A Systematic Review of Human Challenge Trials, Designs, and Safety.

medRxiv preprint DOI: https://doi.org/10.1101/2022.03.20.22272658

Dataset DOI: 10.5281/zenodo.6711717

Dataset

The resulting dataset from this systematic review is provided both as an Excel file and a Google Sheet. These datasets allow filtering for various exclusions:

1. Challenge - describes a traditional challenge trial
2. Prechallenge - describes an immunization phase or a vaccination phase that occurred prior to a traditional challenge phase
3. Rechallenge - describes a cohort of volunteers that have been previously exposed to a challenge agent (in a previous study or in an earlier challenge phase of the current study), that were then challenged again (either with the same strain or a different strain of the challenge agent)
4. Attenuated - describes a challenge with an attenuated challenge agent
5. Vaccine - describes a challenge with a vaccine
6. NAE - studies where AEs were not mentioned/defined, and other reported data (symptoms, illness, etc.) was extracted instead
7. NSAE - studies where SAEs were not mentioned in the text, and the current FDA definition of SAEs was manually applied to reported symptom/illness data in order to identify possible SAEs
8. Excluded - studies that were excluded for any reason (should always remain checked)
9. Summed - previously extracted data from multiple phases, studies, or cohorts that was summed to be treated as a single study

Figures

The figures included for publication were produced directly from the Google Sheet (https://bit.ly/1DSSR22) and the source code is provided in CID-113513.r. This was developend and tested under R 4.1.3.

You may execute this code within a development environment such as RStudio, or simply from the R interpreter by issuing the command Rscript CID-113513.r. In the latter environment, the program will produce and EPS and TIF (1200dpi) version of each figure in the publication.

06/23/2022  11:03 AM            11,547 CID-113513-figure2.eps
06/23/2022  11:03 AM           474,900 CID-113513-figure2.tiff
06/23/2022  11:03 AM            11,552 CID-113513-figure3.eps
06/23/2022  11:03 AM           883,650 CID-113513-figure3.tiff
06/23/2022  11:03 AM            34,883 CID-113513-figure3a.eps
06/23/2022  11:03 AM           463,836 CID-113513-figure3a.tiff
06/23/2022  11:03 AM            11,547 CID-113513-figure3b.eps
06/23/2022  11:03 AM           346,146 CID-113513-figure3b.tiff

Presentation

The presentation given by Danny Toomey outlining the methodology used for this work is provided in both Powerpoint and PDF format.

Repository Contact

Any questions about this repository may be directed to James Wilkinson.