The genomics renaissance

An Executive Interview with GenomeQuest

NGP. Personalized medicine is growing in prominence and is increasingly being seen as the future of treatment for many diseases. How much potential do you think this field of medical science holds?
Ron Ranuro. The field of personalized medicine holds immense potential for human health. We now know that no single drug can be made to treat a specific disease for all of humanity. The variation in our genetic make-up causes differential responses to drugs. With the advent of Next-Generation Sequencing, we can see a clear path 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 knowledge base as a foundation for research in personalized medicine.

NGP. Past approaches to genomics research have been hindered by a number of challenges. Can you outline some of these and highlight what developments have been made in overcoming these constraints?
RR. The main problems associated with past genomic approaches have to do with the use of a single genome as a representative of all genomes for a given 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. For associated technologies such as microarrays, there are additional issues.

We are entering a renaissance period for genomics with the advent of next-generation sequencing technology. 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 chip business with Digital Gene Expression thereby converting today’s analog view of gene expression in a higher resolution, richer digital view.

NGP. 2007 saw great strides in Next-Gen Sequencing, the industry now presents challenges for Bioinformaticians to effectively analyze all the new data produced. How are your company’s solutions solving the latest problems in the field?
RR. GenomeQuest has a complete solution for the management and analysis of the vast amounts of data produced in Next-Gen Sequencing runs. GenomeQuest supports all next-gen vendors and short or long reads. Our users have the ability to proceed from raw sequence output (e.g. a FASTA file) to a fully annotated, sequence and text-searchable database. Our process of transforming the output to usable content is enabled by a suite of extremely fast and very accurate alignment algorithms.

NGP. Increased hiring activity and a renewed focus on economical computer systems are clearly the current trend in the field. How is your business unit providing a low-cost Bioinformatics service?
RR. A fundamental metric of our business is our reliance on commodity computing so as to enable a sustainable scalability model. GenomeQuest employs commodity computing components at the core of our compute cloud that powers the GenomeQuest product. A centrally managed cloud of commodity computers, that is scalable by design, guarantees the delivery of a low-cost informatics solution that can stay ahead of the growth of our customers’ informatics needs.

NGP. Transforming Next-Generation Sequencing Data into knowledge is the next challenge for researchers. Deciphering the sequencing data deluge involves the latest technology and expertise. How can your Bioinformatics solutions enable greater data analysis and interpretation?
RR. We firmly believe we are the only complete solution for dealing with the next-generation data deluge. We are routinely performing all-by-all comparisons of the reads from a next-gen sequencer to all known public sequences. We are achieving these comparisons very quickly, but with unprecedented accuracy, thereby enabling scientists to maximize the utility of the information extracted from their next-gen runs. Once these runs are conducted and analyzed, our On-Demand Informatics solution is also the only one that can manage all of the data from every run. Our solution provides the results in an intuitive, web-based interface that enables the rapid analysis of the data with the follow-on benefit of those analysis results being in a consumable, sharable and reportable form.

NGP. Faster algorithms are the key to achieving better quality results and within a shorter time frame. What key features of your latest technology enable end users to receive reliable and cost effective informatics data at an increasingly competitive speed?
RR. The GenomeQuest solution was designed from its inception to address the inherent limitations of current bioinformatics software. We have rethought the fundamental concepts of sequence comparisons at the core-technology level. The GenomeQuest solution is not yet another workbench of loosely-coupled “Blast-parsers”; it has been designed to be versatile and high-performance. We have circumvented all of the traditional bottlenecks, such as (i) database format conversions (ii) the dichotomy between text searching and sequence searching (iii) flat-text-oriented parsing of various alignment formats (iv) searching my query against a library (v) the non-scalability of an all-against-all paradigm. The result is a highly flexible, extensible solution that has been designed to deliver fast and accurate sequence management in a highly scalable framework.

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.