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ABRF Survey Documents Microarray Growth in Academic Labs

SAN DIEGO, Feb 27 - Eighty-three percent of laboratories using microarrays expect to increase their staff dedicated to the technology over the next year. That’s one of the bullish findings in a survey presented at the annual meeting of the Association of Biomolecular Resource Facilities, which attracted over 1,000 delegates this week to drizzly San Diego.

The web-based survey was conducted in December and January by the ABRF Microarray Research Group, co-chaired by George Grills of Albert Einstein College of Medicine and Chandi Griffin of UC San Francisco. Seventy-eight labs participated in the survey. Reflecting the ABRF membership, they were weighted toward academia (81 percent) and North America (70 percent). The survey looked both at labs using the Affymetrix GeneChip platform as well as those doing their own spotting with oligonucleotide, cDNA and protein technologies.

Compared with a smaller ABRF survey a year ago, the Affy users reported higher satisfaction with the platform. Eighty-three percent of GeneChip users reported they were “very satisfied” or “moderately satisfied” with the Affy technology, with the fraction saying “very” jumping from seven percent in last year’s survey to 33 percent in this year’s. The survey did not drill any deeper but Griffin speculated that the improvement was due to growing experience on the part of users and better support on the part of Affy.

One surprising finding among labs doing their own spotting was the growth in the use of oligonucleotide probes at the expense of cDNAs and PCR products. The fraction of labs using oligos jumped from eleven percent a year earlier to 22 percent in the current survey. Again, the survey did not drill deeper but Griffin suggested that lower prices for oligos might have been a factor.

The survey also took a look at the equipment being used in labs doing their own spotting. Among DNA handling robots, Beckman had the highest market share with 35 percent, followed by Robbins (22 percent) and Qiagen (17 percent). Among slide arrayers, Affy/GMS led with 23 percent, followed by internally-developed systems (17 percnet), GeneMachines (16 percent) and Biorobotics (13 percent). And among scanners, Packard/GSI led with 34 percent, followed by Axon (24 percent) and Affy/GMS (13 percent).

Not surprisingly, all labs reported that their greatest challenges in using microarray technologies are in the area of software. The most commonly reported challenge (57 percent) was bioinformatics and the second most common was software in general (25 percent). There are no clear market leaders in the gene expression analysis software used by the labs. Affy products totaled 19 percent, followed by the academic programs Treeview (15 percent) and Cluster (14 percent). Spotfire was used in twelve percent of labs, followed by GeneSpring (10 percent) and Scanalyze (9 percent).

The MARG plans to post the detailed survey results on the ABRF website in due course – and intends to follow up with “long-term, large-scale studies,” according to Grills.

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