Targeted DNA sequencing of cell-free tumor DNA (circulating tumor DNA, ctDNA) shed into a patients blood holds great promise for detection, diagnosis, and monitoring of cancer. Given that all tumor cells have the potential to shed ctDNA, targeted assays using modern next-generation sequencing methods and digital PCR can provide insight into the entirety of a patients tumor burden. ctDNA is therefore an attractive biomarker for diagnosis and monitoring of cancer patients via non-invasive peripheral blood draw. Such assays, however, require ultra-sensitive sequencing fidelity, flexible target multiplexing, and uniform target amplification for efficient, quantitative, and cost-effective testing. In addition, several challenges arise in the implementation of assays to identify and monitor tumor-specific mutations extracted from blood. First, the mutant DNA from cancer cells is rare compared to the background of normal DNA, requiring detection sensitivities below 0.1% for some clinical applications. Second, cell-free DNA extracted from plasma is limited in mass (<100 ng / 5 ml sample), and typically degraded to very short fragment lengths, requiring efficient capture and amplification of the targets of interest. Third, cancer diagnosis and monitoring may require surveillance of a multitude of tumor or patient-specific mutations, requiring multiplex amplification for efficient sample utilization. In collaboration with our academic partners at Boston University and the University of California San Francisco, we have developed a novel next-generation sequencing sample preparation platform that addresses these critical challenges - PIPSenSeq (Pre-templated Instant Partitions for Sensitive Sequencing). This approach takes advantage of molecular indexing for consensus-read sequencing in combination with single-molecule amplification in Poisson-distributed nanoscale partitions. Furthermore, PIPSenSeq provides a simple, rapid library preparation that does not require complex, expensive instrumentation or microfluidic consumables. In this proposal we will develop PIPSenSeq as a commercial-ready platform for cancer monitoring, and demonstrate clinical utility in a study of 60 - 70 head and neck squamous cell carcinoma patients. These patients will be monitored post-operatively for tumor recurrence using personalized PIPSenSeq panels on longitudinally collected ctDNA samples.
Public Health Relevance Statement: PROJECT NARRATIVE Circulating tumor DNA (ctDNA), obtained via a blood draw, is increasingly seen as a clinically valuable biomarker for cancer detection and diagnosis. The objective of this proposal is to develop and demonstrate the clinical utility of a new technology for personalized cancer detection and longitudinal monitoring. This proposal combines the core innovation of our company, pre-templated instant partitions, with a validated multiplex PCR assay from our collaborator to create a novel technology that overcomes the critical barriers to flexible, multiplexed PCR-based ctDNA tests for cancer monitoring.
NIH Spending Category: Bioengineering; Biotechnology; Cancer; Cancer Genomics; Clinical Research; Genetics; Health Disparities; Human Genome; Minority Health
Project Terms: Abate; Address; amplification detection; Apoptosis; base; Bioinformatics; Biological Assay; Biological Markers; Biological Sciences; Blood; Boston; California; cancer biomarkers; cancer cell; Cancer Detection; cancer diagnosis; Cancer Patient; cancer recurrence; cell free DNA; Cells; Clinical; clinical application; Collaborations; Complex; Computer software; Conflict (Psychology); Consensus; Consumption; cost; cost effective; cost effectiveness; Custom; Data; Data Analyses; design; Detection; Diagnosis; digital; Disease; DNA; DNA sequencing; Excision; flexibility; follow-up; Genomics; Head and Neck Squamous Cell Carcinoma; indexing; Individual; Informatics; innovation; insight; instrumentation; interest; Length; Libraries; Malignant Neoplasms; Manuals; Methods; Microfluidics; Minor; Modernization; Molecular; Monitor; mutant; Mutate; Mutation; nanoscale; neoplastic cell; new technology; next generation sequencing; novel; Output; Patients; Performance; peripheral blood; Phase; Plasma; Population; Postoperative Period; Preparation; Protocols documentation; Reaction; Recurrence; Relapse; research clinical testing; Sampling; San Francisco; self assembly; single molecule; Symptoms; Technology; Testing; Time; Tube; tumor; Tumor Burden; tumor DNA; Universities
