This article was originally published June 29.
By Julia Karow
Approximately 900 next-generation sequencers are installed in laboratories around the world to date, and funding from the 2009 American Recovery and Reinvestment Act, along with Illumina's upcoming iScan sequencing module, could increase that number significantly, according to new research reports on Life Technologies and Illumina from investment bank Leerink Swann.
The reports note that Illumina's Genome Analyzer currently accounts for about two-thirds of next-gen sequencing systems housed at 15 international genome centers, though they add that at more than 40 smaller labs, market share between Illumina's GA, Applied Biosystems' SOLiD, and 454 Life Sciences' GS FLX "is far more equitable."
According to the reports, published this week by Leerink Swann research analysts Isaac Ro and Jody Dai, several genome centers plan to expand their capacity for next-generation sequencing in order to support projects they expect to be funded through stimulus grants.
The analysts contacted consultants at "several top genome centers," last week and "came away with the impression that these institutions stand ready to deploy stimulus funds pursuant to significant expansions in [next-generation sequencing] capacity," they write.
"In several cases we now think capacity expansion could exceed 100 [percent and more] from current levels should funding materialize as expected." Existing lab infrastructure "can support the first wave of these expansion plans immediately," and although Illumina's platform currently dominates the centers, "we note that [Life Technologies'] product exposure is broad-based in these labs."
The Leerink analysts assessed the current number of next-generation sequencing platforms at "the top 15 genome centers globally," including the Broad Institute of MIT and Harvard, Washington University in St. Louis, the Wellcome Trust Sanger Institute, the Beijing Genomics Institute, Baylor College of Medicine, the US Department of Energy Joint Genome Institute, the Beijing Institute of Genomics, the Ontario Institute for Cancer Research , the Genome Institute of Singapore, Cold Spring Harbor Laboratory, Cornell University, the J. Craig Venter Institute, the Translational Genomics Research Institute, the British Columbia Cancer Agency Genome Sciences Center, and Columbia University.
According to their analysis, these centers house almost 300 next-generation sequencers in total, some of which are not yet "fully installed." About two-thirds of them are Illumina GAs, followed by 17 percent ABI SOLiDs, and 14 percent Roche/454 GS FLX instruments. Helicos has a single instrument deployed at one of the centers, the Broad Institute.
Curiously, the reports omit a number of genome centers with sizable next-generation sequencing fleets, including the Max Plank Institute for Molecular Genetics in Berlin; the RIKEN Omics Science Center in Yokohama, Japan; the Centre National de Génotypage in Evry, France; and Duke University. These institutes have at least 29 next-gen sequencing instruments between them, according to previous reporting by In Sequence.
The Leerink analysts say they assume the next-gen sequencing systems installed at the 15 genome centers they analyzed account for about thirty percent of the total market, leading to the estimate that approximately 900 systems are currently installed worldwide. "However, we think pending stimulus dollars along with [Illumina's] Harmonia platform could eventually help expand the global NGS footprint towards 2,000 systems", they note, but do not specify a timeline.
Illumina plans to launch a sequencing module for its iScan array scanner — originally referred to as "Harmonia," — later this year (see In Sequence 5/5/2009). According to the analysts, "we believe the investment community has underestimated the potential for [Illumina's] Harmonia platform to help expand the NGS market."
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In addition, they say, the iScan sequencing module "will pose a threat to SOLiD among smaller institutions given lower upfront costs and functionality with existing array platforms.
"Price and ease of use is always a factor and we believe Harmonia's ability to
interface with iScan and offer array functionality as well could be the Trojan Horse for [Illumina] in this segment of the market."
Separately, the Leerink analysts tallied the number of next-gen sequencing platforms at 42 additional academic and commercial laboratories "known to have NGS systems," many of them single-instrument users, according to the reports. Of the total number of about 60 systems at those centers, about a third are Illumina GAs, about 20 percent are SOLiDs, about 45 percent are GS FLX machines, and about 3 percent — two systems — are Helicos Genetic Analysis systems.
The reports also comment on performance differences between the GA and SOLiD platforms, based on talks with two users of both technologies. "Both suggested that GA's read lengths, error rates, and sample prep remain superior versus SOLiD," the analysts write. "However, it also appears that the real-world differences in performance between the two platforms are likely to shrink as the next wave of chemistry and workflow improvements emerge over the next 12 months."
Users consulted by Leerink commented specifically on a number of pending technical improvements for both platforms. Illumina's goal to achieve 125-base reads and 95-gigabase runs for the GA "looks achievable," according to the report, but "the important transition to semi-ordered arrays pursuant to those metrics is still under development."
For the SOLiD, the emulsion PCR sample prep "can improve," according to the consultants, and a new five-base encoding scheme, which ABI mentioned at a conference earlier this year (see In Sequence 2/10/2009) "while more expensive in terms of reagents and complex in terms of data analysis, could improve accuracy versus GA," which may "find utility in clinical diagnostic settings, where accuracy requirements will likely be higher."
However, the Leerink analysts say, "we continue to think the economics behind such [clinical diagnostic] applications remain prohibitive to this generation of NGS platform (both GA and SOLiD)."
They conclude in their Life Tech report that the SOLiD platform, in the future, "can gain traction in replacing existing gene expression array technologies."
Life Technologies "has done a good job introducing novel whole transcriptome products for SOLiD via Ambion in recent months," they write. "In this area, we believe SOLiD can begin to supplant existing gene expression arrays from [Affymetrix], [Agilent Technologies], and [Illumina] given improve performance (dynamic range and sensitivity) on NGS versus arrays."