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Survey: MiSeq First Choice for Planned Sequencer Purchases; Labs' Data Output Continues to Grow

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Two-thirds of laboratories planning to purchase a sequencer within the next 12 months are considering Illumina's MiSeq, according to a recent survey by investment firm Mizuho Securities USA and GenomeWeb.

In the survey, conducted at the end of the first quarter, researchers ranked the Illumina MiSeq higher than the Ion Torrent PGM in seven out of 10 categories.

The HiSeq scored above the Ion Proton in five out of 10 areas, equal in two, and the Proton came out first in three categories.

Most researchers said they need to see more data in order to make the Ion Torrent Proton more attractive, compared to Illumina's systems.

Respondents continue to see the sequencing output in their labs increase, on average by more than 50 percent this year compared to last year, and by more than 60 percent next year compared to 2013.

The survey was e-mailed to a subset of GenomeWeb Daily News readers, 72 of which responded to at least some questions. Of those, about two thirds said they either produce or analyze sequence data.

About a third of respondents said they work in academia or for the government, about 15 percent for pharmaceutical or biotechnology companies, about 13 percent for diagnostic product companies, and about 10 percent for hospitals. Fifty-nine percent are based in the US or in Canada, and a quarter are based in Europe.

When it comes to short-term purchasing plans for sequencers, Illumina is favored by most. Of 16 survey takers planning to buy a sequencer within the next 12 months, 11 said they are considering the Illumina MiSeq, and seven are considering the HiSeq 2500 or an upgrade to the 2500. One respondent is looking at the HiSeq 1500.

Life Technologies' Ion Torrent is close behind. Six respondents are considering the Ion Torrent PGM, and five are mulling the purchase of an Ion Proton in their 12-month plans.

Interest in Roche's 454 systems continues to wane, however, with only one respondent saying they are considering the 454 GS Junior.

None of the respondents cited an interest in other sequencers currently on the market, such as the 454 GS FLX+, the PacBio RS, or the SOLiD 5500.

Fewer than half of those planning to purchase within 12 months are considering a system that is not yet on the market, with about equal amounts of interest in platforms from Oxford Nanopore Technologies, GnuBio, and Nabsys.

Illumina's MiSeq and Ion Torrent's PGM continue to compete for market share, and among 27 users or prospective users, the MiSeq received higher marks in most categories.

Respondents ranked the MiSeq above the PGM for accuracy, ease of sample prep, promise, current usability, price per base, and read length. The platforms scored about equal in terms of reagent price, and the PGM came out better in terms of instrument price and run time. This is a slight shift from last quarter's survey, where the PGM narrowly won on reagent price and the two systems were considered equal in terms of their promise (IS 1/22/2013).

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Users and prospective users also compared the HiSeq and Ion Proton, where the picture is less clear cut. While the HiSeq scored higher for accuracy, ease of sample prep, current usability, price per base, and throughput, the Proton won out for instrument price, promise, and run time. Both systems scored about equal for reagent price and read length. The results are slightly different from last quarter's survey, where the Proton ranked better for reagent price.

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Asked what would make the Ion Proton more attractive compared to Illumina platforms, nearly half of 19 respondents cited the availability of more data, reflecting the fact that the Proton has only been in users' hands since last fall. More than a quarter said they want to see "better specs" for the instrument.

Desktop sequencers are increasingly used to analyze panels of genes, and vendors of capture or enrichment technologies have released catalog panels as well as custom panels as products. Of 21 respondents who analyze gene panels, about half said they use a combination of custom-designed and off-the-shelf panels, while about a quarter each use either one or the other.

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Overall, sequencing output continues to increase among users, and respondents expect the same to happen both this year and next. Of 44 survey takers who either produce or analyze sequence data, 26 said their sequencing output has increased at least 10 percent over the last three months.

Thirty-five expect their sequencing output to increase over the next three months, and 40 expect it will increase in all of 2013, compared to 2012. Forty-two believe it will grow in 2014, compared to 2013.

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