The main purpose of this core facility is to provide state-of-the-art microarray platforms, one-stop services, integrated database and in collaboration with experts in biostatistics and bioinformatics to assist data analysis for users and investigators who participating in NRPGM or NSC projects. By accessing this “Integrated Core Facility for Functional Genomics” and customized services, researchers are able to perform cutting edge genomic research and achieve research excellence.In addition to provide of high quality microarray core-services (expression microarray, microRNA arrays, methylation array and customized arrays), this core has developed high content cellular imaging analysis systems, integrated functional genomic tools, integrative microarray database, DNA Mass spectrometry, shRNA library screening chip and more user-friendly and powerful on line analysis platforms, increase multi-disciplinary research collaborations and extend the comprehensive microarray services to meet the increasing demands from bio-medical researchers and facilitate their cutting-edge genomic researches. In order to meet the demand from all fields of researchers, the core provide services for assays of genomics (arrayCGH, SNP genotyping, resequencing-based system, and ChIP on chip), epigenomics (methylation chip and Mass Spectrometry), transcriptomics (expression microarray and microRNA quantification), proteomics (protein chip and cytokine chip), Cellomics (high content cellular imaging) and the integrated web-based analysis as well as the liquid association (LA) bioinformatics platform for genetic, epigenetic gene expression, microRNA and protein expressions. However, high cost or expense and advance platform alone are not the guarantee to achieve research excellence. The professional consultation service starting from the experimental design shall be a short cut to assist finishing successful studies of researchers; hence the “customized service and collaboration” group of this core facility is responsible for providing personalized experimental design. This is the uniqueness of our core and the other uniqueness is comprehensive research system built by this core including successful research strategies, collaboration models and expert experience.

   We and core users have published high quality papers (core: 5 papers, users: 19 papers and 9 out of 24 articles were published in the top journals with impact factor greater than 5, 2009-2010). Significantly, three of users papers and two of core’s papers are higher than 10. We apply two patents in which one is applied for PCT (Patent Cooperation treaty) patent and provisional US patents and one got US and AU patents and applied Taiwan regular and national phase (for more than 25 countries). This core facility has four significant progresses in R&D activities. One is that we utilized a nucleotide MALDI-TOF mass spectrometry to analyze clinical outcome and drug response of lung cancer patients. Briefly, the detection limitations were less than 10 copies and 15 copies, respectively. To our best knowledge, it is the most sensitive and most specific up to date. This methodology offered not only a rapid and convenient strategy for early detection of lung cancer and monitor of EGFR mutation status in clinical lung cancer patients but also guided for TKIs (tyrosine kinase inhibitor) treatments. Moreover, we also found that EGFR T790M mutation frequency was correlated to progression-free survival and it can be a negative predictor for clinical outcome. Recently, we also establish a non-invasive diagnosis method to detect the EGFR mutation from peripheral blood in lung cancer patients. The mutation detection and clinical correlation is under investigation. Another is identification of TB (Mycobacterium) infection by DNA Mass Spectrometry. It also helps rapid laboratory diagnosis of TB infection by using respiratory condensate. Just two days need to complete this TB detection. Besides, we tried to identify TB in respiratory condensate of patients. Once the procedure established, we can easily detect TB in patients whose septum is difficultly collected. Third one is that our user discovers a novel mechanism of virus-induced host protein shutdown. Here we showed that the infection of enteroviruses disturbs the expression of miRNAs involved in the pathogenesis and virus propagation. This achievement is currently applying for the PCT and US provisional patents. The last one is that we cooperate with C6 core facility to setup a microarray platform for carrying out the loss of function screening by TRC shRNA library. We design a customized chip by ourselves and optimize the assay condition. Currently, this platform is well established and waiting for open service as users committee approve the service price. We also utilized this system to identify genes related to tumor metastasis and drug resistance. Our effort might help Taiwan researchers to do more excellent studies by using TRC shRNA library.     Importantly, we have established “New Generation Sequencing (NGS)” system and begin to provide NGS service. This core is the biggest DNA sequencing center in Taiwan and 5th in Asia.

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