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Breaking the performance ceiling for neoantigen immunogenicity prediction

Nature Cancer volume 4, pages 1618–1621 (2023)Cite this article

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An Author Correction to this article was published on 15 April 2024

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Neoantigen immunogenicity prediction is a burgeoning field with vast potential; however, the shortage of high-quality data and biases in current datasets limit model generalizability. Here we discuss some of the pitfalls that may underly this limited performance and propose a path forward.

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Fig. 1: Challenges and future directions in cancer neoantigen-prediction methods.

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Acknowledgements

This work is part of the DECOD-Ag project that has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement no. 964998. This publication reflects only the author’s view and the European Commission is not responsible for any use that may be made of the information it contains.

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Authors and Affiliations

  1. Achilles Therapeutics Ltd, London, UK

    Hugh O’Brien, Max Salm, Laura T. Morton, Felix O’Farrell, Pablo D. Becker & Sergio A. Quezada

  2. Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK

    Maciej Szukszto, Charlotte Boulton, Marc R. Mansour & Sergio A. Quezada

  3. Weizmann Institute of Science, Rehovot, Israel

    Yardena Samuels

  4. The Francis Crick Institute, London, UK

    Charles Swanton

  5. Technical University of Denmark, Lyngby, Denmark

    Sine Reker Hadrup

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  1. Hugh O’Brien
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  4. Maciej Szukszto
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Corresponding authors

Correspondence to Max Salm, Sine Reker Hadrup or Sergio A. Quezada.

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Competing interests

S.A.Q. is co-founder and chief scientific officer and own shares in Achilles Therapeutics. C.S. acknowledges grants from AstraZeneca, Boehringer-Ingelheim, Bristol Myers Squibb, Pfizer, Roche-Ventana, Invitae (previously Archer Dx Inc., a collaboration in minimal residual disease sequencing technologies), Ono Pharmaceutical and Personalis. He is chief investigator for the AZ MeRmaiD 1 and 2 clinical trials and is the steering committee chair. He is also co-chief investigator of the NHS Galleri trial funded by GRAIL and a paid member of GRAIL’s scientific advisory board (SAB). He receives consultant fees from Achilles Therapeutics (also an SAB member); Bicycle Therapeutics (also an SAB member); Genentech; Medicxi; the China Innovation Centre of Roche (CICoR), formerly Roche Innovation Centre Shanghai; Metabomed (until July 2022); Relay Therapeutics; and the Sarah Cannon Research Institute. C.S has received honoraria from Amgen, AstraZeneca, Bristol Myers Squibb, GlaxoSmithKline, Illumina, MSD, Novartis, Pfizer and Roche-Ventana; previously held stock options in Apogen Biotechnologies and GRAIL; currently has stock options in Epic Bioscience and Bicycle Therapeutics; and has stock options and is co-founder of Achilles Therapeutics. S.R.H. is the cofounder of PokeAcell and is co-inventor of licensed patents related to T cell detection. H.O’B., M.S., L.M. and F.O’F. are employees of Achilles Therapeutics.

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O’Brien, H., Salm, M., Morton, L.T. et al. Breaking the performance ceiling for neoantigen immunogenicity prediction. Nat Cancer 4, 1618–1621 (2023). https://doi.org/10.1038/s43018-023-00675-z

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