Medical Genome Facility
The Medical Genome Facility is an infrastructure program of the Center for Individualized Medicine that works closely with the Biorepositories Program by bringing together five genomics-oriented cores (shared resources) to provide professional, efficient and low-cost access to the latest genomics technologies for all Mayo Clinic investigators.
The facility also assists researchers and clinicians in interpreting genomic findings and applying them to patient care. This is done in collaboration with the Department of Laboratory Medicine and Pathology, and with support and cooperation among the Center for Individualized Medicine, Mayo Clinic Research Administration and the Mayo Clinic Cancer Center.
Cores in the Medical Genome Facility are:
Areas of focus
The Medical Genome Facility is continuing to expand its technical capabilities and staff to meet investigators' needs within the center's translational programs and across Mayo Clinic. This includes acquiring additional genomic sequencing equipment and adding bioinformatics and information technology specialists who work directly with Medical Genome Facility staff.
Recent work has included a joint effort by members of the sequencing and other cores, the Medical Genome Facility study coordinator, and the facility's information technology and bioinformatics teams to successfully interrogate 90 trillion bases of nucleotide sequences in 2012.
Consulting and advising
Before starting a project, investigators can meet with staff members from Medical Genome Facility cores to discuss plans and logistics for sample collection, processing and analysis.
Such collaborative, coordinated study design is essential for individualized medicine projects, particularly because genomic technologies are ever-changing and a single study may require services from multiple Medical Genome Facility cores.
Two of the many studies the facility is currently supporting in this manner are the beauty and promote studies. Both scientific and operational experts from the Medical Genome Facility are part of these project teams to ensure that sample transfer and data generation meets the needs of these studies, which are led by the Pharmacogenomics Program.
Developing new laboratory methodologies
The Medical Genome Facility has several research technologists who develop and refine new service lines.
Active developmental projects include:
- Utilizing PacBio single-molecule sequencing technology for clinical applications. We have launched a request for applications and supported a diverse set of genomic studies that take advantage of the long read length, low cost and short turnaround time features of the PacBio platform. Studies have focused on critical gene mutation screening, immunoglobulin gene rearrangement and mitochondria genome analyses.
- Developing methods to detect 5 hydroxymethylcytosine (5hmC). DNA methylation is a dynamic state and 5hmC is an intermediary in the demethylation of methylated cytosines, thus allowing analysis of the effects of environmental factors on disease and changes in disease states themselves.
- Single cell genomics. Developing approaches for DNA and RNA derived from single cells. The ability to profile the genome at this level allows analysis of tumor subpopulations, as well as other applications.
- Bringing to production mRNA and miRNA next-generation sequencing library construction using low-input samples. Through extensive testing of various available protocols, we are capable of routinely supporting RNA-seq library constructions using high-quality RNA input as low as 2 nanograms. We also support RNA-seq by NuGen using RNA isolated from formalin-fixed, paraffin-embedded samples.
- In situ detection of gene expression. To assess tumor heterogeneity, the Cytogenetics Core is working to develop a robust method to allow in situ evaluation of mRNA expression using chromogenic stains.
- Proteomics development. Working to complete a principle development of a liquid chromatography-tandem mass spectrometry (LC/MS/MS)-based assay for the protein myostatin and its inhibitors.
Eric D. Wieben, Ph.D. Director