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Illumina Announces Sequencing Technology Innovations

Published: Tuesday, April 23, 2013
Last Updated: Monday, April 22, 2013
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Rich pipeline delivers the most comprehensive end-to-end solutions for next-generation sequencing.

Illumina has announced a series of product and technology innovations for its powerful sequencing ecosystem - from sample preparation to system enhancements to data analysis - that will enable the next breakthroughs in understanding the genome.

“Illumina has consistently led the market in conceptualizing, developing, and executing on industry-changing sequencing technology, and we continue to provide scientific advances that facilitate fully integrated and highly economical sequencing with very rapid turnaround,” said Jay Flatley, President and Chief Executive Officer of Illumina.

Flatley continued, “These capabilities allow us to continue to meet the evolving needs of our customers, as they develop an ever-increasing range of applications, in new and emerging markets from agrigenomics to molecular diagnostics.”

Sample Prep Evolution
Simplifying and accelerating the sample prep process is fundamental to improving sequencing workflows and decreasing turnaround time, an important factor for sequencing to be adopted in clinical settings. Illumina announced and previewed several innovations in sample preparation technology:

Nextera® Rapid Capture Exome Kits represent a new generation of targeted enrichment products, providing the fastest exome enrichment workflow on both the HiSeq® 2500 and the MiSeq®. With a sample-to-data protocol of less than three days, the kits deliver a 70% speed improvement over current technologies, with a solution optimized for efficient enrichment of coding content. Commercial availability for these kits is scheduled for the end of 1Q’13.
Nextera Rapid Capture Custom Kits enable enrichment of hundreds of kilobases to tens of megabases of custom-selected content. Fully automated probe design through DesignStudio™ and the ability to add content to previously designed panels will be provided. Nextera Rapid Capture Custom Kits will begin shipping in 2Q’13.
TruSeq® DNA PCR-Free Kits are a simple, all-inclusive sample prep solution for whole-genome sequencing providing industry-best genome coverage, the ability to sequence the most challenging regions, and the power to identify variants with high accuracy. These kits will be available to order on January 21, 2013.
Nextera Mate-Pair Sample Preparation Kits offer the only gel-free method for preparing up to 15 kb mate-pair libraries in less than two days with the industry’s lowest DNA input; an ideal approach for de novo sequencing, genome finishing, and the detection of structural variation - even in the most complex genomes such as those derived from cancer. These kits are available for immediate order.
TruSeq Targeted RNA Kits bring a new standard to mid-plex gene expression profiling and validation by overcoming significant challenges in cost and workflow. User-defined custom panels of 12-1,000 assays can be created to target genes, isoforms, splice junctions, and cSNPs, all of which can be added to a wide variety of pre-selected gene panels focused on cell pathways and disease states. Commercial availability for the TruSeq Targeted RNA Kit is scheduled for 1Q’13.

Core Technology Enhancements
Illumina also highlighted a number of core sequencing platform enhancements that will increase the throughput, read lengths, and speed of existing systems, as well as decrease running costs.

A new flow cell technology will provide a significant increase in cluster density and number of reads per flow cell while reducing image-processing time. This new technology improves support for counting applications, lowers the cost per data point, and reduces turnaround time for sequencing projects. First customer experience with these new flow cells will occur in the second half of this year.
A novel library prep method and analysis algorithm, enabled by the acquisition of Moleculo Inc., will produce synthetic read lengths up to 10 kb at an extremely low error rate (Q50 or better). This advancement allows more comprehensive coverage and accurate genotyping of clinically important genes and new applications such as phased resequencing of human genomes, and rapid de novo sequencing of complex plant and animal genomes.
HiSeq 2500 chemistry enhancements empower the industry’s highest daily throughput and drive down the price of whole-genome sequencing. With support of paired 250 base pair read lengths in rapid run mode, the HiSeq 2500 will be capable of generating up to 300 Gb in rapid mode with sample to data in less than three days. These enhancements will be available in the second half of this year.

Informatics Advances
Illumina also shared a development in the evolution of its cloud-based data analysis, storage, and sharing platform, BaseSpace™ (

BaseSpace Apps, a dedicated applications store for BaseSpace, has quickly become a seminal environment for the deployment of informatics tools. Today the community has grown to more than 100 independent developers who are working to bring a wide assortment of analysis tools to a growing cloud-enabled user base.

“Our ability to rapidly innovate across the entire workflow of next-generation sequencing ensures we are better positioned than ever to continue creating and delivering value to both our research and clinical customers,” said Christian Henry, Senior Vice President and General Manager of Illumina’s Genomic Solutions business. “With enhancements to our platform, we continue to set the standard for speed, accuracy, output, and workflow.”

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