CASE REPORTS
Profiling viral gene expression in lymphomas
Dirk P. Dittmer
One quarter of human cancers are associated with infectious agents such as viruses. Transcriptional profiling of the viral genome offers the chance to accelerate our investigations, diagnosis and staging of viral-associated lymphomas. Since viral genomes are orders of magnitude smaller than the human genome, we have developed whole viral genome arrays based upon real-time quantitative PCR for Kaposi's Sarcoma-associated herpesvirus and Epstein-Barr virus (1). This technology is technologically robust, rapid and inexpensive. Most clinical laboratories and research centers have extensive experience in real-time QPCR, which has become routine for HIV diagnostics and thuas are in a position to use QPCR-based arrays for lymphoma diagnosis. In adopting real-time QPCR to comparative transcription profiling for KSHV we realized that we could feed the real-time QPCR output (the so-called CT value) directly in existing publicly available cluster analysis programs (2). In fact, the initial step in hybridization-based analysis, e.g. Affymatrix is to compute the logarithm of the signal intensity in order to improve statistical performance. The CT values already represent a logarithmic measure of the target concentration and can be used directly. PCR is the most sensitive detection method available today. It is inherently more sensitive than hybridization-based detection methods and we have been able to quantify 96 different viral mRNAs from a 2x2 mm fine-needle KS biopsy or from as little as 5000 FACS sorted cells.
Publication Dates
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Publication in this collection
06 Jan 2006 -
Date of issue
Oct 2005
