KeyGene licenses Whole Genome Profiling to AGI

Aug. 28, 2012

The Arizona Genome Institute (AGI) and KeyGene announced that they have entered into a broad license agreement that will enable AGI to market and execute sequence-based physical mapping projects using KeyGene’s proprietary Whole Genome Profiling (WGPTM) method.

The agreement includes on-site training to enable AGI scientists to apply the WGP method in their physical mapping projects. The agreement provides AGI with a state-of-the art solution to assemble physical maps of superior quality for internal research programs and customer projects. The WGP maps are used as scaffolds in whole genome sequencing programs, to provide direct access to Bacterial Artificial Chromosomes (BACs), containing genome segments of interest, and as a tool for revealing structural genome changes in evolutionary studies and breeding programs.

KeyGene’s WGP method forms part of KeyGene’s portfolio of Sequence Based Breeding applications. The WGP method uses next generation sequencing to produce short read sequences (“WGP tags”) adjacent to restriction enzyme recognition sites in BACs. For this, BACs are systematically pooled and BAC pool DNA isolated according to protocols developed by Amplicon Express. The WGP tags are used to assemble large numbers of BACs into a physical map of overlapping clones. Integration of whole genome sequence data with the WGP map results in super scaffolds with superior assembly metrics. So far, the WGP method has successfully contributed to many different genome projects covering a broad range of genome sizes and different ploidy levels including melon, cucumber, tomato, sweet pepper, lettuce, oil seed rape, tobacco, wheat and others. The WGP method is particularly valuable for complex genomes with a high fraction of repetitive regions.

Prof. Rod Wing, director of the Arizona Genomics Institute at the University of Arizona said: “AGI is extremely pleased to have established a licensing agreement that will enable AGI to work with KeyGene and its partner Amplicon Express to market and execute Whole Genome Profiling. Next generation sequencing facilitates the rapid generation of genome assemblies that are often missing up to 60 percent of their genome sequence. Rather than calling these assemblies ‘genomes’ I like to call them ‘gene space assemblies’. What WGP offers is the ability to capture the majority of a genome in the form of a sequence based BAC physical map which can then be used as a scaffold to layer deep-coverage multi-platform sequence data (Illumina, 454, PacBio etc.) to create reference quality genome assemblies, or RefSeqs. It is critical that the first genome of any species should be as high a quality as possible as such quality will affect all subsequent downstream analysis activities. Once WGP is established in our institute we will immediately apply it to our ongoing work to sequence the collective Oryza and Brassicales genomes on our quest to help solve the 9-billion-people question – which is how can we grow enough food to feed an additional 2 billion inhabitants in less than 40 years.”

Mark J.J. van Haaren, CEO of Keygene Inc. in Rockville Maryland said: “This agreement with AGI will help us to make the WGP method available to a much larger customer base than KeyGene can serve on its own. We are very pleased with the relationship with AGI and with professor Rod Wing being a prominent expert in the use of physical mapping for assembly of high quality genomes. Combining the long term BAC expertise of AGI with the innovative power of KeyGene and its partner Amplicon Express, will drive the WGP method to a next level and addresses the desire of many genome sequencing consortia and companies for better and more cost effective physical maps and genome assemblies.”