caBIG® in Action: Turning Challenges into Opportunities for Neuro-AIDS Researchers
The National Neuro-AIDS Tissue Consortium (NNTC) is using caArray, a microarray data repository developed for the caBIG® program, to facilitate neuro-AIDS research and data sharing in ways that were previously impossible.
Founded in 1988, the mission of the NNTC is to bolster research on the effects of HIV infection on the human brain by providing high-quality, annotated and molecularly-characterized tissue samples from patients who died with HIV. The ability to quickly and easily share data across multiple geographies was essential to the success of the program because member organizations are spread across six different locations.
The needs of researchers working with the NNTC are not unfamiliar to cancer researchers. "The NNTC needed a system to store and share standard microarray gene expression information with other researchers within the NNTC, as well as other investigators with an interest in this type of data," explains Ganesh Shankar, a bioinformatician at Indiana University-Purdue University Indianapolis (IUPUI), which is a research location for the NNTC. Shankar became familiar with caBIG® tools during their deployment at the Indiana University Simon Cancer Center and immediately thought of caArray, a microarray repository, when consulted by Dr. Yiannoutsos, an IUPUI researcher conducting work under the auspices of the NNTC.
Challenges for Research in a Consortium
"Data is transferred largely by uploading and downloading from websites or by FTP" says Shankar. "The collaborative capabilities of caArray mean that you can work in multiple locations but share information much more quickly and easily. At a pragmatic level, two centers working on a research project can load information into a common repository independent of one another and ensure that the information is up to date. Certainly, this system beats one where folders had to be sent back and forth between research sites."
An unexpected (but not unwelcome) challenge
Tissue samples available for Neuro-AIDS research have become increasingly scarce, as the collection of high-quality samples has not kept pace with the rate first anticipated by the NNTC.
This unexpected shortage of samples is actually a byproduct of medical success. The introduction of anti-retroviral drug therapies has greatly extended the life expectancy of AIDS patients. As life expectancy continues to rise, tissue collection rates are dropping dramatically. caArray has helped the NNTC conduct more longitudinal research because of its extensive annotation capability—providing robust data sets for researchers.
"The value of these tissue samples has increased because now you have more longitudinal data associated with the tissue sample, but the NNTC has fewer samples than it originally expected. The ability to fully utilize the data available is critical to the future viability of neuro-AIDS research," notes Mr. Shankar.
Looking to the future
While caBIG® was conceived and designed to bridge the cancer community, this is just one of an increasing number of examples where caBIG® tools are being used in non-cancer settings.
In fact, Mr. Shankar predicts that the installation of caArray is just the first step towards more collaboration between the Neuro-AIDS community and caBIG®. "The larger vision is to adapt other tools for use in this area of research. We are pushing ahead with this approach and I'm currently investigating the technical steps necessary to achieve this end."
