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Briefings in Functional Genomics Advance Access published online on May 27, 2009
Briefings in Functional Genomics, doi:10.1093/bfgp/elp012
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© The Author 2009. Published by Oxford University Press. For permissions, please email: journals.permissions@oxfordjournals.org

Interesting times for microarray expression profiling

Yvonne Hey and Stuart D. Pepper

Corresponding author. Stuart Pepper, Cancer Research UK Molecular Biology Core Facility, Paterson Institute for Cancer Research, University of Manchester, Wilmslow Road, Withington, Manchester M20 4BX, UK. Tel: +44-161-446-3184; Fax: +44-161-446-3109; E-mail: spepper{at}picr.man.ac.uk

The last 10 years have seen microarrays go from being a nascent technology available only in a limited range of research facilities to becoming a ubiquitous approach to expression profiling. Developments in microarray technology have allowed the content of arrays to increase to the point that complete transcriptomes can be assayed on a single array, whilst developments in RNA labelling technology have reduced the amount of RNA needed down to the point where single cell profiling is technically possible. Recently it has also become possible to generate expression data from formalin-fixed paraffin-embedded archival samples. With the range of samples that can now be successfully profiled by microarray analysis this should be a good time to be running a microarray core facility. However, the arrival of Next Generation Sequencers means that for the first time there is an alternate platform that can potentially give a more complete picture of cellular expression than a microarray. Next Generation Sequencers are still in their infancy as a platform for expression profiling. Currently there are simply not enough Next Generation Sequencers in operation to meet the level of demand for expression profiling that microarray facilities service, but more systems are constantly becoming available. Looking ahead it seems certain that some proportion of expression profiling work will move from microarrays to Next Generation Sequencers, so now is a good time to consider some of the factors that might affect how significant that switch will be.

Keywords: microarray, clonal sequencer, next generation sequencer, expression profiling


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