Data availability of open T-cell receptor repertoire data, a systematic assessment

Huang, Y.-N.; Patel, N. A.; Mehta, J. H.; Ginjala, S.; Brodin, P.; Gray, C. M.; Patel, Y. M.; Cowell, L. G.; Burkhardt, A. M.; Mangul, S.

doi:10.1101/2022.04.13.488243

bioRxiv · 10.1101/2022.04.13.488243

Data availability of open T-cell receptor repertoire data, a systematic assessment

Huang, Y.-N.·Patel, N. A.·Mehta, J. H.·Ginjala, S.·Brodin, P.·Gray, C. M.·Patel, Y. M.·Cowell, L. G.·Burkhardt, A. M.·Mangul, S.

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Abstract

The improvement of next-generation sequencing technologies has promoted the field of immunogenetics and produced numerous immunogenomics data. Modern data-driven research has the power to promote novel biomedical discoveries through secondary analysis of such data. Therefore, it is important to ensure data-driven research with great reproducibility and robustness for promoting a precise and accurate secondary analysis of the immunogenomics data. In scientific research, rigorous conduct in designing and conducting experiments is needed, specifically in scientific and articulate writing, reporting and interpreting results. It is also crucial to make raw data available, discoverable, and well described or annotated in order to promote future re-analysis of the data. In order to assess the data availability of published T cell receptor (TCR) repertoire data, we examined 11,918 TCR-Seq samples corresponding to 134 TCR-Seq studies ranging from 2006 to 2022. Among the 134 studies, only 38.1% had publicly available raw TCR-Seq data shared in public repositories. We also found a statistically significant association between the presence of data availability statements and the increase in raw data availability (p=0.014). Yet, 46.8% of studies with data availability statements failed to share the raw TCR-Seq data. There is a pressing need for the biomedical community to increase awareness of the importance of promoting raw data availability in scientific research and take immediate action to improve its raw data availability enabling cost-effective secondary analysis of existing immunogenomics data by the larger scientific community.

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Huang, Y.-N., Patel, N. A., Mehta, J. H., Ginjala, S., Brodin, P., Gray, C. M., Patel, Y. M., Cowell, L. G., Burkhardt, A. M., Mangul, S.. 2022-04-16. Data availability of open T-cell receptor repertoire data, a systematic assessment. https://doi.org/10.1101/2022.04.13.488243

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