… to provide infrastructure for the
use of genomic technologies ...
• Microarrays
• High throughput genotyping

High-throughput SNP Genotyping

Genes influence all of our physiological and pathological processes. Individual differences in gene sequence lead to differences in the risk for diseases and in the response to treatment. The near-completion of the sequencing of the human genome, along with technological developments, allows us to study genes that affect the risk for complex diseases such as diabetes, hypertension, cancers, and psychiatric diseases.

The most common variations are single nucleotide polymorphisms (SNPs), changes in one base pair out of the 3 billion in the human genome. SNPs can affect susceptibility to disease, the efficacy or side-effects of drugs, and response to treatment. High throughput genotyping allows large-scale studies of how sequence differences affect these processes.

The Center for Medical Genomics has installed the Sequenom MassArray® system, a state-of-the-art, high throughput, mass spectrometer-based SNP genotyping system. Genotyping uses a modified single base extension reaction. The speed and accuracy of this system is excellent. It has the capacity to carry out genotyping for multiple large projects, and has major advantages in speed, accuracy, and lower cost. It can be used to genotype SNPs in any organism. We have generated over 6,000,000 genotypes to date, and have capacity to work even more rapidly.

The Sequenom system is best suited for genotyping multiple SNPs in a set of candidate genes. This technology is most efficient for moderate to large scale projects, working in 384-well format, but we can accommodate smaller projects also.

Another alternative is the use of Affymetrix SNP chips. We are equipped to use the Affymetrix Genome-Wide Human SNP Array 6.0, which has over 906,000 SNPs and 946,000 probes for copy number variants.

The Center for Medical Genomics provides bioinformatics consultation, infrastructure and expertise in high-throughput sequencing. This includes assistance with selection of SNPs and design of the assays. The Center will work with investigators to help organize the DNA samples. Center staff will carry out the PCR and genotyping, and return data to the investigator. Much effort has gone into experimental consistency and quality control at all steps.

Contact the Director, Howard Edenberg ( edenberg@iupui.edu ) for further information.

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The Center for Medical Genomics is partially supported by a competitive, peer-reviewed grant from the State of Indiana 21st Century Research and Technology Fund. Additional support is from the Indiana Genomics Initiative, funded by a generous grant from the Lilly Endowment, and from the Indiana University School of Medicine.