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Illumina Presents Development Roadmap for Scaling its Genome Analyzer
Innovations to substantially increase output, decrease cost, and expand applications

SAN DIEGO--(BUSINESS WIRE)-- Illumina, Inc. (NASDAQ:ILMN) unveiled a development roadmap for its Genome Analyzer system that charts a path to generate greater than 95 Gigabases of high quality data per run in 2009. This roadmap, which was presented at a user-group meeting at this week’s Advances in Genome Biology and Technology (AGBT) conference, outlined advances in chemistry, algorithms, and hardware which will substantially improve accuracy, read length, data density, and ease of use. These developments chart a clear and demonstrable path for researchers to generate 25x coverage of a human genome for less than $10,000 in 2009.

“The demonstrated pace of innovation on the Genome Analyzer has enabled us and end-users to embark on ambitious, new whole-genome sequencing projects that will have a major impact on human health, especially cancer,” said David Bentley, Vice President and Chief Scientist of DNA Sequencing at Illumina. “Currently we can generate greater than 25x coverage of a human genome in three flow cells; a year ago, more than 40 flow cells were used to complete our first African genome. By year’s end, we anticipate generating the same 25x coverage on a single flow cell bringing the cost of acquiring a human genome sequence to below $10,000.”

The current configuration of the Genome Analyzer has the potential to generate in excess of 15 Gigabases of high quality data per run. From this baseline, the performance of the Genome Analyzer is expected to increases greater than six-fold in 2009. The advances to achieve this increase will be commercialized in several phases throughout the year and include the following elements:

  • Chemistry advancements including new polymerases for sequencing and cluster generation to enable faster run times and paired reads in excess of 2x100 base pairs each. These advancements also improve sequencing accuracy to greater than 98.5% for 2x100 paired end reads and 99.9% for 2x50 paired end reads.
  • Hardware upgrades including improved flow cell holder and larger reagent cooler provide an increase in output and walk-away automation for reads of at least 100 cycles. These hardware components will comprise the Genome AnalyzerIIx Upgrade Kit, which current Genome Analyzer users can order immediately to increase the output and enhance the automation of their system.
  • Algorithm improvements including a new approach to cluster detection will increase output up to 80% on high density flow cells and improve basecalling yielding greater accuracy and a larger proportion of perfect reads per run.
  • Data density is increased by use of semi-ordered arrays of one micron and subsequently sub-micron features. These ordered arrays, combined with increases in read length, are expected to yield greater than 55 and 95 Gigabases per run respectively.

The combination of these advances will not only increase the output and decrease the cost of sequencing on a Genome Analyzer, but also expand the menu of applications that researchers can perform on the system. Notably, de novo sequencing and assembly of complex genomes, already possible with the Genome Analyzer, is considerably enhanced by the capability to completely sequence DNA fragments of up to 250 base pairs using the Illumina short-insert libraries and 150 base pair reads. The ability to generate contiguous 250 base pair sequences allows researchers to use a variety of existing long read assemblers for de novo sequencing and metagenomics.

“With the largest installed base of next-generation platforms and over 200 peer-reviewed publications to date, the Illumina Genome Analyzer has enabled a variety of scientists worldwide to conduct groundbreaking research rapidly and cost effectively,” said Joel McComb, Senior Vice President and General Manager of Illumina’s Life Sciences Business unit. “With the planned system enhancements in 2009, we anticipate that the Genome Analyzer will continue to provide a scalable and flexible solution for a broad menu of applications, including large scale whole-genome analysis, de novo sequencing, and metagenomics, and accelerate the rate of discoveries leading to novel insights about human health, biodiversity, and the environment.”

About the Genome Analyzer

Designed for facilities of all sizes, the Illumina Genome Analyzer has been adopted across genome centers worldwide, as well as individual research labs, core and service facilities, and biotechnology and pharmaceutical companies. The Genome Analyzer offers the highest rate of daily output and the simplest, most user-friendly workflow. The Genome Analyzer supports the broadest set of applications, including those used to profile and discover novel transcripts, to create high-resolution genome-wide maps of DNA-protein binding sites and to sequence entire human genomes to greater than 30x coverage.

For more information about the Genome Analyzer and to read what customers are doing with Illumina's sequencing technology, please visit

About Illumina

Illumina ( is a leading developer, manufacturer, and marketer of next-generation life-science tools and integrated systems for the analysis of genetic variation and biological function. Using our proprietary technologies, we provide a comprehensive line of products and services that currently serve the sequencing, genotyping, and gene expression markets, and we expect to enter the market for molecular diagnostics. Our customers include leading genomic research centers, pharmaceutical companies, academic institutions, clinical research organizations, and biotechnology companies. Our tools provide researchers around the world with the performance, throughput, cost effectiveness, and flexibility necessary to perform the billions of genetic tests needed to extract valuable medical information from advances in genomics and proteomics. We believe this information will enable researchers to correlate genetic variation and biological function, which will enhance drug discovery and clinical research, allow diseases to be detected earlier, and permit better choices of drugs for individual patients.

"Safe Harbor" Statement under the Private Securities Litigation Reform Act of 1995: this release may contain forward-looking statements that involve risks and uncertainties. Among the important factors that could cause actual results to differ materially from those in any forward-looking statements are Illumina's ability (i) to develop and commercialize further our BeadArray™, VeraCode®, and Solexa® technologies and to deploy new sequencing, gene expression, and genotyping products and applications for our technology platforms, (ii) to manufacture robust instrumentation and reagents technology, together with other factors detailed in our filings with the Securities and Exchange Commission including our recent filings on Forms 10-K and 10-Q or in information disclosed in public conference calls, the date and time of which are released beforehand. We disclaim any intent or obligation to update these forward-looking statements beyond the date of this release.

Source: Illumina, Inc.

Illumina, Inc.
Maurissa Bornstein
Public Relations Manager
Peter J. Fromen
Sr. Director, Investor Relations