Immune Repertoire Analysis with Vidjil

Lille, France, 21-22 November 2017

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 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 includes two invited talks, hematology, immunology and bioinformatics talks from the users and developers of Vidjil, and practical hands-on sessions on participant data. The previous edition, in March 2016, gathered 34 scientists from 5 countries.


The workshop will start on Tuesday 21st at 9:00 and end on Wednesday 22nd at 16:00. The full program will be available early November. The workshop includes invited talks, including one by Thierry Mora, 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 into user accounts on before the workshop. We will also provide test data for the people who do not currently have their own NGS Rep-Seq data.

Tuesday 21 November

8:00 – 9:30 Registration, coffee
9:30 – 12:00 Talk Session 1: Diagnosis and MRD for Leukemia and Lymphoma
12:00 – 14:00 Lunch
14:00 – 15:30 Talk Session 2: Developer talks, bioinformatics and algorithmics
15:30 – 16:00 Coffee Break
16:00 – 18:00 Practical session 1
19:00 – 20:30 Social event, to be announced

Wednesday 22 November

9:00 – 10:30 Talk Session 3: Clonality and Repertoire Analysis in Hematology and Immunology
10:30 – 11:00 Coffee Break
11:00 – 12:00 Invited talk: Thierry Mora
Quantifying the diversity of immune repertoires
12:00 – 14:00 Lunch
13:30 – 15:00 Practical session 2
15:00 – 16:00 Round table and conclusion
Discussion on library preparation, sequencing instruments and protocols, bioinformatics analysis. Discussion on development priorities.


Grand place de Lille

CC BY SA Velvet (source: Wikimedia Commons)

The workshop is sponsored by SIRIC OncoLille and Inria Lille. 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 e-mail to Florian Thonier :

First name: 
Last name: 

The two lunches (21 and 22 November) are free for all registered participants.
Registration deadline : 26 october 2017

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 Lilliad, in the heart of the Lille 1 Campus, at 20 minutes from Lille center. Lilliad is the brand new university library, which also hosts scientific events. From Lille center, take the metro line 1 (yellow), direction 4 Cantons. Stop at the Cité Scientifique – Professeur Gabillard station. The Lilliad building is 200 meters from the metro station.


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