ARResT/Interrogate: an interactive immunoprofiler for IG/TR NGS data

Bystrý, Vojtěch; Reigl, Tomáš; Krejčí, Adam; Demko, Martin; Barbora, Hanakova; Grioni, Andrea; Knecht, Henrik; Schlitt, Max; Dreger, Peter; Sellner, Leopold; Herrmann, Doris; Marine, Pingeon; Boudjoghra, Myriam; Rijntjes, Jos; Pott, Christiane; Langerak, Anton W.; Groenen, Patricia J.T.A.; Davi, Frédéric; Brüggemann, Monika; Darzentas, Nikos

doi:10.1093/bioinformatics/btw634

Cited by 85 publications

(73 citation statements)

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“…Taken together and properly standardized and validated, these key elements (i.e., comprehensive and consistent annotation of sequences; true representation of the repertoire; meaningful clonotype definition and quantitation; end-userfriendly but unambiguous visualization) can form a consistent computational platform usable by both researchers and clinicians. Within EuroClonality-NGS complementary immunoinformatics expertise is available that covers these key elements with a collection of dedicated computational resources and tools in the form of IMGT (imgt.org) (87-90), Vidjil (vidjil.org) (91), and most recently ARResT/Interrogate (bat.infspire.org/arrest/) (92).…”

Section: Computational Repseq Analysismentioning

confidence: 99%

High-Throughput Immunogenetics for Clinical and Research Applications in Immunohematology: Potential and Challenges

Langerak

Brüggemann

Davi

et al. 2017

The Journal of Immunology

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Analysis and interpretation of Ig and TCR gene rearrangements in the conventional, low-throughput way have their limitations in terms of resolution, coverage, and biases. With the advent of high-throughput, next-generation sequencing (NGS) technologies, a deeper analysis of Ig and/or TCR (IG/TR) gene rearrangements is now within reach, which impacts on all main applications of IG/TR immunogenetic analysis. To bridge the generation gap from low- to high-throughput analysis, the EuroClonality-NGS Consortium has been formed, with the main objectives to develop, standardize, and validate the entire workflow of IG/TR NGS assays for 1) clonality assessment, 2) minimal residual disease detection, and 3) repertoire analysis. This concerns the preanalytical (sample preparation, target choice), analytical (amplification, NGS), and postanalytical (immunoinformatics) phases. Here we critically discuss pitfalls and challenges of IG/TR NGS methodology and its applications in hemato-oncology and immunology.

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Section: Computational Repseq Analysismentioning

confidence: 99%

High-Throughput Immunogenetics for Clinical and Research Applications in Immunohematology: Potential and Challenges

Langerak

Brüggemann

Davi

et al. 2017

The Journal of Immunology

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“…IgGalaxy has the purpose to provide an easy-to-use interface to IgBlast and IMGT/HighV-QUEST results [12]. Some other programs enable to further analyze or visualize statistics on the whole lymphocyte population, such as ARResT/Interrogate [13], tcR [14], ImmunExplorer [15] or VDJviz [16]. …”

Section: Introductionmentioning

confidence: 99%

Vidjil: A Web Platform for Analysis of High-Throughput Repertoire Sequencing

et al. 2016

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BackgroundThe B and T lymphocytes are white blood cells playing a key role in the adaptive immunity. A part of their DNA, called the V(D)J recombinations, is specific to each lymphocyte, and enables recognition of specific antigenes. Today, with new sequencing techniques, one can get billions of DNA sequences from these regions. With dedicated Repertoire Sequencing (RepSeq) methods, it is now possible to picture population of lymphocytes, and to monitor more accurately the immune response as well as pathologies such as leukemia.Methods and ResultsVidjil is an open-source platform for the interactive analysis of high-throughput sequencing data from lymphocyte recombinations. It contains an algorithm gathering reads into clonotypes according to their V(D)J junctions, a web application made of a sample, experiment and patient database and a visualization for the analysis of clonotypes along the time. Vidjil is implemented in C++, Python and Javascript and licensed under the GPLv3 open-source license. Source code, binaries and a public web server are available at http://www.vidjil.org and at http://bioinfo.lille.inria.fr/vidjil. Using the Vidjil web application consists of four steps: 1. uploading a raw sequence file (typically a FASTQ); 2. running RepSeq analysis software; 3. visualizing the results; 4. annotating the results and saving them for future use. For the end-user, the Vidjil web application needs no specific installation and just requires a connection and a modern web browser. Vidjil is used by labs in hematology or immunology for research and clinical applications.

