Skip to main content

Advertisement

SpringerLink
Log in

Tracking cell lineages to improve research reproducibility

  • Correspondence
  • Published:

From Nature Biotechnology

View current issue Submit your manuscript

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1: Genome reading and writing technologies have contributed to an expansion in the number of cell lineages and advanced methods to characterize and track these lineages.
Fig. 2: Evolutionary dynamics and selection in cell line establishment and maintenance.

References

  1. Hughes, P., Marshall, D., Reid, Y., Parkes, H. & Gelber, C. Biotechniques 43, 575, 577–578, 581–582 (2007).

  2. Freedman, L. P., Cockburn, I. M. & Simcoe, T. S. PLoS Biol. 13, e1002165 (2015).

    Article  Google Scholar 

  3. Liu, Y. et al. Nat. Biotechnol. 37, 314–322 (2019).

    Article  CAS  Google Scholar 

  4. Lin, Y.-C. et al. Nat. Commun. 5, 4767 (2014).

    Article  CAS  Google Scholar 

  5. Ben-David, U. et al. Nature 560, 325–330 (2018).

    Article  CAS  Google Scholar 

  6. Boyer, S., Hérissant, L. & Sherlock, G. PLoS Genet. 17, e1009314 (2021).

    Article  CAS  Google Scholar 

  7. Nguyen, Ba,A. N. et al. Nature 575, 494–499 (2019).

    Article  Google Scholar 

  8. Myles, S. et al. Proc. Natl. Acad. Sci. USA 108, 3530–3535 (2011).

    Article  CAS  Google Scholar 

  9. Watson, C. J. et al. Science 367, 1449–1454 (2020).

    Article  CAS  Google Scholar 

  10. Forsberg, L. A. et al. Nat. Genet. 46, 624–628 (2014).

    Article  CAS  Google Scholar 

  11. Fittall, M. W. & Van Loo, P. Genome Med. 11, 20 (2019).

    Article  Google Scholar 

  12. Malm, M. et al. Sci. Rep. 10, 18996 (2020).

    Article  CAS  Google Scholar 

  13. Dumont, J., Euwart, D., Mei, B., Estes, S. & Kshirsagar, R. Crit. Rev. Biotechnol. 36, 1110–1122 (2016).

    Article  CAS  Google Scholar 

  14. Lund, R. J., Närvä, E. & Lahesmaa, R. Nat. Rev. Genet. 13, 732–744 (2012).

    Article  CAS  Google Scholar 

  15. Taapken, S. M. et al. Nat. Biotechnol. 29, 313–314 (2011).

    Article  CAS  Google Scholar 

  16. Weissbein, U. et al. iScience 11, 398–408 (2019).

    Article  CAS  Google Scholar 

  17. Barbaric, I. et al. Stem Cell Reports 3, 142–155 (2014).

    Article  CAS  Google Scholar 

  18. Bai, Q. et al. Stem Cells Dev. 24, 653–662 (2015).

    Article  CAS  Google Scholar 

  19. Sharma, S. V., Haber, D. A. & Settleman, J. Nat. Rev. Cancer 10, 241–253 (2010).

    Article  CAS  Google Scholar 

  20. Yamamoto, H. et al. Cancer Res. 68, 6913–6921 (2008).

    Article  CAS  Google Scholar 

  21. Komor, A. C., Badran, A. H. & Liu, D. R. Cell 168, 20–36 (2017).

    Article  CAS  Google Scholar 

  22. Chen, S. et al. Cell 160, 1246–1260 (2015).

    Article  CAS  Google Scholar 

  23. Richardson, C. D., Ray, G. J., DeWitt, M. A., Curie, G. L. & Corn, J. E. Nat. Biotechnol. 34, 339–344 (2016).

    Article  CAS  Google Scholar 

  24. Lu, C. & Sanjana, N. E. Stem Cell Res. 41, 101643 (2019).

    Article  CAS  Google Scholar 

  25. Kosicki, M., Tomberg, K. & Bradley, A. Nat. Biotechnol. 36, 765–771 (2018).

    Article  CAS  Google Scholar 

  26. Przewrocka, J., Rowan, A., Rosenthal, R., Kanu, N. & Swanton, C. Ann. Oncol. 31, 1270–1273 (2020).

    Article  CAS  Google Scholar 

  27. Ihry, R. J. et al. Nat. Med. 24, 939–946 (2018).

    Article  CAS  Google Scholar 

  28. Haapaniemi, E., Botla, S., Persson, J., Schmierer, B. & Taipale, J. Nat. Med. 24, 927–930 (2018).

    Article  CAS  Google Scholar 

  29. Kimberland, M. L. et al. J. Biotechnol. 284, 91–101 (2018).

    Article  CAS  Google Scholar 

  30. Isasi, R., Namorado, J., Mah, N., Bultjer, N. & Kurtz, A. Stem Cell Res. 40, 101539 (2019).

    Article  Google Scholar 

Download references

Acknowledgements

We thank L.M. de Buy Wenniger and T. Joseph for valuable feedback on the manuscript and K. White for assistance with graphic design. S.Z. is supported by the Jacobs Technion-Cornell Institute, the Elisha M. Friedman Postdoctoral Fellowship and FIND Genomics. S.C.G. is supported by a fellowship from the Gordon and Betty Moore Foundation/Life Sciences Research Foundation through grant GBMF2550.06. N.E.S. is supported by the National Institutes of Health (NIH) National Human Genome Research Institute (grant no. DP2HG010099), NIH National Cancer Institute (grant no. R01CA218668), NIH National Institute of General Medical Sciences (grant no. R01GM138635), Defense Advanced Research Projects Agency (grant no. D18AP00053), Sidney Kimmel Foundation, Melanoma Research Alliance, Brain and Behavior Foundation and Cancer Research Institute, and New York University and New York Genome Center startup funds.

Author information

Author notes

  1. These authors contributed equally: Sophie Zaaijer, Simon C. Groen.

Authors and Affiliations

  1. Cornell Tech, New York, NY, USA

    Sophie Zaaijer

  2. FIND Genomics, New York, NY, USA

    Sophie Zaaijer

  3. Department of Biology, New York University, New York, NY, USA

    Simon C. Groen & Neville E. Sanjana

  4. New York Genome Center, New York, NY, USA

    Neville E. Sanjana

Authors
  1. Sophie Zaaijer
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Simon C. Groen
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Neville E. Sanjana
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

Conception: S.Z., S.C.G., N.E.S. Writing and figures: S.Z., S.C.G., N.E.S.

Corresponding authors

Correspondence to Sophie Zaaijer, Simon C. Groen or Neville E. Sanjana.

Ethics declarations

Competing interests

S.Z. is a co-founder of FIND Genomics, a company that aims to improve reproducible cell-based science and develops cell lineage tracking software. N.E.S is an advisor to Vertex.

Additional information

Peer review information Nature Biotechnology thanks Chad Cowan and Johan Rockberg for their contribution to the peer review of this work.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Zaaijer, S., Groen, S.C. & Sanjana, N.E. Tracking cell lineages to improve research reproducibility. Nat Biotechnol 39, 666–670 (2021). https://doi.org/10.1038/s41587-021-00928-1

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41587-021-00928-1

  • Springer Nature America, Inc.

Search

Navigation