TY - JOUR T1 - Circulating Messenger RNA Profiling with Microarray and Next-generation Sequencing: Cross-platform Comparison JF - Cancer Genomics - Proteomics JO - Cancer Genomics Proteomics SP - 223 LP - 230 VL - 12 IS - 5 AU - CHUN-LIANG SHIH AU - JI-DUNG LUO AU - JOHN WEN-CHENG CHANG AU - TAI-LONG CHEN AU - YU-TZU CHIEN AU - CHIA-JUNG YU AU - CHIUAN-CHIAN CHIOU Y1 - 2015/09/01 UR - http://cgp.iiarjournals.org/content/12/5/223.abstract N2 - 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 high-throughput 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 (RT-qPCR). Results: 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. 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. ER -