Antigen receptor repertoire profiling from RNA-seq data (original) (raw)

• Correspondence
• Published: 11 October 2017
• Stanislav Poslavsky1,3 na1,
• Alexey N Davydov4 na1,
• Felix E Frenkel5 na1,
• Lorenzo Fanchi6,
• Olga I Zolotareva ORCID: orcid.org/0000-0002-9424-80525,
• Saskia Hemmers7,
• Ekaterina V Putintseva2,8,
• Anna S Obraztsova2,9,
• Mikhail Shugay ORCID: orcid.org/0000-0001-7826-79421,2,3,10,11,
• Ravshan I Ataullakhanov5,12,13,
• Alexander Y Rudensky7,14,
• Ton N Schumacher6 &
• …
• Dmitriy M Chudakov ORCID: orcid.org/0000-0003-0430-790X2,3,4,10,11

Nature Biotechnology volume 35, pages 908–911 (2017)Cite this article

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To the Editor:

Somatic recombination and accumulation of mutations in V-D-J segments result in vast heterogeneity of T-cell receptor (TCR) and immunoglobulin repertoires1,[2](/articles/nbt.3979#ref-CR2 "Elhanati, Y. et al. Phil. Trans. R. Soc. Lond. B 370, http://dx.doi.org/10.1098/rstb.2014.0243

             (2015)."). High-throughput profiling of immune receptors has become an important tool for studies of adaptive immunity and for the development of diagnostics, vaccines, and immunotherapies[3](/articles/nbt.3979#ref-CR3 "Greiff, V., Miho, E., Menzel, U. & Reddy, S.T. Trends Immunol. 36, 738–749 (2015)."),[4](/articles/nbt.3979#ref-CR4 "Attaf, M., Huseby, E. & Sewell, A.K. Cell. Mol. Immunol. 12, 391–399 (2015)."),[5](/articles/nbt.3979#ref-CR5 "Boyd, S.D. & Crowe, J.E. Jr. Curr. Opin. Immunol. 40, 103–109 (2016)."),[6](/articles/nbt.3979#ref-CR6 "Heather, J.M., Ismail, M., Oakes, T. & Chain, B. Brief. Bioinform. 
              http://dx.doi.org/10.1093/bib/bbw138
              
             (2017)."),[7](/articles/nbt.3979#ref-CR7 "Hackl, H., Charoentong, P., Finotello, F. & Trajanoski, Z. Nat. Rev. Genet. 17, 441–458 (2016)."). There are efficient molecular and software tools for the targeted sequencing of TCR and immunoglobulin repertoires[6](/articles/nbt.3979#ref-CR6 "Heather, J.M., Ismail, M., Oakes, T. & Chain, B. Brief. Bioinform. 
              http://dx.doi.org/10.1093/bib/bbw138
              
             (2017)."),[8](/articles/nbt.3979#ref-CR8 "Georgiou, G. et al. Nat. Biotechnol. 32, 158–168 (2014)."), including MiXCR, developed by our team[9](/articles/nbt.3979#ref-CR9 "Bolotin, D.A. et al. Nat. Methods 12, 380–381 (2015)."). However, sufficient amount and quality of tissue or extracted RNA or DNA are not always available for analysis.

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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).

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Author notes

1. Dmitriy A Bolotin, Stanislav Poslavsky, Alexey N Davydov and Felix E Frenkel: These authors contributed equally to this work.

Authors and Affiliations

1. MiLaboratory LLC, Skolkovo Innovation Center, Moscow, Russia
   Dmitriy A Bolotin, Stanislav Poslavsky & Mikhail Shugay
2. Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
   Dmitriy A Bolotin, Ekaterina V Putintseva, Anna S Obraztsova, Mikhail Shugay & Dmitriy M Chudakov
3. Pirogov Russian National Research Medical University, Moscow, Russia
   Dmitriy A Bolotin, Stanislav Poslavsky, Mikhail Shugay & Dmitriy M Chudakov
4. Central European Institute of Technology, Brno, Czech Republic
   Alexey N Davydov & Dmitriy M Chudakov
5. BostonGene LLC, Lincoln, Massachusetts, USA
   Felix E Frenkel, Olga I Zolotareva & Ravshan I Ataullakhanov
6. Division of Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
   Lorenzo Fanchi & Ton N Schumacher
7. Howard Hughes Medical Institute and Immunology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, USA
   Saskia Hemmers & Alexander Y Rudensky
8. Centre for Genomic Regulation, The Barcelona Institute for Science and Technology, Barcelona, Spain
   Ekaterina V Putintseva
9. Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
   Anna S Obraztsova
10. Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia
    Mikhail Shugay & Dmitriy M Chudakov
11. Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, Russia
    Mikhail Shugay & Dmitriy M Chudakov
12. Institute of Immunology FMBA, Moscow, Russia
    Ravshan I Ataullakhanov
13. Faculties for Physics and Biology, Lomonosov Moscow State University, Moscow, Russia
    Ravshan I Ataullakhanov
14. Ludwig Center at Memorial Sloan Kettering Cancer Center, Memorial Sloan Kettering Cancer Center, New York, New York, USA
    Alexander Y Rudensky

Authors

1. Dmitriy A Bolotin
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2. Stanislav Poslavsky
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3. Alexey N Davydov
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4. Felix E Frenkel
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5. Lorenzo Fanchi
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6. Olga I Zolotareva
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7. Saskia Hemmers
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8. Ekaterina V Putintseva
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9. Anna S Obraztsova
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10. Mikhail Shugay
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11. Ravshan I Ataullakhanov
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12. Alexander Y Rudensky
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13. Ton N Schumacher
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14. Dmitriy M Chudakov
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Correspondence toDmitriy M Chudakov.

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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)

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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

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• Published: 11 October 2017
• Issue Date: October 2017
• DOI: https://doi.org/10.1038/nbt.3979