SBIR-STTR Award

This SBIR Direct Phase II project will produce a complete platform to perform nucleic acid quantification (NAQ) by digital polymerase chain reaction (dPCR). The platform will consist of a complete instrument that handles devices and executes all phases of the assay (digitization, amplification, and detection) in one instrument, offering true “walk-away” capabilities within a closed system. It will also include a consumable chip specifically tailored to high-sensitivity applications such as circulating tumor DNA (ctDNA) research and diagnostics, a rapidly growing market projected to exceed $6 billion by 2020. The platform will be valuable for biomedical research and clinical diagnostic applications, with specific health related impact in areas such as cancer diagnostics and treatment monitoring, infectious disease diagnostics, viral load monitoring and more. The platform is based on Self-Digitization (SD) technology; a simple, robust method that efficiently uses a network of channels and wells to spontaneously partition samples into an array of predefined compartments. This platform is ideally suited for digital polymerase chain reaction (dPCR) applications. dPCR works by partitioning samples into hundreds, thousands, or even millions of individual volumes where each volume may or may not contain target DNA. Only volumes with target DNA give a positive signal resulting in a “digital” yes/no signal, from which Poisson statistics can then give direct determination of sample concentrations. Digital PCR directly provides absolute quantification, is robust against variations in reaction efficiency, is incredibly sensitive, and has nearly unlimited resolution capabilities, making it technically superior to the current NAQ “gold standard” of qPCR. However, no commercial dPCR system is currently able to be compete with qPCR because of issues with workflow, throughput, and cost. Among dPCR platforms, the SD mechanism is uniquely suited to efficiently handle large sample volumes, which provides a strong value proposition in high- sensitivity applications, and allows for direct competition with qPCR based assays, providing a path to compete in both the dPCR and qPCR market. The primary objective of this proposal is to produce a platform that overcomes the workflow, throughput, cost, and flexibility hurdles that have limited existing commercial dPCR systems, particularly in their inability to penetrate the larger “real time” or qPCR market. The first Aim will be development and construction of the instrument, including a digitization mechanism that will prepare 96 samples in parallel, a high-speed thermalcycling system, an imaging system to rapidly analyze samples, and integrated software to enable all stages from a single “go” command. The second Aim will be development of materials and device designs to enable manufacturing of commercially viable devices. The third Aim will encompass validation of the platform with clinically relevant and valuable NAQ assays. Specifically, it will be validated with an assay relevant to ctDNA research and diagnostics.

Public Health Relevance Statement:
Project Narrative This research will generate a digital PCR (dPCR) platform to perform nucleic acid quantification (NAQ), consisting of a stand-alone instrument with “walk-away” capabilities, and commercially viable devices to perform high-sensitivity assays. This instrument will offer unrivaled workflow capabilities and cost profiles that will transform the dPCR market and enable inroads into the larger qPCR market. It will impact and enable many biological research and clinical applications including cancer diagnostics and treatment monitoring, infectious disease detection, and viral load monitoring.

Project Terms:
abstracting; Address; Air; amplification detection; Area; Automation; base; Biological Assay; biological research; Biomedical Research; Blood; Cancer Diagnostics; cancer therapy; Characteristics; Clinical; clinical application; clinical diagnostics; clinically relevant; Communicable Diseases; Complex; Computer software; Convection; cost; Data; design; Detection; Development; Device Designs; Devices; Diagnostic; Diagnostics Research; digital; DNA; DNA amplification; Drops; Error Sources; flexibility; Glass; Gold; Growth; Health; Hybrids; imaging system; improved; Individual; instrument; Investments; Licensing; Life; Lighting; liquid biopsy; Manuals; manufacturing process; Marketing; Materials Testing; Methods; Microfluidic Microchips; Microfluidics; Modeling; Monitor; Nucleic Acids; Patients; Performance; Phase; Polymerase Chain Reaction; Positioning Attribute; Production; prototype; Pump; Reaction; relative cost; Reproducibility; Research; Resolution; Running; Sampling; scale up; Signal Transduction; single molecule; Small Business Innovation Research Grant; Source; Speed; Staging; Standardization; statistics; System; Technology; Time; tumor DNA; Uncertainty; Universities; Validation; Variant; Viral Load result; Walking; Washington; Work

