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:

Exploring genomic alteration in pediatric cancer using ProteinPaint

Nature Genetics volume 48, pages 4–6 (2016)Cite this article

Subjects

To the Editor:

Genomic information about predisposing germline mutations in normal cells as well as acquired somatic lesions in cancer cells will enable the development and delivery of individualized cancer therapies. Ongoing global initiatives have shown that the spectra of somatic and germline genetic lesions in pediatric cancer are distinct from those found in adult cancer1,2,3. However, existing cancer genome data portals (cBioPortal4 and the Catalogue of Somatic Mutations in Cancer (COSMIC)5) have focused primarily on presenting data generated by adult cancer studies. They also lack features for exploring pathogenic germline mutations, gene fusions and mutation stratification by cancer subtype, all of which are of great importance in pediatric cancer.

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: Comprehensive visualization of sequence mutations, gene fusions and RNA expression using ProteinPaint.

References

  1. Downing, J.R. et al. Nat. Genet. 44, 619–622 (2012).

    Article  CAS  Google Scholar 

  2. Zhang, J. et al. Nature 481, 157–163 (2012).

    Article  CAS  Google Scholar 

  3. Wu, G. et al. Nat. Genet. 44, 251–253 (2012).

    Article  CAS  Google Scholar 

  4. Gao, J. et al. Sci. Signal. 6, pl1 (2013).

    Article  Google Scholar 

  5. Forbes, S.A. et al. Nucleic Acids Res. 43, D805–D811 (2015).

    Article  CAS  Google Scholar 

  6. Zhang, J. et al. N. Engl. J. Med. (http://dx.doi.org/10.1056/NEJMoa1508054 (18 November 2015).

  7. Wang, K., Li, M. & Hakonarson, H. Nucleic Acids Res. 38, e164 (2010).

    Article  Google Scholar 

  8. Chen, X. et al. Nat. Methods 12, 527–530 (2015).

    Article  CAS  Google Scholar 

  9. Liang, S.H. & Clarke, M.F. J. Biol. Chem. 274, 32699–32703 (1999).

    Article  CAS  Google Scholar 

  10. Roberts, K.G. et al. N. Engl. J. Med. 371, 1005–1015 (2014).

    Article  Google Scholar 

Download references

Acknowledgements

We thank J. Klco, P. Northcott and C. Mullighan for helpful suggestions. We thank the reviewers of this manuscript for suggestions of implementing new interface for custom data upload. This study was supported by the St. Jude Children's Research Hospital–Washington University Pediatric Cancer Genome Project, Cancer Center support grant P30 CA021765 from the US National Cancer Institute and the American Lebanese Syrian Associated Charities of St. Jude Children's Research Hospital.

Author information

Authors and Affiliations

  1. Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA

    Xin Zhou, Michael N Edmonson, Mark R Wilkinson, Aman Patel, Gang Wu, Yu Liu, Yongjin Li, Zhaojie Zhang, Michael C Rusch, Matthew Parker, Jared Becksfort, James R Downing & Jinghui Zhang

  2. Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA

    James R Downing

Authors
  1. Xin Zhou
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Michael N Edmonson
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Mark R Wilkinson
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Aman Patel
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Gang Wu
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Yu Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Yongjin Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Zhaojie Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Michael C Rusch
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Matthew Parker
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Jared Becksfort
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. James R Downing
    View author publications

    You can also search for this author in PubMed Google Scholar

  13. Jinghui Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Jinghui Zhang.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Figures and Text

Supplementary Figures 1–8 and Supplementary Note. (PDF 4868 kb)

Supplementary Tutorial

Supplementary tutorial for ProteinPaint. (PDF 3710 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Zhou, X., Edmonson, M., Wilkinson, M. et al. Exploring genomic alteration in pediatric cancer using ProteinPaint. Nat Genet 48, 4–6 (2016). https://doi.org/10.1038/ng.3466

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/ng.3466

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