Industry Insight

University of Texas Facilities Share Big Data Tools in Fight Against Cancer, Infectious Diseases

University of Texas (UT) Southwestern scientists who created a powerful analytic weapon in the fight against cancer and infectious diseases are making that tool available for free via a web-based portal.

The open-source VDJServer provides a data management framework and suite of analytic tools to study the genetic makeup of the disease-fighting receptors located on the surface of a class of white blood cells called lymphocytes. In order to recognize disease-causing pathogens, a well-functioning adaptive immune system creates millions of different proteins for use as cell surface receptors. That protein library is called the immune repertoire.

The new analytic tools—accessible via a web portal—run on high-performance computers at UT Austin’s Texas Advanced Computing Center (TACC), says Lindsay Cowell, PhD, an associate professor of clinical sciences at UT Southwestern Medical Center and leader of the team that developed the software at the core of project.

“A person’s adaptive immune system is remarkable in its ability to detect and respond to a vast and constantly changing array of pathogens and other threats. This response is possible due to the size and diversity of the immune repertoire,” Cowell says.

“The VDJServer software portal provides access to sophisticated computational tools for analyzing immune repertoires in a high-performance computing environment for researchers who currently lack such access, particularly experimental scientists and clinical researchers without bioinformatics training.”

The software—developed with support from the National Institute of Allergy and Infectious Diseases—is relevant for scientists studying a wide range of diseases as well as for basic science researchers investigating the development and function of the immune system. Applications of the software to cancer biology have increased in recent years as immunotherapies have been created to fight a variety of cancers by boosting the immune system’s response, she adds.

The idea for VDJServer started with three UT Southwestern faculty members: Cowell; Nancy Monson, PhD, an associate professor of neurology and neurotherapeutics and of immunology; and Richard Scheuermann, PhD, director of informatics at the J. Craig Venter Institute in San Diego. They teamed up with computational experts at the TACC.

“When high-throughput sequencing became a widely used technology, it was still difficult to apply it to sequencing immune repertoires,” Cowell says. In the last few years, technological advances have enabled the application of high-throughput sequencing to this area.

“We recognized there would be a need in the scientific community for computational tools to facilitate the analysis of the immune repertoire,” Cowell says.

The project took about a year of case analysis and planning and another year of basic infrastructure development followed by the addition of functionality and improvements to the web interface. Designing the portal to appeal intuitively to biologists without backgrounds in bioinformatics proved challenging, she says. The project launched in late 2016, although improvements continue.

Now the team’s challenge is scale—designing algorithms that enable increases in the size of the data sets that are analyzed or even to incorporate new kinds of computations, she says.

This summer and fall, Cowell and her team are conducting community outreach and user recruitment. The project, recently showcased on the TACC website, will be one of the resources discussed at the American Association of Immunologists’ Big Data Analysis in Immunology course in September.

— Source: University of Texas Southwestern Medical Center

Patient Information From Five States Now Available in Michigan

Out-of-state patient information is now available in real-time through Great Lakes Health Connect (GLHC). This health data exchange expands interoperability and reduces barriers to care for providers and residents in five Midwest states. GLHC is the first health information exchange (HIE) within the recently launched Heartland Project to connect to all of the other HIE organizations involved in the initiative. Sponsored as a pilot program by the Health & Human Services (HHS) Office of the National Coordinator and the Strategic Health Information Exchange Collaborative, the seven HIEs involved in the project are creating and testing the Patient Centered Data Home concept and are sharing the funding from HHS over a 12-month period.

In the first phase of the project, patients with home ZIP codes in Michigan who receive care at a facility within one of the other HIEs’ networks are identified. Then, an Admit, Discharge, Transfer (ADT) message for that patient is sent to GLHC. The ADT message contains basic demographic information about the patient and details about the respective admit, discharge, or transfer to/from the inpatient facility. Conversely, when a patient visits a facility within the GLHC network and has an out-of-state ZIP code, the ADT message is sent to the corresponding HIE.

Information that GLHC receives from the other six HIEs is stored within the community health record, called the Virtual Integrated Patient Record (VIPR). The ADT information is available alongside other information about the patient that has been contributed by GLHC participants, such as laboratory results, patient care documents, and other encounter information. The messages are sent between HIEs in real time and are available to any organization/user that has access to VIPR and a Treatment, Payment, or Operations relationship with the patient. More than 8 million patient records are accessible in VIPR.

“Great Lakes Health Connect is proud to participate in the Heartland Project and to offer our participants out-of-state information about their patients in real time,” says Doug Dietzman, executive director of GLHC. “This expanded capability supports our goal of reducing the time required and the financial burden of exchanging health information among health care providers and across communities.”

GLHC is now connected to the following Heartland Project HIE participants:

• Indiana Health Information Exchange, based in Indianapolis;
• HealthLINC, based in Bloomington, Indiana;
• Michiana Health Information Network, based in South Bend, Indiana;
• The Health Collaborative, based in Cincinnati;
• East Tennessee Health Information Network, based in Knoxville, Tennessee; and
• The Kentucky Health Information Exchange, based in Frankfort, Kentucky.

The next phase of the Heartland Project is to provide GLHC participants with the Continuity of Care Document that corresponds with the patient’s care at the out-of-state facility. Another planned service is an electronic notification to the patient’s provider when the Michigan resident seeks care at the out-of-state facility.

— Source: Great Lakes Health Connect