The new sample preparation kit should allow researchers to conduct microarray-based comparative genomic hybridisation (aCGH) experiments on the vast number of FFPE samples that have been stored in connection to various biopsies and as such are associated with a vast wealth of clinical history.

These aCGH experiments allow researchers to analyse copy number variations (CNVs) in one DNA sample compared with another and so identify mutations associated with disease progression.

"People who are conducting cancer research are eagerly awaiting methods that will allow them to run their archived FFPE samples," said Jay Kaufman, Agilent's marketing director for Genomics.

According to Kaufman, these samples are generally old and degraded which leads to problems if standard preparation techniques are used.

He continued by explaining that the sample preparation step first involves the isolation of the RNA from the FFPE matrix.

Typically enzymes would then be used to label the genomic DNA prior to hybridisation to the microarray. However, the degraded samples are often so heavily cross-linked that the enzymes can't label the DNA effectively.

"The enzymes often don't perform well with these systems and can lead to exaggerated noise and bad data, this new method allows the DNA to be labelled using a non-enzymatic method which leads to higher quality data," said Kaufman.

The Universal Linkage System (ULS) developed by Kreatech, makes use of the stable coordinative binding of platinum to nucleic acids to fluorescently label the oligomers so that they can be detected once they are hybridised to the microarray probes.

The number of samples that could be studied using this technique has been estimated to be as large as 400m; however because of the extent of degradation of the samples the number that could be successfully analysed is difficult to accurately predict.

Kaufman said that estimating the market size for any emerging technology can be difficult, but said he believes that by 2008 the market for aCGH of FFPE samples could be in the order of $10 to $50m.

Because of the vast numbers of samples that have, as yet, not been studied using aCGH techniques many companies are trying to provide ways to study this untapped wealth of knowledge.

Indeed, Affymetrix and NuGEN recently announced a collaboration that will work on developing a system that would use NuGEN's whole transcriptome qPCR (quantitative polymerase chain reaction) system to enable such experiments on Affymetrix' GeneChip 3' gene expression platform.

NuGEN has also licensed certain components from Kreatech to create a system for labelling RNA in preparation for gene expression experiments on Agilent microarrays.

While this work is currently being conducted independently of Agilent, Kaufman said that the company has a team currently looking into how the technology works so that they can help customers who are interested in using the technology.

"We have several efforts underway to develop FFPE samples in a wide range of applications including using products that we acquired with our purchase of Stratagene," said Kaufman.

He explained that the older that FFPE samples are, the less likely researchers are to get good results from them, and this is partly due to the fact that before about ten years ago people were less careful with the preparation of the samples and the quality of the formaldehyde used.

Another thing that may slow the adoption is the current debate over the content and overall approach of the next generation of CNV products, which might deter people using up their most valuable samples if there are not compelling tools available for their particular regions of interest.

"Agilent is currently working with collaborators to define what the next generation of CNV products will be and what content they will contain," said Kaufman.

"The challenge is that the market has not yet agreed on what the content for a catalogue product for this application should be. However, because of the flexibility of our microarray printing method Agilent is in a unique position to be able to offer custom arrays to suit needs until the market can agree on what it wants."

The microarray printing facilities at Agilent Life Sciences and Chemical Analysis Centre of Excellence in Santa Clara, California, US, are featured on a 5 minute video recently released by the company, showcasing the company's product and service offerings.