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Right on target
November 2009
by Lloyd Dunlap  |  Email the author
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MADISON, Wis.—Using technologies that include targeted enrichment with Roche NimbleGen's Sequence Capture and ultra-deep sequencing with the Genome Sequencer FLX System from 454 Life Sciences (also a Roche company), Roche Applied Science is providing what is described as "a complete solution for targeted resequencing of the human genome to further our understanding of disease associated regions."

 

Roche and its partner, National Cancer Institute (NCI) contractor SAIC-Frederick Inc., will assess the ability of these technologies to sequence the genomes of cancer research samples. As one example, in a just-published collaborative study between the two partners and the NCI, a detailed map of common genetic variation in the genomic region surrounding the KLK3 gene was generated, which should be useful for fine-mapping the association signal as well as determining the contribution of this locus to prostate cancer risk and/or regulation of PSA expression, the authors state.

 

Together, the NimbleGen Sequence Capture arrays and 454 Sequencing system offer a complete solution by providing comprehensive, relatively unbiased coverage across the desired target enrichment region, says Tom Jarvie, technical applications manager at 454 Life Sciences. Furthermore, he notes, the system is not limited to SNPs, but covers the full range of genomic variation. Known disease-associated regions can be quickly converted into custom-designed target enrichments.

 

"Our ability to understand the impact of particular regions of the human genome with cancer phenotypes is rapidly advancing with the advent of next-generation sequencing technologies," says Joseph Boland, dedicated scientific operations manager of the Core Genotyping Facility at SAIC-Frederick. "Our intent is to implement Roche NimbleGen's solution-based sequence capture technology, SeqCap EZ, to rapidly advance our next-generation sequencing projects and, in turn, increase our knowledge of cancer genetics."

 

The long, accurate reads of the ultra high-throughput Genome Sequencer FLX system provide a unique opportunity to identify classes of variation that are not possible with short read sequencing technologies, Tom Jarvie says. The long reads enable the identification of insertions and deletions, the ability to provide haplotype information on two or more variations (to determine if the variations are linked on the same chromosome), and the ability to discern between variation within nearly identical sequences. The nearly identical sequences are present in closely related genes (gene families, paralogous genes) and within genes that have closely related pseudogenes elsewhere in the genome. 

 

Additionally, all target enrichment technologies must omit areas, such as repeats, from the pool of capture oligos—even when these regions are within the desired target enrichment region. However, these omitted areas are still important to the overall experimental success. NimbleGen Sequence Capture technology successfully captures fragments that border the omitted areas and the long, 454 Sequencing reads span the gap thereby providing comprehensive coverage of the entire target region, Jarvie notes.

 

"The target enrichment, coupled with ultra high-throughput, long-read sequencing, allows researchers to focus in on the regions of interest in the genome that are either biologically significant, such as the whole exome, or a small region that is known from other studies to be of interest for a particular type of cancer. By focusing the sequencing in this way, the data sets are much smaller, quicker to generate, and more readily and quickly interpreted than whole genome data sets," Jarvie states.

 

Kary Staples, manger of global marketing communications at Roche NimbleGen, notes that the SeqCap EZ system was developed by Roche NimbleGen within the past year and is targeted for mass-market launch at the end of October. Some of the differentiators of this product are, it offers more capture oligos (up to 2.1 million) than other technologies, and this together with an optimized design algorithm (or empirically optimized and validated probes), increases the capture uniformity. Compared with other technologies, it achieves better coverage with less sequencing due to the large number of probes and the enhanced uniformity of the capture. In addition, the SeqCap EZ workflow is easily implemented and scalable to a 96-well microplate to achieve 96 discrete captures.

 
Code: E110917

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