The Dream of Personalized Medicine

An Ask the Expert feature with GenomeQuest

Next-generation sequencing takes us closer, but only if we have a sequence data management solution.

The field of personalized medicine holds immense potential for human health. Too many drugs fail because they only treat a portion as opposed to the entire human population. The variation in human genetic make-up causes differential responses to drugs. With the advent of next-generation sequencing, a clear path is visible toward the enumeration of the variation in the human population with the ultimate goal of using those individual genetic variations to provide medicines tailored for each person's genome. However, the dream of personalized medicine will only be achieved by an earlier focus on personalized genomics as a means to build the underlying knowledgebase as a foundation for research in personalized medicine.

Overcoming past hindrances

The limitations of many past genomic approaches have to do with the use of a single genome sequence as representative of an entire species. This approach has provided tremendous insight into the relationship between genetic sequence and biological function at a coarse level, but not at the level of detail associated with personal genetic variation.

The developments made by next-gen sequencing techniques have revolutionized sequencing activities, rapidly bringing forth the era of personalized genomics. In addition, the next-gen advances are expected to supplant a substantial portion of the microarray studies with digital gene expression thereby converting today's analog view of gene expression to a higher resolution, richer digital view.

The data glut

The cost of generating sequence data has dropped ten thousand-fold since 2005, making possible new applications in personalized medicine. By mid-2010, a university laboratory with a next-generation sequencing machine running at 50 percent capacity will produce more sequence data than has been archived in all of GenBank from its inception in 1982 through 2008. As a result, the amount of available genomic data is increasing exponentially, and there is no single point of access to multiple sources of disparate in-house, public and private data.

The information systems to manage all of this sequence data do not exist inside of pharmaceutical and biotech companies. The client-server architectural approaches of these companies are based on relational databases that are too expensive to develop, deploy and maintain causing these companies to increasingly seek commercial solutions to avoid unforeseen scaling risks and hidden costs. How will commercial enterprises and academic institutions deal with all of this data?

The GenomeQuest solution

GenomeQuest provides a software-as-a-service (SaaS) Web portal providing centralized sequence data management resources and applications for biological research, patent research, and for computing and working with all types of sequence data and associated text

GenomeQuest employs commodity computing components at the core of our compute cloud that powers the GenomeQuest product. A centrally managed cloud of commodity computers, scalable by design, guarantees the delivery of a low-cost informatics solution that can stay ahead of the growth of our customers' informatics needs.

We are the only complete solution for dealing with the next-generation data deluge and the management of all sequences across an enterprise. GenomeQuest enables scientists to very quickly accurately extract the maximum information from their next-gen sequence data. The GenomeQuest solution provides this information in an intuitive, web-based interface that enables the rapid analysis of the data with the follow-on benefit that those analysis results are in a consumable, sharable and reportable form.

Return on investment

The GenomeQuest solution provides an ROI to the commercial enterprise by increasing end-user productivity by providing a single, centralized access point for all sequence data from any source (public, corporate, personal, or commercial), across your entire enterprise.

In addition, GenomeQuest improves knowledge transfer and collaboration by enabling end-users to upload and share their sequence data, all within the existing informatics resources, inside your enterprise.

Overall, GenomeQuest's easy-to-use web interface, open system with published APIs, and continuously updated reference data will enable you to reduce your IT costs, minimize your risks and enable you to more effectively redeploy your talented informatics staff to higher value activities.

Ron Ranauro is the Chief Executive Officer of GenomeQuest, Inc., where he oversees the company's day-to-day operations. Prior to joining GenomeQuest, he founded and led Blackstone Technology Group, a grid-computing provider to the life science IT field. Ranauro earned a BS degree in Management and an MS in Computer Science from Worcester Polytechnic Institute.