A sure selection

Agilent Technologies and Wellcome Trust Sanger Institute develop all-exon target enrichment tool for next-generation sequencing

Sep 06, 2010
Lloyd Dunlap
SANTA CLARA, Calif.—Agilent Technologies Inc. has introducedthe SureSelect Human All Exon 50 Mb Target Enrichment kit for next-generationDNA sequencing. The kit enables researchers to streamline experiments bysequencing the expressed genome while discarding regions that are not ofinterest.
 
 
The new kit was developed in collaboration with the WellcomeTrust Sanger Institute (WTSI) and Gencode consortium, where scientists added 12megabases (Mb) of new content to a 38 Mb Agilent SureSelect Human All Exon kit.The original kit was developed with researchers at the Broad Institute atHarvard and MIT. Additional content was defined by researchers at the WTSI aspart of their participation in Gencode.
 
 
Researchers at the WTSI and members of the InternationalCancer Genome Consortium (ICGC) have been using the new SureSelect All HumanExon kit on an early-access basis for about a year. The commercial version ofthe kit is now available.
 
"This new kit is the latest tool to emerge from a longcollaboration between Agilent and the Wellcome Trust Sanger Institute," says Dr.Fred P. Ernani, Agilent SureSelect's platform business manager. "This kit hasthe most complete content to capture exomes. We look forward to continuing thisproductive relationship to bring the genomics community even better tools inthe future."
 
WTSI has standardized on the Agilent SureSelect TargetEnrichment system for its next-generation sequencing work. Due to its status asa charitable organization, the organization does not endorse commercialproducts.
 
 
"Our sequence-capture pipeline is central to the institute'sresearch into understanding gene function," says Dr. Cordelia Langford, head ofgenome analysis production at WTSI. "It is essential that the pipeline deliversreproducibly high-quality and efficiently processed samples for this importantwork."
 
 
There are now 14 products in the SureSelect portfolio, withmany more in development, Ernani notes. SureSelect products are available forenrichment of target sizes ranging from smaller than 200 Kb to more than 50 Mbin a single tube. Protocols now support Illumina end sequencing, paired-endsequencing and indexing protocols in addition to fragment library format,paired-end sequencing and barcoding on the SOLiD System.
 
 
The Agilent SureSelect system enables researchers to focuson genomic regions of interest, rather than sequencing the entire genome. TheAgilent system is based on an in-solution design, making it automation-friendlyand easily scalable from ten reactions through thousands. The product lineoffers customer-specified mixtures of up to 55,000 biotinylated RNA probes,delivered in single tubes. The capture probes are 120 base pairs long, thelongest currently on the market for this application.
 
 
Ernani points out that they are "high-affinity" oligos.Because they are RNA based, rather than DNA based, they have a higher affinityfor single-stranded DNA, which makes the probes very effective at capturingDNA-containing unknown mutations, such as single nucleotide polymorphisms,insertions or deletions. The entire process is accomplished overnight, whereascompetitive techniques can take a week.
 
 
In the near future, Agilent will be launching version 2 ofits 38 Mb kit as it was defined by work with the Broad Institute which has nowsequenced more than 5,100 human genes. The 38 Mb kit has been optimized forunprecedented performance, Ernani says, and is more efficient than the 50 Mbproduct due to its smaller size. And finally, the SureSelect exon capture kitfor sequencing of the kinome (genes expressing all the kinases in a sample), isbeing developed in collaboration with Rene Bernards of the Netherlands CancerInstitute at the Antoni van Leeuwenhoek Hospital (NKI-AVL), Amsterdam.
 
 
 Agilent in biotech collaboration with Malaysiangovernment 
PENANG, Malaysia—In early August, Agilent Technologies Inc.announced a second collaboration with an entity abroad: the Malaysiangovernment.
 
Agilent said it will work with the government of Malaysiathrough the Malaysian Institute of Pharmaceuticals and Nutraceuticals (IPHARM),an agency under the Ministry of Science, Technology and Innovation (MOSTI), topromote and develop cooperation in biotechnology.
 
 
The strategic alliance will focus on the establishment ofthe IPHARM-Agilent Global Reference Research Lab and the development of humancapital in biotechnology. The lab will develop global Halal testing standardsin pharmaceuticals and nutraceuticals. It will also provide access tostate-of-the-art analytical tools and expertise to develop the local industryand small- and medium-size companies in their commercialization efforts.
 
 
"Agilent shares a common desire with the Government ofMalaysia to realize the national agenda for biotechnology," says Gooi SoonChai, president of Agilent Technologies Malaysia and Singapore. "Ourpartnership presents an enormous potential to accelerate the development ofthis field as the next engine of growth for the country."
 
 
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