Agilent Technologies has acquired a license to commercialise a method developed at the Broad Institute for genome partitioning using Agilent's Oligo Library Synthesis (OLS) technology
Recent advances in DNA-sequencing technology have increased the speed of data acquisition.
However, without accompanying improvements in the ability to select relevant portions of the genome, the technology cannot achieve its full potential in studying the relationships between genes and diseases.
The Agilent genome-partitioning portfolio, which is currently in development, holds great potential for eliminating this bottleneck by enabling users to efficiently design and acquire ready-to-use, custom mixtures of biotinylated long RNA probes in a single tube.
Chad Nusbaum, co-director of the genome sequencing and analysis programme at the Broad Institute, described the improved method at an Agilent customer event recently at the American Association of Cancer Research meeting in San Diego, USA.
"We're working on a simple, highly multiplexed, cost-effective way to enable investigators to remove the sample-preparation bottleneck in sequencing targeted regions of mammalian genomes, using relatively small amounts of input DNA," Nusbaum said.
"Agilent's expertise in custom oligo synthesis and our expertise in production-scale sequencing are a natural match-up to overcome these challenges".
"The Broad is part of our early-access programme, in which we made oligo library synthesis capability available to a select number of luminaries to find out how these creative scientists could use custom complex mixtures of long oligonucleotides," said Yvonne Linney, Agilent vice president and general manager, genomics.
"This work to eliminate the sample preparation bottleneck of next-generation sequencing will greatly accelerate our understanding of how genes operate".
Agilent plans to offer kits containing custom mixtures of long biotinylated RNA molecules that can efficiently capture 5-10 megabases of genomic DNA sample in a single tube.
The method is based on the combination of the Agilent SurePrint platform, capable of synthesising high-quality oligo mixtures, and the protocols developed by the Broad Institute to transform these into RNA probes.
These RNA probes can, in turn, be used to capture genomic regions of interest in a simple, scalable and highly multiplexed manner, greatly simplifying the process for targeted re-sequencing.
"The ability to perform the capture reaction in a small volume solution enables a significant increase in the kinetic efficiency and enables users to scale from tens to thousands of samples without adding significant personnel," said Emily LeProust, Agilent R+D chemistry and genome partitioning programme manager.
In February, a researcher from Nusbaum's group presented a paper at the Advances in Genome and Biology Technology conference, describing the use of Agilent Oligo Libraries, the basis of the genome partitioning capability and next-generation sequencing to correctly identify several previously known mutations and several new ones in certain tumour types.
Linney said that this is also an example of how Agilent is leveraging the reagent manufacturing expertise of Stratagene, which joined Agilent in June 2007, to provide high-quality, cost-effective solutions.
The Broad Institute is a research collaboration of the Massachusetts Institute of Technology and Harvard University.
