Roche NimbleGen introduces new version of genome sequencing tool

According to the company, the new and improved microarrays allow researchers to perform their own capture experiment and perform sequencing of enriched regions using next-generation technology such as the Genome Sequencer FLX System from 454 Life Sciences.

The entire workflow, starting from 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. These second version microarrays will also be available through Roche NimbleGen’s Sequence Capture Service.

A critical performance measurement for enrichment technologies is to capture all the target regions with equal efficiency. According to the company, NimbleGen second generation Sequence Capture Arrays deliver improved performance regarding the specificity and uniformity of captured regions.

Thomas Albert, senior director of R&D at Roche NimbleGen, said: “We have observed a high degree of specificity, with 50-70% 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 normalize the capture, and we have developed new algorithms which now make the capture much smoother across all regions.”