Illumina technologies will play a role in a recent attempt by Génome Québec to upgrade its nationwide services.
The organization, one of six government-funded centers designed to support genomic and proteomic research in Canada, has established new research tools in its core facility, added internally developed software to its website, and created a new funding mechanism that encourages Québecois researchers to partner with industry, according to an organization official.
Daniel Tessier, senior director of operations and business development, told BioArray News last week that Génome Québec is currently in the midst of articulating a new three- to five-year strategic plan that will be implemented in the spring of 2008.
But prior to acting on new strategies, the body has already given the Québec genomics community a taste of what is to come. For example, it has added new competencies to the McGill University and Génome Québec Innovation Center, which serves as a core facility for Genome Quebec.
Specifically, Génome Québec recently added Illumina expression services to its offering, complementing the Illumina genotyping services that GQ has offered researchers for several years. While the decision to add Illumina expression is not surprising — Génome Québec is an official genotyping service provider for the company — it is evidence of Illumina’s growing clout in the expression market.
Part of that adoption has been driven by the lower cost of Illumina’s expression arrays compared to those sold by rivals, according to Tessier, who said that price factored significantly in Genome Québec’s decision to choose Illumina. Génome Québec also offers Affymetrix arrays for both genotyping and gene expression.
“The lower cost of an Illumina experiment may allow some of our less fortunate projects to consider the possibility of carrying out more ambitious expression experiments,” he said. “There is a significant — probably a factor of three — price difference between the Affymetrix and the Illumina platform,” he said.
“Affymetrix still offers the widest variety of biological systems. Illumina has initially focused on human, mouse, and rat, but I believe they will be offering custom organisms in the future. Having these two platforms is a way of diversifying our expression profiling service offering,” said Tessier.
An Affymetrix Human U133 Plus 2.0 array currently costs Génome Québec researchers around $650, according to its website. The organization does not list prices for Illumina arrays.
As part of appending its offering to include the new Illumina chips, Tessier said that Génome Québec ran an internal comparative study between the Affy and Illumina platforms.
For the test, identical RNA samples were run on 144 Affy chips versus 64 Illumina arrays and Génome Québec researchers compared the resulting lists of differentially expressed genes from each platform. Tessier said that in Genome Quebec’s opinion, the “two platforms compare very well and the results from both platforms were very equivalent.” Génome Québec will be publishing the results from the study shortly.
As an outgrowth of the Illumina-Affymetrix comparative work, Génome Québec decided to upgrade a software program it helped develop called FlexArray that was launched in March for analyzing Affymetrix data. According to Tessier, FlexArray is also now capable of importing and analyzing Illumina expression data, and, if necessary, comparing between the two platforms. It can also compare data from other sources, such as genotyping or sequencing experiments.
FlexArray “tracks how you did the analysis and it’s an integrated, preventative software that prevents you from doing things like normalizing twice in a row,” said Tessier. “It was originally designed for Affy data, but because of the comparative study with Illumina, we designed a plug-in that works with Illumina expression,” he said.
According to GQ bioinformatician Michal Blazejczyk, who helped develop the software, FlexArray is “essentially a statistical data-analysis program for expression microarrays” designed with biologists in mind.
“The main goal was to reach the biologists; the target audience is really the biologists, which means that it has to be easy to use, it has to he easy to understand, but we didn't have to sacrifice the statistical complexity,” Blazejczyk told BioArray News last week.
“We didn't see any packages that could do that. My impression is that a lot of the free packages for array data analysis out there are created as parts of academic research projects and they are fairly limited in scope in terms of number of algorithms you have available,” he said. “Of course there are some tools that are more comprehensive, but there is actually no tool that I think would fit this description.”
Génome Québec has recognized that FlexArray has some value and is currently debating the path forward for the software.
“Because of the mission and mandate of Génome Québec we are planning to make FlexArray fully accessible to academic researchers at no cost,” Blazejczyk said. “We are currently exploring different models to make FlexArray available to industrial clients. Nothing is cast in stone on that end yet,” he added.
In terms of the future of the program, Blazejczyk said that Génome Québec would also like to “extend FlexArray to exchange data with more tools upstream and downstream, like data-mining tools.” The experience with tweaking the software to accept both Affy and Illumina data has also encouraged Blazejczyk to consider adding capabilities for other platforms.
“Now we are thinking about two-color arrays, doing Agilent chips and CodeLink chips, and it should be pretty straightforward,” he said. “We have projects going that apply FlexArray to genotyping and sequencing data. So it is flexible to meet all of these needs,” he added.
Beyond Academia ... and Québec
Researchers who wish to download FlexArray may do so through Génome Québec’s recently updated website, where it is offered as part of its Nanuq web application, an interface designed to support all the genomic services provided at the center to its customers.
“What prompted us to offer it is that the Illumina platform will allow some of our less fortunate PIs, in terms of funding, to explore the possibility of running expression experiments in terms of cost.”
According to Tessier, Nanuq — the Inuit word for “polar bear” — enables its administrators to create accounts for clients and produce reports for production. The application also offers a lab information-management system for Génome Québec’s operators to follow and track samples. Nanuq modules exist for genotyping, sequencing, and gene expression so that technicians are able to register not only progress but enter results into it.
“This will happen practically on a live basis as our clients have access to data as soon as it comes off the sequencer or genotyping machine,” Tessier said.
Nanuq also provides a cross-platform tool to analyze sequencing data in the context of genotyping or arrays. The ability to compare genomics and proteomics data is also being formulated.
“One of the things that we are migrating to is that link between the genomics into the proteomics platform,” said Tessier. “For example, ‘How do you correlate the expression data with proteomics data?’ We are probably looking at 18 months or so deployment for that capability,” he said. “This is something that a lot of people want to do and that is a strategic direction. To index genomics data and proteomics data so that it speaks to one another.”
As with FlexArray, Génome Québec has recognized that there is value in Nanuq. According to Tessier, the system has already been licensed to three users — Johns Hopkins University, the University of Tartu in Estonia, and the Mexico Institute of Genomics.
Beyond licensing deals is a greater motivation to push the great majority of Génome Québec users that are academics into alliances with commercial partners. To that end the organization initiated its Privac program last autumn, hoping to match $10 million with funding from other state agencies and, most importantly, industry, which must foot one third of the project cost. Deadlines for Privac were in March and the program is expected to fund six to 10 academic-commercial projects over the next three years.
“This is one mechanism that we feel will improve the technology transfer from fundamental research to commercial outcomes, whether it be a new drug or a new drug target,” said Tessier.