Analysis of Heterogeneous Immune Repertoires with Vidjil

Lille, France, 15-16 March 2016

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 workshop was 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 included two invited talks, hematology, immunology and bioinformatics talks from the users and developers of Vidjil, and practical hands-on sessions on participant data. The workshop gathered 34 scientists from 5 countries.


The workshop will start on the Tuesday at 9:30 and end on the Wednesday at 16:00. 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 into user accounts on before Sunday 13 March. There will be no internet connection in the workshop rooms, but all the data uploaded before March 13 will be available on a local server. We will also provide test data for the people who do not currently have their own NGS Rep-Seq data.

Tuesday 15 March

9:30 – 9:50 Registration, coffee
9:50 – 10:00 Introduction
10:00 – 11:00 Invited talk: John Moppett
Evolving the role of MRD in the management of childhood leukaemia
University Hospitals Bristol, NHS (UK)
11:00 – 12:30 Diagnosis and MRD for Leukemia and Lymphoma
  • Jona Van der Straeten, Marleen Bakkus (Brussels), Identification of leukemic clone(s) and minimal residual disease quantification in acute lymphoblastic leukemia
  • Nathalie Grardel et al. (Lille), Multi-loci diagnosis of acute lymphoblastic leukaemia in routine hospital practise in Lille
  • Odile Avinens (Montpellier), Clonality analysis of TCRg and IgH loci: Experience of Montpellier
  • Marie Lorena Guinea Montalvo, Riccardo Rossi (Bergamo, Milano), A capture-based NGS approach for Ig/TCR clonality assessment at diagnosis in adult acute lymphoblastic leukemia : our molecular biology and bioinformatics perspectives
12:30 – 14:00 Lunch
14:00 – 15:30 Developer talks: Bioinformatics and algorithmics
  • Mikaël Salson, Mathieu Giraud (Lille), Gathering reads and analyzing clones
  • Marc Duez, Ryan Herbert (Bristol, Lille), The Vidjil web application, an autonomous platform to process RepSeq data
  • Tatiana Rocher (Lille), Towards a clone database based on a Burrows-Wheeler-Transform
15:30 – 16:00 Coffee Break
16:00 – 17:30 Practical session 1
20:30 Dinner, Art-Déco restaurant La Paix in Lille

Wednesday 16 March

9:00 – 10:00 Invited talk: Mikhail Shugay
A general-purpose framework for immune repertoire sequencing: applications to aging and autoimmune disorder studies
Genomics of Adaptive Immunity Lab
Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow (Russia)
10:00 – 10:30 Coffee Break
10:30 – 12:00 Clonality and Repertoire Analysis in Hematology and Immunology
  • Nicolas Denis-Lagache (Limoges), VDJ repertory of B cells undergoing Locus Suicide Recombination (LSR)
  • Ludovic Lhermitte, Amélie Trinquand (Paris Necker), Applications of Vidjil software in Haemato-oncology: the Necker-Enfants-Malades Hospital experience
  • Frédéric Davi (Paris, La Pitié), IG repertoire of B-cell tumors : evidence for antigen selection
  • Lana Mhaldien, Soragia Athina Gkazi (London), Using Vidjil in discovering the diversity of T cells
12:00 – 13:30 Lunch
13:30 – 15:00 Practical session 2
15:00 – 15:20 Coffee Break
15:20 – 16:00 Round Table Discussion, with Martin Figeac, Mathieu Giraud, John Moppett, Mikaël Salson and Mikhail Shugay. Discussion on library preparation, sequencing instruments and protocols, bioinformatics analysis. Perspectives and possible collaborations.

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.

List of hotels with available rooms

The workshop will take place at Institut Gernez Rieu (IGR), in the heart of the Lille Hospital, at 15 minutes from Lille center. From Lille center, take the metro line 1 (yellow), direction CHR B Calmette. Stop at the CHR Oscar Lambret station. The IGR building is 600 meters from the metro station.

How to get to IGR


The workshop is organized by Mathieu Giraud, Ryan Herbert, Tatiana Rocher, Mikaël Salson, Maximilien Vanleene and Aurélie Wieczorek, from CRIStAL, Inria Lille and SIRIC OncoLille.