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5AM Solutions Sets Up Shop out West to Tap into Bay Area Life Sciences Market

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By Uduak Grace Thomas

5AM Solutions recently opened a new office in San Francisco to provide bioinformatics development and analysis services to its life science customers on the West Coast.

The company tapped James Ireland, its principal bioinformatics scientist, to lead the Bay Area operations and hired additional staff to man the new office, bringing its total headcount to 50.

“The Bay Area is a hotbed of both technology and life science innovation,” Brent Gendleman, 5AM’s president and CEO, said in a statement. “We are expanding on the West Coast, so it made sense to formalize our operations by opening a San Francisco office.”

Prior to this, the company, which spun out of a software engineering company called Number 6 in 2004, conducted its business dealings out of its East Coast offices in Reston, Va., and Rockville, Md.

From there the company has worked with groups at Howard Hughes Medical Institute's Janelia Farms and Celera and has also provided services for federal agencies like the National Cancer Institute, which has licensed the company as a Support Service Provider for the Cancer Biomedical Informatics Grid.

William Fitzhugh, 5AM's chief scientific officer and head of the company's bioinformatics core, told BioInform that his team is currently collaborating with researchers involved in the Cancer Genome Atlas Project to develop methods to analyze comparative genomic hybridization data. He explained that his team is enhancing the Broad Institute's Gene Set Enrichment Analysis tool by enabling its use on copy number data.

He said the bioinformatics team, which has five members in total in its East and West Coast offices, provides consulting and services for projects involving microarray, DNA sequence, and proteomics data. It primarily relies on bioinformatics workhorses such as R, Bioconductor, Perl, Matlab, Python, and Blast, among other data analysis tools. The rest of the company's employees work in the software development and strategic consulting arms of the business.

In addition to services, Fitzhugh said the company stores software that it writes for its clients on its own infrastructure "so that we can go back and rerun analysis if we need to."

Fitzhugh pointed out that his team's strength is "that we know how to use publicly available tools for bioinformatics analysis and also know the databases that people use and the tools that people need to get the most out of their data." Ireland added that 5AM is a "heavy believer in using open source software and, when we can, open sourcing our own software."

Ireland said that the company's clientele on the West Coast includes pharmaceutical and biotechnology companies as well as academic and non-profit research institutes.

He noted that the company sees an opportunity in the Bay Area among small start-up biotechs who don't have bioinformatics capabilities in house. While these firms have projects that might be too small for larger services companies to take on, they are a "nice fit" for 5AM because "we are a small company as well," and, as such, "partnering with us usually makes a lot of sense for both parties."

In the start-up arena, 5AM has worked with Sequenta, a San Francisco-based company that's focused on developing sequencing-based diagnostic tests for immune-related diseases. The company recently raised $13 million in a Series B financing round (IS 12/14/2010).

Malek Faham, Sequenta's chief scientific officer, explained to BioInform that in order to develop its tests, the company looked for "associations between clinical outcomes and specific characteristics in B- and T-cell receptor sequences" and that 5AM provided some algorithms that enabled the company to make these correlations.

Another early-stage company that has worked with 5AM is PCR technology developer QuantaLife, a Pleasanton, Calif.-based firm that also recently closed a Series B financing round valued at $17.2 million (PCR Insider 12/16/2010).

Serge Saxonov, vice president of application development at QuantaLife, told BioInform that the company has developed a digital PCR platform that separates samples into several thousand droplets and then performs individual PCR reactions on each droplet, providing "better quantification and precision" than existing real-time PCR technologies.

En route to the final product, Saxonov said the company worked with 5AM to design "appropriate" primers and probes for the system to ensure that the PCR reactions are accurate.

Ireland said that 5AM will continue to do more to grow its business in its current locations as well as in other biotech hotbeds like Boston and San Diego.

He noted that diagnostic development and next-generation sequencing will likely be the key drivers for the company's growth in the years to come.

"I think a lot of people are looking at [diagnostics] as an application area ... as far as companion diagnostics with drugs and standalone diagnostics," he said. "The other obvious one is next-generation sequencing, where ... clients bring us the data and say, 'How do we work with this?'"

He pointed out that the sheer volume of the data that’s generated as well as methods to integrate the data in meaningful ways are two areas that still remain challenging for most groups. He added that the company is working with its clients on methods to do both.

Fitzhugh echoed Ireland's comments on moving into the next-gen sequence analysis arena, noting that now that 5AM has "dipped its toe" into the market, it is looking to work on more projects in the space.

Ireland also said that 5AM is considering cloud-based technology as a way to "remain nimble and dynamic as far as being able to quickly scale up and scale down both computation and storage" in a competitive climate.


Have topics you'd like to see covered in BioInform? Contact the editor at uthomas [at] genomeweb [.] com.

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