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Survey Finds Exome Arrays on the Upswing as GWAS, Gene Expression Apps Decline

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By Bernadette Toner

Exome analysis is the most promising application area for microarrays in the foreseeable future, according to a survey of genomic researchers GenomeWeb recently conducted in partnership with investment firm Mizuho Securities.

While the survey results indicate that arrays face continued competition from next-generation sequencing platforms, exome arrays represented a bright spot for the technology. Respondents expect to increase spending on exome arrays by 3.7 percent on average over the next 12 months, while they anticipate a .2 percent decline in spending on gene expression studies and a 1.7 percent fall in genome-wide association studies (see chart 1, below).

Likewise, around 30 percent of respondents said they expect exome analysis to be the "most relevant" application for arrays over the next two years, followed by cytogenetics/diagnostics (26 percent), and genotyping (19 percent) (see chart 2, below).

The optimism around exome arrays is in line with the results of a survey conducted in December by investment bank William Blair (BAN 12/13/2011) and follows the launch of new exome arrays from Illumina and Affymetrix last fall (BAN 10/18/2011).

The broader outlook for arrays is not positive, however, as the technology generally fared "poorly" in the survey, Mizuho analyst Peter Lawson wrote in a research note outlining the results.

Similar to the results of a survey GenomeWeb and Mizuho conducted in October (BAN 10/25/2011), next-generation sequencing is clearly the technology of most interest to the genomics research community. Around 80 percent of respondents said they use or plan to use sequencing, while only 40 percent said the same for arrays.

In terms of budgets, single-molecule sequencing, informatics, and next-gen sequencing were the top three areas where respondents expect to increase their spending over the next 12 months.

By contrast, the survey found that a net of 26 percent of respondents plan to spend less on gene expression arrays over the next year, while a net of 34 percent said the same for array-based genotyping — marking them "the only technologies with negative scores in the survey," Lawson noted (see chart 3, below).

Furthermore, the results echo the findings of previous GenomeWeb/Mizuho surveys that found that RNA-seq is making inroads into the gene expression array market. Around 83 percent of respondents in the current survey expect RNA-seq to replace gene expression arrays within five years (see chart 4, below).

Respondents on average expect RNA-seq to replace RNA arrays in just under six years, which is "faster than expected," Lawson wrote, adding that this finding underscores "the overriding stance from the survey that sequencing is replacing arrays."

Overall, the survey's findings indicate a "substantially more positive outlook for sequencing spending versus array spending," Lawson said.

The array outlook, "on one hand, is a positive for Illumina, as more work migrates to sequencing, but also cannibalizes their own array business," Lawson noted, adding that the survey results "continue to be a negative for Affymetrix."

Another negative for Affy is the finding that 34 percent of array users said they were more likely to use Illumina arrays, while only 18 percent were more likely to buy Affy arrays (see chart 5, below).

Lawson noted, however, that these results differ from a fourth-quarter Mizuho survey of the drug discovery sector, "where Affymetrix led Illumina as the most likely microarray platform to be purchased, likely due to drug development's focus on gene expression."

In general, Lawson noted, "while the outlook for array spending is less robust than sequencing, arrays continue to have a place in research – they still command a significantly lower price point versus sequencing, and also offer complementary technology to sequencing — both upstream and downstream."

The GenomeWeb/Mizuho survey, which was intended to assess broad trends in the genomics R&D market, collected responses from 91 GenomeWeb readers in late December and early January.

The 25-question survey was e-mailed to a small subset of GenomeWeb readers comprising researchers in academic organizations or biopharmaceutical firms. Around 57 percent of the 91 respondents said they work in a government or academic setting, while 27 percent were from industry. Around 77 percent of respondents work in or manage a lab.

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