Bioinformatics Shared Resource

Jean-Pierre A. Kocher, Ph.D.
Director

The Bioinformatics Shared Resource was created in mid-2006 to answer the increasing demand for bioinformatics support from investigators of the Cancer Center and across Mayo Clinic. The growing adoption of genomics tools to probe the cellular machinery at the molecular level and the fast development pace of 'omics' technology platform had led to a new need for data management, data analysis and data interpretation.

The mission of the Shared Resource is to develop and maintain state of the art services to help investigators take advantage of new 'omics' technologies to enable discoveries that will impact patient care. To this end, the Shared Resource has assembled a team of informatics experts specialized in the analysis of high throughput genomics, proteomics and metabolomics data. This team includes computer scientists and bioinformatics specialists with strong backgrounds in molecular biology, genetics, biophysics, chemistry and statistics. The Shared Resource also works collaboratively with the Division of Biomedical Statistics and Informatics and Experimental Cores to ensure coordination of experimental and analytics through the different phases of a project.

The Shared Resource provides services for Mayo Clinic Cancer Center investigators in the following areas:

The Shared Resource also contributes to the development of the IT infrastructure needed to manage and analyze data. Some of these developments are done in collaboration with other IT teams at Mayo Clinic. Current activities include:

Facilities and Equipment

The Bioinformatics Shared Resources is part of the Division of Biomedical Statistics and Informatics. It operates in a state of the art facility including an Access Grid® enabled media room for multi-site multi-media conferencing. Additional conferencing technologies are deployed for supporting standard videoconferencing, web casting, and video on demand. Multiple OC-3 connections to Mayo Clinic group practices across all three Mayo Clinic campuses in Scottsdale, Ariz., Jacksonville, Fla. And Rochester, Minn., and DS3 connections to Internet2 Consortium members ensure fast data transfer between remote sites.

Bioinformatics takes advantage of the multiple compute resources available at Mayo including blade-server computer clusters, comprising roughly of 40 IBM Intel nodes running Linux. They are maintained by Mayo's IT server support group explicitly for moderately compute-intensive tasks. The Shared Resource also has access to a Beowulf-style Linux cluster with production research storage that is administered and maintained by the Mayo's Research Computer Facility. This cluster is designed specifically for distributed computing. It includes 40 Athlon nodes, each consisting with 1-2 gigabytes (Gb) memory, 50Gb individual storage and 1.5 terabytes shared storage. A number of smaller Xeon-based 'compute engines' are also available for ad-hoc processor-intensive tasks. The bioinformatics software commonly used by the Shared Resource are installed on this system.

Recent Publications

Following are a selection of recent publications involving staff of the Bioinformatics Shared Resource:

• Overlapping human leukocyte antigen class I/II binding peptide vaccine for the treatment of patients with stage IV melanoma: evidence of systemic immune dysfunction. Cancer, 2007.
• Protein Kinase C inhibitor enzastaurin induces in vitro and in vivo antitumor activity in Waldenstrom's Macroglobulinemia. Blood, 2007.
• Proteomic Analysis of Waldenstrom Macroglobulinemia. Cancer Research, 2007.
• Early Cutaneous Gene Transcription Changes in Adult Atopic Dermatitis and Potential Clinical Implications. Experimental Dermatology, 2007.
• Patterns of Gene Expression in a Pituitary Carcinomas and Pituitary Adenomas by High-Density Oligonucleotide Arrays, Reverse Transcriptase-Quantitative PCR and Protein Expression. Endocrine, 2007.
• Intranasal exposure to staphylococcal enterotoxin B elicits an acute systemic inflammatory response. Shock, 2006.
• Inherited variation in carcinogen metabolizing enzymes and risk of colorectal polyps. Carcinogenesis, 2007.