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Vol. 10, Issue 9, 1393-1402, September 2000

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

W. Troy Loging,1,5 Anita Lal,1,5 I-Mei Siu,1 Tania L. Loney,1 Carol J. Wikstrand,1 Marco A. Marra,2 Christa Prange,3 Darell D. Bigner,1 Robert L. Strausberg,4 and Gregory J. Riggins1,6

1 Duke University Medical Center, Durham, North Carolina 27710, USA; 2 Washington University Genome Sequencing Center, St. Louis, Missouri 63108, USA; 3 The I.M.A.G.E. Consortium, Biology and Biotechnology Research Program, Lawrence Livermore National Laboratory, Livermore, California 94550, USA; 4 Cancer Genome Anatomy Project, Office of the Director, National Cancer Institute, Bethesda, Maryland 20892, USA

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).]

5 These authors contributed equally to this work.

6 Corresponding author.

10:1393-1402 ©2000 by Cold Spring Harbor Laboratory Press  ISSN 1088-9051/00 $5.00
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