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Survey Finds Affy Is Dominant Platform in Microarray Cores; Expression Profiling Is Most Common App

SALT LAKE CITY – Despite the emergence of many new application areas for microarrays over the last several years – such as whole-genome SNP analysis, comparative genomic hybridization, chromatin immunoprecipitation-on-chip studies, and microRNA analysis – core labs are still running more arrays for gene expression studies than for any other area, according to a recent survey by the Association for Biomolecular Research Facilities’ Microarray Research Group.
The 2008 MARG survey also found that Affymetrix GeneChips are used more than any other array platform, followed by Agilent arrays, in-house spotted arrays, and Illumina’s BeadChip.
Furthermore, the study found that in spite of the recent rise of next-generation sequencing technologies, which some consider to be a promising alternative to microarrays for many research applications, only 9 percent of respondents think that these sequencers will replace microarray technology over the next five years.
MARG member Christina Harrington, manager of the Affymetrix Microarray Core at Oregon Health & Science University, presented the preliminary results of the study on Sunday at the annual ABRF conference here. She said that the group expects to publish the complete results on its website next week.
The survey was conducted in November and December of 2007 and had 149 respondents. Of those, 77 percent were academic or government microarray facilities and the remainder were commercial service facilities or pharmaceutical labs. The majority of respondents – 74 percent – were based in the US or Canada.
Harrington noted that new applications and new technologies that have emerged over the last several years have led to “much discussion” in the microarray community about where the field is going, and that one aim of the study was to provide a snapshot of the current state of the art, as well as the future of the technology. 
The study found that the Affymetrix platform is the most widely used, with around 60 percent of respondents noting that they run Affy GeneChips. Agilent arrays and in-house spotted arrays were the next most popular, with about 50 percent of labs saying they used those platforms. Around 30 percent of respondents said they are using Illumina BeadChips, while less than 10 percent of respondents are using arrays from Applied Biosystems, NimbleGen, or Combimatrix.
Regarding applications, whole-genome expression profiling is still the most widely used research area. Around 98 percent of Affy customers said they use the arrays for this application, while 86 percent of Illumina customers run gene expression studies on the BeadChip platform.
Around 29 percent of Affy users and 27 percent of Illumina users run whole-genome genotyping studies with more than one million markers, while 44 percent of Affy users and 60 percent of Illumina users run whole-genome genotyping studies with fewer than a million markers. 
Affy arrays appear to be the most popular platform for gene expression analysis in most labs. In response to the question, “What arrays do your investigators prefer to use for gene expression analysis?” 48 percent of respondents said Affy arrays. Agilent arrays are used preferentially for gene expression studies in 21 percent of labs, Illumina arrays in 20 percent of labs, and in-house spotted arrays are used in 16 percent of labs. Less than 2 percent of respondents said they prefer to use arrays from ABI, NimbleGen, or Exiqon for expression studies.
Harrington said MARG was particularly interested in finding out what sort of impact high-throughput sequencing technologies are expected to have on microarray facilities, and whether sequencing would eventually displace arrays, as some have predicted.
“In essence,” she said, “the answer was no.”
Only 9 percent of respondents said they thought next-gen sequencers would “completely” replace microarrays within five years, although 62 percent of respondents said they thought the technology would “partially” replace arrays. Around 17 percent of respondents said they thought next-gen sequencing would have no impact on arrays at all, while 12 percent were unsure.
Of the responding labs, 28 percent, or 23, currently have a next-gen sequencer: 10 Illumina Genome Analyzers, 9 Genome Sequencers from 454 Life Sciences, and 7 ABI SOLiDs. Around 46 percent of respondents said they plan to purchase a high-throughput sequencer in the “near future,” however.

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