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Thursday, February 14, 2008

Scientists remove bottleneck in genetic sequencing

Researchers at the Broad Institute of MIT and Harvard, USA, have successfully employed a new technique developed by Agilent that could potentially eliminate one of the biggest bottlenecks in the genetic sequencing process.

The researchers, who presented their work at the Advances in Genome and Biology Technology conference in Florida, USA last week, successfully identified previously unknown somatic mutations in tumours. It represents one of the first instances in which Agilent's inkjet-printing method of rapidly creating oligonucleotide probes has been successfully deployed in real scientific research.

When studying genetic variations, researchers frequently only need to study specific sections that are relevant to a particular disease, instead of studying the whole genome. "They can use custom oligonucleotide mixtures to isolate and enrich genomic segments they're interested in, rather than having to sequence the entire genome," Emily LeProust, Agilent's manager of chemistry development, told

To do this, they need to create many copies of the sections that they want to study which can then act as probes for further research. All of the other steps in the sequencing process have seen improvements in new, "parallel" techniques that can study many different sequences simultaneously, but until now there has been no equivalent technique for creating artificially amplifying sections of the genome in this way. Current techniques, such as polymerase chain reactions, are length processes that create a bottleneck that holds up genomic projects.

Agilent's new technique, called Oligo Library Synthesis, could be the answer. It is quicker and less costly than other methods, with the capacity to create up to 55,000 customer-defined oligonucleotides in a single tube.

"To create a mixture of 55,000 oligos individually using PCR would take many months and cost millions of dollars. The OLS capability creates these mixtures very quickly and cost-effectively," explained LeProust. "We use a sophisticated inkjet type 'printer' to synthesise as many as 244,000 oligonucleotide probes on a one-inch by three-inch glass wafer."

Chad Nusbaum, co-director of the genome sequencing and analysis programme at the Broad Institute, believes it is a very effective technique: "We prepared a labelled derivative of Agilent's oligo libraries to use for direct capture of target sequences by hybridisation. The method is highly multiplexed, with a simple, efficient and inexpensive laboratory process, thus overcoming the sample preparation bottleneck."

The technique reportedly offers many other advantages in addition to its speed. According to LeProust, customers have reported that the oligonucleotides are of a better quality than traditional techniques. It can also create very long sections of DNA, up to 200 base pairs in length, which would not have been possible using previous methods.

Agilent is currently providing its Oligo Library Synthesis to a small set of research groups before it becomes a commercially available product or service.

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