With the ever-increasing utilisation of nucleic acid-based analyses, there is a demand for higher sample throughput. An obvious way of achieving such increase in sample processing is to combine separate assays into a multiplex format. However, this approach may lead to a compromise in assay specificity, as efforts are made to accommodate all targets in one reaction. Microarrays offer the potential to screen thousands of DNA, RNA or cDNA targets simultaneously thereby increasing throughput and reducing costs considerably. Most applications of microarray technology have been concentrated on expression arrays, where gene expression levels in two samples are compared. Recently, more applications have turned to the use of oligonucleotide based arrays for detection and discrimination of Single Nucleotide Polymorphisms (SNPs) and other DNA sequences. Generic control sequences that can indicate the discriminatory power of the system when incorporated into array-based assays, will increase confidence in the performance and comparability of these technologies.

The overall aim of the initial project was to develop and validate protocols and toolkits, including reference materials, to improve the performance of multiplexed genetic measurements and increase confidence in their validity and comparability. The main problem with a multiplex assay lies with the optimisation of reaction conditions for multiple DNA targets, whilst maintaining specificity and selectivity. We have developed a set of array standards and demonstrated their use as performance indicators to monitor specificity and efficiency of hybridisation, aid assay optimisation, and act as a generic tool for cross experiment and platform comparisons. A more detailed report can be downloaded from this page.

In the current programme of work we are evaluating the potential of the standards for monitoring the performance of expression arrays, through in house and inter-laboratory trials. We also plan to produce certified reference batches of the standards to be made available for distribution to the scientific community. If you would like to participate in, or would like further information on the evaluation of the standards, please contact the VAM helpdesk ([email protected]).