New potential unleashed for microarrays

By Jeremy Torr
Monday, 12 May, 2003



With the 3rd Australian Microarray Conference just around the corner, Jeremy Torr takes a look at what's new in the technology.

With microarrays being touted as the ultimate solution for everything from defrosting tasty peas, curing the common cold to avoiding genetic defects, there is little wonder the industry is increasing its levels of interest in the technology.

"The big news at the moment is protein arrays," says Geoff Kornfeld, director of the Ramaciotti Centre for Gene Function Analysis, based at the University of NSW. This move to protein arrays combined with ever more available and refined DNA sets is opening up the scope of microarray research to what Ian Dawes of the School of Biotechnology and Biomolecular Sciences at UNSW calls "wonderful times."

Kornfeld notes that although the number of labs investing in new microarray equipment is not increasing, there is increasing consolidation of the facilities where existing microarray services were being offered.

"The number of machines being sold has levelled off, and there is a trend away from individual labs buying their own new equipment," he says.

"But what is happening is that some of the more established people are now buying second and third machines and consolidating the market, providing services for a wide range of other facilities."

In terms of the overall uses of microarrays as a research tool, changes to the technology itself are making their use more attractive to a wider range of users. Major influences are the widespread introduction of oligos rather than cDNA (printed) arrays. The move away from cDNA samples, with their intensive preparation, PCR implementation, checking then printing stages to the much faster and easier to use oligos has made a considerable difference both to speed and accuracy, notes Kornfeld.

"You can simply get the oligos out of the machine and go. You can be much more specific about splice variants, and they also offer higher accuracy and convenience," he says. Another development spurring activity within the science is the clustering of experimental data.

"As more microarray work and results get done, the opportunities for clustering increase exponentially," says Dawes.

"Every experiment can be clustered with results from similar work. Things like reaction for heat shock, cold shock and so on can all be clustered to give a broader picture."

Dawes also predicts exciting discoveries on the horizon in the fields of genetic disorders, virus typing, anti-oxidants, haemophilia and cancer research.

"Using gene identification within secondary tumours to pinpoint treatment of primary tumours is quite possible. This should give us a really good predictive tool," he claims.

Also making a difference in the technology itself are the introduction of new substrate materials, which boost both accuracy and sensitivity.

Kornfeld explains the conventional glass or plastic substrate is likely to be edged aside by new materials designed to offer higher levels of convenience and repeatability. As an example, the use of 'porous' or 'flow-through' glass is being investigated. In this case, the samples are printed onto a semi-permeable surface, which allows a much higher level of sensitivity -- many multiples of times that of conventional glass.

These new materials offer up to one hundred times the sensitivity, due to the greatly increased surface area and better hybridisation.

Other advances include notable progress in the reliability of data underpinning microarray use. Both Dawes and Kornfeld point out that not only is there more raw data now available than ever before, but that improvements in statistical analysis have made results easier and more accurate to obtain.

"People are now working on proteins, with researchers at Yale having completed 5000 proteins in the yeast gene. That's really exciting, impressive stuff," comments Dawes.

Talking microarrays

The 3rd Australian Microarray Conference will be held on the Gold Coast, July 23-26. Registrations are still open, and there is still a chance to submit abstracts to the event's organisers.

Confirmed speakers include:

  • Nigel Carter, leader of the Molecular Cytogenetics Team at the Wellcome Trust Sanger Institute
  • Orly Alter, principal investigator in the Department of Genetics, Stanford University
  • Timothy Hughes, assoc prof in the Banting and Best Department of Medical Research at the University of Toronto
  • Alvis Brazma, team leader of the microarray informatics team at the European Bioinformatics Institute
  • Donna Albertson, assoc prof at the Cancer Research Institute, UC San Francisco
  • Thomas Preiss, laboratory head of the molecular genetics program at the Victor Chang Cardiac Research Institute
  • Paul Bertone, of Yale University
More information is on the conference web site, www.microarrays.org.au
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