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Jun Cheng, Guido Novati, Joshua Pan, Clare Bycroft, Akvilė Žemgulytė, Taylor Applebaum, Alexander Pritzel, Lai Hong Wong, Michal Zielinski, Tobias Sargeant and 6 more
The vast majority of missense variants observed in the human genome are of unknown clinical significance. We present AlphaMissense, an adaptation of AlphaFold fine-tuned on human and primate variant population frequency databases to predict missense variant pathogenicity. By combining structural context and evolutionary conservation, our model achieves state-of-the-art results across a wide range of genetic and experimental benchmarks, all without explicitly training on such data. The average pathogenicity score of genes is also predictive for their cell essentiality, capable of identifying short essential genes that existing statistical approaches are underpowered to detect. As a resource to the community, we provide a database of predictions for all possible human single amino acid substitutions and classify 89% of missense variants as either likely benign or likely pathogenic.
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Cheng, J., Novati, G., Pan, J., Bycroft, C., Žemgulytė, A., Applebaum, T., Pritzel, A., Wong, L. H., Zielinski, M., Sargeant, T., Schneider, R. G., Senior, A., Jumper, J., Hassabis, D., Kohli, P., & Avsec, Ž. (2023). Accurate proteome-wide missense variant effect prediction with AlphaMissense. Science, 381(6664), eadg7492. https://doi.org/10.1126/science.adg7492
Cheng, Jun, et al. "Accurate proteome-wide missense variant effect prediction with AlphaMissense." Science, vol. 381, no. 6664, 2023, pp. eadg7492, https://doi.org/10.1126/science.adg7492.
Cheng, Jun, Guido Novati, Joshua Pan, Clare Bycroft, Akvilė Žemgulytė, Taylor Applebaum, Alexander Pritzel, et al. "Accurate proteome-wide missense variant effect prediction with AlphaMissense." Science 381, no. 6664 (2023): eadg7492. https://doi.org/10.1126/science.adg7492.
Cheng J., Novati G., Pan J. [и др.] Accurate proteome-wide missense variant effect prediction with AlphaMissense // Science. — 2023. — Vol. 381, № 6664. — P. eadg7492. — URL: https://doi.org/10.1126/science.adg7492
@article{cheng2023accurate,
title = {{Accurate proteome-wide missense variant effect prediction with AlphaMissense}},
author = {Jun Cheng and Guido Novati and Joshua Pan and Clare Bycroft and Akvilė Žemgulytė and Taylor Applebaum and Alexander Pritzel and Lai Hong Wong and Michal Zielinski and Tobias Sargeant and Rosalia G. Schneider and Andrew Senior and John Jumper and Demis Hassabis and Pushmeet Kohli and Žiga Avsec},
journal = {Science},
year = {2023},
volume = {381},
number = {6664},
pages = {eadg7492},
doi = {10.1126/science.adg7492},
url = {https://doi.org/10.1126/science.adg7492}
}TY - JOUR AU - Cheng, Jun AU - Novati, Guido AU - Pan, Joshua AU - Bycroft, Clare AU - Žemgulytė, Akvilė AU - Applebaum, Taylor AU - Pritzel, Alexander AU - Wong, Lai Hong AU - Zielinski, Michal AU - Sargeant, Tobias AU - Schneider, Rosalia G. AU - Senior, Andrew AU - Jumper, John AU - Hassabis, Demis AU - Kohli, Pushmeet AU - Avsec, Žiga TI - Accurate proteome-wide missense variant effect prediction with AlphaMissense JO - Science VL - 381 IS - 6664 SP - eadg7492 PY - 2023 DA - 2023/09/19 DO - 10.1126/science.adg7492 UR - https://doi.org/10.1126/science.adg7492 ER -
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