RT Journal Article
SR Electronic
T1 Circulating Messenger RNA Profiling with Microarray and Next-generation Sequencing: Cross-platform Comparison
JF Cancer Genomics - Proteomics
JO Cancer Genomics Proteomics
FD International Institute of Anticancer Research
SP 223
OP 230
VO 12
IS 5
A1 SHIH, CHUN-LIANG
A1 LUO, JI-DUNG
A1 CHANG, JOHN WEN-CHENG
A1 CHEN, TAI-LONG
A1 CHIEN, YU-TZU
A1 YU, CHIA-JUNG
A1 CHIOU, CHIUAN-CHIAN
YR 2015
UL http://cgp.iiarjournals.org/content/12/5/223.abstract
AB 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.