Spanish partners to develop low-cost informatics methods for clinical genomics
GRANADA, Spain—Integromics SL, a company that provides IT solutions for life sciences in the areas of genomics and proteomics, has entered into a partnership with Prof. Angel Carracedo and his team at the Galician Foundation of Genomic Medicine (FPGMX), a recipient of the European Life Technologies Ion Torrent Visionary Winners Award, for the development of inexpensive solutions for clinical genomics.
Life Technologies acquired Ion Torrent in late 2010 in a move targeting acquisition of the services of life-sciences pioneer Dr. Jonathan Rothberg, as well as his company that has spawned the latest innovation in gene sequencing. At that time, Life Technology’s CEO Mark Stevenson noted that Rothberg and his DNA semiconductor-based sequencing technology were key to the acquisition. Now, via its awards program, Ion Torrent appears to acknowledge that data interpretation is the next hurdle in reaching the goal of clinical and diagnostic use of next-generation sequencing (NGS).
The first product using Ion Torrent technology is the Personal Genome Machine (PGM), an easy-to-use, highly accurate benchtop instrument that is initially being marketed for mid-scale sequencing projects, such as targeted and microbial sequencing. The instrument is being provided free to Ion Torrent Award winners and is pegged at an entry cost of less than $100,000. In less than a year since Life Technologies commercially launched the PGM, the semiconductor-based instrument has become the best-selling, next-generation sequencing machine in the world, and it is democratizing DNA sequencing, the company claims. The PGM enabled two independent teams of scientists in Germany and China to quickly decipher the deadly E. coli bacterium that recently caused more than 50 deaths in Europe.
Based on the strength of its R&D work, the new partnership between the two Spanish organizations has also been awarded a $1.3 million grant from the European Regional Development Fund and the Spanish government for a project called “Advanced analysis and interpretation of low-cost next generation sequencing data for clinical applications (ApliClinics LC-NGS).” The interpretation of NGS data has been recognized as a major bottleneck in the adoption of personalized medicine, both in terms of cost and time. The ApliClinics collaboration is designed to address the issues, at the bench and bioinformatics levels, being faced by the clinical labs trying to apply NGS technology.
The project aims to improve procedures and optimize tools to make the use of NGS faster in the routine healthcare environment, which will alleviate the current lack of applications critically needed by clinicians, as well as helping to lessen their workload.
“This will be the first time that Integromics will be working side-by-side with clinicians to bridge the gap between our NGS technology and how it translates into healthcare for patients,” says Eduardo González Couto, chief strategy officer of Integromics. “The synergy of the clinical genomic pioneers from the FPGMX and the expertise of the bioinformaticians we have at Integromics will undoubtedly help to accelerate the development of solutions for clinical genomics. Automated next-gen sequencers have increased the speed and reduced the cost of sequencing, making it possible to offer genetic testing to consumers. Producing the genomic data is no longer a problem, however; it is the analysis and interpretation of the data that has become the ‘new frontier.’ In order to characterize and interpret the data for medical usage, novel bioinformatics tools are crucially needed.”
“The interest of the group, in addition to genomic research, is the practical translation of next generation sequencing to clinical routine casework,” says Carracedo, director of the FPGMX. “For this reason this project is essential for us. In this moment the bottleneck is not data production but to have bioinformatic tools allowing us to obtain reliable and accurate information of the variation found after DNA sequencing using NGS facilities, which is the main objective of this project.”
Integromics expects to announce the first results of the ApliClinics project before year-end.
The Integromics solution
Integromics’ OmicsOffice offers an all-in-one software platform for straightforward analysis and management of genomic data, combining real-time PCR (RT-qPCR), microarray gene expression and next generation sequencing (NGS) data to meet the needs of modern genomics research.
Part of the platform is SeqSolve, an advanced and user-friendly software solution for the tertiary analysis of NGS data. By integrating state of-the-art bioinformatics methods into one-click analysis workflows, SeqSolve provides scientists with a unique combination of cutting edge algorithms and intuitive user experience. Its Click And Go technology enables the automatic processing of the data and includes a Smart Quality Control system, which makes it both simple to use for non-experts and reliable in terms of biological results.