ARCHITECTURE AND TOOLS FOR THE QUERY OF ANTIBODY AND T-CELL RECEPTOR SEQUENCING DATA REPOSITORIES FOR ENABLING IMPROVED PERSONALIZED MEDICINE AND IMMUNOTHERAPY

Livrables

D4.1 Critical analysis tools identified for integration

D6.3 Integrated multi-omics tranSMART repository

Integrated multiomics tranSMART repository with available datasets within the iReceptor Plus platform

A handson workshop where potential users can test and interact with iReceptor Plus giving feedback and exploring how they might incorporate the platform into their workflow

D3.1 Holistic Security and Privacy Concept

D2.6 iReceptor Plus Turnkey repository available for AIRR Community

Working documented and production iReceptor Plus Turnkey repository available for AIRR Community

D8.3 Project-specific innovation approach

D4.3 Analysis tool mgt and vis UI impl, in Scientific Gateway

D1.5 ImmuneDB release

Adapt and incorporate the developments made through work packages WP2 through WP7 to enhance the capabilities of the ImmuneDB web interface

D4.5 Basic toolkit of advanced AIRR-seq analysis tools integrated

Basic toolkit of advanced AIRRseq analysis tools integrated into the iReceptor Plus Platform

D3.3 Monitoring and GDPR Aspects

Monitoring the changes in security and privacy developments and will carefully monitor latest research and industry developments

D3.4 Recommendations and proposals for new regulatory regimes

ecommendations will be made regarding improved legal regimes as to facilitate flexibility to a large audience and to facilitate wide adoption of project results while allowing rewarding those that invested Focus will be on a realistic regulatory solution

D9.1 Communication plan finalised

D1.4 VDJServer release

Release of VDJServer a cloudbased analysis portal for AIRRseq data that provides access to a suite of tools for a complete analysis workflow

D10.1 Establishing governance structure

D2.1 iReceptor Plus IPA repository interactively explore

iReceptor IPA repository that can interactively explore 100s of millions or billions of annotated sequences M36

D9.5 A final dissemination report

At the end of the project M48 a dissemination report will be delivered

D1.1 Protocol Kick-off meeting

D2.5 iReceptor Plus REST API available for platform integration

Production version of iReceptor Plus REST API available for platform integration

D7.1 An updated MiAIRR standard

An updated MiAIRR standard containing a proper representation of singlecell AIRRseq data and a corresponding API supporting singlecell queries

D1.3 iReceptor Plus Gateway implementing use case scenarios

Implementation of the iReceptor Scientific Gateway based on user feedback and the needs of the other work packages

D4.2 Tool integration methodology and implementation completed

D5.1 A list of features that can be used for potential biomarkers

D2.3 Data repositories from partner institutions (6) integrated

Data repositories from partner institutions 6 integrated into the AIRR Data Commons

D6.1 A multi-omic data model

D2.2 iReceptor repositories able to link data related to single cell

D7.3 Tool for automated import and annotation into iReceptor Plus

A tool for automated import and annotation for flow cytometry data into iReceptor Plus

D9.6 Protocol Concluding Conference

A concluding conference will be organised at the end of the project in Brussels to present the final results to key target audiences opinion leadersregulators researchers healthcare providers industry owners providers of data repositories the media and the general public A webinar will be recorded and made publicly available

D7.2 A generic single-cell data import toolkit for iReceptor Plus

D5.2 S/W to apply ML approaches for classifying individuals

Software to apply machine learning approaches for classifying individuals from different clinical cohorts

D1.2 Use cases identified and documented for development

Use cases identified and documented for development and further iteration

D4.4 User interface release candidates for deployment

User interface release candidates for deployment in Scientific Gateway

D8.2 Legal, ethics, privacy & security framework

D9.4 Protocols participation in AIR Community activities

To maximize the project impact partners will take all opportunities to disseminate and raise awareness of the project and encourage joining the AIRR Community

D9.3 Communication tools

Creating communication tools required to support the successful implementation of the communication plan

D1.6 Intermediate beta release of platform wide system

D5.3 Implementation of networks and AI-functionality iReceptor

Implementation of networks and AI-functionality iReceptor for querying the AIRR space for biomarker signatures

D3.2 Layered Security Framework

Implementation of a software framework that ensures that the FAIR principles of scientific data management and stewardship are attained, while the security of personal data is not compromised.

