Immune Repertoire Analysis
with Vidjil

Lille (France) + online, 16-17 May 2022

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 fifth 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 invited talks, hematology, immunology and bioinformatics talks from the users and developers of Vidjil, and practical hands-on sessions on participant data. The Vidjil Workshop usually takes place every 18 months. The previous workshops (2016, 2017, 2019, special edition 2020) gathered at each edition between 30 and 40 scientists from 5 to 7 countries.

Hybrid participation.The 2022 edition comes backs physical, in Lille! However, it's also possible to follow remotely part of the workshop (hybrid): Zoom link, Meeting ID: 943 7024 7582, Passcode: 089129

Program

The workshop includes 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 app.vidjil.org before the workshop. We also provide public test data for the people who do not currently have their own NGS Rep-Seq data.

Monday 16 May

9:00 – 9:45 Registration, coffee
9:45 – 10:00 hybrid Introduction
10:00 – 11:30 hybrid Talks: Hematology and Immunology (session 1)
  • Marie-Laure Boulland (CHU Rennes 🇫🇷), Reliable IGHV status assessment by next-generation sequencing in routine practice for Chronic Lymphocytic Leukemia
  • Guilherme Giusti (Boldrini Center 🇧🇷), Spike-in controls for MRD with Vidjil
  • Mindaugas Stoškus (Vilnius Univ. Hospital 🇱🇹), IG/TR Recombination Analysis in Oncohematology Setting: Experience of Vilnius University Hospital
  • Claire Mauduit (CHU Lyon 🇫🇷), Evaluation of TCR gamma repertoire in the diagnosis and the residual disease of the most common cutaneous T-cell lymphoma, Mycosis Fungoides
  • Valérie Rimelen (CHU Strasbourg 🇫🇷), *NGS amplicon for IgVH mutational status determination in CLL. From Sanger to NGS: preliminary results and technical considerations.
11:30 – 12:30 hybrid Talks: Algorithmics and bioinformatics
  • Florian Thonier (Rennes), Marc Duez (Lille), The Vidjil web platform for RepSeq/AIRR data: presentation, 2021-22 news
  • Mikaël Salson (Lille), Faster clonal analysis of reads with Ig/TR recombinations
12:30 – 14:00 Lunch
14:00 – 15:30 Practical sessions 1
  • Usage of the Vidjil Web platform, analysis of participant and/or public data
    • (both tutorial and advanced usage)
15:30 – 16:00 Coffee Break
16:00 – 17:00 hybrid Keynote Talk
Nina Luning Park (U. Pennsylvania 🇺🇸) and Anne Eugster (TU Dresden 🇩🇪), AIRR Community: Biological Resources Working Group and challenges regarding IgH gene rearrangement analysis
17:00 – 17:30 hybrid Talks: Bioinformatics software, regulation and certification
  • Mikaël Salson, Tests and continuous integration
  • Mathieu Giraud, Regulation and Certification
20:00 Dinner, restaurant L'Assiette du Marché, in Lille.
800m from the Rihour metro station.

Tuesday 17 May

9:00 – 10:30 hybrid Talks: Hematology and Immunology (session 2)
  • Aurore Touzart (Hôpital Necker, Paris 🇫🇷), Immunogenetics and High-Throughput Sequencing in the onco-hematological lab in Paris-Necker
  • Shivangi Harankhedkar (Tata Memorial Hospital, Mumbai 🇮🇳), Determination of IGVH mutation status by NGS in CLL using Leader primers
  • Laura Rengifo (UZ Leuven 🇧🇪), Dynamic Follow-up of Tumor Burden in Multiple Myeloma Using Circulating Cell-Free DNA
  • Yannick LeBris (CHU Nantes 🇫🇷) Analysis of CLL mutation status by HTS capture and Vidjil
10:30 – 11:00 Coffee Break
11:00 – 12:30 Practical session 2 (in parallel)
  • Continuation of Practical Session 1 and identification of software issues
  • Bioinformatics meeting on Command-line, API, and interaction between RepSeq/AIRR software
12:30 – 14:00 Lunch
14:00 – 15:30 Round table
  • Discussion on most wanted features, development priorities
  • Meeting of the Scientific and Technic Commitee (N. Grardel, Y. Le Bris, C. Pastoret, with D. Margery and the Vidjil team)
15:30 – 16:00 Conclusion
Discussion on library preparation, sequencing instruments and protocols, bioinformatics analysis. Conclusion on development priorities.

Registration

The workshop is sponsored by the VidjilNet consortium at Inria. There is no registration fee. To register, please copy, paste and fill the following lines into an email to Florian, Marc, Mathieu and Mikaël : 

================================================
First name: 
Last name: 
Function: 
Laboratory/hospital: 
City: 
Country:

I will be present in Lille:
    [ ] Both days
    [ ] Monday 16 May 2022
    [ ] Tuesday 17 May 2022

[ ] I will attend the workshop remotely

My 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 (16 and 17 May) and the dinner of the evening of the 17 May are free for registered participants. The registration for the full workshop with the lunches in the Lille is now closed, but stays open for the online participation.

Grand place de Lille

Lille, CC BY SA Velvet (source: Wikimedia Commons)

Practical information in Lille

The workshop takes place at CRIStAL ESPRIT building, in the heart of the Université de Lille Campus, at 20 minutes from Lille center. From Lille center, take the metro line 1 (yellow), direction 4 Cantons. Stop at the terminus, 4 Cantons -- Stade Pierre Mauroy station. The CRIStAL ESPRIT building is 300 meters from the metro station.

Organizers

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