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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.”