Core Services

The Department of Genomics and Precision Medicine and Research Center for Genetic Medicine host a series of regional and national core facilities. The goal of these core facilities is to facilitate research in many remote laboratories, through application of specialized technologies and expertise to investigators’ projects. 

The Department of Genomics and Precision Medicine cores house state-of-the-art equipment purchased through institutional funds, philanthropic donations, and research grants, totaling over $10 million. Providing other investigators easy access to these facilities and equipment is an important value shared by all Department of Genomics and Precision Medicine faculty. 

Core facilities in most institutions are stand-alone units that are staffed by personnel dedicated to the core services. In the Department of Genomics and Precision Medicine, we have taken an alternative approach to core services. All cores are integrated into the research laboratories; expertise and technical assistance derive from the research laboratories in the Department of Genomics and Precision Medicine. A consequence of this is that the Core user and their research project are typically aligned with a faculty member that shares research interests and/or technologies. In this manner, we feel we provide more expert help and guidance with regards to experimental design, data generation, and data interpretation.

Department of Genomics and Precision Medicine/GenMed support for Core functions derives from NIH Center grants (NCMRR, IDDRC, CTSA), the Department of Defense (CDMRP), US Department of Education, and foundations (www.duchennemd.org, others). 

Many core functions are provided at highly subsidized charge-back that covers reagent costs.

Investigators may qualify for pilot funding from the NCMRR grant (if the project is related to medical rehabilitation research and includes functional outcome measures), or other NIH or DoD grants.  Center investigators are also aligned with a number of foundations, and have frequently arranged for promising translational research to be underwritten by non-profits.  Please contact ehoffman@cnmcresearch.org to enquire about pilot funding options.  

A brief overview of Core facilities run by Department of Genomics and Precision Medicine faculty include DNA/mRNA technologies, Proteomics, Microscopy, Pre-clinical drug testing, Neuromuscular natural history and clinical trials (CINRG), and Bioinformatics.

DNA and mRNA technologies. (Contact: ehoffman@cnmcresearch.org; sknoblach@cnmcresearch.org)

  • Funding: NIH NCMRR, NIH IDDRC, NIH CTSA
  • Genotyping.
    • TaqMan allele discrimination assays (two units)
    • BioTrove/ABI highly parallel TaqMan assays
    • Illumina beadarrays for CGH/CNVs
    • GWAS by Affymetrix SNP chips (two units) or Illumina beadarrays
    • Epigenomics
      • Illumina 24k site epigenomics panel (human only)
      • Pacific BioSciences epigenomics by sequencing
      • MicroRNA profiling (Affymetrix, Illumina, TaqMan)
      • Nextgen sequencing
        • RainDance emulsion PCR (highly parallel re-sequencing)
        • Pacific BioSciences single molecule sequencing
        • mRNA profiling
          • Affymetrix (many species)
          • Illumina beadarrays
          • RNAseq nextgen sequencing

Proteomics technologies. (Contact: kbrown@cnmcresearch.org; sknoblach@cnmcresearch.org)

  • Funding: NIH NCMRR, NIH IDDRC, NIH CTSA
  • Electrospray – ion trap
    • Finnigan LTQ
    • Finnigan Orbitrap
    • MALDI-TOF
      • ABI TOF/TOF
      • Methods
        • Protein identification
        • Quantitative proteomic profiling in vitro using SILAC
        • Proteomic profiling by non-labeled methods

Microscopy. (Contact: jtjaiswal@cnmcresearch.org )

  • Funding: NIH IDDRC
  • Confocal microscopy
    • Imaging cell movement and interactions during growth and tumor formation.
    • Monitoring signaling pathways regulating tumor formation and metastasis.
    • Studying the trafficking and secretion hormones that play a role in obesity at tissue and cellular level.
  • Live cell imaging
    • Spinning disc confocal imaging
    • High speed imaging (>100 frames per second)
    • Continuous imaging for long period (> 1 day) with losing focus or damaging cells
    • High spatial resolution imaging (~ 50 nanometer at the cell surface)
    • Imaging single molecules dynamics
    • Monitoring biomolecular interactions
    • Photoactivation and photoablation of cells or parts of cells

Pre-clinical murine drug testing. (Contact: knaragaraju@cnmcresearch.org)

This facility is heavily utilized by academic labs, private companies (pharma, biotech), and foundations.

  • Funding: NIH NCMRR, Department of Defense CDMRP, Foundation to Eradicate Duchenne
  • Drug testing in mouse models of muscular dystrophy
    • Strains
      • Dystrophin
      • Dysferlin
      • Calpain 3
      • Emerin, Lamin A/C
      • Sarcoglycans
      • Inflammatory myopathy
  • Methods
    • Functional outcomes
      • Ex vivo muscle contractile strength
      • Grip strength
      • Activity monitors, wheel running
      • Imaging methods
        • Live animal CTSB imaging (Baudy et al. 2010)
        • Micro-echocardiography
        • MRI
        • Histological assays (regeneration, inflammation, collagen, central nuclei)

Patient natural history studies and clinical trials (CINRG network).  (Contact abronsen@cnmcresearch.org), further information at www.cinrgresearch.org

As with the pre-clinical facility, CINRG is utilized by academic labs, private companies, and foundations.

  • Funding: Department of Education NIDDR, NIH NCMRR, Department of Defense CDMRP
  • Data on functional outcomes and molecular outcomes in 348 Duchenne dystrophy patients (5 yr follow up)
  • Training in clinical evaluation methods
  • Natural history studies
  • Clinical trials

Bioinformatics. (Contact ehoffman@cnmcresearch.org, sknoblach@cnmcresearch.org, zwang@cnmcresearch.org).