Patterns of immune response to a vaccine or virus as measured by intracellular cytokine staining in flow cytometry: hypothesis generation and comparison of groups.

Candidate HIV vaccines must show an immune response in order to be considered for further testing and development. What constitutes a "response," however, is still not clear. While the hunt for a protective vaccine continues, hypotheses are being formed by studying the immune responses across cohorts of people with differing responses to the infection, as well as the immune responses formed by healthy people to other viruses, ones that are generally common and well controlled. Here we examine the functional profile of the immune responses of a group of HIV+ long-term non-progressors as measured by intracellular cytokine staining using polychromatic flow cytometry, and compare these responses to those of a larger group of other HIV+ people. We describe some of the types of patterns in immune response that are of interest to vaccine researchers, and compare several statistical tests appropriate for this type of data.