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Despite Downturn, Investment Firm Survey Sees Emerging Uses for Microarrays

NEW YORK (GenomeWeb News) – Despite recent concerns about declining interest in and uses for microarray technology, the results of a survey conducted by investment firm William Blair suggest the technology still has a place in the research world, though likely in certain emerging applications.

The advent of next-generation sequencing and the costs of NGS-based experiments have been falling dramatically, resulting in a migration away from microarray-based research, has led to forecasts that microarray technology may be on its deathbed. Though the technology may be limited primarily to its use for genome-wide association studies, "We believe there is still a place for microarrays in the experimental world given the ongoing cost differential between the platforms," William Blair analyst Amanda Murphy wrote in a note accompanying the results of the survey.

Furthermore, she added, "While we expect many applications currently performed on microarrays to ultimately shift to next-generation sequencing, we expect the per-base cost decline of next[-generation] sequencing to slow relative to historical levels and thus believe a general shift from microarrays to sequencing could be more protracted than investors currently expect."

The e-mail survey was based on a total of 84 responses and follow-up conversations with thought leaders about GWAS and the use of microarrays in genetic analysis going forward. The purpose of the survey and a conference call following its release was to evaluate Illumina's microarray business, but the results also shed light on its competitors.

While Illumina is known for its sequencing business, the microarray business comprises about 35 percent of its total revenues, Murphy said, and in particular GWAS has become a crucial driver of the company's array business. GWAS makes up between 40 percent and half of Illumina's array sales, she said.

However, GWAS has so far provided only limited insight into disease heritability, especially for complex diseases, and "there has been great debate around the value derived from GWAS, as well as the utility of these methods to successfully identify the genetic component of disease," Murphy said, adding that GWAS is now viewed as "'yesterday's experiment.'"

In response, microarray firms have begun incorporating lower frequency mutation content into their arrays to address the weakness of GWAS.

In the midst of continuing proof-of-concept studies around the new arrays with lower-frequency mutations, Illumina reported a 9 percent drop in its microarray business in the third quarter, compared to a year ago, spurring on worries that the technology is being phased out in favor of alternative technologies such as NGS, Murphy said.

And the problem of declining array revenues extends beyond Illumina. Affymetrix, which has long been the leader in gene expression arrays, has struggled over the past couple of years and recently reported a decline in array sales year over year.

The William Blair survey bears out some of the skepticism. One finding, for example, is that most of the respondents, 55 percent, are not currently conducting active GWAS. The majority, 54 percent, also said that they expect array use to be flat during the next year.

In addition, with government funding for scientific research also expected to take a hit in the coming years, concerns were voiced about a potential decline in funding for array-based studies, with 89 percent of respondents currently using microarrays saying they expect funding in 2013 to be flat or to decrease, and 70 percent saying their labs have no plans to buy additional array instruments during the coming year.

But Murphy maintained that the technology still has relevance in the research world, and noted particular interest in exome arrays in discussions she had with thought leaders.

At the combined International Congress of Human Genetics/American Society of Human Genetics meeting in October, both Illumina and Affy introduced new chips targeting the exome. According to GenomeWeb Daily News sister publication BioArray News, the firms believe those products will provide users with the ability to validate such variants in large sample numbers in a "fast and economical way."

Murphy said she expects arrays to continue to be used in applied markets, such as diagnostics and agricultural genomics, and in large-scale GWAS outside of European populations in larger centers, as well as in targeted approaches, such as exome arrays. However, "We see a scenario for flat array revenues over the next two years, compared with buy-side expectations of down 5 percent or more."

Among other findings from the survey was that, on average, the price tipping point at which respondents felt they would switch from arrays to NGS was $500 per sample. Also among respondents 57 percent said they have array technology in their laboratories, primarily for discovery purposes.

The number of those who use an Affymetrix array platform (32) slightly outnumbered those using an Illumina platform (31). Eleven said they use Agilent's high-resolution microarray scanner, five use Roche Nimblegen's MS 200 Microarray Scanner, and four said they use another platform.

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