A Highly Multiplexed PCR Platform for Gene Expression Profiling from FFPE Tissue

Information

  • Research Project
  • 8432665
  • ApplicationId
    8432665
  • Core Project Number
    R33CA160011
  • Full Project Number
    1R33CA160011-01A1
  • Serial Number
    160011
  • FOA Number
    RFA-CA-12-003
  • Sub Project Id
  • Project Start Date
    9/19/2012 - 12 years ago
  • Project End Date
    8/31/2013 - 11 years ago
  • Program Officer Name
    OSSANDON, MIGUEL
  • Budget Start Date
    9/19/2012 - 12 years ago
  • Budget End Date
    8/31/2013 - 11 years ago
  • Fiscal Year
    2012
  • Support Year
    01
  • Suffix
    A1
  • Award Notice Date
    9/19/2012 - 12 years ago
Organizations

A Highly Multiplexed PCR Platform for Gene Expression Profiling from FFPE Tissue

DESCRIPTION (provided by applicant): The overall goal of this application is to deliver a highly multiplexed, quantitative, and automated system for the rapid identification of diffuse large B-cell lymphoma (DLBCL) subgroups using formalin-fixed paraffin-embedded (FFPE) material as the sample source; a technology that is not yet available to the research and clinical communities. DLBCL accounts for ~30% of all non-Hodgkin lymphomas and thus is the most common subtype of this cancer in the United States. While many patients respond well to treatment, there is a sizable subset that remains refractory or suffers relapse. Gene expression profiling has revealed that this difference in response is reflected in the biology of the tumor an two subgroups have been defined based on the origin of the tumor cell. Molecular signatures within a panel of 17 genes can differentiate these subgroups. Technologies to detect gene expression patterns currently center around two existing formats: microarrays and real-time PCR. The former, although able to detect hundreds to thousands of genes, suffer from their lack of sensitivity and quantitative capacity, while PCR, although quantitative and exceedingly sensitive, has extremely limited multiplexing capability. Therefore, technologies that combine attributes of multiplexing with sensitive, quantitative analysis are critically needed to advance the understanding of tumor biology toward translation into clinical diagnostic utility. Archives of FFPE tumors represent a valuable resource for translational cancer genomic research. However, utilizing FFPE tissue is challenging since it is often derived from small biopsies containing RNA that is fragmented during fixation and storage, thus rendering it less suitable for microarray analysis. As a result there is a lack of quantitative, multiplexed, sensitive, and robus assays that are able to utilize FFPE as a source of tissue for genetic analysis. In order to overcome these above obstacles we propose to develop a novel, rapid, and automated assay to detect, quantify, and classify the two main subtypes of DLBCL, thus facilitating timely diagnosis of the tumor type in order to inform clinical treatment options. Such a technology, that can detect and quantify multiple gene targets in a single-tube reaction using FFPE specimens as the source material, does not currently exist. The objective of this proposal will be met by completing three Specific Aims. These consist of (i) developing the technology, to be termed the 'ICEPlex Multiplex FFPE Assay', by adapting PrimeraDx's emerging STAR technology and ICEPlex instrument system for this purpose; (ii) validating the analytical performance characteristics of the resultant assay; and (iii) verifying performance of the assay by conducting a concordance study comparing results from the newly developed assay with a reference microarray technology currently used for DLBCL subtyping. PUBLIC HEALTH RELEVANCE: The past decade has seen a major shift in cancer diagnostics with the ascendance of gene expression profile analysis of tumors, which is leading to improvements in cancer detection, diagnosis, and treatment. However, to achieve the full potential of this approach, technology impediments involving the number of genes that can be detected in a single assay and the use of stored tissue samples that may be degraded need to be overcome. PrimeraDx will address these problems by providing an automated solution for a single-reaction, multi-sample analysis from stored tumor tissue material in order to classify types of a common human lymphoma, thereby facilitating rapid diagnosis, determination of treatment options, and analysis of response to therapy.

IC Name
NATIONAL CANCER INSTITUTE
  • Activity
    R33
  • Administering IC
    CA
  • Application Type
    1
  • Direct Cost Amount
    244661
  • Indirect Cost Amount
    90525
  • Total Cost
    335186
  • Sub Project Total Cost
  • ARRA Funded
    False
  • CFDA Code
    394
  • Ed Inst. Type
  • Funding ICs
    NCI:335186\
  • Funding Mechanism
    Non-SBIR/STTR RPGs
  • Study Section
    ZCA1
  • Study Section Name
    Special Emphasis Panel
  • Organization Name
    PRIMERADX, INC.
  • Organization Department
  • Organization DUNS
    602547932
  • Organization City
    MANSFIELD
  • Organization State
    MA
  • Organization Country
    UNITED STATES
  • Organization Zip Code
    020481172
  • Organization District
    UNITED STATES