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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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).

Author information

Author notes

    • Mikhail Shugay
    • , Olga V Britanova
    • , Ekaterina M Merzlyak
    •  & Maria A Turchaninova

    These authors contributed equally to this work.

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

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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.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Dmitriy M Chudakov.

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DOI

https://doi.org/10.1038/nmeth.2960

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