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Feb 15, 2009 (Vol. 29, No. 4)

Recent Advances in NextGen Sequencing

  • Illumina just released new sequencing chemistry kits and complementary software for its Genome Analyzer system. These new products reportedly enable researchers to generate 40% more reads per run and extend read length to greater than 75 bp.

    Also launched is the new Mate Pair Library Preparation Kit, which provides support for generating longer insert paired-end libraries and is complementary to Illumina’s existing short-end paired libraries.

    “These new improvements enable researchers to generate 10 to 15 Gb of high-quality data per run, more than doubling the output previously attainable on the Genome Analyzer,” explains David Bentley, vp and chief scientist of DNA sequencing at Illumina.

    “The availability of mate pair library kits and long paired-end reads has greatly increased the flexibility and capacity of our Illumina sequencers. I believe that they have greatly improved our ability to sequence cDNA libraries and may even open up the possibility to do de novo sequencing on the Illumina sequencer,” adds W. Richard McCombie, Ph.D., professor at the Cold Spring Harbor Laboratory.

    “They are also greatly helping our medical resequencing by giving us more data and the ability to look for small insertions and deletions in patient samples.”

    “In addition to providing new solutions for de novo sequencing, the combination of short insert paired-end reads with the new longer insert mate pair sequencing is the most powerful approach for maximal coverage across the genome,” says Bentley. “This combination enables detection of the widest range of structural variant types and is essential for accurately identifying complex rearrangements.

  • Moving Toward Personalized Medicine

    Researchers at Roche NimbleGen and 454 Life Sciences believe a key milestone for personalized medicine has been achieved via the application of novel technologies to resequence all human exons from individual genomes. Roche NimbleGen launched Sequence Capture 2.1M Human Exome microarrays, built on the HD2 platform, which allows researchers to capture all exons in the genome (i.e., the exome) on a single array with 2.1 million long oligonucleotide probes.

    “Coupled with the Genome Sequencer FLX system from 454, life science investigators now have the capability to assess genetic variation within the exome of any individual,” notes Gerd Maass, CEO of Roche NimbleGen.
    Exons are the most functionally relevant portion of the genome and are comprised of short segments of DNA that provide the genetic blueprint for proteins. As such, exome sequencing enables the discovery of much of the functional variation that is responsible for many common and rare diseases. Exome sequencing research is also expected to shed light on why diseases like diabetes occur more often in certain populations, and can help uncover why drugs are effective only in a subset of the individuals or population.

    “Prior to the release of NimbleGen Sequence Capture Human Exome microarrays, the sequencing of the exome was neither technically nor economically feasible, as conventional PCR methods for the preparation of all human-coding exons are expensive and time-consuming,” continues Maass.

    “In 2009, the technologies of Roche NimbleGen’s Sequence Capture and the 454 Sequencing System have made complete human exome sequencing a reality, and can ultimately produce technology to feed the research pipeline and nourish the development of personalized healthcare.”

    Maass explains that offering reliable next-generation tools can lead to dramatically reducing the costs of DNA sequencing and opens up new and quicker means for discoveries about biological disease pathways.

    “In the future, these types of technologies, and the data and knowledge they provide are expected to allow comprehensive understanding of any information from the genome and enable personalized healthcare strategies for diagnosis, prevention, and treatment,” he says.


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