Spanish partners to develop low-cost informatics methods for clinical genomics

GRANADA, Spain—Integromics SL, a company that provides ITsolutions for life sciences in the areas of genomics and proteomics, hasentered into a partnership with Prof. Angel Carracedo and his team at theGalician Foundation of Genomic Medicine (FPGMX), a recipient of the EuropeanLife Technologies Ion Torrent Visionary Winners Award, for the development ofinexpensive solutions for clinical genomics.

Life Technologies acquired Ion Torrent in late 2010 in amove targeting acquisition of the services of life-sciences pioneer Dr.Jonathan Rothberg, as well as his company that has spawned the latestinnovation in gene sequencing. At that time, Life Technology's CEO Mark Stevensonnoted that Rothberg and his DNA semiconductor-based sequencing technology werekey to the acquisition. Now, via its awards program, Ion Torrent appears toacknowledge that data interpretation is the next hurdle in reaching the goal ofclinical and diagnostic use of next-generation sequencing (NGS).

The first product using Ion Torrent technology is thePersonal Genome Machine (PGM), an easy-to-use, highly accurate benchtopinstrument that is initially being marketed for mid-scale sequencing projects,such as targeted and microbial sequencing. The instrument is being providedfree to Ion Torrent Award winners and is pegged at an entry cost of less than$100,000. In less than a year sinceLife Technologies commercially launched the PGM, the semiconductor-basedinstrument has become the best-selling, next-generation sequencing machine inthe world, and it is democratizing DNA sequencing, the company claims. The PGMenabled two independent teams of scientists in Germany and China to quicklydecipher the deadly E. coli bacterium that recently caused more than50 deaths in Europe.

Based on the strength of its R&D work, the newpartnership between the two Spanish organizations has also been awarded a $1.3million grant from the European Regional Development Fund and the Spanish governmentfor a project called "Advanced analysis and interpretation of low-cost nextgeneration sequencing data for clinical applications (ApliClinics LC-NGS)." Theinterpretation of NGS data has been recognized as a major bottleneck in theadoption of personalized medicine, both in terms of cost and time. TheApliClinics collaboration is designed to address the issues, at the bench andbioinformatics levels, being faced by the clinical labs trying to apply NGStechnology.

The project aims to improve procedures and optimize tools tomake the use of NGS faster in the routine healthcare environment, which willalleviate the current lack of applications critically needed by clinicians, aswell as helping to lessen their workload.

"This will be the first time that Integromics will beworking side-by-side with clinicians to bridge the gap between our NGStechnology and how it translates into healthcare for patients," says EduardoGonzález Couto, chief strategy officer of Integromics. "The synergy of theclinical genomic pioneers from the FPGMX and the expertise of thebioinformaticians we have at Integromics will undoubtedly help to acceleratethe development of solutions for clinical genomics. Automated next-gensequencers have increased the speed and reduced the cost of sequencing, makingit possible to offer genetic testing to consumers. Producing the genomic datais no longer a problem, however; it is the analysis and interpretation of thedata that has become the 'new frontier.' In order to characterize and interpretthe 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 routinecasework," says Carracedo, director of the FPGMX. "For this reason this projectis essential for us. In this moment the bottleneck is not data production butto have bioinformatic tools allowing us to obtain reliable and accurateinformation 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 theApliClinics project before year-end.

TheIntegromics solution

Integromics'OmicsOffice offers an all-in-one software platform for straightforward analysisand management of genomic data, combining real-time PCR (RT-qPCR), microarraygene expression and next generation sequencing (NGS) data to meet the needs ofmodern genomics research.

Partof the platform is SeqSolve, an advanced anduser-friendly software solution for the tertiary analysis of NGS data. Byintegrating state of-the-art bioinformatics methods into one-click analysisworkflows, SeqSolve provides scientists with a unique combination of cutting edgealgorithms and intuitive user experience. Its Click And Go technology enablesthe automatic processing of the data and includes a Smart Quality Controlsystem, which makes it both simple to use for non-experts and reliable in termsof biological results.