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Reply to "Evaluation of immune repertoire inference methods from RNA-seq data"

Nature Biotechnology volume 36, pages 1035–1036 (2018)Cite this article

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Bolotin et al. reply:

Clinical and biological studies are often aimed at discovering a small fraction of T cell receptor (TCR) or immunoglobulin variants shared between samples or groups of samples—for example, when searching for the common clonotypes involved in response to tumor antigens, infectious agent antigens or self antigens1. In this context, even a single false intersection between immune repertoires extracted from different samples may compromise the utility of the results. Among the scientific community, complementarity-determining region 3 (CDR3) with designated V and J gene segments is the accepted identifier that unambiguously defines TCR α- or a β-chain sequence.

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Figure 1: A comparison of the outputs of TRUST v2.1 and MiXCR.

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Acknowledgements

Research work supported by grant of the Ministry of Education and Science of the Russian Federation Number 14.W03.31.0005.

Author information

Author notes

  1. Dmitriy A Bolotin and Stanislav Poslavsky: These authors contributed equally to this work.

Authors and Affiliations

  1. MiLaboratory LLC, Skolkovo Innovation Center, Moscow, Russia

    Dmitriy A Bolotin & Stanislav Poslavsky

  2. Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia

    Dmitriy A Bolotin & Dmitriy M Chudakov

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

    Dmitriy A Bolotin, Stanislav Poslavsky & Dmitriy M Chudakov

  4. Central European Institute of Technology, Brno, Czech Republic

    Alexey N Davydov & Dmitriy M Chudakov

  5. Privolzhsky Research Medical University, Nizhny Novgorod, Russia

    Dmitriy M Chudakov

  6. Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia

    Dmitriy M Chudakov

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. Dmitriy M Chudakov
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Corresponding author

Correspondence to Dmitriy M Chudakov.

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

Supplementary information

Supplementary Note 1

Commands used for STAR alignment (PDF 60 kb)

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Bolotin, D., Poslavsky, S., Davydov, A. et al. Reply to "Evaluation of immune repertoire inference methods from RNA-seq data". Nat Biotechnol 36, 1035–1036 (2018). https://doi.org/10.1038/nbt.4296

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