Welcome to the 2nd CMI-PB Prediction challenge. We expect to have data from 20+ 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 to base the prediction on
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
- Gene expression in PBMC by RNA-Seq
- Cell type frequencies in PBMC by cytometry
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.
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
- Spearman correlation
- AUC value for an ROC curve where the top half of observed measurements are considered ‘positive’ and the lower half are considered ‘negative’
Feel free to Sign-in at https://www.cmi-pb.org/mycmipb/2021_prediction_challenge/ for more information.
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
[2] CMI-PB Submission Template 2022: 2nd CMI-PB Prediction Challenge: Submission Template - Google Sheets