by Byron Connolly

Cancer foundation in quest to create giant genomic database

Apr 11, 20143 mins
Big Data

Amanda Haddock is on a mission. She wants to create a database containing at least 50,000 human genomes – our genetic material – to find better treatments and cures for cancers.

Last year, Haddock and her husband established Dragon Master Foundation, an organisation based in Wichita in the United States after their 16-year-old son lost his battle with glioblastoma multiforme, a highly aggressive form of brain cancer in 2012.

“We weren’t looking to start a foundation … we were volunteering with a few large groups here in the US and as part of that we attended a conference and heard a researcher speaking from the University of Arizona who was well respected in the cancer research community,” Haddock said.

“I’m paraphrasing here but basically she said if we [the university] could compare 50,000 genomes, ‘we could probably cure cancer,’” Haddock said.

Haddock and her husband Richard Haddock – a former software developer with more than 30 years experience in the technology industry – spoke to the researcher. They quickly realised that there were no large databases available for scientists to access and analyse a large amount of genomics data.

Read: Big data to advance cancer genomics

Haddock said existing databases are only collecting “pieces of information” such as tumour tissue or data regarding a specific tumour type. There are foundations that are collecting genomic data for healthy people – but it’s all very segmented, said Haddock.

Dragon Master is trying to change this with plans to create a giant database where hospitals, medical schools and non-profit organisations can add and share molecular, genetic, clinical and environmental data related to brain cancer.

The project is still in its infancy but Haddock said the organisation is in talks with researchers interested in the initiative and data specialists on the best way to build the database.

“The beginning is important because we need to build it with the proper scale in mind,” Haddock said.

Haddock said the organisation was also in talks with NetApp – one of Dragon Master’s board members works at the vendor – as well as IBM.

IBM is already looking at big data analysis of brain cancer. In March, the computing giant announced that its Watson supercomputer is being used to solve the mysteries of brain cancer by examining individual genetic mutations.

IBM Watson will soon help clinicians at New York Genome Center search for mutations in patients with glioblastoma that may be referenced in medical literature and genomic databases. Findings will then be presented to the patient’s doctor.

Haddock said collecting 50,000 genomes is a “big enough number to do data analytics.” But the database would also need to collect environmental data (where patients are living and the food they are eating for instance), as well as clinical information.

Haddock said the database will enable researchers to access information live.

“For instance, if they are working on a cancer vaccine and they know the vaccine is starting to work for a certain subgroup of patients, we want them to be able to find those patients, and submit requests to talk to their doctors.”

Haddock pointed out that genomic information is residing in many databases and not necessarily in usable form as it has been developed by different people and is in multiple formats.

“We anticipate having to have staff on site at most of the institutions that want to participate to help them figure out the protocols to get data from their database into our database,” she said.

The foundation is currently raising funds to hire a project co-ordinator for the initiative.