Complex Mixtures of Targeting Oligonucleotides Unlock the Power of Next-Generation DNA Sequencers

22-Oct-2007

A group of researchers at Harvard Medical School, Virginia Commonwealth University, Agilent Technologies Inc., Codon Devices Inc., and Stanford University has used complex mixtures of oligonucleotides in the form of oligonucleotide library synthesis to overcome a major bottleneck in realizing the potential of the newest generation of DNA sequencers to reduce costs and increase throughput on a grand scale. Their findings are reported in Nature Methods.

The full potential of the new DNA sequencers is severely constrained by the lack of massively parallel "front end" methods to replace traditional polymerase chain reactions, according to the article. The team synthesized complex oligonucleotide probe mixtures using programmable "inkjet" technology, and then applied the oligonucleotide probe mixtures to simultaneously capture and amplify approximately 10,000 human exons in a single reaction. The researchers then demonstrated how this technique can be integrated with ultra-high-throughput sequencing for economical, high-quality targeted variation discovery.

"Agilent adapted its in-situ oligonucleotide synthesis technology to oligo library synthesis, and the oligo length and low error rates had already been helping us with massively parallel synthetic constructs," said co-author George Church, Ph.D., professor of genetics, Department of Genetics, Harvard Medical School. "It was clear that this approach could also be harnessed for second-generation sequencing primer tools."

The article compares the new oligo library protocol to conventional targeted discovery of genetic variation using Sanger sequencing of PCR amplicons. With PCR as the "front end" enabling the amplification of discrete regions that can be covered by an individual Sanger sequencing read - about one kilobase - the bottleneck becomes apparent when used with new sequencing techniques.

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