A microfluidic chip-based assay outperforms common methods for quantification of cell-free DNA and RNA

Abstract

Plasma and serum contain cell-free DNA and RNA and are common specimens used for pathology investigation. Circulating nucleic acids in plasma and serum (CNAPS) represent an important target for analyzing several conditions including prenatal diagnostics, tumors, infections, and inflammatory disorders. It is highly expected that plasma and serum contain potential biomarkers for the detection of cancers and other pathological conditions. The major challenges are that CNAPS are present in small quantities and are highly degraded, hampering their downstream analysis. For example, obtaining acceptable quality and quantity of CNAPS remains a bottleneck for advanced studies such as those using next-generation sequencing (NGS) platforms as the currently available platforms require nanogram to microgram levels of deoxyribonucleic acid or ribonucleic acid (DNA/RNA) input. This paper examines the use of various methods to quantify CNAPS, including quantitative real-time polymerase chain reaction (qRT-PCR), digital PCR (dPCR), fluorometric assay, gel electrophoresis, and Bioanalyzer. In particular, the results of CNAPS quantification using a fluorometer, a NanoDrop spectrophotometer, and a microfluidic chip-based assay were compared. It is asserted that spectrophotometry, fluorometric assay and gel electrophoresis lack sensitivity for detecting CNAPS; thus, highly sensitive methods such as qRT-PCR, dPCR, and Bioanalyzer are required.