Bioinformatics and Applications in Hematology and Immunology
Workshop W5 at ECCB 2016, The Hague, Netherlands, Saturday 3 september 2016

High-throughput sequencing now enables profiling the repertoires of lymphocyte antigen receptor on an unprecedented scale. RepSeq 2016 workshop will cover emerging methods and software dedicated to Immune Repertoire Sequencing data, as well as best analysis practices. The workshop is targeted both to bioinformaticians developing RepSeq methods and software and hematologists or immunologists using RepSeq software for research and clinical applications.

Adaptive immunity is a process by which T- and B-lymphocytes are able to mount an effective and specific immune response against invading pathogens. It has been estimated that about 1012 different lymphocytes are present in an individual at any given time, each one of which is able to recognize a single antigen. This striking diversity required to withstand a multitude of pathogens is generated by a process called V(D)J recombination producing a set of unique T- and B-cell receptors. The original repertoire of immune receptors is then shaped by thymic selection of T-cells and affinity maturation B-cells. While encoding the antigen specificity of T- and B-cells, immune receptors also appear to be ideal targets for tracking malignant cells in leukemia and lymphoma.

With the advent of high-throughput sequencing (HTS) it is now possible to sequence millions of T- and B-cell receptors and study the structure and dynamics of adaptive immune system using a family of techniques called Immune Repertoire Sequencing (RepSeq). RepSeq technique produces huge amounts of highly complex data that should be handled using dedicated bioinformatic methods. Indeed, commonly used bioinformatic tools are not well-suited for such data. For example, resolving V(D)J junctions that are only partially encoded in genome within a set of highly homologous amplicons is a challenging task for common alignment algorithms. The first dedicated RepSeq software and algorithms started to emerge around 2011. Currently, there are more than a dozen tools able to manage, process, visualize and perform statistical analysis of RepSeq data: ARResT, Change-O, Decombinator, IgBlast, IGGalaxy, IMGT/HighV-QUEST, ImmunExplorer, IMSEQ, miTCR, MiXCR, pRESTO, tcR, TCRKlass, VDJtools/VDJviz, and Vidjil.

Implementation of aforementioned software tools required developing complex algorithms, for example, V(D)J mapping that utilizes string matching techniques such as optimized dynamic programming, spaced seeds, statistical models, clustering or text indexing. Combining high-throughput sequencing techniques and dedicated bioinformatic algorithms provided us with a much better understanding of immune repertoire structure and allowed immunologists all around the world to gain novel insights into age-related repertoire dynamics, mechanisms behind autoimmune diseases and cancer immunity. Notably, those techniques appear to be highly effective in applied immunology tasks, such as disease stratification and tracking minimal residual disease in patients with leukemia.


The registration can only be done on the conference website. It is possible either to register for the workshop only (60€ for students, 110€ otherwise; respectively raised to 90€ and 165€ after July 29th) or to the whole conference. All the details are specified on the conference website.


