Credits

Vidjil is an open-source platform for the analysis of high-throughput sequencing data from lymphocytes, developed and maintained by the Bonsai bioinformatics lab at CRIStAL (UMR CNRS 9189, Université Lille) and the VidjilNet consortium at Inria.

Contact: Mathieu Giraud and Mikaël Salson

Vidjil core development

Other contributors

.should-vdj.fa tests with curated V(D)J designations

Acknowledgements

We thank all our users, collaborators and colleagues who provided feedback on Vidjil and proposed new ideas. Our special thanks go to:

Vidjil is developed in collaboration or in connection with the following groups:

Funding

The development of Vidjil is funded by:

References

If you use vidjil-algo, please cite [Giraud, Salson 2014]. If you use the web platform, please cite [Duez 2016].

Marc Duez et al., Vidjil: A web platform for analysis of high-throughput repertoire sequencing, PLOS ONE 2016, 11(11):e0166126 http://dx.doi.org/10.1371/journal.pone.0166126

Mathieu Giraud, Mikaël Salson, et al., Fast multiclonal clusterization of V(D)J recombinations from high-throughput sequencing, BMC Genomics 2014, 15:409 http://dx.doi.org/10.1186/1471-2164-15-409

Some publications using Vidjil

Chrystelle Abdo et al., Caution encouraged in next-generation sequencing immunogenetic analyses in acute lymphoblastic leukemia, Blood, 2020, 136(9):1105–1107, https://doi.org/10.1182/blood.2020005613

Jean-Sebastien Allain et al., IGHV segment utilization in immunoglobulin gene rearrangement differentiates patients with anti-myelin-associated glycoprotein neuropathy from others immunoglobulin M-gammopathies, Haematologica, 2018, 103:e207-e210, http://dx.doi.org/10.3324/haematol.2017.177444

Jack Bartram et al., High throughput sequencing in acute lymphoblastic leukemia reveals clonal architecture of central nervous system and bone marrow compartments, Haematologica, 2018, https://dx.doi.org/10.3324%2Fhaematol.2017.174987

Sébastien Bender et al., Immunoglobulin variable domain high-throughput sequencing reveals specific novel mutational patterns in POEMS syndrome, Blood, 2020, https://doi.org/10.1182/blood.2019004197

Marie-Laure Boulland et al., Reliable IGHV status assessment by next generation sequencing in routine practice for chronic lymphocytic leukemia, Leukemia & Lymphoma, 2021, https://doi.org/10.1080/10428194.2021.1933476

Monika Brüggemann et al., on behalf of the EuroClonality-NGS working group, Standardized next-generation sequencing of immunoglobulin and T-cell receptor gene recombinations for MRD marker identification in acute lymphoblastic leukaemia; a EuroClonality-NGS validation study, Leukemia, 2019, 33, 2241–2253, https://doi.org/10.1038/s41375-019-0496-7

Roberta Cavagna et al., Capture-based Next-Generation Sequencing Improves the Identification of Immunoglobulin/T-Cell Receptor Clonal Markers and Gene Mutations in Adult Acute Lymphoblastic Leukemia Patients Lacking Molecular Probes, Cancers, 2020, 12(6), 1505, https://doi.org/10.3390/cancers12061505

Rodolfo P. Correia et al., High‐throughput sequencing of immunoglobulin heavy chain for minimal residual disease detection in B‐lymphoblastic leukemia, Int. Journal of Laboratory Hematology, 2021, https://doi.org/10.1111/ijlh.13453

Frédéric Davi et al., on behalf of ERIC, the European Research Initiative on CLL, and the EuroClonality-NGS Working Group, Immunoglobulin gene analysis in chronic lymphocytic leukemia in the era of next generation sequencing, 2020 Leukemia, 2020, https://doi.org/10.1038/s41375-020-0923-9

Yann Ferret et al., Multi-loci diagnosis of acute lymphoblastic leukaemia with high-throughput sequencing and bioinformatics analysis, British Journal of Haematology, 2016, 173, 413–420, https://hal.archives-ouvertes.fr/hal-01279160

Henrike J. Fischer et al., Modulation of CNS autoimmune responses by CD8+ T cells coincides with their oligoclonal expansion, Journal of Neuroimmunology, 2015, S0165-5728(15)30065-5, http://dx.doi.org/10.1016/j.jneuroim.2015.10.020

Navarro Nilo Giusti et al., 2020 Test trial of spike-in immunoglobulin heavy-chain (IGH) controls for next generation sequencing quantification of minimal residual disease in acute lymphoblastic leukaemia, British Journal of Haematology, 2020, 189: e150-e154, https://doi.org/10.1111/bjh.16571

Irene Jo et al., Considerations for monitoring minimal residual disease using immunoglobulin clonality in patients with precursor B-cell lymphoblastic leukemia, Clinica Chimica Acta, 2019, https://doi.org/10.1016/j.cca.2018.10.037

Natalia Izotova et al., Long-term lymphoid progenitors independently sustain naïve T and NK cell production in humans, Nature Communications, 2021, https://doi.org/10.1038/s41467-021-21834-9

Vincent Jauvague et al., RNA-based immunoglobulin repertoire sequencing is a new tool for the management of monoclonal gammopathy of renal (kidney) significance. Kidney International, 2021, https://doi.org/10.1016/j.kint.2021.10.017

Takashi Kanamori et al., Genomic analysis of multiple myeloma using targeted capture sequencing in the Japanese cohort, British Journal of Haematology, 2020, https://doi.org/10.1111/bjh.16720

Kenji Kimura et al., Identification of Clonal Immunoglobulin λ Light-Chain Gene Rearrangements in AL Amyloidosis Using Next-Generation Sequencing, Experimental Hematology, 2021, 101:34-41.e4 https://doi.org/10.1016/j.exphem.2021.08.001

