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The missing diversity in human epigenomic studies

Recent work has highlighted a lack of diversity in genomic studies. However, less attention has been given to epigenomics. Here, we show that epigenomic studies are lacking in diversity and propose several solutions to address this problem.

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Fig. 1: Diversity in epigenomic data samples over time.
Fig. 2: Diversity in epigenomic data samples by assay.

References

  1. Popejoy, A. B. & Fullerton, S. M. Nature 538, 161–164 (2016).

    CAS  Article  Google Scholar 

  2. Sirugo, G., Williams, S. M. & Tishkoff, S. A. Cell 177, 26–31 (2019).

    CAS  Article  Google Scholar 

  3. The ENCODE Project Consortium. Nature 489, 57–74 (2012).

    Article  Google Scholar 

  4. Maurano, M. T. et al. Science 337, 1190–1195 (2012).

    CAS  Article  Google Scholar 

  5. Claussnitzer, M. et al. N. Engl. J. Med. 373, 895–907 (2015).

    CAS  Article  Google Scholar 

  6. Bravo González-Blas, C. et al. Nat. Methods 16, 397–400 (2019).

    Article  Google Scholar 

  7. Grafodatskaya, D., Chung, B., Szatmari, P. & Weksberg, R. J. Am. Acad. Child Adolesc. Psychiatry 49, 794–809 (2010).

    Article  Google Scholar 

  8. Husquin, L. T. et al. Genome Biol. 19, 222 (2018).

    CAS  Article  Google Scholar 

  9. Breeze, C. E. et al. Genome Med. 13, 74 (2021).

    CAS  Article  Google Scholar 

  10. Fraser, H. B., Lam, L. L., Neumann, S. M. & Kobor, M. S. Genome Biol. 13, R8 (2012).

    CAS  Article  Google Scholar 

  11. Tsai, P.-C. et al. Clin. Epigenetics 10, 126 (2018).

    CAS  Article  Google Scholar 

  12. Philibert, R. et al. Front. Psychol. 6, 656, https://doi.org/10.3389/fpsyg.2015.00656 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  13. Lu, A. T. et al. Aging (Albany NY) 11, 303–327 (2019).

    CAS  Article  Google Scholar 

  14. Birney, E., Smith, G. D. & Greally, J. M. PLoS Genet. 12, e1006105 (2016).

    Article  Google Scholar 

  15. van Dongen, J. et al. Nat. Commun. 7, 11115 (2016).

    Article  Google Scholar 

  16. Min, J. L. et al. Nat. Genet. 53, 1311–1321 (2021).

    CAS  Article  Google Scholar 

  17. Bell, J. T. et al. Genome Biol. 12, R10 (2011).

    CAS  Article  Google Scholar 

  18. Heyn, H. et al. Genome Res. 23, 1363–1372 (2013).

    CAS  Article  Google Scholar 

  19. Visscher, P. M. et al. Am. J. Hum. Genet. 101, 5–22 (2017).

    CAS  Article  Google Scholar 

  20. Visscher, P. M., Brown, M. A., McCarthy, M. I. & Yang, J. Am. J. Hum. Genet. 90, 7–24 (2012).

    CAS  Article  Google Scholar 

  21. Welter, D. et al. Nucleic Acids Res. 42, D1001–D1006 (2014).

    CAS  Article  Google Scholar 

  22. Edwards, S. L., Beesley, J., French, J. D. & Dunning, A. M. Am. J. Hum. Genet. 93, 779–797 (2013).

    CAS  Article  Google Scholar 

  23. Trynka, G. et al. Nat Genet. 45, 124–130 (2013).

    CAS  Article  Google Scholar 

  24. Tehranchi, A. et al. Elife 8, e39595 (2019).

    Article  Google Scholar 

  25. Taitt, H. E. Am. J. Mens Health 12, 1807 (2018).

    Article  Google Scholar 

  26. Mills, K. T. et al. Circulation 134, 441–450 (2016).

    Article  Google Scholar 

  27. GBD Chronic Kidney Disease Collaboration. Lancet 395, 709–733 (2020).

    Article  Google Scholar 

Download references

Acknowledgements

This project was supported in part by the Intramural Research Program of the Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health (C.E.B. and S.I.B.) and National Institutes of Health R01 MD012765, HL163972, DK117445 (grants to N.F.).

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Correspondence to Charles E. Breeze.

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The authors declare no competing interests.

Supplementary information

Supplementary Table

Experiment-specific information from publicly available IHEC data (downloaded 20 July 2021). Information includes ethnicity, experiment ID, assay, target of assay, biosample summary, biosample term name, lab, project status, and date of release of the experiment.

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Breeze, C.E., Beck, S., Berndt, S.I. et al. The missing diversity in human epigenomic studies. Nat Genet 54, 737–739 (2022). https://doi.org/10.1038/s41588-022-01081-4

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