Blood biopsy test for pan-cancer mutations with error-checking probes Confidential PI: Shafer, David A., PhD PROJECT SUMMARY GeneTAG Technology (www.genetagtech.com) has developed a series of molecular diagnostic assays for cancer and infectious diseases based on DNA amplification and proprietary detection methods. Our primary system, internal DDS (iDDS) probes, comprises two interacting components, a fluor-labeled probe and a quencher-labeled antiprobe nearly complementary to the probe. In the absence of the intended target, paired probes and antiprobes bind together, quenching fluorescence and preventing off-target detection. This unique system provides highly specific single-base discrimination over a wide temperature range (10?30C). Recently, we merged iDDS probe technology with Wild Terminator (WTx) methods to enable detection of low-abundance mutants by blocking amplification of the wild-type sequence (patent pending). By combined these technologies, we can reliably detect single-base variants of numerous targets at trace levels (0.01%) in a background of wild type genomic DNA. This enhanced qPCR sensitivity meets or exceeds the sensitivity of specialized platforms (such as droplet digital PCR, next-generation sequencing [NGS], and MALDI-TOF), which have been used to study rare mutations in the plasma of cancer patients. Our primary goal is to develop a pan-cancer screening test based on this combined method. This new method should enable the detection of low frequency diagnostic driver mutations in the blood that derive from a somatic tumor located elsewhere in the body. Our probes can reliably detect specific mutations that are indicative of a particular cancer or of a drug resistant variant. By covering ten or more of the common cancer-specific mutations in one assay we can identify the presence of an unknown cancer at an early stage, and in some cases, we can pin-point which cancer is likely.
The Specific Aims of this Phase I grant are: 1, to test and compare selective-amplification methods for detecting low- abundance, pan-cancer driver mutations and 2, to develop and test a prototype assay for pan-cancer driver mutations in plasma based on iDDS probes and selective amplification. To demonstrate feasibility, we will study pan-cancer mutations in plasma samples from early- and late-stage patients with cancers that show high levels of ctDNA, such as neuroblastoma, prostate, ovarian, colorectal, hepatocellular, and breast cancer. Our long-range goal by the end of Phase II is to market a generalized test for ~100 circulating cancer biomarkers (actionable and drug-resistant variants), based on a synthesis between WTx, iDDS, NGS, and statistical methods. Such information would guide physicians in follow-up testing and selecting appropriate first-line targeted therapy. This, in turn, would provide a public health benefit by enabling early cancer detection through a non-invasive approach.
Blood biopsy test for pan-cancer mutations with error-checking probes Confidential PI: Shafer, David A., PhD PROJECT NARRATIVE GeneTAG Technology specializes in developing molecular diagnostic assays for cancer, with high sensitivity and unparalleled specificity. We have also developed selective amplification methods that enable detection of low-abundance cancer-specific mutations (0.01%) in a background of genomic DNA. The combination of these methods enable the detection of common cancer related mutations that are shed by a somatic tumor into circulating blood. Our goal is to develop a blood-based ?liquid biopsy? assay to screen for 10 or more cancer- specific mutations that are indicative of a high cancer risk, or that identifies a specific cancer probability. Such a test could be employed on a routine basis or as part of an annual physical exam, and would provide an enormous benefit to public health. The Specific Aims of this Phase I grant are: 1) to test and compare selective-amplification methods for detecting low-abundance, pan-cancer driver mutations and 2) to develop and validate our prototype assay for pan-cancer driver mutations in plasma genomic DNA samples. Success in Phase I will enable early cancer detection through a non-invasive approach, and it will justify expanded Phase II studies with ~100 circulating cancer biomarkers (actionable and drug-resistant variants) in preparation for FDA approval.
