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.

Antigen receptor repertoire profiling from RNA-seq data

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

Relevant articles

Open Access articles citing this article.

Access options

Buy article

Get time limited or full article access on ReadCube.

$32.00

All prices are NET prices.

Figure 1: Sensitivity and specificity of extraction of TCR and immunoglobulin repertoires from tumor RNA-seq data.
Figure 2: Immune repertoire analysis in human melanoma and sorted mice T cells.

References

  1. Murugan, A., Mora, T., Walczak, A.M. & Callan, C.G. Jr. Proc. Natl. Acad. Sci. USA 109, 16161–16166 (2012).

    Article  CAS  Google Scholar 

  2. Elhanati, Y. et al. Phil. Trans. R. Soc. Lond. B 370, http://dx.doi.org/10.1098/rstb.2014.0243 (2015).

  3. Greiff, V., Miho, E., Menzel, U. & Reddy, S.T. Trends Immunol. 36, 738–749 (2015).

    Article  CAS  Google Scholar 

  4. Attaf, M., Huseby, E. & Sewell, A.K. Cell. Mol. Immunol. 12, 391–399 (2015).

    Article  CAS  Google Scholar 

  5. Boyd, S.D. & Crowe, J.E. Jr. Curr. Opin. Immunol. 40, 103–109 (2016).

    Article  CAS  Google Scholar 

  6. Heather, J.M., Ismail, M., Oakes, T. & Chain, B. Brief. Bioinform. http://dx.doi.org/10.1093/bib/bbw138 (2017).

  7. Hackl, H., Charoentong, P., Finotello, F. & Trajanoski, Z. Nat. Rev. Genet. 17, 441–458 (2016).

    Article  CAS  Google Scholar 

  8. Georgiou, G. et al. Nat. Biotechnol. 32, 158–168 (2014).

    Article  CAS  Google Scholar 

  9. Bolotin, D.A. et al. Nat. Methods 12, 380–381 (2015).

    Article  CAS  Google Scholar 

  10. Weinstein, J.S. et al. Blood 124, 3719–3729 (2014).

    Article  CAS  Google Scholar 

  11. Pulko, V. et al. Nat. Immunol. 17, 966–975 (2016).

    Article  CAS  Google Scholar 

  12. Böttcher, J.P. et al. Nat. Commun. 6, 8306 (2015).

    Article  Google Scholar 

  13. Li, B. et al. Nat. Genet. 48, 725–732 (2016).

    Article  CAS  Google Scholar 

  14. Brown, S.D., Raeburn, L.A. & Holt, R.A. Genome Med. 7, 125 (2015).

    Article  CAS  Google Scholar 

  15. Mose, L.E. et al. Bioinformatics 32, 3729–3734 (2016).

    Article  CAS  Google Scholar 

  16. Li, B. et al. Nat. Genet. 49, 482–483 (2017).

    Article  CAS  Google Scholar 

  17. Stubbington, M.J.T. et al. Nat. Methods 13, 329–332 (2016).

    Article  Google Scholar 

  18. Britanova, O.V. et al. J. Immunol. 196, 5005–5013 (2016).

    Article  CAS  Google Scholar 

  19. Charoentong, P. et al. Cell Rep. 18, 248–262 (2017).

    Article  CAS  Google Scholar 

  20. Tumeh, P.C. et al. Nature 515, 568–571 (2014).

    Article  CAS  Google Scholar 

  21. Reddy, S.T. et al. Nat. Biotechnol. 28, 965–969 (2010).

    Article  CAS  Google Scholar 

  22. Kotlan, B. et al. J. Immunol. 175, 2278–2285 (2005).

    Article  CAS  Google Scholar 

  23. Khalil, D.N., Smith, E.L., Brentjens, R.J. & Wolchok, J.D. Nat. Rev. Clin. Oncol. 13, 273–290 (2016).

    Article  CAS  Google Scholar 

  24. Shalapour, S. et al. Nature 521, 94–98 (2015).

    Article  CAS  Google Scholar 

  25. Rubtsov, Y.P. et al. Immunity 28, 546–558 (2008).

    Article  CAS  Google Scholar 

  26. Shugay, M. et al. PLOS Comput. Biol. 11, e1004503 (2015).

    Article  Google Scholar 

  27. Kosmrlj, A., Jha, A.K., Huseby, E.S., Kardar, M. & Chakraborty, A.K. Proc. Natl. Acad. Sci. USA 105, 16671–16676 (2008).

    Article  CAS  Google Scholar 

  28. Jordan, M.S. et al. Nat. Immunol. 2, 301–306 (2001).

    Article  CAS  Google Scholar 

  29. Feng, Y. et al. Nature 528, 132–136 (2015).

    Article  CAS  Google Scholar 

  30. Hsieh, C.S., Zheng, Y., Liang, Y., Fontenot, J.D. & Rudensky, A.Y. Nat. Immunol. 7, 401–410 (2006).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

Research supported by grant of the Ministry of Education and Science of the Russian Federation Number 14.W03.31.0005. Human melanoma SPX6730 and SPX8151 sample preparation supported by European Union's Horizon 2020 Research and Innovation Programme Number 633592 (to T.N. Schumacher). Foxp3yfpcre mice sample preparation supported by NIH/NCI Cancer Center Support Grant P30 CA008748 (to A.Y. Rudensky).

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Dmitriy M Chudakov.

Ethics declarations

Competing interests

MiLaboratory LLC develops MiXCR software and has exclusive rights for its commercial distribution

Supplementary information

Supplementary Figures

Supplementary Figures 1–4, Supplementary Tables 1–3 and 5,Supplementary Notes 1–3 and Supplementary Methods (PDF 8248 kb)

Reporting Summary

Life sciences reporting summary (PDF 1295 kb)

Supplementary Table 4

Dominant and hypermutating intratumorally produced Ig clones (XLSX 27 kb)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Bolotin, D., Poslavsky, S., Davydov, A. et al. Antigen receptor repertoire profiling from RNA-seq data. Nat Biotechnol 35, 908–911 (2017). https://doi.org/10.1038/nbt.3979

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nbt.3979

This article is cited by

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing