Nuclease Probe Mediated Sequencing

Information

  • Research Project
  • 8126388
  • ApplicationId
    8126388
  • Core Project Number
    R43HG005949
  • Full Project Number
    5R43HG005949-02
  • Serial Number
    5949
  • FOA Number
    PA-09-080
  • Sub Project Id
  • Project Start Date
    8/13/2010 - 14 years ago
  • Project End Date
    12/30/2012 - 12 years ago
  • Program Officer Name
    SCHLOSS, JEFFERY
  • Budget Start Date
    7/1/2011 - 13 years ago
  • Budget End Date
    12/30/2012 - 12 years ago
  • Fiscal Year
    2011
  • Support Year
    2
  • Suffix
  • Award Notice Date
    6/27/2011 - 13 years ago

Nuclease Probe Mediated Sequencing

DESCRIPTION (provided by applicant): Sequencing is very powerful for identifying differences in genomic DNA that may regulate cell function and diseases, pre-dispose persons to certain diseases, or warn of adverse drug metabolism. It provides a basis for identifying differences in gene expression, though such applications have been limited and are problematic because each expressed gene can vary from a single copy per cell to 10's of thousands of copies. Further, its application to formalin fixed paraffin-embedded tissue (FFPE) is quite challenging. Millions of such samples, along with the corresponding treatment modalities and known clinical outcomes, are archived at clinical centers and hospitals. Millions of such samples have also been archived from in vivo studies of safety, metabolism, and animal models of disease. In addition, the utility of sequencing for routine experiments where array-based measurements are used today is limited by cost, and might also be limited by accuracy, sensitivity, and reproducibility of the sequencing data. This Phase I proposal develops and validates a new approach for addressing these challenges, "Nuclease Probe Mediated Sequencing," provides a variation of candidate capture methods used to focus sequencing onto genes of interest, and addresses issues with array-based methods. The method proposed uses a lysis-only assay and either a variation of HTG's quantitative Nuclease Protection Assay (qNPA") or ligation/exonuclease generated Padlock probes to generate DNA probes for sequencing by synthesis, combined with gene tagging and experiment tagging methods to permit pooling to provide cost reduction and higher sample throughput. PUBLIC HEALTH RELEVANCE: This Phase I project will address challenges to using sequencing for measuring gene expression. The proposed method will enable researchers to use archived fixed tissue samples. It will also lower the cost per sample and increase the number of samples tested per sequencing run, while potentially increasing the accuracy, dynamic range and reproducibility of measurement, expanding the utility of sequencing to measure gene expression and providing a more cost effective and precise platform than currently provided by high density array-based measurement.

IC Name
NATIONAL HUMAN GENOME RESEARCH INSTITUTE
  • Activity
    R43
  • Administering IC
    HG
  • Application Type
    5
  • Direct Cost Amount
  • Indirect Cost Amount
  • Total Cost
    299390
  • Sub Project Total Cost
  • ARRA Funded
    False
  • CFDA Code
    172
  • Ed Inst. Type
  • Funding ICs
    NHGRI:299390\
  • Funding Mechanism
    SBIR-STTR
  • Study Section
    ZRG1
  • Study Section Name
    Special Emphasis Panel
  • Organization Name
    HTG MOLECULAR DIAGNOSTICS, INC.
  • Organization Department
  • Organization DUNS
    020238841
  • Organization City
    TUCSON
  • Organization State
    AZ
  • Organization Country
    UNITED STATES
  • Organization Zip Code
    857065009
  • Organization District
    UNITED STATES