Parallel and high throughput isolation of cfDNA to target detection of rare, highly conserved nucleotide polymorphisms

Blood contains a wealth of biomarkers that can be potentially used to diagnose cancer at early stages and to successfully manage its treatmentBiomarkers include circulating tumor cellsCTCscell free DNAcfDNAand extracellular vesiclesEVswhich comprise theliquid biopsyportfoliooriginate from the developing primary tumor and the metastatic sitesHoweverthe disease associated blood based biomarkers are rareand the isolation of each from aliquid biopsyrequires different approachesThusthe development of new technologies that afford efficient and cost effective isolation of each biomarker holds the key to advancing precision medicine approaches for individualizedpatient specific careand treatmentBioFluidica has demonstrated a platform with superior performance capabilities of the isolation of CTCs using microfluidic technologyBuilding on this technologythe objective of this Phase I proposal is to develop a novel microfluidic platform and operational peripherals for the automatedsolid phase extractionSPEof cfDNALeveraging our previous successwe will develop a SPE microfluidic chip for the efficient isolation of cell free DNA fragments from plasmaAimThe microfluidic chip will be made from polycarbonate that can be moldedallowing for high scale production at low costThe chip will be designed to accommodate pipette tips associated with an FDA compliant liquid handling station to automate operation of the chipAimWe will demonstrate the utility of our microfluidic chip by enriching cfDNA isolated from plasma spiked with cfDNA containing mutant alleles of several oncogenes ranging fromEnriched cfDNA will be analyzed by a highly sensitive ligase detection reactionThe final SPE product will enrich cfDNA with high recovery and reproducibilityprovide high specificity and high throughputand be an automatedcost effectiveand commercially viable technology Blood based liquid biopsies are emerging as the preferred approach to manage a variety of cancer related diseasesall from a simple blood drawIn this proposalwe aim to develop a cost effective and highly efficient approach for the isolation of cell free DNAcfDNAusing an automatic microfluidic approachThis technology will advance a patient centricprecision medicine approach to diagnose and improve treatment success for patients with a variety of cancer related diseases