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Survey Finds MiSeq, Ion PGM Tied for Most Likely Sequencing Purchase over Next 12 Months

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Genomic researchers planning to purchase a new sequencer over the next 12 months are most likely to choose Illumina's MiSeq or Life Technologies' Ion Torrent PGM, according to a recent survey conducted by GenomeWeb in collaboration with investment firm Mizuho Securities.

The survey, which collected responses from 81 GenomeWeb readers in late March, found that 20 participants, or 25 percent, plan on buying a next-gen sequencer over the next 12 months. Of those, nine, or 35 percent, said they are considering a MiSeq among sequencers that are currently on the market and the same number said an Ion PGM.

Five respondents said they are considering purchasing a HiSeq 2000 over the next 12 months, two said a SOLiD 5500, and one said a Pacific Biosciences RS. No respondents said they were considering purchasing a Roche 454 FLX+ or GS Junior system over the next twelve months (see chart 1, below).

Among systems scheduled for launch in 2012, Life Tech's Ion Proton generated the most interest, with 12 participants, or 32 percent, considering the system. This was followed by Oxford Nanopore Technologies' GridIon, with 10 responses, and a tie between Oxford's MinIon and Illumina's HiSeq 2500, with six responses each. One respondent was most interested in the GnuBio system, which is slated for commercial launch before the end of the year (IS 2/28/2012). (see chart 2, below)

The survey also gauged respondents' opinions of the performance of the two leading benchtop sequencers — MiSeq and PGM.

Of the 20 respondents who answered this question, 18, or 75 percent, ranked MiSeq higher for accuracy and 16, or 70 percent, scored the Illumina system higher for throughput. Meantime, 18 people, or 75 percent, ranked the PGM higher for instrument price; 16, or 64 percent, said that the PGM had a better run time than the MiSeq; and 15, or 56 percent, said that the PGM had the "most promise."

These results were largely in line with an independent comparison of the MiSeq, PGM, and GS Junior that was published this week in Nature Biotechnology (see story, this issue).

"We would classify MiSeq as the box with the most current potential; high accuracy, and high throughput, while the Ion Torrent as the box that’s priced competitively, fast, and [has] the most potential in the future," wrote Mizuho analysts Peter Lawson and Eric Criscuolo in a research note outlining the survey findings (see chart 3, below).

With regard to clinical sequencing, 20 of the 81 respondents said that they are either already running sequencing-based diagnostic tests or plan to do so in the next 12 months. Of those, six, or 28 percent, cited Illumina's HiSeq as the instrument they use or plan to use, followed by Roche's GS FLX+, with four responses. MiSeq and Ion PGM were again neck-and-neck, with three responses each, and two respondents said they are considering the Ion Proton.

These results are "promising for Illumina’s strategy of taking sequencing into new, clinical markets," the analysts note, but they add that Ion's desktop systems appear "well positioned" for the clinical market as well (see chart 4, below).

The 26-question survey, intended to gauge broad trends in the genomics R&D sector, was e-mailed to a small subset of GenomeWeb readers comprising researchers in academic organizations, hospital or reference labs, and biopharmaceutical firms. Around 74 percent of the 81 respondents work in a government or academic setting.

Of the 81 respondents, 96 percent said they use DNA sequencing.

Respondents said that over the next three months, they expect their sequencing output to grow by more than 16 percent. For full-year 2012, respondents expect sequencing data output to increase by around 32 percent, which is in line with the results of the fourth-quarter 2011 GenomeWeb/Mizuho survey (IS 1/17/2012).

However, respondents reported slower sequencing growth in 2013 compared to the prior survey. The Q1 survey found that respondents expected an average increase in sequencing output of 25 percent in 2013 compared to 2012, while respondents to the Q4 survey reported an average expected increase of 38 percent.

This falloff in expected growth could be a "negative for volumes in a space where pricing is falling," the Mizuho analysts concluded.

The survey results indicate that Illumina has the largest share of the sequencing market. According to the 38 respondents to a question on system installations, more than half — 58 percent — of currently deployed systems are made by Illumina, while 23 percent are Life Tech, 13 percent are 454, and 6 percent are PacBio.

In terms of specific instruments, the HiSeq 2000 is the most common, with 50 percent of the total systems reported by respondents. The Ion PGM followed with 18 percent of respondents' systems (see chart 5, below).

However, in terms of overall spending by vendor, more respondents said they plan to increase their spending with Life Tech than with Illumina over the next 12 months — 45 percent of 59 respondents to the question said they plan to spend more with Life Tech compared to 42 percent who said the same for Illumina.

Lawson and Criscuolo said this shift was "potentially driven by the success of [Life Tech's] Ion Torrent Personal Genome Machines" in the marketplace.

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