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Human genetics and genomics

Improving estimates of loss-of-function constraint for short genes

Genetic constraint identifies genes under selection against loss-of-function, but existing methods are inaccurate for shorter genes. A new study overcomes this key limitation to ascribe more confident predictions to all human protein-coding genes.

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Fig. 1: A machine-learning model incorporating gene features improves genetic constraint estimates for short genes.

References

  1. Fuller, Z. L., Berg, J. J., Mostafavi, H., Sella, G. & Przeworski, M. Nat. Genet. 51, 772–776 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Chen, S. et al. Nature 626, E1 (2024).

    Article  CAS  PubMed  Google Scholar 

  3. Lek, M. et al. Nature 536, 285–291 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Karczewski, K. J. et al. Nature 581, 434–443 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Cassa, C. A. et al. Nat. Genet. 49, 806–810 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Seaby, E. G. et al. Genet. Med. 24, 1697–1707 (2022).

    Article  CAS  PubMed  Google Scholar 

  7. He, X. et al. PLoS Genet. 9, e1003671 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Kaplanis, J. et al. Nature 586, 757–762 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Gudmundsson, S. et al. Hum. Mutat. 43, 1012–1030 (2022).

    Article  PubMed  Google Scholar 

  10. Minikel, E. V. et al. Nature 581, 459–464 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Whiffin, N. et al. Nat. Med. 26, 869–877 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Pilz, D. T. et al. Hum. Mol. Genet. 7, 2029–2037 (1998).

    Article  CAS  PubMed  Google Scholar 

  13. Zeng, T. et al. Nat. Genet. https://doi.org/10.1038/s41588-024-01820-9 (2024).

    Article  PubMed  PubMed Central  Google Scholar 

  14. Singer-Berk, M. et al. Am. J. Hum. Genet. 110, 1496–1508 (2023).

  15. MacArthur, D. G. & Tyler-Smith, C. Hum. Mol. Genet. 19, R125–R130 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

N.W. is supported by a Sir Henry Dale Fellowship jointly funded by the Wellcome Trust and the Royal Society (220134/Z/20/Z).

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Correspondence to Nicola Whiffin.

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N.W. receives research funding from Novo Nordisk and has consulted for ArgoBio studio.

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Whiffin, N. Improving estimates of loss-of-function constraint for short genes. Nat Genet 56, 1544–1545 (2024). https://doi.org/10.1038/s41588-024-01829-0

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