Patricia F. Fitzpatrick Dimond Ph.D. Technical Editor of Clinical OMICs President of BioInsight Communications

Strategy provides a feedback loop to improve instrumentation and develop new applications.

Next-generation DNA sequencing fundamentally changed basic genomic research. It made possible the analysis of entire genomes or transcriptomes, processes that used to be too technically complex or expensive without massively parallel technology.

As genomics becomes big business worldwide, sequencing manufacturers have worked to cover their bases. They’ve been growing sales and grooming new markets by forming customer networks and in some cases providing direct funding.

Currently three major players provide most sequencing machines: Illumina, Life Technologies, and Roche’s 454 Life Sciences. All three companies now market benchtop sequencers based on either the platforms in their larger machines or completely novel technology.

Life Technologies announced on January 10 that it is taking orders for its new benchtop Ion Proton Sequencer, priced at $149,000, built on the Ion Torrent semiconductor sequencing technology. Illumina said its HiSeq 2500 will be available in the second half of the year, and Roche offers its GS Junior benchtop sequencing machine, based on its pyrosequencing technology, priced at about $125,000.

All of them are working with early adopters to define and develop applications for the sequencers and develop new user bases. By developing customer networks and supporting research collaborations, these companies maintain pipelines of new applications for their instrumentation as well build a feedback loop in which their customers can support improvements in the instrumentation.

The Power of Networking

Illumina provides a model for staying ahead of the curve in a highly competitive industry. The company works its customer base by not only providing technical support but also through its Illumina Genome Network (IGN). The IGN links researchers needing large-scale whole-genome sequencing with leading institutions that provide this service using Illumina’s platforms.

All IGN partners are experienced and well-published with regard to the firm’s TruSeq™ technology, according to Illumina. Partners have also obtained Illumina’s Certified Service Provider (CSPro®) certification. Each network partner hastens use of more Illumina sequencing systems, providing the scalability to handle the largest sequencing projects with rapid completion times.

Illumina also has a significant stake in the future of its own industry, working to propose and provide applications standards through collaborations with its IGN companies and institutions. Illumina’s svp and GM, genetic analytic business unit, Christian Henry told GEN that Illumina collaborates with genome centers. “We try to understand the characteristics of our systems in their hands. We want to understand the areas in which clients have challenges and know their workflows to help simplify production-scale work as much as possible.”

The New York Genome Center’s (NYGC’s) founding executive director, Nancy Kelley, told GEN that Illumina has become a go-to source for new scientific collaborators as well as technical know-how. The $125 million NYGC, set to start operations in the spring, unites 11 academic medical centers, with the shared goal of developing one of North America’s largest genomics facilities.

To date, the Center has two industrial partners: Roche and Illumina. Kelley says both Illumina and Life Technologies were invited to make presentations on how they would partner with NYGC. “In the end, there’s just been enormous progress made by Illumina in their productivity and turnaround times this year, and that proved to be one of the deciding factors,” she said in an interview with Bio IT World.

In March 2007, Roche enlarged its presence in the sequencing world with its $154.9 million acquisition of 454 Life Sciences from Curagen, and now, it’s making a play for Illumina. On January 25, Roche went public with a $5.7 billion bid, valuing the firm at $44.5 per share, a 43% premium over the one-month average. As of February 16, Illumina was trading at $53.94.

Roche’s acquisition of 454 grew out of collaboration between the firms and gave Roche access to 454 sequencer pyrosequencing technology. Roche’s 454 has been particularly nimble in focusing its collaborations on other companies that can ultimately provide enhancements to its product offerings and solve customers’ problems.

These include partnerships with NuGEN Technologies to construct sequencing-ready cDNA libraries from RNA samples. This collaborative effort provides researchers an end-to-end solution for transcriptome profiling on samples with as little as 500 pg of total RNA.

Investigators that use Roche’s sequencing platforms also provide research results that attest to the capabilities of the GS Junior Benchtop. For example, on January 17, the Center for Human Genetics and Laboratory medicine of Martinsread, Germany, reported using the Roche GS Junior Benchtop system to sequence clinically relevant exons and identify genomic variations in solid tumors treated with an antibody-based medicine. This sequencing approach, the investigators said, easily expanded to complete coding regions, has great potential for personalized medicine, where individual treatment success is largely dependent on the mutation status of tumor genes.

As part of a tried and true business strategy, company-supported collaborations with academic institutions yield novel instrument application development and publications as well as testimonials. Companies can facilitate their customers’ business growth and sustainability, hooking them up with new clients and seeding new partnerships for investigators.

Sequencing centers that use their instruments at academic institutions provide a sort of self-replicating advertisement for companies’ sequencing machines. For example, the center at the University of California, Davis, in marketing its services on its website, describes its capabilities as “massively parallel sequencing using Illumina sequencing platforms to generate many gigabases of high-quality sequence data for each sample” and points potential customers to Illumina websites.

New funding for genome centers as well as ongoing industry-academic collaborations will sustain markets for genome machine providers and inform the development of new technologies and applications.








































Patricia F. Dimond, Ph.D. ([email protected]), is a principal at BioInsight Consulting.

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