Circulating nucleic acids from dying tumor cells may yield an early indication of cancer if they could be detected at sufficiently low abundance in body fluids in the presence of background DNA from healthy cells as well as contaminants inherent to blood serum, urine, and stool samples. Methods capable of enriching for small quantities of partially intact tumor DNA from body fluids while rejecting contaminants and background DNA from healthy cells would be a great advantage. This would be particularly true, if the DNA could be enriched for sequence mutations that signal oncogene activation or other tumor related sequence signatures. We have developed a method of DNA concentration and extraction (SCODA) that, in its simplest form, promises to increase the amount and purity of DNA extracted from body fluids, while reducing the amount of processing steps and cost. SCODA will allow facile extraction of nucleic acid biomarkers from samples such as urine, stool, or blood serum for non-invasive cancer detection, and for genomic studies of cancer. SCODA provides a means for high efficiency concentration of low abundance DNA with a high degree of contaminant rejection. Applications of this technology to forensics and genomics research are being commercialized, and its value has been proven in both fields.
We aim to apply SCODA technology to extraction of circulating DNA from body fluids ranging from blood serum to stool. We expect that its outstanding efficiency and rejection of contaminants, as proven in our forensics work, will yield benefits in biomarker extractions. Furthermore, we plan to make modifications to SCODA that will allow enrichment for specific low abundance DNA sequences. This will be done by altering the concentration mechanism, such that only DNA fragments containing specific sequences relating to tumor cells will be concentrated. This promises to provide a pre-concentration tool that would enable exceptionally sensitive detection of tumor DNA biomarkers in body fluids.
