Welcome to the 3rd (Public) CMI-PB Prediction Challenge. We expect to have data from 50+ individuals on their response to the Tdap boost. These will include individuals primed in infancy with either aP or wP. The data generated will be similar to what is described in our paper [1]. We will make information on the new sets of individuals available as described below in the Pre-vaccination Information section. We will then ask each prediction team to make their best call on the questions asked in the Immune responses to predict section. We will evaluate the answers to these questions using the metrics suggested in the Evaluation Metrics section.
Pre-vaccination Information
Demographic data
- Age
- biological sex at birth
- vaccine priming status
Assays characterizing the immune status just before the vaccine is given (day 0)
- Antibody titers in plasma
- Secreted cytokine levels in plasma by OLINK and LegendPlex
- Gene expression in PBMC by RNA-Seq
- Cell type frequencies in PBMC by cytometry
- T cell polarization using FluoroSpot assay
- T cell activation using AIM assay
Immune responses to predict
1) Antibody titers
1.1) Rank the individuals by IgG antibody titers against pertussis toxin (PT) that we detect in plasma 14 days post booster vaccinations.
1.2) Rank the individuals by fold change of predicted IgG antibody titers against pertussis toxin (PT) that we detect in plasma 14 days post booster vaccination compared to titer values at day 0.
2) Cell Frequencies
2.1) Rank the individuals by predicted frequency of Monocytes on day 1 post boost after vaccination.
2.2) Rank the individuals by fold change of predicted frequency of Monocytes on day 1 post booster vaccination compared to cell frequency values at day 0.
3) Gene Expression
3.1) Rank the individuals by predicted gene expression of CCL3 on day 3 post booster vaccination.
3.2) Rank the individuals by fold change of predicted gene expression of CCL3 on day 3 post booster vaccination compared to gene expression values at day 0.
4) T-cell response task (A Bonus task) - Updated on Oct 03, 2024**
4.1) Rank the individuals by predicted Th1/Th2 (IFN-γ/IL-5) polarization ratio on day 30 post-booster vaccination.
Evaluation Metrics
All predictions made will be in the form of ranking readouts from the highest response (=rank 1) to the lowest response in the N donors tested (=rank N). We will compare these to experimental readouts using the Spearman correlation.
References
[1] da Silva Antunes, R., Soldevila, F., Pomaznoy, M., Babor, M., Bennett, J., Tian, Y., … & Peters, B. (2021). A system-view of Bordetella pertussis booster vaccine responses in adults primed with whole-cell versus acellular vaccine in infancy. JCI insight , 6 (7). Available at: https://insight.jci.org/articles/view/141023