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Nucleic Acids Research 2006 34(6):e46; doi:10.1093/nar/gkl086
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Published online 22 March 2006

© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

I1 monitoring gene expression and K1 nucleic acid amplification

Multiplex degenerate PCR coupled with an oligo sorbent array for human endogenous retrovirus expression profiling

Jean-Philippe Pichon, Bertrand Bonnaud, Philippe Cleuziat1 and François Mallet*

Unité Mixte de Recherche 2714 CNRS–bioMérieux, IFR128 BioSciences Lyon-Gerland, ENS-Lyon 46 allée d'Italie, 69364 Lyon cedex 07, France 1Centre de Biologie Moléculaire et des Microsystèmes, bioMérieux, Parc Polytec 5 rue des Berges, 38024 Grenoble Cedex 01, France

*To whom correspondence should be addressed. Tel: +33 472 728 358; Fax: +33 472 72 8533; Email: francois.mallet{at}ens-lyon.fr

Received January 20, 2006. Revised February 7, 2006. Accepted March 7, 2006.

Human endogenous retroviruses (HERVs) can be divided into distinct families of tens to thousands of paralogous loci. The expression of HERV elements has been detected in all tissues tested to date, particularly germ cells, embryonic tissues and neoplastic tissues. Hence, the study of HERV expression could represent added value in cancer diagnosis. We developed a quantitative assay combining a multiplex degenerate PCR (MD-PCR) amplification, based on the relative conservation of the pol genes, and a colorimetric Oligo Sorbent Array (OLISA®). Nine HERV families were selected and amplification primers and capture probes were designed for each family. The features required to achieve efficient amplification of most of the elements of each HERV family and balanced co-amplification of all HERV families were analyzed. We found that MD-PCR reliability, i.e. equivalence of amplification and dose-effect relationship, relied on the adjustment of three critical parameters: the primer degeneracy, the relative concentration of each primer and the total amount of primers in the amplification mixture. The analysis of tumoral versus normal tissues suggests that this assay could prove useful in tumor phenotyping.


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