By Julia Karow
Illumina last week launched its own in-solution human exome capture product, called TruSeq Exome Enrichment kit, and plans to launch a liquid-handling platform to automate target enrichment sample prep early next year.
The TruSeq exome kit will compete with existing products from other vendors, in particular Agilent's SureSelect human exome kits and NimbleGen's SeqCap EZ Human Exome Library v2.0. Both Illumina and Agilent say they are moving toward automating target enrichment for large-scale studies.
Developing an exome enrichment kit of its own was "not an unnatural thing" for Illumina to do, given its expertise in oligonucleotide synthesis and molecular biology, Omead Ostadan, the company's vice president of marketing, told In Sequence at the sidelines of the American Society of Human Genetics conference last week.
The TruSeq exome kit requires about a microgram of input DNA and allows users to pool up to six barcoded DNA libraries in a single exome capture reaction. Libraries are prepared using the TruSeq DNA sample prep kit, with a recommended library insert size of 300 to 400 base pairs.
The exome kit uses biotinylated 95-base DNA oligonucleotide probes and streptavidin to pull out exon DNA, followed by a second round of enrichment. Approximately 340,000 probes target 62 megabases of coding DNA, comprising about 200,000 exons from 20,800 genes and some non-coding RNAs, or 91 percent of the RefSeq database and 95 percent of the Collaborative Consensus Coding Sequence database. After enrichment, the DNA is amplified before it enters the cluster station and the Illumina sequencer.
According to Ostadan, Illumina sought to improve on the specificity, uniformity, target regions, workflow, and cost of competing products. Based on list prices, the per-sample cost of using the TruSeq kit is less than $300, enabled by the pre-enrichment sample pooling, or about $1,800 per capture for six samples.
Roche NimbleGen said that the cost of its SeqCap EZ Exome is "well below" $1,000 per capture, and multiplexing is possible as well.
While Agilent did not provide specific pricing information for SureSelect, Chris Grimley, senior marketing director for genomics at Agilent, said that the company's SureSelect XT system, which it launched last week, is "cost competitive with all other products on the market when considering sequencing costs."
He noted that the company's new exome designs have "a recommended shear size of 150-250 bps," which correlates with biological exon sizes and "reduces sequencing costs associated with off-target reads by requiring only 2x76 base pair sequencing compared to 2x125 base pair reads required by some competitors."
Grimley added that the company's new exome designs "are the most comprehensive on the market," and currently target more than 99.9 percent of the CCDS database and 96.7 percent of RefSeq.
The TruSeq exome kit will be available later this month. Early-access customers who have tested it include Jay Shendure's lab at the University of Washington in Seattle.
At the moment, Illumina does not offer customized capture kits for genomic regions other than the exome, but Ostadan said that customization would be a "natural extension" of the product line that the company will be looking into.
The TruSeq exome kit has been designed with automation in mind. Reagents are pre-mixed in master mixes, and reaction volumes are compatible with liquid-handling platforms. During the first quarter of 2011, Illumina also plans to launch its own automation hardware, Ostadan said, consisting of a robot made by an unnamed partner under an OEM agreement, as well as a LIMS and protocols from Illumina. That system, though compatible with other reagents and workflows, is expected to be "better tuned to work with our own sample prep," he said.
Agilent, meantime, launched the SureSelect XT target-enrichment system last week, which combines existing SureSelect kits with sequencing library-preparation kits and a preparative kit for isolating genomic DNA. The kits are compatible with both the Illumina and the SOLiD platform, according to the company. SureSelect uses 120-base RNA oliognucleotides as probes.
Grimley said that the SureSelect XT "can be fully automated using a turn-key automation system available from Agilent’s Automation Solutions group, which further reduces operating costs for higher throughput customers."
Agilent is now offering its Bravo automated liquid-handling system and other automation modules — such as plate stackers, a carousel, and a plate sealer — specifically configured for automating next-gen sequencing library preparation and target capture. The Broad Institute recently revealed that it has standardized on the Bravo platform for next-gen sequencing sample prep automation (IS 10/12/2010).
Agilent offers a variety of SureSelect capture kits, including two human exome kits, a mouse exome kit, a human kinome kit, a human X chromosome kit, and custom target-enrichment kits ranging in size from 200 kilobases to 6.8 megabases.
This summer, the company launched the SureSelect Human All Exon v2 kit, which targets 38 megabases of DNA, 99 percent of the CCDS database, and 95 percent of the RefSeq database; and the SureSelect Human All Exon 50 Mb Target Enrichment kit, which covers 50 megabases of DNA that includes additional content besides the exome.
Roche NimbleGen, the third major player in the in-solution target-capture market, recently launched its SeqCap EZ Human Exome Library v2.0, which has been optimized for use with short-read sequencing platforms like the Illumina and SOLiD systems, according to a company representative. The SeqCap EZ exome kit uses 2.1 million DNA probes to target 44.1 megabases of DNA, including 36.5 megabases from more than 30,000 genes, or 300,000 exons, from the RefSeq, CCDS, and miRBase databases.
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