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“…The resulting fastq files were analyzed using the bioinformatics tools Vidjil (19) and ARResT/Interrogate (20). After the second PCR, the concentration of the resulting products was measured using the Quant-iT™ PicoGreen ® dsDNA Assay Kit (Thermo Fisher Scientific, Waltham, MA).…”

Section: Next-generation Sequencingmentioning

confidence: 99%

“…The raw sequencing data were demultiplexed using the bcl2fastq conversion software (Illumina) with 0 mismatches in barcode sequences allowed. The resulting fastq files were analyzed using the bioinformatics tools Vidjil (19) and ARResT/Interrogate (20). Only clones with a frequency >15% were reported.…”

Section: Next-generation Sequencingmentioning

confidence: 99%

Next‐generation amplicon TRB locus sequencing can overcome limitations of flow‐cytometric Vβ expression analysis and confirms clonality in all T‐cell prolymphocytic leukemia cases

et al. 2018

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T-cell receptor (TCR) β repertoire analysis can distinguish monoclonal from polyclonal T-cell proliferations and crucially aid in the diagnosis of T-cell malignancies. TCR repertoire can be assessed either by flow cytometry (FCM), or by molecular genetic techniques. We compared the results of parallel analyses of Vβ expression by FCM and TRB rearrangements by DNA-based next-generation sequencing (NGS) in 80 diagnostic peripheral blood samples of patients with T-cell prolymphocytic leukemia (T-PLL) for (1) the diagnosis of clonality and (2) the assessment of dominant Vβ usage. FCM-based analysis of the surface expression was performed using the IOTest Beta Mark kit. The NGS-based analysis employed the multiplex Biomed-2 VB-JB primers. In all the samples, one or two clonal TRB rearrangements were detected by NGS. Although a dominant Vβ domain usage was detected by FCM in only 41/80 (51%) samples, clonality was suspected in all of them. In a total of 12 cases, the FCM missed the clone detected by NGS, despite theoretical coverage by the antibodies, the functionality of the rearrangement, and the expression of TCRαβ on the cell surface. Partly overlapping with those cases, FCM discovered predominant Vβ usage in the T-PLL population that differed from the one detected by NGS in 10 cases. Overall, the concordant NGS and FCM results were obtained on 61/80 (76%) of samples. We conclude that NGS-based TRB analysis can overcome certain limitations of FCM-based analysis by the identification of both productive and nonproductive rearrangements and by covering the whole Vβ spectrum. Currently available FCM analysis of Vβ expression lacks this breadth but has advantages, such as parallel immunophenotyping and a more accurate quantification of the Vβ usage.

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ARResT/Interrogate: an interactive immunoprofiler for IG/TR NGS data

Abstract: Supplementary data are available at Bioinformatics online.

Cited by 85 publications

References 5 publications

High-Throughput Immunogenetics for Clinical and Research Applications in Immunohematology: Potential and Challenges

High-Throughput Immunogenetics for Clinical and Research Applications in Immunohematology: Potential and Challenges

Vidjil: A Web Platform for Analysis of High-Throughput Repertoire Sequencing

Next‐generation amplicon TRB locus sequencing can overcome limitations of flow‐cytometric Vβ expression analysis and confirms clonality in all T‐cell prolymphocytic leukemia cases

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