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Towards error-free profiling of immune repertoires

Nature Methods volume 11, pages 653–655 (2014)Cite this article

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Abstract

Deep profiling of antibody and T cell–receptor repertoires by means of high-throughput sequencing has become an attractive approach for adaptive immunity studies, but its power is substantially compromised by the accumulation of PCR and sequencing errors. Here we report MIGEC (molecular identifier groups–based error correction), a strategy for high-throughput sequencing data analysis. MIGEC allows for nearly absolute error correction while fully preserving the natural diversity of complex immune repertoires.

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Figure 1: MIGEC analysis.
Figure 2: MIGEC analysis for control clones.

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Acknowledgements

We are grateful to M. Eisenstein for the English editing. This work was supported by the Molecular and Cell Biology program RAS, Russian Foundation for Basic Research 12-04-33139 (to D.M.C.), 13-04-00998 (to O.V.B.) and 14-04-01247 (to E.M.M.), Russian President grant MD-3044.2014.4 (to D.M.C.) and European Regional Development Fund (CZ.1.05/1.1.00/02.0068).

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Author notes

  1. Mikhail Shugay, Olga V Britanova, Ekaterina M Merzlyak and Maria A Turchaninova: These authors contributed equally to this work.

Authors and Affiliations

  1. Shemiakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, Russia

    Mikhail Shugay, Olga V Britanova, Ekaterina M Merzlyak, Maria A Turchaninova, Ilgar Z Mamedov, Timur R Tuganbaev, Dmitriy A Bolotin, Dmitry B Staroverov, Ekaterina V Putintseva, Dmitriy Shagin, Sergey Lukyanov & Dmitriy M Chudakov

  2. Pirogov Russian National Research Medical University, Moscow, Russia

    Mikhail Shugay, Dmitriy Shagin, Sergey Lukyanov & Dmitriy M Chudakov

  3. Central European Institute of Technology, Masaryk University, Brno, Czech Republic

    Ilgar Z Mamedov, Karla Plevova, Sarka Pospisilova & Dmitriy M Chudakov

  4. Division of Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands

    Carsten Linnemann & Ton N Schumacher

Authors
  1. Mikhail Shugay
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  2. Olga V Britanova
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  3. Ekaterina M Merzlyak
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  4. Maria A Turchaninova
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  6. Timur R Tuganbaev
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  7. Dmitriy A Bolotin
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  9. Ekaterina V Putintseva
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  16. Dmitriy M Chudakov
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Contributions

M.S., O.V.B., D.A.B., D.S., S.P. and D.M.C. designed experiments. O.V.B., E.M.M., M.A.T., I.Z.M., T.R.T., D.B.S., E.V.P., K.P. and C.L. performed experiments. M.S., D.A.B. and D.M.C. designed the MIGEC algorithm and analyzed and interpreted results. M.S., S.L., T.N.S. and D.M.C. wrote the manuscript.

Corresponding author

Correspondence to Dmitriy M Chudakov.

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The authors declare no competing financial interests.

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Supplementary Figures 1–11 and Supplementary Tables 1–4 (PDF 4939 kb)

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Shugay, M., Britanova, O., Merzlyak, E. et al. Towards error-free profiling of immune repertoires. Nat Methods 11, 653–655 (2014). https://doi.org/10.1038/nmeth.2960

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