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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