Microarray and next-generation sequencing – cross-platform comparison shows only modest-to-moderate correlation in poor quality samples

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. Researchers from Chang Gung University explored and compared the ability of two high-throughput platforms for the profiling of circulating mRNA regarding their ability to retrieve useful information out of this type of samples.

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 (RT-qPCR).

The overall expression profiles derived from the two platforms showed modest-to-moderate correlation. Genes with higher expression levels had higher cross-platform concordance than those of medium- and low-expression 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.

Correlation of the expression data determined by the DASL assay and RNA sequencing. The Pearson’s correlation coefficients for genes with different expression levels in each sample were plotted.

Genes with higher expression levels have cross-platform concordance and can be potential biomarkers. Furthermore, RNA-Seq is a better tool for profiling circulating mRNAs.