Support Services

Infrastructure to support the mission of STSI

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Capabilities and Core Functions

STSI drives the integration of genomics into the realm of personalized medicine by providing key services via our Core Laboratories, by supporting the Scripps Genomic Medicine projects, by leading the Scripps Genomic Health Initiative, and by initiating with partners in industry, academia, and health to improve patient access to the best medical research available.

1. Targeted DNA Sequencing Using State of the Art Next Generation Technology

  • Illumina Genome Analyzer IIx (GAIIx)
  • Life Technologies Solid3 (SOLiD3)

  • 2. High Throughput Genotyping

  • Sequenom MassArray iPLEX genotyping (custom content: 1-25 SNPs)
  • Illumina Goldengate genotyping (384-1536 SNPs) for fixed and custom content
  • Illumina Infinium whole-genome genotyping products, including:

  •                 Human660W-Quad beadchip kits
                    Human1M-Duo beadchip kits
                    HumanOmni-1 Quad beadchip kits
                    HumanCytoSNP-12 beadchip kits

    3. Biostatistics

    STSI’s biostatistics expertise and research capabilities include:

    • General biostatistical analysis including multivariate analysis.
    • DNA sequence analysis, including DNA sequence assembly and polymorphism characterization analysis, and statistical genetics including linkage and association analysis.
    • Clinical trials design and analysis.
    • Population science, including epidemiology, population genetics, risk profiling and ancestry assessment analysis.
    • Power and sample size calculations.

    Rigorous and comprehensive computational and data analysis strategies and resources characterize the research programs.

    In addition to our on-site resources, STSI researchers are able to take advantage of the exceptional storage and computing facilities of the San Diego Supercomputer Center (SDSC) and the computing cluster of The Scripps Research Institute (TSRI). SDSC, a world leader in high performance computing, has developed specific computational resources and research capacity for “omically’-oriented translational research.

    3. Bioinformatics Support

  • Study design and power analysis
  • SNP selection for genotyping studies
  • Bioinformatics pipeline and variant calling for next-generation sequencing data
  • Association analysis of genome-wide association genotyping data
  • Association analysis of candidate gene SNP data

  • 4. Clinical Trials Design

  • Support service available for all aspects of design and execution of randomized clinical trials, emphasizing individualized medicine

  • 5. Science/Medicine Matchmaker

  • Bringing together basic scientists with clinical investigators to enhance understanding of a particular disease or condition and to foster close collaborations

  • 6. ResearchMatch

  • A CTSA consortium initiative (coordinated via the Vanderbilt Institute for Clinical and Translational Research) to develop the first national, disease-neutral, centralized volunteer recruitment agency
  • Connecting individuals who wish to participate in research with eligible researchers nationwide
  • www.researchmatch.org

  • 7. CTSA Pharmaceutical Assets Portal

    The CTSA Pharmaceutical Assets Portal invites you to join in the effort to find new uses for discontinued drugs.
    The Portal members are given an unprecedented opportunity to collaborate with Pfizer Indications Discovery Unit, a division of Pfizer vested with finding new uses for old drugs.
    In addition to the compounds that you may be aware of from publically-available sources, Pfizer is also encouraging inquiries about the existence/availability of little known Pfizer compounds that target specific mechanisms in which you may have an interest. We call these “unknown” assets “Dream Compounds”.
    The ultimate goal is to leverage existing compounds to advance mechanistic understanding of human disease, resulting in novel treatments for patients. Integration of academic investigators into collaborative repositioning efforts with Pfizer would substantially increase the knowledge base and the pool of methodologies available for proof of concept studies. These matches will undoubtedly result in an increased number of approved drugs for new indications and considerable public benefit. Membership in the Portal is free for CTSA researchers (which includes TSRI, SH and any additional STSI Consortium Members).Visit their website for more information and to register: CTSA Pharmaceutical Assets Portal

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