Support for Biomedical Researchers
With a service-first mentality and a mission to improve population health by facilitating biomedical research advancements with state-of-the-art genomic technologies for studying gene expression and genetics, the Center for Medical Genomics at IU School of Medicine provides infrastructure and consults for the use of genomic technology in studies of disease and in other biomedical research.
The professional staff of the Center for Medical Genomics are available to investigators at all stages of the experiment, including study design, sample quality assessment, data delivery and analysis consultation. In collaboration with the Bioinformatics Core and the Center for Computational Biology and Bioinformatics, the Center for Medical Genomics can also provide fee-for-service bioinformatics analysis on sequencing, microarray and genotyping experiments. This center is an Indiana CTSI core facility open to investigators from Indiana University, Purdue University and University of Notre Dame.
Services and Instrumentation
The Center for Medical Genomics provides full scale high-throughput sequencing services, including genomic DNA sequencing (whole genome sequencing, whole exome sequencing and gene panel target sequencing), transcriptome RNA sequencing (whole transcriptome sequencing, mRNA sequencing and small RNA sequencing), methylation capture following sequencing, and protein DNA/RNA interaction (ChIP-seq, ChIP-exo and CLIP-seq).
Center staff has experience in conducting sequencing experiment from standard samples, blood samples, low quantity samples (as long as 10ng total RNA), and low quality or degraded samples (from FFPE or micro-dissection). Investigators are responsible for conducting the pulled-down assay and provide the core with good quality DNA. Staff of the Center for Medical Genomics can work with investigators on adopting/developing other assays that require high-throughput sequencing technology.
Next Generation Sequencing instrumentation at the center includes:
- Illumina HiSeq 4000
- Illumina NextSeq 500
- LifeTech Ion Proton sequencing system
The Center for Medical Genomics provides consultation, infrastructure and expertise in use of Affymetrix microarrays technology. The team also offers data analysis and bioinformatics expertise needed to interpret the large amount of data generated in these experiments. Much effort has gone into experimental consistency and quality control at all steps.
Microarray instrumentation at the center includes the Affymetrix GeneChip ® cartridge system. Services include gene expression from Total RNA (wide range of organisms), gene expression from limited samples (<5ng Total RNA), gene expression from FFPE or other degraded samples, and miRNA expression (miRNA array 4.0 – multi organism array).
The Center for Medical Genomics uses the Sequenom MassArray® system for targeted genotyping, generally in groups of up to 25 or 30 SNPs per assay. The Sequenom is a mass spectrometer-based SNP genotyping system that uses a modified single base extension reaction. It is an excellent choice for candidate gene studies and for following up results from GWAS and next- generation sequencing. To date, the center has produced more than 20 million targeted SNP genotypes. The Sequenom MassArray® system can be used to genotype SNPs in any organism. Services include high-throughput targeted genotyping using SNPs, allele-specific expression and validation of methylation sites.
DNA/RNA Analysis services include quality/ quantity assessment as well as shearing and sample extraction:
- DNA/RNA quality/quantity assessment instrumentation at the center include the Nanodrop, an Agilent 2100 Bioanalyzer and the Qubit Fluorometer. Services include DNA/RNA quantification, DNA quality-control and fragment-size analysis, RNA quality (measure of fragmentation/degradation) and miRNA quality.
- DNA/RNA shearing instrumentation at the center includes the Covaris S2.
- DNA/RNA sample extraction is also available. For information regarding extraction, email Dr. Yunlong Liu, the Center for Medical Genomics director.