Roche Nimblegen and the Human Genome Sequencing Center at Baylor College of Medicine in Houston, Texas, have improved the Sequence Capture 385K arrays.
These arrays enrich targeted genomic regions for high-throughput sequencing.
The new version of the microarrays allows researchers to perform capture experiments and quick sequencing of enriched regions using next-generation technology such as the Genome Sequencer FLX System from 454 Life Sciences.
The entire workflow, from genomic DNA to enriched DNA of target regions and sequencing results, takes about two weeks compared with months or years for traditional PCR-based methods coupled with capillary sequencing.
These second version microarrays will be available from Roche Nimblegen's Sequence Capture Service.
A critical performance measurement for enrichment technologies is the ability to capture all target regions with equal efficiency.
Dr Thomas Albert, senior director of research and development at Roche Nimblegen, said: 'We have observed a high degree of specificity, with 50-70 per cent of reads mapping back to target regions.
'Further improvements will have a limited effect on overall sequencing efficiency.
'Capture uniformity, however, is actually far more important for improving overall efficiency.
'For example, if the variation in sequencing coverage between or across target regions is high, many sequencing reads will be wasted on regions that have high coverage, at the expense of regions with low coverage.
'Therefore, much deeper coverage will be needed to provide adequate depth at poorly captured regions.
'We have focused our research efforts on ways to normalise the capture and we have developed new algorithms which now make the capture much smoother across all regions.' Dr Richard Gibbs, director of the Human Genome Sequencing Center, Baylor College of Medicine, said: 'Iterations of chip designs using new algorithms have resulted in well balanced captures by reducing low and high coverage regions, which has in turn reduced the overall amount of sequencing required by 50 per cent to achieve effective coverage.' Baylor has successfully implemented Nimblegen Sequence Capture technology into its sequencing pipeline in concert with the 454 Genome Sequencer FLX System.
Gibbs added: 'In more than 200 capture experiments, including those directed to the 1,000 Genomes project, as well as whole exome analyses and disease gene allele discoveries, we have had a success rates of >90 per cent.' Roche Nimblegen can deliver the custom-designed Sequence Capture Arrays to the researcher with the essential equipment, reagents and consumables.
On-site customer workshops are also available for researchers to gain hands-on experience under the guidance of certified sequence-capture trainers.
Nimblegen will soon release high density HD2 (2.1 million probes) arrays to enable the capture of all human coding exons on a single array.
Gibbs has generated human exome sequencing results by combining Nimblegen Sequence Capture and the 454 GS FLX System.