9:00Opening remarks
9:15Keynote: Thierry Mora
Quantifying the diversity of immune repertoires
The diversity of repertoires of B-cell and T-cell receptors is generated by a stochastic process of gene rearrangement called VDJ recombination. This diversity is later shaped by selection, clonal proliferation, and somatic hypermutations in the case of B cells. I will show how these processes can be learned quantitatively from high-throughput repertoire sequencing data, and used to estimate the diversity of repertoires, their overlap between individuals, and development.
10:00 Yana Safonova, Alexander Shlemov, Sergey Bankevich, Andrey Bzikadze and Pavel Pevzner
Y-Tools: a Toolkit for Construction and Analysis of Adaptive Immune Repertoires
10:30Coffee break and Posters
11:00 Mikaël Salson, Aurélie Caillault, Marc Duez, Yann Ferret, Alice Fievet, Michaela Kotrova, Florian Thonier, Patrick Villarese, Stephanie Wakeman, Gary Wright and Mathieu Giraud
A Dataset of Sequences with Manually Curated V(D)J Designations
11:30 Barbera DC Van Schaik, Paul L Klarenbeek, Marieke E Doorenspleet, Sabrina Pollastro, Anne Musters, Giulia Balzaretti, Rebecca EE Esveldt, Frank Baas, Niek de Vries and Antoine HC van Kampen
T- and B-cell Receptor Repertoire Sequencing: Quality Control and Clone Identification
12:00Informal discussions
13:45Keynote: Anton Langerak
Impact of high-throughput immunogenetics in clinical and research hematology
High-throughput immunogenetic studies are finding their way in hematological and immunological research for clonality assessment and monitoring of malignant leukemic cells, as well as evaluation of immune repertoires. In this lecture the potentials and pitfalls of such studies will be discussed and current standardization and validation efforts in the EuroClonality-NGS consortium will be highlighted that aim to allow implementation of this new technology in routine clinical diagnostics.
14:30 Elisa Genuardi, Marco Beccuti, Greta Romano, Luigia Monitillo, Marco Ladetto, Simone Ferrero and Francesca Cordero
IGH screening by NGS in mantle cell lymphoma: the DNA input matters
15:00Coffee break and Posters
15:30 Ivan Zvyagin, Ilgar Mamedov, Olga Tatarinova, Ekaterina Komech, Yuri Lebedev, Michael Maschan and Dmitry Chudakov
T cell repertoire profiling after hematopoietic stem cell transplantation with alpha-beta T cell depletion
16:00Round Table : Challenges of Rep-Seq bioinformatics and applications, methodologies, interactions between Rep-Seq software
16:45 – 17:00Closing remarks

Call for contributions

As this field has emerged only recently, there is still little consensus on the techniques, protocols and algorithms that should be used in RepSeq studies. The RepSeq 2016 workshop will thus be a platform to encourage discussions on immune repertoire sequencing allowing bioinformaticians and biologists to exchange ideas on RepSeq analysis and to better understand forthcoming challenges that will answer real-world immunogical and hematological questions.

We welcome both methodological and algorithmic contributions in bioinformatics as well as contributions in fundamental or applied immunology and hematology on the following themes:

  • Library preparation and sequencing protocols for RepSeq
  • Bioinformatic methods to manage and analyze RepSeq data: reads pre-processing, V(D)J mapping, clone clustering, statistics, visualization
  • Fundamental and applied RepSeq studies in immunology and hematology
  • Expected developments in RepSeq methodology: paired-chain sequencing, functional annotation of repertoires

Keynote speakers

Anton Langerak is associate professor in immunology in Erasmus MC (Rotterdam). He is chairing the working group EuroClonality-NGS that gathers hematological labs around Europe. His talk will include an overview of what RepSeq studies can bring in clinical and research hematology.

Thierry Mora is working at Laboratoire de Physique Statistique in ENS (Paris). He works on the statistical physics modelling of biological systems, focusing on systems comprising many interacting units and displaying emergent behaviours. His talk will include an overview of modeling and statistics of V(D)J recombinations.

Key dates

Submission server opens5 April 2016
Abstract/Paper submission deadline
The submission is now closed.
1 May 201623 May 2016
Abstract/Paper acceptance notification30 May 20168 June 2016
Detailed program14 June 2016
Final version of accepted abstract/papers20 June 20161 July 2016
Workshop at ECCB 2016, 3 September 2016


The abstract or papers, in .pdf, should be submitted through EasyChair. They should be between 4 pages (around 2000 words) and 12 pages. Download the LaTeX template and the Word/LibreOffice template.

The proceedings of the workshop will be published in open access for authors willing to distribute their contribution. We are in the process of contacting editors to publish selected extended abstracts from the workshop as articles in a special issue of a journal.



  • Jack Bartram, University College London, UK
  • Eva Froňková, Charles University Prague, Czech Republic
  • Mathieu Giraud, CNRS, Lille, France (program co-chair)
  • Peter N. Robinson, Charité Berlin, Germany
  • Mikaël Salson, Université de Lille, France (proceedings chair)
  • Mikhail Shugay, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia (program co-chair)
  • Andrew P. Stubbs, Erasmus MC, Rotterdam, The Netherlands