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Survey: Sequencing Output to Grow by 32 Percent in 2012; High Interest in Single-Molecule Systems

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By Bernadette Toner

Genomic researchers expect their sequencing output to increase by 32 percent in 2012 over 2011, according to a survey conducted by GenomeWeb in partnership with investment firm Mizuho Securities.

The survey, which collected responses from 91 GenomeWeb readers in late December and early January, also found that single-molecule sequencing is expected to see the greatest increase in spending over the next 12 months — a finding that was "somewhat surprising given respondents' prior ambivalence to single-molecule sequencing in the past," wrote Mizuho analyst Peter Lawson in a research note outlining the results of the survey.

Indeed, 85 percent of respondents in the current survey said they plan to increase their spending on single-molecule sequencing over the next 12 months, compared to just 20 percent who said they planned to so in a similar survey that GenomeWeb and Mizuho conducted in October (IS 10/25/2011).

Lawson noted that the expected increase in spending on single-molecule systems is a "surprising positive" for Pacific Biosciences and may "signal the transition we are seeing from genome centers to stay competitive."

Next-generation sequencing as a general category ranked third as the technology most likely to see a spending boost over the next 12 months, behind single-molecule sequencing and informatics.

RNA-seq, which respondents identified in the previous survey as the technology most likely to see a spending increase, dropped to fifth place, though the portion of respondents who indicated they planned to increase their spending on the technology remained flat at 63 percent (see chart 1, below).

Around 83 percent of respondents expect RNA-seq to replace gene expression arrays within five years or less (see chart 2, below).

According to a weighted average of the results, respondents 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."

The 25-question survey, intended to assess broad trends in the genomics R&D market, 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.

In total, 85 percent of respondents said they use or plan to use next-generation sequencing — more than twice as many as said they use or will use arrays.

Around 88 percent of participants agreed with the statement that they will generate more sequence data in 2012 than 2011.

In terms of the specific increase in sequencing output over the next year, respondents indicated that they will see a 32 percent increase in sequencing data in 2012 over 2011, and expect to see a 38 percent increase in 2013 over 2012 (see chart 3, below).

As far as instrument purchasing plans, around 14 percent of respondents strongly agreed with the statement that they expected to purchase a new sequencer in the 12 months, while 37 percent strongly disagreed with this statement, indicating that they do not expect to purchase a new sequencer. In total, 35 percent either somewhat or strongly agreed they would purchase a new sequencer, while 43 percent either somewhat or strongly disagreed.

The survey also found that respondents were more likely to use software from instrument vendors for base calling, but open source tools for secondary and tertiary analysis (see chart 4, below).

Overall, "only 17 percent to 22 percent of alignment and analytics was conducted using commercial programs — a significant opportunity for commercial application development," according to Lawson.

In terms of informatics market share, Illumina's software for primary analysis is used more than that of any other vendor, while CLC Bio has the largest share among commercial vendors for secondary and tertiary analysis (see chart 5, below).

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