Unclogging informatics workflows
Mayo Clinic, U of Minn. to create shared data analysis solution
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MINNEAPOLIS, Minn.—The Minnesota Partnership for Biotechnology and Medical Genomics recently awarded the Mayo Clinic and the University of Minnesota $1.2 million to fund a project aimed at streamlining management and analysis of high-throughput sequence analysis data produced by the two research groups' collaborative genomic research projects.
The project, called High-throughput Sequence Analysis Infrastructure Technology Investigation (HAITI), was one of four recent grants worth a total of $7 million awarded by the Partnership, a collaborative venture among the Mayo Clinic, the University of Minnesota and the state of Minnesota.
According to the Partnership, the HAITI Project received the award as part of its commitment to build Minnesota's bioscience infrastructure while avoiding duplication of technologies.
The HAITI Project seeks to solve a clog in the two research groups' informatics workflow. While the university uses a 454 Genome Sequencer to analyze high-throughput sequence data, the clinic uses Illumina Genome Analyzers. The funds will be used to create a new informatics workflow that allows researchers to run jobs on sequencing instruments at either site and easily share and analyze data.
"Both platforms have unique data output—the 454 generates longer reads, but the Illumina system generates much more data," says Dr. Sushmita Singh, a research associate at the university's BioMedical Genomics Center. "A big problem came into play where we had to figure out the best method in which we can do our data analysis. What we wanted to do is make our platforms complementary."
Dr. Jean-Pierre Kocher, chair of the Mayo Clinic's Division of Biomedical Statistics and Informatics, says the project leverages past efforts to create a structure for the rapid evaluation of new software algorithms and routine analysis. "Using an infrastructure grant can either support acquisition of a new experimental tool, like a next-generation sequencing platform, or it can be quite broad," he says. "In this case, what the state pushed us to do is share an instrument instead of duplicating it at both sites."
Although the two institutions have not decided if they will use a commercial software vendor for the project, Singh says the solution that is created will not become the exclusive IP of either group.
"We're both academic institutions, so in that same spirit, we will share whatever we can that will help people," she says. DDN
The project, called High-throughput Sequence Analysis Infrastructure Technology Investigation (HAITI), was one of four recent grants worth a total of $7 million awarded by the Partnership, a collaborative venture among the Mayo Clinic, the University of Minnesota and the state of Minnesota.
According to the Partnership, the HAITI Project received the award as part of its commitment to build Minnesota's bioscience infrastructure while avoiding duplication of technologies.
The HAITI Project seeks to solve a clog in the two research groups' informatics workflow. While the university uses a 454 Genome Sequencer to analyze high-throughput sequence data, the clinic uses Illumina Genome Analyzers. The funds will be used to create a new informatics workflow that allows researchers to run jobs on sequencing instruments at either site and easily share and analyze data.
"Both platforms have unique data output—the 454 generates longer reads, but the Illumina system generates much more data," says Dr. Sushmita Singh, a research associate at the university's BioMedical Genomics Center. "A big problem came into play where we had to figure out the best method in which we can do our data analysis. What we wanted to do is make our platforms complementary."
Dr. Jean-Pierre Kocher, chair of the Mayo Clinic's Division of Biomedical Statistics and Informatics, says the project leverages past efforts to create a structure for the rapid evaluation of new software algorithms and routine analysis. "Using an infrastructure grant can either support acquisition of a new experimental tool, like a next-generation sequencing platform, or it can be quite broad," he says. "In this case, what the state pushed us to do is share an instrument instead of duplicating it at both sites."
Although the two institutions have not decided if they will use a commercial software vendor for the project, Singh says the solution that is created will not become the exclusive IP of either group.
"We're both academic institutions, so in that same spirit, we will share whatever we can that will help people," she says. DDN
