Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Correspondence
  • Published:

Uncertainties in tumor allele frequencies limit power to infer evolutionary pressures

Nature Genetics volume 49, pages 1288–1289 (2017)Cite this article

Subjects

To the Editor:

We read with great interest the paper by Williams et al.1, who reported evidence for neutral evolution in tumors by analyzing data from The Cancer Genome Atlas (TCGA). They supported this conclusion by showing high R2 values for fits to a neutral evolutionary model predicting M ∝ 1/f, where M is the number of somatic mutations with allele frequency ≥f. However, we believe a conclusion of neutrality must be treated with caution, as high R2 values are consistent with many evolutionary models.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Comparison of evolutionary models for TCGA and simulated data.

References

  1. William, M.J., Werner, B., Barnes, C.P., Graham, T.A. & Sottoriva, A. Nat. Genet. 48, 238–244 (2016).

    Article  Google Scholar 

  2. Cibulskis, K. et al. Nat. Biotechnol. 31, 213–219 (2013).

    Article  CAS  Google Scholar 

  3. Gerstung, M. et al. Nat. Commun. 3, 811 (2012).

    Article  Google Scholar 

Download references

Acknowledgements

We would like to thank H.S. Kim for helpful discussions and J. Cha for graphics design. J.H.C. was supported by the National Cancer Institute of the NIH under award R21CA191848 and supplement R21CA191848-01A1S1. Research was also partially supported by the National Cancer Institute under award P30CA034196.

Author information

Authors and Affiliations

  1. The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA

    Javad Noorbakhsh & Jeffrey H Chuang

  2. Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, Connecticut, USA

    Jeffrey H Chuang

Authors
  1. Javad Noorbakhsh
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Jeffrey H Chuang
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Jeffrey H Chuang.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Note

Supplementary Note (DOCX 132 kb)

Supplementary Code

ipython notebook with code used for computations. (TXT 174 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Noorbakhsh, J., Chuang, J. Uncertainties in tumor allele frequencies limit power to infer evolutionary pressures. Nat Genet 49, 1288–1289 (2017). https://doi.org/10.1038/ng.3876

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/ng.3876

This article is cited by

Search

Advanced search

Quick links

Nature Briefing: Cancer

Sign up for the Nature Briefing: Cancer newsletter — what matters in cancer research, free to your inbox weekly.

Get what matters in cancer research, free to your inbox weekly. Sign up for Nature Briefing: Cancer