The Netherlands
July 14, 2015
Molecular genetics Ag Biotech company KeyGene and biomedical big data solutions company GENALICE, jointly mark the significant mutual benefits of their first two years of partnership, running GENALICE MAP in full production as their preferred tool for primary (Next-Generation Sequencing (NGS) data analysis.
The AgBio challenge
KeyGene supports its customers and partners with cutting edge breeding technologies and plant trait platforms. For many important agronomical crops, KeyGene has elucidated their highly complex genomes. With its in-house MultiVariome Analysis Platform for the processing of high volume resequencing data, and the CropPedia system for data integration, the company has brought crop genomics to a next level. The platforms create the perfect view on exploitable genetic variation, enabling more efficient use of germplasm and elite breeding material, and revealing the genetic basis of commercial traits.
KeyGene’s multivariome analysis pipeline focuses on different types of variation, like SNPs, indels, and CNV’s, and on the discovery of novel genes in the germplasm. Back in 2013, the initial version of the Multivariome Analysis Platform used open source mapping and genotyping tools that were running on a powerful in-house compute cluster. KeyGene’s NGS big data production, however, consumed an increasing part of that compute capacity, calling for either brute expansion or innovative data analytics.
The starting point
In the partnership with GENALICE, KeyGene was the first company to benchmark GENALICE MAP on agronomical crops. Prof. Dr. Roeland van Ham, VP Bioinformatics and modeling at KeyGene, was attracted to the amazingly fast short read mapping speed of GENALICE MAP, as presented at the ECCB conference in 2012. He comments: “The early results on simulated data seemed too good to be true, but also intrigued me and triggered us to do further exploration of the product”. Based on the excellent results obtained, KeyGene incorporated GENALICE MAP into its Multivariome Analysis Platform. Running it on commodity hardware, this now saves compute capacity for an expanding array of downstream tools in KeyGene’s Lead Discovery pipeline. The fast execution also provides great flexibility to tune the system for higher quality results in variation discovery. Roeland van Ham: “With a shared passion for innovation, it was the starting point of an extremely pleasant and productive partnership. Together, we first went through the validations for alignment and variant calling on smaller plant genomes. Still a complex job, as plant genomes consist of many repetitive areas. Thereafter we covered the adaptation of GENALICE MAP to also process larger plant genome sizes. The GENALICE team operates in an agile fashion, and together we are able to define and implement new functionality very fast and precise. Two of the new modules they are finalizing in the coming months are population calling and RNA-Seq alignment and quantification. Two important research areas and valuable product extensions for us. Since about a year we use GENALICE MAP in all of our high volume NGS projects. The key factors backing our decision to move to GENALICE MAP were the quality and speed of the product enabling the development of better genetic solutions for KeyGene’s partners and customers”.
More to come
Jos Lunenberg, Chief Business Officer of GENALICE, says in a statement: “We are very pleased with the partnership with KeyGene. It is exemplary for its kind. In a very short time, we have managed to complete product development and make sure it excels in the AgBio genomics environment, with all its specific challenges. The synergy between KeyGene and GENALICE is the foundation of true collaboration and innovation. The companies are continuing on this path towards innovative Big Data analytics solutions to add real value to genomic workflows in business and research”.
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