Ultra-Rare Circulating Tumor DNA Detection with PAP and Digital Bead Technologies

DESCRIPTION (provided by applicant): Diagnosis and prognosis of cancer have increasingly benefited from the use of molecular markers and molecular approaches. Accumulating lines of evidence have shown that there is tumor DNA circulating in the peripheral blood of patients with a variety of cancers. Multiple studies have shown that circulating DNA carries genetic and epigenetic alterations that are found in the corresponding primary tumors. Therefore, the presence of circulating DNA in blood is a strong dia gnostic and prognostic indicator, making blood a valuable solid tumor surrogate for non-invasive and preventive cancer diagnostics as well as monitoring of patients who are actively under cancer therapy. One of the most commonly used targets for detecting tumor DNA in blood are p53 mutations. The p53 tumor suppressor gene product (TP53) is playing an important role in early cancer initiation. Maxwell Sensors Inc. together with City of Hope National Medical Center proposes to develop a TP53-TYPER system fo r early cancer screening. The prototype TP53-TYPER will be designed to (i) amplify ultra-rare TP53 mutations within the excess of normal genomic DNA circulating in blood, (ii) capture the amplified alleles onto digitally bar-coded beads by hybridization, a nd (iii) identify, detect and quantify the amplified alleles. The technology combining Bi-directional PAP allele specific amplification (Bi-PAP) with the capture of Bi-PAP amplified TP53 somatic mutations on digital microbeads along with identification and fluorescent scanning of allele abundance, we are enabling high-throughput and high resolution genotyping to be performed in a reliable, cost-effective and time-saving manner. The combination of Bi-PAP, an amplification technology with ultra-high sensitivi ty (1 mutant DNA molecule) and selectivity (1 mutant in 109 to 1011 wild-type molecules), with addressable bead-based microfluidic detection will enable the routine use of biomarkers in blood in early clinical cancer diagnostics. The TP53-TYPER system is a menable to commercial system integration and automation for efficient large scale analyses. The Phase I work will focus on system fabrication and feasibility testing.