Journal Article

Sensitivity Issues in DNA Array-Based Expression Measurements and Performance of Nylon Microarrays for Small Samples

François Bertucci, Karine Bernard, Béatrice Loriod, Yi-Chung Chang, Samuel Granjeaud, Daniel Birnbaum, Catherine Nguyen, Konan Peck and Bertrand R. Jordan

in Human Molecular Genetics

Volume 8, issue 9, pages 1715-1722
Published in print September 1999 | ISSN: 0964-6906
Published online September 1999 | e-ISSN: 1460-2083 | DOI: http://dx.doi.org/10.1093/hmg/8.9.1715
Sensitivity Issues in DNA Array-Based Expression Measurements and Performance of Nylon Microarrays for Small Samples

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DNA or oligonucleotide arrays are widely used for large-scale expression measurements, using various implementations: macroarrays in which DNA is spotted onto nylon membranes of relatively large dimensions (with radioactive detection) on the one hand; microarrays on glass slides and oligonucleotide chips, both used with fluorescent probes, on the other hand. Nylon microarrays with colourimetric detection have also been described recently. The small physical dimensions of miniaturized systems allow small hybridization volumes (2–100 µl) and provide high probe concentrations, in contrast to macroarrays. We show, however, that actual sensitivity (defined as the amount of sample necessary for detection of a given mRNA species) is in fact similar for all these systems and that this is mostly due to the very different amounts of target material present on the respective arrays. We then demonstrate that the combination of nylon microarrays with 33P-labelled radioactive probes provides 100-fold better sensitivity, making it possible to perform expression profiling experiments using submicrogram amounts of unamplified total RNA from small biological samples. This has important implications in basic and clinical research and makes this alternative approach particularly suitable for groups operating in an academic context.

Journal Article.  5976 words.  Illustrated.

Subjects: Genetics and Genomics

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