Vidjil, une plateforme web pour l’ etude de populations ...
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Vidjil, une plateforme web pour l’´ etude de populations lymphocytaires par NGS Aur´ elien B´ eliard, Marc Duez, Mathieu Giraud, Ryan Herbert, Tatiana Rocher, Mika¨ el Salson, Florian Thonier Bonsai bioinformatics Hˆ opital Rennes CRIStAL (Universit´ e Lille, CNRS), Inria, GBMHM/Inca GBMHM/Inca June 23, 2017 [email protected]
Transcript of Vidjil, une plateforme web pour l’ etude de populations ...
Vidjil, une plateforme web pour l’etudede populations lymphocytaires par NGS
Aurelien Beliard, Marc Duez, Mathieu Giraud, Ryan Herbert,Tatiana Rocher, Mikael Salson, Florian Thonier
Bonsai bioinformatics Hopital Rennes
CRIStAL (Universite Lille, CNRS), Inria, GBMHM/Inca GBMHM/Inca
June 23, [email protected]
Conflicts of interest
MS : Novartis funded his living expenses for a 2-day workshop inDieppe, France
Vidjil, une plateforme web pour l’etudede populations lymphocytaires par NGS
Aurelien Beliard, Marc Duez, Mathieu Giraud, Ryan Herbert,Tatiana Rocher, Mikael Salson, Florian Thonier
Bonsai bioinformatics Hopital Rennes
CRIStAL (Universite Lille, CNRS), Inria, GBMHM/Inca GBMHM/Inca
June 23, [email protected]
Immune Repertoire Sequencing (RepSeq)
1. Monitor the immune re-sponse (vaccine, immunotherapy)
2. Identify markers for leukemiastratification and follow-up
The Adaptive Immune System
TCR and Antibody Specificity – V(D)J Recombination
TCR and Antibody Specificity – V(D)J Recombination
Indexing Labelled Immune Sequences
antibody
V(D)J recombinations are responsible for receptor diversity
V1 V2 V3 V65 D1 D2 D3 D27. . . J1 J2 J3 J4 J5 J6 C1. . .
Intron Intron
V D J
N N
Diversity region
V J
N
V(D)J recombinations are responsible for receptor diversity
V1 V2 V3 V65 D1 D2 D3 D27. . . J1 J2 J3 J4 J5 J6 C1. . .
Intron Intron
V D J
N N
Diversity region
V J
N
V(D)J recombinations are responsible for receptor diversity
V1 V2 V3 V65 D1 D2 D3D4J3 J4 J5 J6 C1 C2. . .
Intron Intron
V D J
N N
Diversity region
V J
N
V(D)J recombinations are responsible for receptor diversity
V1 V2 V3 V65 D1 D2 D3D4J3 J4 J5 J6 C1 C2. . .
Intron Intron
V D J
N N
Diversity region
V J
N
V(D)J recombinations are responsible for receptor diversity
V1 V2 V3 V17D4J3 J4 J5 J6 C1 C2. . .
Intron Intron
V D J
N N
Diversity region
V J
N
V(D)J recombinations are responsible for receptor diversity
V1 V2 V3 V17D4J3 J4 J5 J6 C1 C2. . .
Intron Intron
V D J
N N
Diversity region
V J
N
V(D)J recombinations are responsible for receptor diversity
V1 V2 V3 V17D4J3 J4 J5 J6 C1 C2. . .
Intron Intron
V D J
N N
Diversity region
V J
N
V(D)J recombinations are responsible for receptor diversity
V1 V2 V3 V17D4J3 J4 J5 J6 C1 C2. . .
Intron Intron
V D J
N N
Diversity region
V J
N
V(D)J recombinations are responsible for receptor diversity
V1 V2 V3 V17D4J3 J4 J5 J6 C1 C2. . .
Intron Intron
V D J
N N
Diversity region
V J
N
V(D)J recombinations are responsible for receptor diversity
V1 V2 V3 V17D4J3 J4 J5 J6 C1 C2. . .
Intron Intron
V D J
N N
Diversity region
V J
N
V(D)J recombinations are responsible for receptor diversity
V1 V2 V3 V17D4J3 J4 J5 J6 C1 C2. . .
