flowCAP II Challenge 3

This data set is a subset of the ICS data generated for HVTN049 (pubmed ID 21451004). The data is intracellular cytokine staining data of CD4 and CD8 T-cells from a safety and immunogenicity vaccine trial, testing for IL2, IL4, IFNg, and TNFa cytokine producing antigen specific T-cells. The goal of this experiment within the context of the flowCAP II challenge was to have automated gating methods identify cell populations that can distinguish between Gag stimulated and Env stimulated samples. The data set contains 54 samples, half of which were used from training and half of which were used for testing purposes in the challenge. Post-hoc analysis included a comparison against manually gated data and a placebo-treated control group.
Conclusion:
Many of the automated gating methods were able to identify IL2+/CD4+ populations that discriminated between Env and Gag stimulated samples. These same features were found using manual gating, demonstrating that automated gating can perform as well as manual gating for this particular data set.
Notes:
Several control and stimulated samples in the flowCAP II data set were taken from mismatched plates, meaning that the control and stimulated samples from an individual were run on different plates. This led to an observable plate-effect in some of the features. The mismatched samples are annotated in the data set submission. Note that this issue does not impact the original HVTN049 trial data, but is a data manipulation error in the preparation of the flowCAP II challenge 3 data set. The HVTN049 data was subject to extensive quality controls as described in PMID 21451004, and related publications.