Roche NimbleGen’s Revolutionary Sequence Capture Technology Now Available for Use in Research Laboratories

04 Sep 2008
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This spring, Roche NimbleGen announced the launch of their Sequence Capture Technology, a groundbreaking technique for enriching targeted genomic regions for high-throughput sequencing. Initially offered as a service, the Sequence Capture Technology is now available for delivery, or use in research laboratories.

Roche NimbleGen delivers the custom-designed Sequence Capture Arrays to the researcher, together with the essential equipment, reagents, and consumables. On-site customer workshops are also available for researchers to gain valuable hands-on experience under the guidance of certified Sequence Capture trainers. Researchers then perform their own capture experiment following the instructions of a user’s guide validated for human and mouse, and perform quick sequencing of enriched regions using next-generation technology such as the 454 Genome Sequencer FLX. The entire workflow, from starting genomic DNA, to enriched DNA of target regions, and sequencing results takes about two weeks, compared to months or years for traditional PCR-based methods coupled with capillary sequencing. Hence, the selective enrichment of target DNA using custom-designed high-density oligonucleotide microarrays, consisting of 385,000 probes, is a very efficient alternative to PCR-based approaches, especially in terms of time, cost, and scalability. Up to 5 Mb of contiguous or noncontiguous genomic sequence can be captured on a single array. Currently, NimbleGen Sequence Capture Arrays and Service are the only commercially available technology for researchers to perform large-scale targeted sequencing with quick turnaround time.

At the High-Throughput Sequencing Solutions lab of the University of Washington in Seattle, Sequence Capture 385K Custom Delivery Arrays are already in full use – with very good success. “We found NimbleGen Sequence Capture Arrays and protocol very easy to use and routinely observed successful capture experiments,” says Michael Dorschner, Director of the unit. He also appreciates the quality control that comes with the system. “It not only provides robust equipment for the elution of target-specific templates but also a qPCR-based assay to evaluate the degree of enrichment.” Besides Sequence Capture Delivery Arrays, Roche also provides validated equipment and kits, including a new instrument called Elution Station, to facilitate researchers to achieve consistent and reproducible capture results. Moreover, the cost savings of performing such cutting-edge research using NimbleGen Sequence Capture Arrays is a big advantage when compared with previous techniques. As Dorschner explains, the “Roche NimbleGen’s Sequence Capture Technology provides a cost-effective alternative to PCR for the enrichment of genomic targets facilitating large-scale resequencing projects and the development of a multitude of next-generation sequencing-based assays.”

Not only does the use of Sequence Capture Arrays tackle a major bottleneck in DNA sequencing system, the isolation of target genomic regions, but it also enhances the advantages of next-generation sequencing. The arrays are a perfect fit for the long reads of the 454 sequencing technology and thus enable haplotyping and identification of variations such as insertions, deletions, and SNPs down to single base pairs. Currently, captured DNA fragments can be directly utilized in the 454 system library preparation process as input for sequencing. “The Roche NimbleGen Sequence Capture System has revolutionized the way genomic regions of interest can be sequenced,” says Lynne Nazareth, Associate Professor at the Human Genome Sequencing Center at Baylor College of Medicine, Houston. “The system provides the scientific community with an invaluable tool for the rapid interrogation of genetic sequences, especially when combined with the next-generation sequencing technologies. We have successfully used the capture technology to enrich for targeted genes and found the system to be user-friendly and cost-effective, thereby facilitating our resequencing projects.”

Roche NimbleGen is currently developing protocols that will allow the direct addition of 454 adapters into the Sequence Capture workflow, thereby further streamlining the workflow and facilitate even faster turnaround time. The goal is to provide researchers with a more complete solution for targeted next-generation sequencing – in their own lab, on their own bench, on their own schedule.

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