Customized Molecular Phenotyping by Quantitative Gene Expression and Pattern Recognition Analysis

  1. Shreeram Akilesh,
  2. Daniel J. Shaffer, and
  3. Derry Roopenian1
  1. The Jackson Laboratory, Bar Harbor, Maine 04609, USA

Abstract

Description of the molecular phenotypes of pathobiological processes in vivo is a pressing need in genomic biology. We have implemented a high-throughput real-time PCR strategy to establish quantitative expression profiles of a customized set of target genes. It enables rapid, reproducible data acquisition from limited quantities of RNA, permitting serial sampling of mouse blood during disease progression. We developed an easy to use statistical algorithm—Global Pattern Recognition—to readily identify genes whose expression has changed significantly from healthy baseline profiles. This approach provides unique molecular signatures for rheumatoid arthritis, systemic lupus erythematosus, and graft versus host disease, and can also be applied to defining the molecular phenotype of a variety of other normal and pathological processes.

Table 1.

Genes Included in the ImmunoQuantArray

Footnotes

  • [Supplemental material—The primer sequences for genes included in the ImmunoQuant Array (and listed in Table 1) are available online at www.genome.org. The GPR algorithm, documentation, and sample data sets are available at http://www.jax.org/staff/roopenian/labsite/index.html.The following individuals kindly provided reagents, samples, or unpublished information as indicated in the paper: D. Mathis and C. Benoist.]

  • Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.533003.

  • 1 Corresponding author. E-MAIL dcr{at}jax.org; FAX (207) 288-6383.

    • Accepted April 1, 2003.
    • Received November 13, 2002.
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