3rd Millennium of Cambridge, Mass. is planning to develop a microarray analysis system that both manages data flow and uses statistical methods to determine expression levels and values, using the proceeds of a Phase I Small Business and Innovation and Research contract from the US Department of Defense.
The system is being developed for Shiela Peel’s lab at the US Department of Defense, which studies infectious diseases of military importance. The work is supported by the US Army Medical Research and Material Command under Contract No. DAMD17-02-C-0040.
The basic idea behind the software is to jump into microarray analysis on the front-end, using statistical tools to help determine whether genes are absent, present, or differentially expressed, then link this information to biological context and a LIMS system recording experimental conditions.
“Most microarray analytics platforms really function after the fact,” said Jack Pollard, 3rd Millennium’s Principal Investigator on this project. “You get votes on what [expression levels] are statistically relevant, what genes are thumbs up and thumbs down, and everybody else goes off and does their principal components analysis, their clustering et cetera. Our platform actually sits in front of that in that it helps people determine the ‘thumbs up, thumbs down’ votes for gene expression.”
The software includes information on the biological context of a sample along with the “absent or present, up or down” number of the gene. “You can ask the system questions like: ‘show me all biological conditions where my set of marker genes have the behavior that I am expecting,’” said Pollard. “You get back from that a list of all biological conditions that meet those criteria as opposed to a list of genes. That lets you tease out what phenotypes are connected to given gene expression profiles.”
The LIMS aspect of the software will also connect this information on phenotype, context, and gene expression level to the experimental design and experimental conditions. The basic format is MIAME-supportive (or supportive of the standard for the Minimum Information about a Microarray Experiment). But it is up to the Peel Lab, said Pollard, to determine whether the specific package will be MIAME-compliant.
Through this grant, 3rd Millennium hopes to develop a technology platform that can be adopted for its various clients other than the Peel lab, but not necessarily a shrink-wrapped product.
“The goal of [an] SBIR grant is to produce some type of commercially applicable technology,” said Pollard. “If this piece of software is unique enough, we at 3rd Millennium are interested in pushing it on to become a product. But we are interested in underlying technology that we can redeploy for clients and technology engagements.”
This bioinformatics consultancy has had several recent departures, including bioinformaticists Nat Goodman and Eric Neuman, causing some to speculate on deeper trouble at the company But 3rd Millennnium has been “very aggressive about hiring new people,” said Pollard. “We are in many ways much more focused.”