title: Application of unique sequence index (USI) barcode to gene expression profiling in gastric adenocarcinoma.
abstract: Accurate expression profiling is imperative for understanding the biological roles of mRNAs. Real-time PCR have been at the forefront of biological innovation in detection and monitoring of gene expression, however, fluorophore-labeled oligonucleotides and double-stranded DNA binding dyes, the two most frequently used dyes in RNA detection, are not very cost effective and have poor specificity, respectively. We have developed a cost effective and specific approach for mRNA expression profiling via added unique sequence index (USI) to cDNAs before amplification. USI is a barcode which enable the detection of each target RNA. Using this method, caudal type homeobox 1 (CDX1) and FAT atypical cadherin 4 (FAT4) expressions were investigated in tumoral and non-tumoral tissues of gastric cancer patients and compared with commercial ABI kit. Both methods indicated that FAT4 and CDX1 expression were significantly reduced in gastric cancer tissues compared with adjacent noncancerous tissues. Moreover, we have shown that this assay is highly sensitive, linear and reproducible. USI barcode not only provides a powerful tool for mRNA detection due to its sensitivity, specificity and cost-effectiveness, but also allows comfortable design for real-time qPCR assays within the least time and empowers the analysis of many transcripts of virtually any organism. Furthermore, USI barcode is highly affordable for large numbers of different samples or small sample sizes without microarray and expensive commercial platforms.
authors.affiliation: Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran.|North Research Center-Pasteur Institute of Iran, Amol, Iran.
authors.forename: Sadegh
authors.initials: S
authors.lastname: Fattahi
authors.affiliation: Department of Genetics, Faculty of Medicine, Babol University of Medical Sciences, Babol, Iran.
authors.forename: Maryam
authors.initials: M
authors.lastname: Pilehchian Langroudi
authors.affiliation: Department of Biology, Islamic Azad University, Ghaemshahr, Iran.
authors.forename: Ali Akbar
authors.initials: AA
authors.lastname: Samadani
authors.affiliation: Department of Surgery, Rouhani hospital, Babol University of Medical Sciences, Babol, Iran.
authors.forename: Novin
authors.initials: N
authors.lastname: Nikbakhsh
authors.affiliation: North Research Center-Pasteur Institute of Iran, Amol, Iran.
authors.forename: Mohsen
authors.initials: M
authors.lastname: Asouri
authors.affiliation: North Research Center-Pasteur Institute of Iran, Amol, Iran. Halehakhavan@yahoo.com.|Department of Genetics, Faculty of Medicine, Babol University of Medical Sciences, Babol, Iran. Halehakhavan@yahoo.com.
authors.forename: Haleh
authors.initials: H
authors.lastname: Akhavan-Niaki
keywords: CDX1, cancer; FAT4; Gene expression; QPCR; Taqman