Hutch News

Bridging the digital divide

June 19, 2003
Dr. Dan Geraghty and lab members

Dr. Dan Geraghty, front right, is one of several scientists whose research will benefit from a project with IBM to develop a system for sharing complex data. Geraghty lab members pictured are Rahul Joshi, front left, and Simon Fortelny, Ruihan Wang, Anupama Vasanth and Priti Sawant, background.

Photo by Todd McNaught

Dr. Dan Geraghty uses the most sophisticated DNA-sequencing equipment available to study genes that determine a person's unique tissue type.

Yet when he and Clinical Research Division colleagues, Drs. Effie Petersdorf and John Hansen, want to compare data, they must resort to a decidedly low-tech method. Each must copy thousands of bits of sequences and other complex information onto a CD-ROM and walk from one office or lab to another to share information critical to their collaborative studies.

"Each of our laboratories uses different software platforms for managing data," Geraghty said. "We also organize our databases differently. There is no way for me to sit at a computer terminal in my lab and compare a new result with information in their databases or with the databases of my collaborators around the country. It slows research down."

This scientific logjam soon may ease thanks to a new collaboration between Fred Hutchinson and IBM Life Sciences Division, a branch of the company that provides information-technology support for biotechnology and pharmaceutical research.

IBM donated computer hardware, software and staff time through its Shared University Research Award program. The donation will help the center develop a system that will allow immune-system geneticists in the Clinical Research Division to share and integrate data as well as execute searches of multiple databases and formats with a single query. In the future, the network of users could be expanded to include any doctor's office or research laboratory around the world where access to tissue-type information is needed.

"A coordinated data-sharing system would be a much more productive and efficient way for research colleagues to interact," said Hansen, head of the center's Immunogenetics Program and chair of the International Histocompatibility Working Group, an organization of scientists who study tissue-type genes.

"If we can make this approach work-and I am optimistic that we can-it will provide opportunities and impetus for new collaborations. Right now, we spend too much time planning and positioning to overcome obstacles to managing increasingly complex data."

The tissue-type signatures that Hansen and his colleagues study are determined by a set of genetic instructions known as MHC and immune-regulator genes, which differ in DNA sequence among all individuals except identical twins. Databases of the sequences of these immune-system blueprints from thousands of individuals around the world are used to match leukemia patients with appropriate stem-cell transplant donors, for studies on why some individuals are more susceptible to certain diseases, and to develop new vaccines and other therapies.

Advances in all of these fields depend on international collaborations of researchers sharing and comparing thousands of DNA sequences and other medical data. But the ideal information-technology infrastructure required to facilitate these interactions is difficult for academic institutions to build on their own.

That's where an industry collaboration can be valuable, said Chuck Hirsch, a Fred Hutchinson trustee and chair of the board's Strategic Implementation Committee. The committee seeks to establish alliances with industry to help tackle complex research problems.

"While Fred Hutchinson is at the forefront of so much scientific research, it needs strong technical support to derive the most from its work," he said. "IBM offers this deep technical capacity, as well as an understanding of the needs of life-science initiatives. The center will build upon this collaboration to forge other key alliances with strong technology companies to further its important work."

An effective collaboration benefits both partners, and this project is no exception, said Mary Erichsen, a business development executive at IBM Life Sciences.

"At IBM, when we enter into a collaboration, we like to establish a long-term relationship with a client," she said. "What we're working on now is a proof-of-concept phase of the project. We hope to continue to work with Fred Hutchinson as they increase the scale of the project."

Hands-on work for the project began in April, when a team of life-sciences computing experts from IBM set up camp in the Thomas building, where they worked closely with Derek Walker, a member of the center's Information Technology department and project manager for the collaboration, and scientists from the Clinical Research Division.

"The idea is to develop a database of databases-what's called a federated database," Walker said. "This is made possible with IBM's DiscoveryLink technology. Essentially, it will enable scientists to search data from many laboratory databases through a Web-based interface."

A successful prototype

Walker said that the first phase of the project was to develop a prototype based on a small subset of the data at the center. The successful prototype was completed last month and offers researchers a glimpse at the future possibilities of the technology.

The next phase of the project, to begin later this year, will focus on enhancing the prototype tools, expanding to additional data sources and developing standards and conventions for data representation and exchange.

Working on-site has provided tremendous benefit for the project, said Dr. Jaya Kaja, a senior information technology architect at IBM.

"We can address any infrastructure issues much more easily when we're here," she said. "In addition, bringing together the teams from both institutions has fostered a productive working relationship. I'm excited about helping the Fred Hutchinson team fulfill their data integration needs and improve productivity by cutting down the amount of manual work they need to do to accomplish their research goals."

Key to the ultimate success of the project will be to guarantee the security of computer-transmitted medical information. At a recent planning meeting with the IBM team, Petersdorf said that concerns about information privacy have hampered collaborations with other countries, which may have different confidentiality and security regulations than the United States.

"For international transplant studies, the reason our colleagues in Asia are hesitant to participate in public databases is because of confidentiality issues," she said. "We can't have data going all over the world without security."

The team's efforts to build privacy safeguards into the system will benefit from Walker's recent work to secure the transfer of medical information between Fred Hutchinson, the University of Washington, and Children's Hospital and Regional Medical Centers-partners in the Seattle Cancer Care Alliance and the Fred Hutchinson/University of Washington Cancer Consortium.

Geraghty's intention is that the next phase of the project will expand the data-sharing system to include other cancer centers. Upon completion of a workable prototype for center investigators, he hopes to approach the National Cancer Institute for funding of a multicenter collaboration.

Expanding the network

"We need to think about how to expand this system beyond just being useful for us," he said. "Right now, I can name 10 collaborators outside the center who would be very interested in this. Every small genetics lab has the same complaint-that they don't have any way to manage and share data. It's enough of a bottleneck to prevent more people from obtaining genetic data because it's too hard to manage."

One of the challenges to the creation of an international network of users is the fact every lab uses a different system for classifying and describing the information in their databases, said Anajane Smith, manager of the Clinical Immunogenetics Laboratory at the Alliance. The lab determines the tissue types of Alliance patients who will undergo bone-marrow or stem-cell transplants as well as those of potential donors.

"We'll need to establish universal naming conventions," she said. "It's difficult to link data when labs organize their data differently and use different names for the same thing."

Despite the obstacles, Geraghty predicts that with some hard work, thousands of individual labs could benefit from the technology within the next five years.

"Ultimately, this could be in every doctor's office," he said.

 


Immune-system genetics IT project development team

Team leaders:

  • Drs. Dan Geraghty, John Hansen, Effie Petersdorf and Gary Schoch from the Clinical Research Division.
  • Dr. Bob Robbins, vice president for Information Technology
  • Project manager:

  • Derek Walker, Information Technology
  • Working group members:

  • Anajane Smith, manager of the Alliance Clinical Immunogenetics Laboratory
  • Dr. Mari Malkki, Caroline McKallor, Madeline Kesten, Dr. Keith Eaton, Ruihan Wang and Simon Fortelny, Clinical Research Division
  • Eric Mickelson, manager of the center's Research Cell Bank
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