Comprehensive Genomics

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Michael Crowley, Ph.D.
– Co-Director

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Shawn Levy, Ph.D.
– Co-Director

Contact: (205) 975-2013

Overview:

Cancer research in the modern era has taken advantage of advances in sequencing technologies, the most obvious being the ability to sequence the human genome quickly with relatively low cost. Over the last ten years, cancer genomic studies have illustrated the vast diversity that exists between and within different cancer types at the molecular level. As the push for precision (personalized) medicine continues and the use of genomic assays in the clinic matures, the requirement for sequence data on individual tumors compared with the patient’s normal constitutive DNA will be a necessity for proper treatment. In addition, basic researchers investigating the mechanisms of tumor development, progression and metastasis benefit from low cost, highly specific integrated data sets.

Next-Generation sequencing is only part of the broader repertoire of genomic tools available to cancer researchers.  Many of the assays applicable to cancer research require specific expertise and equipment, which would be prohibitive for individual labs to implement. The Comprehensive Genomics Shared Facility is a single entity that was developed by combination of three previously separate facilities: Sanger DNA Sequencing, Microarray and Next-Generation Sequencing. In recent years the use of microarray technology for many projects, especially expression studies, has been supplanted by sequencing methodologies. The consolidation of the three facilities and continued partnership with HAIB also allows far more efficient management and investment in equipment and related tools in the rapidly evolving genomic technology space. This consolidation of the three previous facilities into one entity, the Comprehensive Genomics Shared Facility (CGSF), provides a single entry point to genomic services for all investigators. The combined facility has the following specific aims:

  1. The CGSF will provide comprehensive consultative services for basic research and clinical assay design and development for cancer genomics. Since the inception of the shared facility a primary mission of the directors has been to consult with CCC investigators about their experimental and analysis needs related to genomic technologies.  These consultations include recommendations on using the appropriate genomic platform to most efficiently and effectively support their research.  They also include information on the technical capabilities and services offered and on study design and data interpretation.
  1. The GCSF will fully support and maintain state-of-the-art genomic technology platforms including Next-Generation sequencing and high dimensional genotyping platforms and provide access to those platforms to all Cancer Center investigators. The integrated CGSF will continue to provide Cancer Center members access to high-throughput, state-of-the art genetic and genomic technologies to augment existing research and to open new avenues of genetic and genomic research.  The CGSF is physically located at both UAB and HAIB with capabilities unified by shared staff as well as LIMS tools.
  1. Provide continued, expert service for standard Sanger DNA sequencing and support for various experiments run on the ABI sequencers. Sanger DNA sequencing is still a workhorse of molecular biology and a valuable technology to determine sequence information from cloned genes, gene specific PCR amplification, mutation screening, etc.  In addition, the sequencing instruments are able to perform a variety of assays including, but not limited to, Human Cell Line Identification for conformation of cell type.
  1. The shared facility has been and will continue to be the sequencing provider to the Microbiome/Gnotobiotic Shared Facility. The microbiome has been shown to have a major impact on host metabolism and homeostasis. The GCSF provides support to determine qualitatively and quantitatively the microbial population present at various sites in or on the human body and for animal model research. This support consists of sequencing the V4 region of the 16S ribosome gene and whole bacterial genomes for metagenomic analysis.

 

Contact Information:

Co-Director: Michael Crowley, Ph.D.
Email: mcrowley@uab.edu
Phone: (205) 975-2013

Co-Director: Shawn Levy, Ph.D.
Email: slevy@hudsonalpha.org
Phone: (256) 327-9426