1. The Center for Medical Genomics facilitates cutting-edge research with state-of-the-art genomic technologies for studying gene expression and genetics, with the aim of improving health. Affymetrix microarray technology Gene expression on a global scale Tiling arrays Genomic SNP arrays (if needed) SNP Genotyping, targeted at particular genes or regions Epigenetics (genome-wide with tiling arrays or targeted) Bioinformatics support for the above Affymetrix microarray technology Gene expression on a global scale Tiling arrays SNP Genotyping, targeted at particular genes or regions Epigenetics (genome-wide with tiling arrays or targeted) Bioinformatics support for the above includes: consultation on experimental design collaboration on microarray data analysis SNP selection and consultation on LD coverage Affymetrix microarray technology Measurement of global gene expression We have carried out the biochemistry for and scanned about 4500 Affymetrix GeneChips, including human, mouse, rat and many model organisms. We have assisted many scientists with analysis of the complex datasets produced. These data have been part of many publications and grants in different areas. Differentiation and development (animals, plants) Treatment response (hepatitis C, vitamin A deficiency, UV) Gene expression in different tissues (brain, lymphoblastoid cells) Rat and mouse models of disease (alcoholism, schizophrenia, bipolar) Disease susceptibility (Haemophilus ducreyi infection) We developed a method of improving the ratio of reproducible data to false positives by screening out probe sets that are not expressed in a given cell or tissue McClintick and Edenberg, 2006. BMC Bioinformatics 7: 49 SNP Genotyping Targeted at candidate genes or regions Follow-up of Genome Wide Association Studies or linkage studies We have generated about 13 million SNP genotypes to date These data have been part of many publications and grants in fields such as: Alcoholism Bipolar disorder Osteoporosis Hypertension Director: Howard J. Edenberg, Ph.D. edenberg@iupui.edu Primary Contacts Gene Expression studies: Jeanette McClintick, Ph.D. jnmcclin@iupui.ed Howard Edenberg, Ph.D. edenberg@iupui.edu Genotyping studies: Xiaoling Xuei, Ph.D. xxuei@iupui.edu Howard Edenberg, Ph.D. edenberg@iupui.edu Epigenetics: Xiaoling Xuei, Ph.D., Howard Edenberg, Ph.D Ingenuity Pathways Assist: Jeanette McClintick, Ph.D. jnmcclin@iupui.ed We follow carefully tested procedures. Affymetrix GeneChip data quality is assessed with internal controls and external validation: 1.We have tested many of the differentially expressed genes by qRT-PCR and confirmed the vast majority (the expected fraction, given the calculated False Discovery Rate) 2.For some experiments, we have run replications with results that are very consistent. Genotyping: the high quality is demonstrated both by concordance of duplicates and testing segregation in family samples. Affymetrix microarray technology. The Center for Medical Genomics is equipped with the latest instrumentation from Affymetrix, capable of scanning all of their currently available arrays. Affymetrix GeneChip microarrays can measure expression of nearly all genes in humans, rats, mice and most model organisms. We consult on experimental design. We accept total RNA, and carry out all of the biochemistry, hybridization and scanning, and return the data to the investigator. We can assist with data analysis, which is a significant undertaking. SNP Genotyping targeted at particular genes or regions. The Sequenom MassArray system is an excellent choice for candidate gene studies in which much of the variation within the candidate gene can be captured by tagging SNPs and functional SNPs, and for following up results from genome-wide association studies (GWAS) or fine-mapping after linkage studies. CMG recently upgraded to a new iPLEX genotyping assay which allows multiplexing of SNPs in the range of 20-30 per assay. Epigenetics Targeted Epigenetics: Sequenom EpiTYPER. The CMG is introducing a new assay for methylated C in specific regions of the genome. We can make quantitative measurements of multiple potential methylation sites within targeted regions of 200-400 bp (smaller regions for FFPE samples). There are pre-designed assays for imprinting studies and for studies of selected genes important in cancer. We can design assays for other genes or regions. We can run Affymetrix tiling arrays (whole genome or promoters of known genes) for ChIP-Chip studies to detect which sequences are bound by a transcription factor, a methylated-DNA binding protein, or modified histones. This provides a genome-wide assessment of the epigenetic markings. Bioinformatics support for the above We consult on experimental design for all of the kinds of experiments we conduct. We are available for consultation and collaboration on microarray data analysis and for SNP selection and consultation on LD coverage for genotyping, and for design of assays and targeting regions for epigenetic studies. OVERVIEW RESOURCES and SERVICES RESEARCH CONTRIBUTION HIGHLIGHTS QUALITY CONTROL AND ASSURANCES CONTACT INFORMATION Center for Medical Genomics LIST OF SERVICES