Aug 15, 2005 | Putting personalized medicine into practice is a high priority for many IT specialists. With the right tools — an enterprise-level, integrated infrastructure, for example — an IT department can accelerate genetic and genomic science from discovery through clinical care.
Category: Infrastructure: IT Hardware
and Systems Software
Title: Gateway for Integrated Genomics
-Proteomics Applications and Data (GIGPAD)
Company: Harvard Partners Center for
Genetics and Genomics
This is precisely what Sandy Aronson’s group at the Harvard Partners Center for Genetics and Genomics (HPCGG) set out to create in 2003. The result: the Gateway for Integrated Genomics-Proteomics Applications and Data (GIGPAD).
“When you discover something in the lab, getting it to the clinic requires a dramatic change in IT infrastructure,” Aronson says. GIGPAD supports both research and clinical processes on the same platform so that research processes can be easily adapted when a clinically relevant breakthrough occurs. This allows a smooth transition from discoveries to translational medicine and provides IT support for new diagnostics sooner.
For example, less than three months after the correlation between epidermal growth factor receptor (EGFR) mutations and Iressa efficacy was first reported last year (see “Minority Report,” June 2004 Bio-IT World, page 6), HPCGG released a physician-ready, routine test, and the GIGPAD team was able to respond quickly and provide IT support.
“GIGPAD’s strength lies in its ability to integrate infrastructure,” says Raju Kucherlapati, HPCGG’s scientific director. “Building this [infrastructure] in the context of constantly evolving genetics, genomics, and proteomics technology has been challenging, but the resulting flexibility is important.”
“We are now validating several different types of microarray technologies for clinical use,” says Peter Verlander, associate director, strategic development, Laboratory for Molecular Medicine, HPCGG. “There are a lot of moving pieces that have to come together when a new diagnostic is being validated and launched. While the technologies we work in are new to the clinic, they are not new to the research environment, and GIGPAD allows us to get IT support up and running quickly by leveraging this fact.”
The first GIGPAD modules were released in May 2004, but the roots of the project began a year earlier, as HPCGG sought one system that would provide uniform access to all of its laboratories, centralize finance and administration, ensure flexible collection of structured annotations from researchers and physicians, support research and clinical security models, and be extremely user friendly.
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As part of a build-versus-buy decision, HPCGG evaluated several generic laboratory information management systems (LIMS) and some that were packaged with instruments. Ultimately, they chose a hybrid approach — leveraging the integration capabilities of products such as Affymetrix’s GeneChip Operating System and Thermo Finnigan’s Excalibur and designing an enterprise architecture to make build-versus-buy decisions on each LIMS for each laboratory while keeping the rest of HPCGG’s infrastructure consistent.
In August 2003, HPCGG and Partners HealthCare’s IT department assembled a team to code the enterprise components of this architecture. Hewlett-Packard contributed onshore and offshore designers and programmers to help accelerate GIGPAD development and build common components (a generic protocol system, for example) to simplify custom LIMS development.
Today, GIGPAD supports more than 200 users, including principal investigators, research associates, laboratory directors and technicians, and, importantly, clinicians with different levels of IT expertise. Its architecture consists of a portal layer, interface layer, common laboratory interface layer, several independent but integrated LIMS, and a unified file repository. LIMS are entirely encapsulated within the architecture and not exposed to end users outside HPCGG. Management and reporting are handled centrally, which leads to a consistent look and feel and simplifies data integration. By reducing errors, simplifying communication, and automating steps, laboratory directors and technicians estimate that the system reduces the effort required to process each transaction by 20 to 30 percent.
Also, “GIGPAD addresses the need for comprehensive data standards, data views, and underlying system support, allowing for a flexible environment for insights, discovery, and advancements in patient care,” says V.K. Holtzendorf, Hewlett-Packard’s life science strategic program manager.
Much of GIGPAD’s success rests on its security and code generation layer developed by HPCGG senior software architect Eugene Clark. GIGPAD leverages J2EE, Struts, Oracle, and XDoclet. Users strictly access the database through Entity Beans, which allows system architects to construct security at this layer. It also allows the generation of data transfer objects, Oracle tables, and security configurations based on tags in the class files, which speeds development.
In addition to supporting research, GIGPAD provides the transactional base required to practice personalized medicine, requiring the synthesis and analysis of genetic and medical data. “We hope GIGPAD will serve as a model that other institutions can leverage as they seek to integrate genetic, genomic, and ultimately proteomic information into their research or clinical processes,” says Aronson.