Immune Repertoire Analysis with Vidjil

Lille, France, 18-19 March 2019

V(D)J recombinations in lymphocytes are essential for immunological diversity. They are also useful markers of pathologies, and in leukemia, are used to quantify the minimal residual disease during patient follow-up. High-throughput sequencing (NGS/HTS) now enables the deep sequencing of lymphoid populations. With dedicated Rep-Seq bioinformatics methods and software, clinicians and researchers can now qualify and sometimes quantify the heterogeneity of these lymphoid populations.

This third workshop is intended for users and developers of Vidjil, to share experience, protocols and results, to raise questions and decide development priorities, and possibly to set up new collaborations between biologists and bioinformaticians. The workshop will include an invited talk by Jack Bartram, hematology, immunology and bioinformatics talks from the users and developers of Vidjil, and practical hands-on sessions on participant data. The previous workshop gathered 36 scientists from 6 countries.


The workshop will include invited talks, hematology and bioinformatics talks from the users and developers of Vidjil, and practical hands-on sessions on participant data. We expect that one participant from each group will do a short presentation of his research or clinical work, and, if applicable, of the results obtained with Vidjil or with other software.

For the practical sessions, the participants are invited to bring a laptop and some of their NGS data (fasta / fastq / fastq.gz files). The data can also be uploaded before the workshop into user accounts on before the workshop. We also provide public test data for the people who do not currently have their own NGS Rep-Seq data.

Monday 18 March

9:00 – 9:45 Registration, coffee
9:45 – 10:00 Introduction
10:00 – 11:00 Diagnosis and MRD for Leukemia and Lymphoma
  • Chrystelle Abdo, Patrick Villarèse (Paris Necker), Ig/TR sequencing and analysis for ALL and mature B hemopathies in Paris Necker
  • Nathalie Grardel (Lille), A four-year experience in using routinely Vidjil in a hematological lab for diagnosis and follow-up of ALL
  • Naïs Prade (Toulouse), Ig/TCR sequencing at diagnosis for ALL and CLL using Vidjil in Toulouse
11:00 – 11:30 Break
11:30 – 12:30 Keynote talk: Jack Bartram
Great Ormond Street Hospital for Children, London (UK)
Application of IG/TCR sequencing to advanced clinical diagnostics in acute lymphoblastic leukaemia and beyond
12:30 – 14:00 Lunch
14:00 – 15:30 Algorithmics and bioinformatics
  • Mikaël Salson (Lille), Faster clonal analysis of reads with Ig/TR recombinations
  • Florian Thonier (Rennes), Mathieu Giraud (Lille), The Vidjil web platform for RepSeq data: presentation, 2018-19 news
  • Joao Meidanis (Boldrini Center, Brazil), Spike-In Controls for MRD with Vidjil
15:30 – 16:00 Coffee Break
16:00 – 17:30 Practical sessions 1 (in parallel)
  • Usage of the Vidjil Web platform, analysis of participant and/or public data
  • (both tutorial and advanced usage)
  • Command-line, API, and interaction between RepSeq software
19:30 Dinner, restaurant De Rode Koe, in Lille.
Stop at the Rihour metro station.

Tuesday 19 March

9:30 – 10:30 Talks: Hematology and Immunology
  • Esteban Arrieta-Bolanos (Essen, Germany), T cell receptor repertoires in alloreactivity against HLA molecules and their relevance for hematopoietic stem cell transplantation
  • Aurélie Caye-Eude (Paris Debré), Identification of clonal Ig/TCR rearrangements at diagnosis in pediatric Acute Lymphoblastic Leukemia
  • Julie Drémaux (Amiens), Uncommon Kappa recombination analysis with high-throughput sequencing and pediatric ALL MRD quantification with digital PCR
10:30 – 11:15 Round table
Discussion on most wanted features, development priorities
11:15 – 11:45 Coffee Break
11:45 – 12:30 Bioinformatics software, regulation and certification
  • Mikaël Salson (Lille), Towards software certification
  • Mathieu Giraud (Lille), The VidjilNet consortium at Inria
12:30 – 14:00 Lunch
14:00 – 15:30 Practical session 2
  • Continuation of Practical Session 1
  • Identification of software issues
15:30 – 16:00 Round table and conclusion
Discussion on library preparation, sequencing instruments and protocols, bioinformatics analysis. Conclusion on development priorities.


Grand place de Lille

CC BY SA Velvet (source: Wikimedia Commons)

The workshop is sponsored by the VidjilNet consortium. There is no registration fee, but, as the capacity is limited, it is mandatory to register. To register, please copy, paste and fill the following lines into an email to Florian, Mathieu and Mikaël :

First name: 
Last name: 
I will be present:
    [ ] Both days
    [ ] Monday 18 March
    [ ] Tuesday 19 March
Usage of Vidjil:
    [ ] I use Vidjil at least once a month
    [ ] I use Vidjil occasionnaly
    [ ] I am a new user or I don't use Vidjil

The two lunches (18 and 19 March) and the dinner of the evening of the 18 March are free for registered participants. Registration deadline : 28 february 15 march 2018. It is still possible to register for the workshop, however we do not guarantee now places for the lunches and the dinner.

Practical information

Lille is a lovely city at the heart of French Flanders. With TGV, Lille is 1h from Paris, 1h20 min from London and 35 min from Brussels.

The workshop takes place at CRIStAL M3 building, in the heart of the Lille 1 Campus, at 20 minutes from Lille center. From Lille center, take the metro line 1 (yellow), direction 4 Cantons. Stop at the Cité Scientifique – Professeur Gabillard station. The CRISTAL M3 building is 500 meters from the metro station.


The workshop is organized by Mathieu Giraud, Mikaël Salson, Florian Thonier, from CRIStAL, Inria Lille and the VidjilNet consortium.