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As CEO Departs, GenomeQuest Sets Sights on Growing Footprint in Whole-Genome-Analysis Market


By Bernadette Toner

GenomeQuest CEO Ron Ranauro has resigned after eight years with the company, and will be temporarily replaced by Richard Resnick, vice president of products and services, as the firm searches for a permanent replacement.

It wasn't immediately clear why Ranauro resigned, though Resnisk said he is "investigating new opportunities."

Resnick said that GenomeQuest's board "is going to take the time it needs" to ensure that it appoints "the best possible permanent CEO available to the company."

The change in the corner office comes as the company looks to gain a foothold in the whole-genome sequence-analysis market, which GenomeQuest believes will grow rapidly as next-generation sequencing technologies continue to gain traction in research labs.

In an interview with BioInform, Resnick pointed to the oft-cited statistic that the cost of sequencing is plummeting more sharply than Moore's law, which means that "as vendors manufacture better and better machines to produce more sequence, the compute can't keep up."

GenomeQuest was founded in 1999 as Gene-IT, and over the ensuing decade it has weathered the ebb and flow of industry interest in adopting commercial bioinformatics tools in general and its GenomeQuest Engine core technology in particular.

But Resnick said the tide is beginning to turn as sequence data grows in volume and complexity. In a statement announcing Ranauro's departure, Resnick said that the company is seeing an "incremental change" in the market when it comes to next-gen sequencing. The focus over the last several years has been on validating sequencing technology and fundamental analysis questions regarding mapping and assembly.

But today, "the industry is … talking about next-generation sequencing as a whole-genome-sequencing and -analysis problem … and asking [questons like], 'How do I overlay these 100 exomes against these 50 genomes?'" he said.

This shift could represent a significant opportunity for GenomeQuest. "When you're looking at a whole human genome at 30X coverage, that's when we really start to shine," Resnick said.

Resnick estimated that the worldwide sequencing capacity is currently on the order of 5,000 whole human genomes at 30X coverage. "In 2011 it's going to be about 50,000 …and in 2012 it might be 250,000, and then it's going to be a million," he told BioInform. "This is not going to stop."

In the meantime, academic and commercial organizations are more open to working with companies like GenomeQuest to help with these large data sets, he said.

GenomeQuest does not consider its tools to be an alternative to in-house bioinformatics activities, but rather a "framework that enables bioinformaticists to stop doing the things that don't really add value to their enterprise [and to allow them to] really work on the higher-level science."

He described the company's contribution as the "raw janitorial stuff — managing the enormous volumes of sequence data to provide an interactive report for users" — enabled by the company's core technology, the GenomeQuest Engine.

Based on a framework for parallelizing various alignment tools that was developed in the 1990s by company founder Jean-Jacques Codani to support the Human Genome Project, the technology has continued to evolve in step with new sequencing technologies.

Crops to Clinics

At its core, the GQ-Engine does two things, Resnick said: "It represents, stores, compresses, indexes, and allows you to search sequence and annotation; and it represents, stores, indexes, and compresses mapping information. And because of these two things … focused on sequence, we can really shrink the footprint of NGS data significantly more than anyone else in the industry."

The company has also worked closely with SGI, the Sunnyvale, Calif.-based server and data-visualization and –storage company to design a computational architecture optimized for the GQ-Engine. GenomeQuest has deployed this architecture in its in-house data center to support its software-as-a-service delivery model.

The data center currently runs "thousands of cores" and is growing rapidly, Resnick said. With its current computational capacity, GenomeQuest is able to process 150 whole human genomes at 30X coverage per month, "and we'll be scaling into the thousands through the course of the remainder of the year and into 2011," he said.

Going forward, Resnick said GenomeQuest sees an opportunity for its tools to be used in several key markets, including pharma and biotech, agricultural biotech, academic sequencing, and genomic medicine.

The company has recently forged alliances on several of these fronts, including one with a large ag-bio company and one with a leading medical center. GenomeQuest is also working with a high-profile genome center. These collaborators are currently undisclosed.

Ag-bio is a particularly promising short-term market for GenomeQuest and represents a "major source of revenue," Resnick said. He noted that while there are fewer ag-bio companies than pharma companies, "they do a lot more sequencing" because they work with comparatively non-model organisms.

Genomic medicine, on the other hand, is a longer-term opportunity, according to Resnick. "What we're setting our sights on is the adoption of NGS for whole-genome analysis in the clinic, and ultimately that's where GenomeQuest will play," he said.

However, he noted that it's too soon to accurately predict how NGS might penetrate the clinical market largely because there are many open questions asking "whether there's any clinically actionable information that we can get out of NGS."

Still, with that goal in mind, GenomeQuest plans to launch a consortium that will include GenomeQuest Personalized Medicine Research and a handful of undisclosed pharmaceutical firms. The goal of the consortium, called GQ-PMR, will be to improve whole-genome analysis tools for personalized medicine.

As part of the project, GenomeQuest has begun collecting "all of the public genome data – from the 1000 Genomes Project down to the very reads that are available on NCBI's Short Read Archive." When it goes live, GQ-PMR will process those data in the GQ-Engine to enable its pharma partners to "overlay their next-generation-sequencing project on the world's sequence."

The consortium also expects to develop new genome annotations "that are relevant to specific diseases, to clinically actionable variation and so on."

GenomeQuest is not the only bioinformatics firm to have recognized an opportunity to use its tools to improve clinical annotations for whole-genome sequencing. San Francisco-based start-up Omicia, for example, has set out to specialize in analyzing whole human genomes with an eye toward clinical use (BI 6/25/2010), while Knome, based in Cambridge, Mass., has built its business model on sequencing and annotating whole human genomes.

Resnick acknowledged these and other competitors in the sequence-analysis market, such as CLC Bio, GenoLogics, and Geospiza. He added that GenomeQuest has not lost a deal to another commercial entity in the last six months.

When GenomeQuest does lose a deal, he said, it is due to "internal expertise, and we think that's a lose-lose for everyone," he said.

Despite hints that customers are more open to working with commercial bioinformatics firms, such a trend reversal won't happen overnight.

"What we're finding is that the sales cycles are longer in some enterprises, particularly within academia, because of the in-house expertise and investment in partially built solutions," he said.