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Evaluation of immune repertoire inference methods from RNA-seq data

Nature Biotechnology volume 36, page 1034 (2018)Cite this article

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To the Editor:

Characterizing tumor-infiltrating T cell receptor (TCR) repertoire is a critical step toward identifying cancer antigens and developing new immunotherapies1. We previously developed a computational algorithm named TRUST2,3 to extract TCR hypervariable complementarity-determining region 3 (CDR3) sequences from unselected bulk tumor RNA sequencing (RNA-seq) data. When applied to large cancer cohorts, TRUST found associations between tumor mutation load and TCR repertoires2. A recent study by Bolotin et al.4 reported a new version of their MiXCR tool that enables assembly of TCR clonotypes from RNA-seq data. In comparing MiXCR to TRUST, Bolotin et al.4 concluded that MiXCR was superior and that the output of TRUST includes unconfirmed and potentially false positive results. Here, we point out important differences between TRUST and MiXCR, as well as differences in interpretation of results, which may complicate direct comparison of the tools.

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Acknowledgements

This work was supported by CPRIT RR170079 (B.L.), Chinese Scholarship Council funding (J.Z.), and NCI U01 CA226196 and the Breast Cancer Research Foundation (X.S.L.).

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Author notes

  1. Xihao Hu and Jian Zhang: These authors contributed equally to this work.

  2. Bo Li and Xiaole Shirley Liu: These authors jointly supervised this work.

Authors and Affiliations

  1. Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA

    Xihao Hu & Xiaole Shirley Liu

  2. Beijing Institute of Basic Medical Sciences, Beijing, China

    Jian Zhang

  3. Statistics Department, Harvard University, Boston, Massachusetts, USA

    Jun S Liu & Xiaole Shirley Liu

  4. Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, Texas, USA

    Bo Li

Authors
  1. Xihao Hu
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  2. Jian Zhang
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  3. Jun S Liu
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  4. Bo Li
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  5. Xiaole Shirley Liu
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Corresponding author

Correspondence to Xiaole Shirley Liu.

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The authors declare no competing financial interests.

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Hu, X., Zhang, J., Liu, J. et al. Evaluation of immune repertoire inference methods from RNA-seq data. Nat Biotechnol 36, 1034 (2018). https://doi.org/10.1038/nbt.4294

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