Intron Intron
V D J
N N
Diversity region
V J
N
TCR and Antibody Specificity – V(D)J Recombination
Indexing Labelled Immune Sequences
antibody
Immune Repertoire Sequencing (RepSeq)Strategies – Sequencing millions of V(D)J recombinations from T-cells or B-cells
V D J
V D J
V D J
CDR3 specific primer
Consensus PCR primers
Capture probe
DNA
CDR3
Quantitative PCRa)
b)
c)
RNA-Seq
RNA
d)
Rep-Seq
HTS
Immune Repertoire Sequencing (RepSeq)Identification of all VDJ recombinations
1 000 000 VDJ = 100 000 s1 000 000 VDJ = 100 sGiraud, Salson et al., BMC Genomics, 2014
Immune Repertoire Sequencing (RepSeq)Identification of all VDJ recombinations
1 000 000 VDJ = 100 000 s1 000 000 VDJ = 100 sGiraud, Salson et al., BMC Genomics, 2014
Immune Repertoire Sequencing (RepSeq)Identification of all VDJ recombinations
1 000 000 VDJ = 100 000 s1 000 000 VDJ = 100 sGiraud, Salson et al., BMC Genomics, 2014
Ching-Hon Pui Childhood leukemias
0 70 140 210 280 3500,0001
0,001
0,01
0,1
1
10
100
Jours
Pou
rcen
tage
Concentration du lymphocyte cancereux
, by () — —
0 70 140 210 280 3500,0001
0,001
0,01
0,1
1
10
100
Jours
Pou
rcen
tage
Concentration du lymphocyte cancereux
, by () — —
A strong collaboration with Lille hospital since 2011
N. Grardel
N. DuployezA. Caillault
S. Sebda
M. Figeac
C. Preudhomme
Vidjil Platform
High-throughput Repertoire Sequencing (RepSeq) analysis
Web Application
Algorithm
C++
Client
Javascript, d3.js
Patient databaseServer
Python, web2py,AJAX
I all the Vidjil components are open-source (GPL v3)
I code on http://www.vidjil.org/ and on GitHub
I continuous integration, > 2, 000 unit and functional tests
Duez et al., PLOS One, 2016
Web application: traceability– Reports for medical records
Patient database and server
Autonomous RepSeq analysis pipeline in a clinical/research lab
Patient database and server
Autonomous RepSeq analysis pipeline in a clinical/research lab
Upload
Patient database and server
Autonomous RepSeq analysis pipeline in a clinical/research lab
Upload Process
Patient database and server
Autonomous RepSeq analysis pipeline in a clinical/research lab
Upload Process Analyze
Web Application, October 2014 to June 2017Public test server app.vidjil.org, >100 users, including 30 regular users
10,000samples
Web Application, October 2014 to June 2017Public test server app.vidjil.org, >100 users, including 30 regular users
1,000ALL/CLL patients at diagnosis in 5 labs
Web Application, October 2014 to June 2017Public test server app.vidjil.org, >100 users, including 30 regular users
1,000ALL/CLL patients at diagnosis in 5 labs
Web Application, October 2014 to June 2017Public test server app.vidjil.org, >100 users, including 30 regular users
1,000ALL/CLL patients at diagnosis in 5 labs
Lille, 2015: routine diagnosis of patients with ALL5 tubes, mainly BIOMED-2 primers
January-March34 patients
3 patients with Sanger failurecomparison with IMGT and igBlast
January-December120 patients
Y. Ferret, A. Caillault et al., British J. of Haematology, 2016
Analyze your immune repertoire data with Vidjil
Interactively process all lymphocyte receptorsReady-to-use platform to handle HTS/RepSeq data
1. Upload, 2. Process, 3. View and Annotate
Analyze your immune repertoire data with Vidjil
Interactively process all lymphocyte receptorsReady-to-use platform to handle HTS/RepSeq data
1. Upload, 2. Process, 3. View and Annotate
Open-source softwareFeel free to use: app.vidjil.org
Feel free to contribute: git.vidjil.org
Analyze your immune repertoire data with Vidjil
Interactively process all lymphocyte receptorsReady-to-use platform to handle HTS/RepSeq data
1. Upload, 2. Process, 3. View and Annotate
Open-source softwareFeel free to use: app.vidjil.org
Feel free to contribute: git.vidjil.org
New academic and industrial collaborationsALL/CLL diagnosis and follow-up, other pathologies
Immunological studies, immune monitoring
