Circulating messenger RNA profiling with microarray and next-generation sequencing: Cross-platform comparison

Background: Circulating mRNA is a less invasive and more easily accessed source of samples for biomedical research and clinical applications. However, it is of poor quality. We explored and compared the ability of two highthroughput platforms for the profiling of circulating mRNA regarding their ability to retrieve useful information out of this type of samples. Materials and Methods: Circulating mRNAs from three non-small cell lung cancer patients and three healthy controls were analyzed by the cDNA-mediated annealing, selection, extension, and ligation (DASL) assay and high-throughput RNA sequencing (RSEQ). Twelve genes were selected for further confirmation by reverse transcription-quantitative polymerase chain reaction (RTqPCR). Results: The overall expression profiles derived from the two platforms showed modest-to-moderate correlation. Genes with higher expression levels had higher crossplatform concordance than those of medium- and lowexpression levels. In addition, the pathway signatures identified by gene set enrichment analysis from both platforms were in agreement. The RT-q PCR results for the selected genes correlated well with that of RSEQ. Conclusion: Genes with higher expression levels have cross-platform concordance and can be potential biomarkers. Furthermore, RSEQ is a better tool for profiling circulating mRNAs.