Identifying Potential Tumor Markers and Antigens by Database Mining and Rapid Expression Screening

  1. W. Troy Loging1,5,
  2. Anita Lal1,5,
  3. I-Mei Siu1,
  4. Tania L. Loney1,
  5. Carol J. Wikstrand1,
  6. Marco A. Marra2,
  7. Christa Prange3,
  8. Darell D. Bigner1,
  9. Robert L. Strausberg4, and
  10. Gregory J. Riggins1,6
  1. 1Duke University Medical Center, Durham, North Carolina 27710, USA; 2Washington University Genome Sequencing Center, St. Louis, Missouri 63108, USA; 3The I.M.A.G.E. Consortium, Biology and Biotechnology Research Program, Lawrence Livermore National Laboratory, Livermore, California 94550, USA; 4Cancer Genome Anatomy Project, Office of the Director, National Cancer Institute, Bethesda, Maryland 20892, USA

Abstract

Genes expressed specifically in malignant tissue may have potential as therapeutic targets but have been difficult to locate for most cancers. The information hidden within certain public databases can reveal RNA transcripts specifically expressed in transformed tissue. To be useful, database information must be verified and a more complete pattern of tissue expression must be demonstrated. We tested database mining plus rapid screening by fluorescent-PCR expression comparison (F-PEC) as an approach to locate candidate brain tumor antigens. Cancer Genome Anatomy Project (CGAP) data was mined for genes highly expressed in glioblastoma multiforme. From 13 mined genes, seven showed potential as possible tumor markers or antigens as determined by further expression profiling. Now that large-scale expression information is readily available for many of the commonly occurring cancers, other candidate tumor markers or antigens could be located and evaluated with this approach.

[The expression data described in this paper have been submitted to the NCBI SAGEmap database under library name SAGE_Duke_GBM_H1110, SAGE_pooled_GBM, SAGE_BB542_whitematter, and SAGE_normal_pool(6th).]

Footnotes

  • ↵5 These authors contributed equally to this work.

  • ↵6 Corresponding author.

  • E-MAIL greg.riggins{at}duke.edu; FAX (919) 681-2796.

  • Article and publication are at www.genome.org/cgi/doi/10.1101/gr.138000.

    • Received February 24, 2000.
    • Accepted July 18, 2000.
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  1. doi: 10.1101/gr.138000 Genome Res. 10: 1393-1402 Cold Spring Harbor Laboratory Press

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