This SBIR Direct Phase II project will produce a complete platform to perform nucleic acid quantification (NAQ) by digital polymerase chain reaction (dPCR). The platform will consist of a complete instrument that handles devices and executes all phases of the assay (digitization, amplification, and detection) in one instrument, offering true ?walk-away? capabilities within a closed system. It will also include a consumable chip specifically tailored to high-sensitivity applications such as circulating tumor DNA (ctDNA) research and diagnostics, a rapidly growing market projected to exceed $6 billion by 2020. The platform will be valuable for biomedical research and clinical diagnostic applications, with specific health related impact in areas such as cancer diagnostics and treatment monitoring, infectious disease diagnostics, viral load monitoring and more. The platform is based on Self-Digitization (SD) technology; a simple, robust method that efficiently uses a network of channels and wells to spontaneously partition samples into an array of predefined compartments. This platform is ideally suited for digital polymerase chain reaction (dPCR) applications. dPCR works by partitioning samples into hundreds, thousands, or even millions of individual volumes where each volume may or may not contain target DNA. Only volumes with target DNA give a positive signal resulting in a ?digital? yes/no signal, from which Poisson statistics can then give direct determination of sample concentrations. Digital PCR directly provides absolute quantification, is robust against variations in reaction efficiency, is incredibly sensitive, and has nearly unlimited resolution capabilities, making it technically superior to the current NAQ ?gold standard? of qPCR. However, no commercial dPCR system is currently able to be compete with qPCR because of issues with workflow, throughput, and cost. Among dPCR platforms, the SD mechanism is uniquely suited to efficiently handle large sample volumes, which provides a strong value proposition in high- sensitivity applications, and allows for direct competition with qPCR based assays, providing a path to compete in both the dPCR and qPCR market. The primary objective of this proposal is to produce a platform that overcomes the workflow, throughput, cost, and flexibility hurdles that have limited existing commercial dPCR systems, particularly in their inability to penetrate the larger ?real time? or qPCR market. The first Aim will be development and construction of the instrument, including a digitization mechanism that will prepare 96 samples in parallel, a high-speed thermalcycling system, an imaging system to rapidly analyze samples, and integrated software to enable all stages from a single ?go? command. The second Aim will be development of materials and device designs to enable manufacturing of commercially viable devices. The third Aim will encompass validation of the platform with clinically relevant and valuable NAQ assays. Specifically, it will be validated with an assay relevant to ctDNA research and diagnostics.

Thesaurus Terms:
Address; Air; Amplification Detection; Area; Automation; Base; Biological Assay; Biological Research; Biomedical Research; Blood; Cancer Diagnostics; Cancer Therapy; Characteristics; Clinical; Clinical Application; Clinical Diagnostics; Clinically Relevant; Communicable Diseases; Complex; Computer Software; Convection; Cost; Data; Design; Detection; Development; Device Designs; Devices; Diagnostic; Digital; Dna; Dna Amplification; Drops; Error Sources; Flexibility; Glass; Gold; Growth; Health; Hybrids; Imaging System; Improved; Individual; Instrument; Investments; Life; Lighting; Liquid Biopsy; Manuals; Manufacturing Process; Materials Testing; Methods; Microfluidic Microchips; Microfluidics; Modeling; Monitor; Nucleic Acids; Patients; Performance; Phase; Polymerase Chain Reaction; Positioning Attribute; Production; Prototype; Pump; Reaction; Relative Cost; Reproducibility; Research; Resolution; Running; Sampling; Scale Up; Signal Transduction; Single Molecule; Small Business Innovation Research Grant; Source; Speed; Standardization; Statistics; System; Technology; Time; Tumor Dna; Uncertainty; Universities; Validation; Variant; Viral Load Result; Walking; Washington; Work;