Genotyping Shared Resource

Julie Cunningham, Ph.D.
Director

The Genotyping Shared Resource is dedicated to high-throughput genotyping, genetic linkage analysis, analysis of genetic variants in gene association studies, and in characterization of tumor tissues. Shared Resource studies seek to understand the molecular basis of disease and other processes such as response to medications and vaccines. These studies may one day translate into new treatments for disease, new means of assessing risk, and many other clinical applications.

The goal of the Genotyping Shared Resource is to provide the highest quality genotyping data using sophisticate technology to enhance the understanding of human diseases, improve health, and promote excellent patient care. With the growing awareness that cancer has a genetic basis, it becomes crucial that cancer researchers have access to high quality, high throughput genomic based methodologies. A subsection of Mayo Clinic’s Advanced Genomics Technology Center, the Genotyping Shared Resource combines linkage analysis and molecular epidemiology activities, providing a single resource for the genotyping needs of Mayo Clinic Cancer Center investigators, conducting:

• Genotyping support for investigators at all three campuses in Phoenix/Scottsdale, Ariz.; Jacksonville, Fla.; and Rochester, Minn.; as well as external collaborators
• Support to ongoing, population-based epidemiological and family-based studies
• Genotyping assays to provide pilot studies incorporating novel genetic markers with either clinical and/or etiological relevance
• A platform for exploring technologically advanced, state-of-the-art genomic approaches to oncology research
• Genotyping of single nucleotide polymorphisms and other common inherited susceptibility markers in support of research into the etiology and progression of cancer
• Linkage analysis
• Genotyping of repeat polymorphisms and other micro-satellite-based applications
• Custom and genome-wide SNP determinations in blood derived DNA and DNA from fixed and unfixed tissues
• Custom single genotyping from many to thousands of SNPs
• Genome-wide genotyping, from linkage analysis t100, 300, 500 or 650 thousand or even 1 million
• Custom genotyping for repeat length polymorphisms
• Custom genotyping for insertion/deletion polymorphisms
• DNA quantity checks and sample verification

Facilities, Equipment and Staffing

The Genotyping Shared Resource occupies several spaces, including a pre-PCR and post-PCR area, a specialized Illumina pre-PCR room with controlled access and an isolated ventilation system, and a separate analysis room for the 10 staff/technologists.

Illumina BeadLab System

Illumina Genotyping is an ultra-high throughput technology using a BeadArray technology with two different array formats, the Sentrix® Array Matrix and the Sentrix® BeadChip. The Illumina BeadLab facility also supports gene expression analyses using DASL (cDNA mediated Annealing, Selection, extension and Ligation), which is based on GoldenGate® methodology. Through use of this specialized equipment, the Shared Resource is able to provide:

• Custom GoldenGate® Genotyping
• Linkage GoldenGate® Genotyping
• Infinium® Whole-Genome Genotyping
• iSelect - Custom Infinium® Genotyping
• Methylation assays
• Infinium® Linkage BeadArray