Enhancing the compatibility of BioCaRGOS silica sol-gel technology with ctDNA extraction and droplet digital PCR (ddPCR) analysis

Abstract

Previously, our group had demonstrated long term stabilization of protein biomarkers using BioCaRGOS, a silica sol-gel technology. Herein, we describe workflow modifications to allow for extraction of cell free DNA (cfDNA) from primary samples containing working concentrations of BioCaRGOS, as well as the compatibility of BioCaRGOS with droplet digital PCR (ddPCR) analysis for pancreatic cancer biomarkers i.e., KRAS circulating tumor DNA (ctDNA). Preliminary attempts to extract ctDNA from BioCaRGOS containing samples demonstrated interference in the extraction of primary samples and the interference with ddPCR analysis when BioCaRGOS was directly introduced to stabilize sample extracts. In our modified technique, we have minimized the interference caused by methanol with ddPCR by complete removal of methanol from the activated BioCaRGOS formulation prior to addition to the biospecimen or ctDNA extract. Interference of the silica matrix present in BioCaRGOS with ctDNA extraction was eliminated through the introduction of invert filtration of the sample prior to extraction. These modifications to the workflow of BioCaRGOS containing samples allow for use of BioCaRGOS for stabilization of trace quantities of nucleic acid biomarkers such as plasma ctDNA, while retaining the capability to extract the biomarker and quantify based on ddPCR.