Blood biopsy test for pan-cancer mutations with error-checking probes

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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 (10–30ºC). 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.