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Benchmarking immunoinformatic tools for the analysis of antibody repertoire sequences

Smakaj, Erand ; Babrak, Lmar ; Ohlin, Mats ; Shugay, Mikhail ; Briney, Bryan ; Tosoni, Deniz ; Galli, Christopher ; Grobelsek, Vendi ; D’Angelo, Igor ; Olson, Branden ; Reddy, Sai ; Greiff, Victor ; Trück, Johannes ; Marquez, Susanna ; Lees, William ; Miho, Enkelejda Birols, Inanc

Bioinformatics, 2020-03, Vol.36 (6), p.1731-1739 [Revista revisada por pares]

England: Oxford University Press

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  • Título:
    Benchmarking immunoinformatic tools for the analysis of antibody repertoire sequences
  • Autor: Smakaj, Erand ; Babrak, Lmar ; Ohlin, Mats ; Shugay, Mikhail ; Briney, Bryan ; Tosoni, Deniz ; Galli, Christopher ; Grobelsek, Vendi ; D’Angelo, Igor ; Olson, Branden ; Reddy, Sai ; Greiff, Victor ; Trück, Johannes ; Marquez, Susanna ; Lees, William ; Miho, Enkelejda
  • Birols, Inanc
  • Materias: Antibodies ; Benchmarking ; Engineering and Technology ; High-Throughput Nucleotide Sequencing ; Humans ; Medical Engineering ; Medical Laboratory and Measurements Technologies ; Medicinsk laboratorie- och mätteknik ; Medicinteknik ; Original Papers ; Reproducibility of Results ; Teknik
  • Es parte de: Bioinformatics, 2020-03, Vol.36 (6), p.1731-1739
  • Notas: ObjectType-Article-1
    SourceType-Scholarly Journals-1
    ObjectType-Feature-2
    content type line 23
    The authors wish it to be known that, in their opinion, Erand Smakaj and Lmar Babrak should be regarded as Joint First Authors.
  • Descripción: Abstract Summary Antibody repertoires reveal insights into the biology of the adaptive immune system and empower diagnostics and therapeutics. There are currently multiple tools available for the annotation of antibody sequences. All downstream analyses such as choosing lead drug candidates depend on the correct annotation of these sequences; however, a thorough comparison of the performance of these tools has not been investigated. Here, we benchmark the performance of commonly used immunoinformatic tools, i.e. IMGT/HighV-QUEST, IgBLAST and MiXCR, in terms of reproducibility of annotation output, accuracy and speed using simulated and experimental high-throughput sequencing datasets. We analyzed changes in IMGT reference germline database in the last 10 years in order to assess the reproducibility of the annotation output. We found that only 73/183 (40%) V, D and J human genes were shared between the reference germline sets used by the tools. We found that the annotation results differed between tools. In terms of alignment accuracy, MiXCR had the highest average frequency of gene mishits, 0.02 mishit frequency and IgBLAST the lowest, 0.004 mishit frequency. Reproducibility in the output of complementarity determining three regions (CDR3 amino acids) ranged from 4.3% to 77.6% with preprocessed data. In addition, run time of the tools was assessed: MiXCR was the fastest tool for number of sequences processed per unit of time. These results indicate that immunoinformatic analyses greatly depend on the choice of bioinformatics tool. Our results support informed decision-making to immunoinformaticians based on repertoire composition and sequencing platforms. Availability and implementation All tools utilized in the paper are free for academic use. Supplementary information Supplementary data are available at Bioinformatics online.
  • Editor: England: Oxford University Press
  • Idioma: Inglés;Noruego
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