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Microarray Facility Description and Use InformationThe Microarray Analysis facility at Ordway functions as an integral component of the Translational & Functional Genomics laboratory and consists of state-of-the-art Affymetrix Microarray Suite which is based on the latest version of the Affymetrix GeneChip System. The principal use of this facility has been to develop genetic tests which can be used to facilitate the clinical implementation of the concept of personalized genomics-enabled disease management for more than twenty major human disorders including: Alzheimer’s disease (AD); bipolar disease (BD); rheumatoid arthritis (RA); coronary artery disease (CAD); Crohn's disease (CD); type 1 diabetes (T1D); type 2 diabetes (T2D); hypertension (HT); ankylosing spondylitis (AS); Graves' disease (autoimmune thyroid disease; AITD); multiple sclerosis (MS); breast cancer (BC); prostate cancer (PC); colorectal cancer (CRC); lung cancer (LC); ovarian cancer (OC); systemic lupus erythematosus (SLE); vitiligo-associated multiple autoimmune disease (VIT); Huntington’s disease (HD); schizophrenia (SCHZ); ulcerative colitis (UC); autism (AUT); and obesity (OB). The Microarray Analysis facility at Ordway will provide a service to Ordway’s investigators and local research community, which includes pharmaceutical and biotechnology companies. The Affymetrix GeneChip System is one of the most widely accepted and mature microarray technologies currently commercially available to the research community. A variety of GeneChips are available in the Affymetrix product lines, including Human UniGene sets, Human SNPs, P450 SNPs, P53, mouse and rat genomes, mouse neurobiology, mouse toxicology, and many others. With its integrated data analysis tools and databases, in one single experiment one can study ~ 22,000 protein-coding genes at the mRNA expression level; or survey the expression status of ~ 300,000 exons; or examine over 3.1 million SNPs. However, the truly unique and fascinating analytical high-throughput capabilities of the microarray analysis platform is best illustrated by the tiling array experiments which facilitate genome-wide expression analysis of vast transcriptional output of human genomes and measure expression profiles of hundreds of thousands (perhaps, millions) of small non-coding RNAs. The Affymetrix suite includes the Affymetrix Data Analysis and Data Mining Tools. The real-time PCR machine, ABI 7900HT, is used for gene expression validation. It functions based on detection of time-resolve fluorescence and melting temperature. The important applications of this instrument are for quantitative RT-PCR for SNP detection, microRNA and small non-coding RNA expression analysis. We plan to expand the Microarray Analysis facility into a mature Analytical Genomics core which will be supported by the Bioinformatics Core in data storage, curation, data analysis, creation and maintenance of databases, as well as database applications. The Analytical Genomics core will provide the genotyping services of human tissues and cell lines for confirming identities, expansion of tissue banks and validating inventories. This may include the wide rage of forensic applications. In collaboration with the Analytical Genomics Core, the Bioinformatics Core will host a number of web-based applications for Internet users which will provide storage capabilities and statistical data analysis of microarray-derived databases. |