title: Circulating Messenger RNA Profiling with Microarray and Next-generation Sequencing: Cross-platform Comparison.
abstract: 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.
  
  
  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.
  
  
  CONCLUSIONS
  Genes with higher expression levels have cross-platform concordance and can be potential biomarkers. Furthermore, RSEQ is a better tool for profiling circulating mRNAs.
authors.affiliation: Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan, R.O.C.
authors.forename: Chun-Liang
authors.initials: CL
authors.lastname: Shih
authors.affiliation: Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan, R.O.C. Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan, R.O.C.
authors.forename: Ji-Dung
authors.initials: JD
authors.lastname: Luo
authors.affiliation: Division of Hematology-Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital, Taoyuan, Taiwan, R.O.C. School of Medicine, College of Medicine, Chang Gung University, Taoyuan, Taiwan, R.O.C.
authors.forename: John Wen-Cheng
authors.initials: JW
authors.lastname: Chang
authors.affiliation: Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan, R.O.C. Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan, R.O.C.
authors.forename: Tai-Long
authors.initials: TL
authors.lastname: Chen
authors.affiliation: Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan, R.O.C.
authors.forename: Yu-Tzu
authors.initials: YT
authors.lastname: Chien
authors.affiliation: Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan, R.O.C. ccchiou@mail.cgu.edu.tw yucj1124@mail.cgu.edu.tw.
authors.forename: Chia-Jung
authors.initials: CJ
authors.lastname: Yu
authors.affiliation: Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan, R.O.C. Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan, R.O.C. ccchiou@mail.cgu.edu.tw yucj1124@mail.cgu.edu.tw.
authors.forename: Chiuan-Chian
authors.initials: CC
authors.lastname: Chiou
mesh_terms: D002289:Carcinoma, Non-Small-Cell Lung / Q000235:genetics; D016022:Case-Control Studies; D020869:Gene Expression Profiling / Q000379:methods; D015972:Gene Expression Regulation, Neoplastic; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods / Q000592:standards; D006801:Humans; D008175:Lung Neoplasms / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods / Q000592:standards; D012333:RNA, Messenger / Q000097:blood / Q000235:genetics*; D015203:Reproducibility of Results; D059467:Transcriptome
chemical_list: D012333:RNA, Messenger
keywords: Circulating mRNA; DASL assay; RNA sequencing; transcriptomic profiling