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Agilent's Upgrade Plans for SureSelect Target Enrichment Include Support for SOLiD, 454

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This article was originally published June 17.

Agilent Technologies is working on several enhancements for its SureSelect Target Enrichment system for targeted resequencing, In Sequence has learned.

This summer, Agilent plans to introduce a SureSelect kit for paired-end sequencing on the Illumina GA, according to Emily LeProust, Agilent's director for applications and chemistry R&D for genomics, who spoke at an Agilent seminar at Rockefeller University in New York last week. The company is also working on versions of SureSelect for use with Applied Biosystems' SOLiD sequencer and the 454 Life Sciences platform.

The company launched its first kits for the hybridization-based in-solution capture method, which it developed in collaboration with researchers at the Broad Institute, in February (see In Sequence 2/24/2009). The product allows users to select and enrich on the order of 3.3 megabases of target DNA, using custom-designed 120-mer RNA probes, or "baits."

Later this year, Agilent plans to launch SureSelect DNA capture arrays, developed in conjunction with researchers at Cold Spring Harbor Laboratory. Both the in-solution and array-based products rely on Agilent's proprietary SurePrint injet technology, which allows the company to synthesize high-quality oligonucleotides up to 200 base pairs in length.

SureSelect Target Enrichment kits come in different sizes and include all required reagents and consumables for the hybridization except for magnetic beads, which customers have to purchase separately. Protocols are currently optimized only for single-end sequencing with the Illumina Genome Analyzer, and Agilent and Illumina have a co-marketing agreement for the product in place.

Agilent does not publicly disclose the price of the product, but LeProust said the price per reaction drops up to tenfold with larger kit sizes. Kits range from 10 to 5,000 reactions.

In addition to the customized SureSelect offer, Agilent is also developing a catalog kit to analyze the human exome, which will be optimized for paired-end sequencing on the GA with paired 75-base reads. It is also considering further catalog products, based on customer demand.

Another future goal, LeProust said, is to increase the target size up to 10 megabases, which will be synchronized with Illumina's development of longer reads and higher throughput for its GA platform. To work with 36-base Illumina reads, Agilent currently recommends a probe design where probes overlap by 50 percent. In the future, when 75-base paired-end reads are in common use, probes may not need to overlap anymore..

Further, the company plans to support sample indexing for sequencing with the GA, allowing customers to analyze DNA from several samples in parallel, for example a one-megabase target from 10 samples instead of a 10-megabase target from a single sample.

LeProust also mentioned that a new protocol for SureSelect kits is underway that will be simpler and will improve the performance of the target selection. Researchers at the Wellcome Trust Sanger Institute have contributed their changes to the DNA sample protocol, she said, which increases the number of on-target reads to approximately 80 percent, from a current range of 40 to 60 percent.

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