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Alex's Lemonade Stand Foundation to Open Bioinformatics Lab to Support Pediatric Oncology Research


NEW YORK (GenomeWeb) – Alex's Lemonade Stand Foundation, a national childhood cancer charity, plans to open a dedicated bioinformatics laboratory for analyzing genomic data from pediatric oncology projects.

The bioinformatics lab will employ data scientists, computer scientists, bioinformaticians, computational biologists, and other scientists who will use computational tools to search for patterns in existing tumor datasets in order to identify new molecular targets, cancer therapies, and opportunities for research. The lab will also provide free bioinformatics analyses services to help ALSF-funded researchers and other scientists focused on childhood cancers analyze and explore existing and new pediatric oncology datasets generated in various research facilities across the country.

"Currently, the childhood cancer research community does not have a non-affiliated center to objectively analyze existing science and look for patterns to share with scientists," Jay Scott, co-executive director of ALSF, said in a statement. "This is a true privilege to be able to offer this resource to the community and ultimately advance the pace of finding cures."

The foundation expects to have the lab up and running within the next 12 to 18 months. It will most likely be based in the Philadelphia area near institutions such as the University of Pennsylvania, Scott told GenomeWeb. For its first steps, the foundation plans to hire a scientist who will initially work from ALSF's offices and be responsible for setting up the lab infrastructure, running the place, and hiring a team of computational researchers, he said. The foundation hopes to hire a manager by the end of the year and to have lab space ready for business by the middle of 2017. It expects to spend up to $2 million per year on the lab initially, according to Scott.

The idea for the setting up a bioinformatics lab came from ALSF's scientific advisory board.  The foundation was seeking opportunities to bring its resources and expertise to bear on the childhood cancer space. One idea, suggested by John Maris, a professor of pediatric oncology at the Children's Hospital of Philadelphia and an ALSF board member, was to set up a "dry lab" that specialized in analyzing pediatric cancer data, Scott told GenomeWeb.

"It would really address the issue that big data remains inaccessible to many labs because of a lack of a bioinformatician or a computational biologist who can really work with the data," Maris told GenomeWeb in an interview. "This lab could fill that gap by being available to both ALSF-funded investigators or other pediatric cancer researchers to try to solve problems collaboratively."

The lab would help defray some of the costs of pediatric oncology research projects, he added. Researchers involved in existing grants have in some cases spent as much as $25,000 and in at least one case as much as $50,000 out of their budgets for bioinformatics analyses alone. Once the lab is up and running, researchers could leverage the resource for their analysis for free rather than pay a third party for the analysis. There could also be opportunities for nearby elementary and high schools to send students on educational field trips that introduce them to childhood cancer research and bioinformatics. "We'll be able to expose kids to science and technology and math and statistics and things like that in a fun way," Scott said. Also, "we'll be able to aggregate a lot of [pediatric] data and make better use of it," he added.

It is still early days for the lab so the exact details of how it will be operated and what it will offer researchers are unclear. But Maris said that he envisions that initially lab researchers will focus on assessing and evaluating available pediatric data in repositories such as the Genomic Data Commons with an eye towards helping to improve annotations and harmonize datasets. They could then develop computational tools and pipelines for processing and querying these datasets.

"The vision is that it will be a collaborative core or research environment for investigators who have biological questions or questions of a translational nature that could benefit from accessing, analyzing, and understanding data that's available," he said.

In addition to establishing the bioinformatics lab, ALSF has also committed to doubling its investment in childhood cancer research projects and family services to the tune of $150 million over the next five years. A portion of those funds will support the bioinformatics labs' activities while other funds will be funneled into a number of research grants where researchers will be required to work with collaborators across multiple institutions, Scott told GenomeWeb. ALSF funds about 100 projects annually.