PT  - JOURNAL ARTICLE
AU  - SHIH, CHUN-LIANG
AU  - LUO, JI-DUNG
AU  - CHANG, JOHN WEN-CHENG
AU  - CHEN, TAI-LONG
AU  - CHIEN, YU-TZU
AU  - YU, CHIA-JUNG
AU  - CHIOU, CHIUAN-CHIAN
TI  - Circulating Messenger RNA Profiling with Microarray and Next-generation Sequencing: Cross-platform Comparison
DP  - 2015 Sep 01
TA  - Cancer Genomics - Proteomics
PG  - 223--230
VI  - 12
IP  - 5
4099  - http://cgp.iiarjournals.org/content/12/5/223.short
4100  - http://cgp.iiarjournals.org/content/12/5/223.full
SO  - Cancer Genomics Proteomics2015 Sep 01; 12
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.