Michaela Kotrova et al., The predictive strength of next-generation sequencing MRD detection for relapse compared with current methods in childhood ALL, Blood, 2015, 126:1045-1047, http://dx.doi.org/10.1182/blood-2015-07-655159

Michaela Kotrova et al., 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, Cytometry Part A, 93(11):1118-1124, 2018 http://dx.doi.org/10.1002/cyto.a.23604

Anton W. Langerak, High-Throughput Immunogenetics for Clinical and Research Applications in Immunohematology: Potential and Challenges, Journal of Immunology, 2017, 198(10):3765-3774, https://dx.doi.org/10.4049/jimmunol.1602050

Zhenhua Li et al., Identifying IGH disease clones for MRD monitoring in childhood B-cell acute lymphoblastic leukemia using RNA-Seq, Leukemia, 2020, 34:2418-2429, http://dx.doi.org/10.1038/s41375-020-0774-4

Ralf A. Linker et al., Thymocyte-derived BDNF influences T-cell maturation at the DN3/DN4 transition stage, European Journal of Immunology, 2015, 45, 1326-1338, http://dx.doi.org/10.1002/eji.201444985

Ming Liang Oon et al., T-Cell Lymphoma Clonality by Copy Number Variation Analysis of T-Cell Receptor Genes, Cancers, 2021, 13(2), 340, https://dx.doi.org/10.3390/cancers13020340

Alejandro Medina et al., Comparison of next-generation sequencing (NGS) and next-generation flow (NGF) for minimal residual disease (MRD) assessment in multiple myeloma, Blood Cancer Journal, 10, 108, https://doi.org/10.1038/s41408-020-00377-0

Dai Nishijima et al., Capture Sequencing Is a Useful Method for Comprehensive Clonality Analysis Based on Ig/TCR Gene Rearrangements in Acute Lymphoblastic Leukemia, ASH 2018, Blood, 132(S1):1543, https://doi.org/10.1182/blood-2018-99-115624

Edit Porpaczy et al., Aggressive B-cell lymphomas in patients with myelofibrosis receiving JAK1/2 inhibitor therapy, Blood, 2018, https://dx.doi.org/10.1182/blood-2017-10-810739

Rathana Kim et al., Adult T-cell acute lymphoblastic leukemias with IL7R pathway mutations are slow-responders who do not benefit from allogeneic stem-cell transplantation, Leukemia, 2020, 34, 1730-1740, https://dx.doi.org/10.1038/s41375-019-0685-4

Mikaël Salson et al., High-throughput sequencing in acute lymphoblastic leukemia: Follow-up of minimal residual disease and emergence of new clones, Leukemia Research, 2017, 53, 1–7, http://dx.doi.org/10.1016/j.leukres.2016.11.009

Masashi Sanada et al., Targeted-Capture Sequencing Is a Useful Method for MRD Markers Screening in KMT2A (MLL) Rearranged Leukemia, ASH 2019, Blood, 134(S1):2759, https://doi.org/10.1182/blood-2019-125421

Florian Scherer et al., Distinct biological subtypes and patterns of genome evolution in lymphoma revealed by circulating tumor DNA, Science Translational Medicine, 2016, 8, 364ra155, http://dx.doi.org/10.1126/scitranslmed.aai8545

V. Seitz et al., Evidence for a role of RUNX1 as recombinase cofactor for TCRβ rearrangements and pathological deletions in ETV6-RUNX1 ALL Scientific Reports, 2020, 10:10024, https://doi.org/10.1038/s41598-020-65744-0

Udo zur Stadt et al., Characterization of novel, recurrent genomic rearrangements as sensitive MRD targets in childhood B-cell precursor ALL, Blood Cancer Journal, 2019, https://doi.org/10.1038/s41408-019-0257-x

Lucia Stranavova et al., Heterologous Cytomegalovirus and Allo-Reactivity by Shared T Cell Receptor Repertoire in Kidney Transplantation, Frontiers in Immunology, 2019, https://doi.org/10.3389/fimmu.2019.02549

Manuela Tosi et al., MRD-Based Therapeutic Decisions in Genetically Defined Subsets of Adolescents and Young Adult Philadelphia-Negative ALL Cancers 2021, 13(9), 2108, https://doi.org/10.3390/cancers13092108

Amelie Trinquand et al., Towards molecular stratification of pediatric T-cell lymphoblastic lymphomas based on Minimal Disseminated Disease and NOTCH1/FBXW7 mutational status: the French EURO-LB02 experience (preprint), medRxiv 2020.09.08.20189829, https://www.medrxiv.org/content/10.1101/2020.09.08.20189829v1

Patrik Villarèse et al., One step next generation sequencing of immunoglobulin and T-cell receptor gene recombinations for MRD marker identification in acute lymphoblastic leukemia, ed. Anton W. Langerak, Methods in Molecular Biology, forthcoming

Gary Wright et al., Clinical benefit of a high‐throughput sequencing approach for minimal residual disease in acute lymphoblastic leukemia, Pediatric Blood & Cancer, 2019, https://doi.org/10.1002/pbc.27787

Wen‐Qing Yao et al., Angioimmunoblastic T‐cell lymphoma contains multiple clonal T‐cell populations derived from a common TET2 mutant progenitor cell, The Journal of Pathology, 2019, https://doi.org/10.1002/path.5376

Yasuda et al., Clinical utility of target capture‐based panel sequencing in hematological malignancies: A multicenter feasibility study, Cancer Science, 2020, 111(9):3367-3378, https://dx.doi.org/10.1111/cas.14552