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In Sequence Survey: Illumina Holds Two-Thirds of Sequencing Market, Splits Desktop Share with Ion PGM

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Illumina currently holds around 66 percent of the total sequencing market, but the company's share of the desktop market is split evenly with Life Technologies' Ion Torrent PGM, according to a recent survey of 150 In Sequence readers.

The survey, conducted in collaboration with investment firm Mizuho Securities, found that Illumina's HiSeq 2000, GA IIx, and MiSeq claim a total of 66 percent of the sequencing market — 42 percent, 10 percent, and 11 percent, respectively.

Life Technologies, meantime, holds 23 percent of the total market — 9 percent for its SOLiD 5500xl and 12 percent for the Ion Torrent PGM. Roche holds around 8 percent of the market and Pacific Biosciences just over 2 percent.

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The survey — In Sequence's fifth assessment of the sequencing market — underscores how rapidly the sector has changed over the last year with the launch of desktop systems from Illumina and Ion Torrent. Our previous survey, published in January 2011 (IS 1/25/2011), found that Illumina had similar market share — at 60 percent — but that a third of respondents had either a 454 or SOLiD.

And while our prior survey found that around half of respondents felt that PacBio would provide the "next big leap" in sequencing, that honor rests solely with Oxford Nanopore Technologies this year.

The following is a high-level analysis of the survey results. Complete results are available in a supplementary document here.

Desktops Grab Market Share

An invitation to the survey was sent via e-mail in late August to In Sequence subscribers and responses were collected via SurveyMonkey. Mizuho Securities analysts Peter Lawson and Eric Criscuolo collated the results.

Of the 150 respondents, around 60 percent worked in an academic setting or research institute, 26 percent in an academic medical center, 9 percent in a government lab or agency, and 3 percent were commercial service providers.

Around 63 percent of respondents were from North America, 30 percent from Europe, and 7 percent from Asia.

The survey results made it clear that desktop sequencers are having a measurable impact on market dynamics. While only 23 percent of current sequencers are desktops (11 percent MiSeq, 12 percent Ion PGM), 55 percent of respondents said they plan to buy a desktop system over the next 12 months.

As far as the competition in this sector, Ion Torrent appears to have an edge. Around 18 percent of respondents said they would purchase a MiSeq and the same number said they would buy an Ion Proton. An additional 7 percent of respondents said they'd purchase a PGM.

Interestingly, 25 percent of respondents said they are considering purchasing an Oxford Nanopore sequencer — 12 percent a GridIon and 13 percent a MinIon — even though the company has not provided an update on the launch of these systems since it announced them at the Advances in Genome Biology and Technology meeting in February (IS 2/21/2012).

Illumina's HiSeq, currently the market leader with 42 percent share, captured around 14 percent of the vote for respondents' next sequencing purchase.

The PacBio RS and Roche/454 GS Junior were on the purchase list for one respondent each, while no one said they plan to purchase a Roche/454 GS FLX or FLX+ over the next year.

Only 24 percent of respondents said they don't plan to purchase a sequencer in the next 12 months.

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Meantime, Illumina's GAIIx was the most common instrument to be retired over the last 12 months, driven by upgrades to the HiSeq. Around 36 percent of respondents said they retired a GAIIx in the last year.

Around 26 percent of respondents said they retired a SOLiD system in the last 12 months, while 22 percent retired their Roche/454 system.

Meeting Expectations

Overall, most current systems met user expectations, though Roche was on average slightly below expectations and PacBio was above, due largely to a very high score for read length. Survey participants were asked to respond based on their experience and expectations for a given system, so the results are not suitable for cross-platform comparisons.

In general, among the "large box" systems, HiSeq scored well for throughput, accuracy, and service but ranked poorly for instrument and consumable price and run time; SOLiD ranked well for accuracy and service, but poorly for ease of data analysis and reagent price; Roche scored well for read length, ease of data analysis, and accuracy, but poorly for reagent price and sample prep; and PacBio excelled for read length, did well for run time, and ranked poorly for reliability and instrument price (see supplementary information for details, including instrument-specific performance assessments).

Among desktops, the MiSeq scored well for sample prep and throughput, but ranked below expectations for reagent price, while the PGM ranked well for throughput, price, and read length, but poorly for accuracy and sample prep.

Several respondents reported issues with homopolymer reads with the Ion PGM and cited the system's emulsion PCR as a disadvantage. The company is currently developing a new emulsion-free chemistry, dubbed Avalanche (IS 9/18/2012), which Mizuho's Lawson said "should help alleviate a lot of the negativity surrounding sample prep/homopolymers."

