Agilent Technologies removes major bottleneck for DNA sequencing
16 February 2009
Agilent Technologies, Inc. (NYSE:A) has introduced the Agilent SureSelect Target Enrichment System, a unique tool for greatly streamlining DNA-sequencing research by enabling scientists to sequence only genomic areas of interest with next-generation sequencing instrumentation.
The system will initially be available for the Illumina Genome Analyzer system. In addition, Agilent is in the process of optimizing the platform for the SOLiD System from Applied Biosystems, a division of Life Technologies Corp.
“There have been amazing advances in next-generation sequencing in recent years, driving down the cost of whole genome sequencing dramatically,” said Nick Roelofs, Ph.D., Agilent vice president and general manager, Life Science Solutions Unit.
“We’ve succeeded in developing a front-end method for isolating complex subsets of genomes that greatly enhances the efficiency of next-generation sequencing technologies by focusing them on the areas most interesting to DNA researchers. Agilent’s new platform will significantly reduce sample complexity, allowing researchers to analyze a greater number of samples per study with fewer resources.”
Target Enrichment, also referred to as “targeted resequencing,” “genome partitioning,” or “DNA capture,” is useful when a researcher is only interested in sequencing a particular segment of the genome, just the translated part, for example.
In this case, the Agilent SureSelect platform can be used to capture a subset of exons or other genome targets and wash away the rest of the genome prior to sequencing. SureSelect replaces other labor-intensive methods of targeted re-sequencing such as polymerase chain reaction (PCR) techniques that are a major bottleneck in most next-generation sequencing workflows.
“We have been highly impressed by the performance of Agilent’s SureSelect Target Enrichment System,” said early access user Daniel Turner, head of Sequencing Technology Development, Wellcome Trust Sanger Institute.
“There are several important features of this technology that set it apart from its competitors: It is simple to perform and easily scalable to a 96-well format; it requires far less genomic DNA than on-array or PCR-based approaches; and it provides unparalleled specificity. In fact, the amount of input DNA needed for a successful target enrichment experiment is approximately one tenth that required by other platforms, enabling experiments that would not be possible otherwise by preserving precious sample.”
“Our experience of using Agilent’s SureSelect Target Enrichment System resulted in significant enrichment of our targeted regions for studying healthy aging,” said Kelly Frazer, Ph.D., director of Genomic Biology, Scripps Genomic Medicine, another early access user. “The resulting sequence data showed excellent uniform coverage of the targeted regions.”
“We attribute this evenness of coverage to SureSelect’s long RNA-based oligos and optimized design algorithms, which avoids introducing sequencing bias, a common concern about other target enrichment methods,” said Fred Ernani, Ph.D., Agilent’s emerging genomics applications product manager.
The initial Agilent genome partitioning product is a ready-to-use kit containing a customer-specified mixture of up to 55,000 biotinylated RNA probes delivered in a single tube. The capture probes are 120 base pairs long, the longest currently on the market for this application.
This makes them very effective at capturing DNA containing unknown mutations such as single nucleotide polymorphisms, insertions or deletions. SureSelect kits are packaged for a range of study sizes from tens to thousands of samples, and are well-suited for automation in very high throughput workflows, unlike other commercially available products for this application.
Users can design their own custom SureSelect mixtures using the Agilent eArray online design tool, which contains many key genomes and also lets users upload their own sequences. This intuitive Web-based design tool is the heart of Agilent’s custom genomics product manufacturing capability, proven popular with the microarray community and now expanded to the new SureSelect platforms. eArray allows biologists to easily design the tools they need to do the science they want to do, without up-front design fees.
Later in the year, Agilent also plans to introduce an array-based genome partitioning method for smaller-scale experiments, providing researchers a complete range of products for target enrichment.
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