uProcess: A novel home and lab system to improve cfDNA screening and monitoring using transrenal DNA

About This Grant

Abstract/Summary Cell free DNA (cfDNA) analysis is a translational method that has revolutionized both basic science and clinical medicine. It has allowed basic understanding of gene function to impact clinical decisions and allowed clinical specimens to be used for basic science. It has become part of the standard of care for perinatal screening, monitoring transplants, and choosing therapy for cancer. Clinical trials evaluating cfDNA in virtually every disease, including diseases of heart function, infections, vascular disease, neurology, psychiatry, organ transplantation, eclampsia, fetal health, inflammatory/autoimmune diseases, and cancer are showing promising results. Even just the easily measured level of cfDNA is a useful screening tool for maternal risk, many other tests use relatively simple PCR. cfDNA is the basis of highly sophisticated multiple cancer early detection (MCED) and potentially screening for other diseases, even including Alzheimer’s. Most applications use blood cell free DNA (BcfDNA). BcfDNA turns over in under 2 hours, it is subject to variation over the course of the day, it needs to be collected in special tubes to be stable, or immediately processed with biohazard care, to obtain plasma, which needs to be stored frozen or immediately processed by “moderate complexity” lab cfDNA isolation methods, which yield variable amounts of BcfDNA. Typically, patients’ visits are weeks or months apart and only 1 -20 mls of blood is obtained yielding 10s of nanograms of cfDNA. For MCED, MRD, CNS diseases, and occult infections, this small amount limits sensitivity. Urine also contains cfDNA (ucfDNA), at comparable or a bit lower concentration. Urine can be collected multiple times a day and on as many days as desired at home without the cost, inconvenience and potential exposure to infectious diseases, of the often immunosuppressed patients, inherent in a clinic visit. However, existing methods to extract ucfDNA only allow small amounts of urine to be processed; they too are complex methods that have variable, generally low, efficiency. When scaled up they are prohibitively expensive. Even with preservatives, there is immediate degradation of a fraction of the DNA before the specimens reach the lab. Numerous studies show ucfDNA contains cfDNA from the blood and that this trans-renal DNA can be used to understand system functions. Included preliminary data document a use anywhere, all resource sites (even home use), simplified and inexpensive method collects 20x to 100x more cfDNA, immediately separates the cfDNA from enzymes that cause degradation by affinity binding, and allow transport, without biofluid and cold chain concerns. Each of the underlined items are in themselves novel. The aims are to confirm and extend this data to commercialize a system, which once received in the lab can generate cfDNA suitable for PCR and next generation sequencing in 10 minutes. ucfDNA collected over time complements the snapshot BcfDNA provides. Larger total amounts of cfDNA improve sensitivity and provide excess material so this clinical resource will be more available for basic research. While BcfDNA is a limited resource, ucfDNA is virtually unlimited. Such translational research is expected to continue to rapidly change clinical practice. Other methods are for collection or lab isolation, uProcess does both, less expensively and in 1/10 the lab time. Most importantly, the variation featured herein selects for the trans-renal DNA indicative of systemic disease; all current kits yield >80% urothelial DNA.