s Block Retrieval Department will coordinate specimen retrieval for all OnkoSight cases, and ensure that blocks are returned.
TISSUE REVIEW
- For myeloid disorder testing, either GenPath will complete the specimen work-up (if ordered) to confirm diagnosis and disease presence, or, if GenPath is not doing the work-up, pathology results must be submitted with the specimen. GenPath will then confirm the diagnosis and sample adequacy before proceeding with testing to avoid false negative results.
- For solid tumors, a GenPath molecular pathologist will review an H&E slide for every case to ensure that: 1) a tumor is present, 2) tumor nuclei are present in >10% of cells, and 3) the most appropriate section of tissue is tested.
DNA ISOLATION
- For myeloid disorders, DNA is isolated from the blood or bone marrow, typically taking between 2-4 hours.
- For solid tumors, samples are incubated overnight to increase the overall DNA yield from the FFPE tissue. For small samples, GenPath may increase the incubation period to maximize the amount of DNA isolated from the sample.
DNA QUALITY CONTROL
- Nucleic acid derived from fresh tissue like blood and bone marrow is generally high quality. Receiving inadequate amounts of blood or bone marrow is typically the only difficulty in ensuring there is enough DNA to run OnkoSight; 2-4 mL of blood or bone marrow is requested.
- For solid tumors, tissue fixation can damage DNA. Many competitors run their NGS panels on all specimens regardless of DNA quality. GenPath, on the other hand, has devised stringent quality control protocols to ensure DNA quality and amount is sufficient to increase overall success rates. If GenPath scientists deem the DNA insufficient, we will communicate with clients early in the testing process.
LIBRARY PREPARATION
- For myeloid disorder testing, our library preparation utilizes an Illumina kit that has been enhanced with GenPath customizations.
- For solid tumor testing, GenPath built a proprietary technology that has been optimized to work with very low DNA input amounts.
These custom library prep solutions allow GenPath to work with small and poor quality specimens as well as to provide flexibility to build upon our existing test offerings.
SEQUENCING
- OnkoSightTM Myeloid Disorder and Solid Tumor panels are sequenced on the Illumina platform. This technology has a low false positivity rate for insertion and deletion mutations and sequences every DNA molecule in both directions for improved accuracy compared to competitor products that only sequence in one direction.
BIO – INFORMATICS
- GenPath’s bio-informatics pipeline is OnkoSightTM Analytics, a proprietary set of algorithms that find mutations in the millions of reads that come off the sequencer. OnkoSightTM Analytics is designed by a clinician and has undergone grueling quality measures to increase accuracy and decrease false negative results. Most labs use off-the-shelf panels and bio-informatics software; there is no standard for validating that their informatics is producing accurate results.
REPORT GENERATION
- OnkoSightTM reports are designed to provide clinically relevant information for optimal patient management. Reports will be clearly classified as ABNORMAL, NORMAL, or, rarely, as VARIANT OF UNKNOWN SIGNIFICANCE.
Each variant detected by ClearView Analytics is annotated with our dynamic knowledge database. Each night, this database is updated with the most recent national guidelines, prognostic associations, available therapies, and clinical trials so that the reports GenPath releases are up-to-date and actionable. Clinical trials are specific to the mutation(s) found in the patient’s tumor.
POPULATION ANALYTICS
- Through our population analytics, healthcare providers can track patient results as they relate to their entire patient population. Equipped with analytical tools, healthcare providers can easily identify cohorts of patients eligible for new clinical trial enrollment. GenPath is also willing to engage clients on collaborative projects and publications.
