This SBIR phase I application is being submitted in response to the Program Announcement PAR-13-203 entitled Methods of Development for Obtaining Comprehensive Genomic Information from Human Specimens that are Easy to collect and store. This proposal specifically addresses the request for sensitive and cost-effective technologies for obtaining high-quality and comprehensive genomic data from urine, which is both an easy to collect and easy to handle form of human specimen. We have already developed the standard operating procedures (SOP) to collect urine for genetic studies, which can be used for research purposes that have been implemented in the NCI EDRN-funded validation study (protocol ID320). We have also developed a patented fractionation method that enables us to separate the DNA into two distinct species based on fragment sizes. DNA larger than 1 kb is designated as high molecular weight (HMW) DNA, which is mostly derived from the cell debris of the urinary tract. Conversely, the DNA ranging from 100 to 400 bp is designated as low molecular weight (LMW) DNA, which is derived mostly from the circulation. We have shown that LMW DNA can be used for the detection of circulation-derived genetic markers of cancer, if the tumor is present. In phase I, Aim 1 of this application is to demonstrate that HMW urine DNA can replace whole blood as a DNA source for obtaining comprehensive and high-quality genomic information. We will also demonstrate that LMW urine DNA can be a source for cell-free apoptotic DNA for detecting somatic/acquired genetic variants from the entire body, similar to plasma DNA (Aim 2). We propose to use TP53 codon 249 mutations as a somatic mutation marker to compare the LMW urine DNA and plasma DNA for the sensitivity of detecting circulation-derived mutations. In phase II, we propose to develop the urine DNA collection kit (JBS Hi-Lo urine DNA kit) to optimize the use of urine, which is both easy to collect and easy to handle (including sample transportation and storage) for clinical use. It is anticipated that this proposal will lead to the development of a kit that will provide a complete end-to-end solution that addresses all the steps from sample collection and nucleic acid extraction to sequencing, for obtaining complete genomic information with various applications in both clinic and research.
With advancing genomic technologies and simultaneous falling costs of whole genome sequencing and analysis, there is an opportunity to enhance clinical and public health value of genetic tests by expanding them to deliver comprehensive genomic data from human specimens that are easy to collect and handle. We propose our method of using urine DNA which is absolutely non-invasive and is of particular value in remote and under-sourced environments. The goal of this project is to develop the JBS Hi-Lo urine DNA kit that will provide a complete end-to-end solution to address all the steps from sample collection and nucleic acid extraction to next generation sequencing (NGS) for obtaining complete genomic information for various applications in clinic and research.