Why Buy?

We asked respondents why they purchased their existing sequencers. Among large box systems, accuracy and throughput were the most important factors for Illumina and SOLiD purchase decisions, while read length was most important for Roche and PacBio.

In terms of the least important purchasing decisions, instrument price was the lowest-ranking factor for Illumina instruments, while ease of data analysis was least important for SOLiD users. Reagent price was the least important factor for Roche customers, and instrument price for PacBio customers.

On the desktop side, accuracy and read length were the highest-ranking factors for purchasing the MiSeq, while reliability and reagent price were the least important considerations.

For the Ion PGM, run time and throughput were the most important factors in the purchasing decision, and reliability and ease of data analysis the least important factors.

Tasks and Projects

The survey results indicate that users are finding certain sequencing platforms to be better suited to particular tasks and projects, indicating that there may be plenty of room for different types of systems that meet various research needs.

For example, respondents overwhelmingly use SOLiDs and Illumina HiSeq and GAIIx systems for exome sequencing, RNA-seq, and whole-genome sequencing, with well over 70 percent of respondents indicating they use these systems for these tasks (details available in supplementary information).

Around 71 percent of respondents, meantime, said they use Roche for targeted/amplicon sequencing, while 62 percent use that platform for de novo whole-genome sequencing and metagenomic sequencing.

Lawson said that the use of Roche for de novo sequencing is not surprising, as the system's long reads make it well suited for this purpose. However, he said, "the lack of throughput compared to HiSeq and SOLiD platforms limit this de novo sequencing to organisms with smaller genomes or for filling gaps and aligning reads from Illumina or SOLiD."

Likewise, respondents said they primarily use PacBio for de novo whole genome sequencing and targeted/amplicon sequencing.

Respondents use both the Ion PGM and MiSeq primarily for targeted/amplicon sequencing — 78 percent of MiSeq users and 93 percent of PGM users said they use their systems for this purpose. However, Lawson noted that the responses indicate that MiSeq is used "for a modestly broader set of applications versus Ion Torrent."

He added that Ion "is perhaps focused on more targeted sequencing applications, areas where homopolymer/accuracy are less of an issue."

In terms of the types of projects for which these systems are used, there was a clear breakdown among available systems: The Illumina and Life Tech "large box" systems are primarily used in basic human genome research; the Roche and PacBio systems have found a niche in microbiology; and the MiSeq and PGM are finding use in clinical or diagnostic applications (see supplementary information for details).

Around 37 percent of respondents said they are currently performing clinical sequencing. Among these respondents, capillary electrophoresis is still the most common platform, with 34 percent of participants saying they use CE for this purpose. The Ion PGM was a close second, with 28 percent of respondents, followed by the HiSeq and GAIIx with 17 percent, the MiSeq with 11 percent, SOLiD with 6 percent, and 454 with 2 percent.

The clinical sequencing landscape is poised to change over the next year, however, as 30 percent of respondents indicated they plan to purchase a MiSeq for clinical use over the next 12 months. This was followed by 24 percent who said they will purchase a HiSeq for that application, 22 percent who will purchase an Ion Torrent PGM or Proton, and only 13 percent who plan to buy a new CE instrument for clinical sequencing. Around 5 percent said they plan to purchase a 454 for clinical sequencing and 3 percent said a SOLiD.

Sample Prep and Enrichment

Overall, respondents ranked Illumina as the best provider of DNA sample-prep technology, with 47 percent ranking the company highest in this category, "likely driven by Nextera sample prep kits and on-board cluster generation on the MiSeq," Lawson said.

Agilent came next, with 40 percent of respondents citing the company as the best provider of DNA sample prep for next-gen sequencing.

In terms of market share for DNA enrichment technology, Agilent holds around 32 percent of this sector, followed by Illumina with 24 percent. Around 19 percent of respondents said they still use traditional PCR for DNA selection.

Sample prep was cited as the most important improvement required for next-gen sequencing, followed by data accuracy, read length, and consumables cost. Respondents ranked lower instrument cost as the least important improvement for the field.

The Next Big Leap

Around 70 percent of respondents selected Oxford Nanopore as the company most likely to provide the "next big leap" in sequencing technology, followed by Ion Torrent, which garnered around 31 percent of responses, and Illumina with 23 percent.

Among some emerging technologies listed as choices, GnuBio snagged 5 percent of responses; 454/IBM received 4 percent; Intelligent Bio-Systems/Qiagen, LaserGen, Genia, NabSys, and Quantapore each garnered 2 percent; and 454/DNA Electronics and NobleGen each had 1 percent.

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