Lessons learned from the IMMREP23 TCR-epitope prediction challenge

Research output: Contribution to journal › Research article › Contributed › peer-review

Contributors

  • Morten Nielsen - , Technical University of Denmark (Author)
  • Anne Eugster - , Chair of Preclinical stem cell therapy and diabetes (Author)
  • Mathias Fynbo Jensen - , Technical University of Denmark (Author)
  • Manisha Goel - , Center for Regenerative Therapies Dresden (Author)
  • Andreas Tiffeau-Mayer - , University College London (Author)
  • Aurelien Pelissier - , Zurich University of Applied Sciences (ZHAW) (Author)
  • Sebastiaan Valkiers - , University of Lausanne (Author)
  • María Rodríguez Martínez - , Yale University (Author)
  • Barthélémy Meynard-Piganeeau - , Laboratory of Computational and Quantitative Biology (LCQB) (Author)
  • Victor Greiff - , University of Oslo, Oslo University Hospital Rikshospitalet (Author)
  • Thierry Mora - , École normale supérieure Paris-Saclay (Author)
  • Aleksandra M. Walczak - , École normale supérieure Paris-Saclay (Author)
  • Giancarlo Croce - , University of Lausanne (Author)
  • Dana L Moreno - , University of Lausanne (Author)
  • David Gfeller - , University of Lausanne (Author)
  • Pieter Meysman - , University of Antwerp (Author)
  • Justin Barton - , University of London (Author)

Abstract

Here, we present the findings from IMMREP23, the second benchmark competition focused on predicting the specificity of TCR-pMHC interactions. The interaction of T cell receptors (TCR) towards their pMHC target is a cornerstone of the cellular immune system. Over the last decade, substantial progress has been made within the field of TCR specificity prediction, providing proof of concept for predicting TCR-pMHC interactions in a narrow space of “seen” pMHC targets where substantial training data is available. However, a significant challenge persists in extending the predictive capability to novel “unseen” pMHC targets. Furthermore, the performance of proposed methods is often challenged when evaluated outside the initial publication and data sets. To address these issues, IMMREP23 challenge invited participants to predict, for a given test set of TCR-pMHC pairs, the likelihood that a pair would bind. A total of 53 teams participated, providing a total of 398 submissions. The benchmark confirms that current methods achieve reasonable performance in the "seen" pMHC setting. However, most participating methods had close to random performance on the subset of “unseen” peptides, underlining that this prediction challenge remains essentially unsolved. Finally, another key lesson from the benchmark is the critical issue of data leakage. Specifically, the data set construction procedure employed in IMMREP23 led to biases in the negative test data set. These biases were identified by several participating teams, and complicated the interpretation of the benchmark results. Based on these results, we put forward suggestions on how future competitions could avoid such data leakages and biases.

Details

Original languageEnglish
Article number100045
JournalImmunoInformatics
Volume16
Publication statusPublished - Dec 2024
Peer-reviewedYes

External IDs

Mendeley b04933ef-48c9-3d3a-aea7-236dd7d76cbe
unpaywall 10.1016/j.immuno.2024.100045

Keywords