D6.2 Data curation and integration pipeline within tranSMART

Data curation and integration pipeline within a tranSMART repository

D2.4 Integration testing completed across all repositories

Integration testing completed across all repositories in the AIRR Data Commons, Capstone Demonstration completed

D9.2 A project identity and specific project website

D7.4 A version of iReceptor Plus that can be queried using (Kd)

A version of iReceptor Plus that can be queried using target affinity (Kd) as search parameter

Publications

Benchmarking of T cell receptor repertoire profiling methods reveals large systematic biases

Auteurs: Pierre Barennes, Valentin Quiniou, Mikhail Shugay, Evgeniy S. Egorov, Alexey N. Davydov, Dmitriy M. Chudakov, Imran Uddin, Mazlina Ismail, Theres Oakes, Benny Chain, Anne Eugster, Karl Kashofer, Peter P. Rainer, Samuel Darko, Amy Ransier, Daniel C. Douek, David Klatzmann, Encarnita Mariotti-Ferrandiz
Publié dans: Nature Biotechnology, 2020, ISSN 1087-0156
Éditeur: Nature Publishing Group
DOI: 10.1038/s41587-020-0656-3

Polymorphisms in human immunoglobulin heavy chain variable genes and their upstream regions

Auteurs: Ivana Mikocziova, Moriah Gidoni, Ida Lindeman, Ayelet Peres, Omri Snir, Gur Yaari, Ludvig M Sollid
Publié dans: Nucleic Acids Research, Numéro 48/10, 2020, Page(s) 5499-5510, ISSN 0305-1048
Éditeur: Oxford University Press
DOI: 10.1093/nar/gkaa310

Diversity in immunogenomics: the value and the challenge

Auteurs: Kerui Peng, Yana Safonova, Mikhail Shugay, Alice B. Popejoy, Oscar L. Rodriguez, Felix Breden, Petter Brodin, Amanda M. Burkhardt, Carlos Bustamante, Van-Mai Cao-Lormeau, Martin M. Corcoran, Darragh Duffy, Macarena Fuentes-Guajardo, Ricardo Fujita, Victor Greiff, Vanessa D. Jönsson, Xiao Liu, Lluis Quintana-Murci, Maura Rossetti, Jianming Xie, Gur Yaari, Wei Zhang, Malak S. Abedalthagafi, Khalid
Publié dans: Nature Methods, Numéro 18/6, 2021, Page(s) 588-591, ISSN 1548-7091
Éditeur: Nature Publishing Group
DOI: 10.1038/s41592-021-01169-5

Machine Learning Analysis of Naïve B-Cell Receptor Repertoires Stratifies Celiac Disease Patients and Controls

Auteurs: Or Shemesh, Pazit Polak, Knut E. A. Lundin, Ludvig M. Sollid, Gur Yaari
Publié dans: Frontiers in Immunology, Numéro 12, 2021, ISSN 1664-3224
Éditeur: Cold Spring Harbor Laboratory
DOI: 10.3389/fimmu.2021.627813

Animal Immunization, in Vitro Display Technologies, and Machine Learning for Antibody Discovery

Auteurs: Andreas H. Laustsen, Victor Greiff, Aneesh Karatt-Vellatt, Serge Muyldermans, Timothy P. Jenkins
Publié dans: Trends in Biotechnology, 2021, ISSN 0167-7799
Éditeur: Elsevier BV
DOI: 10.1016/j.tibtech.2021.03.003

Mining adaptive immune receptor repertoires for biological and clinical information using machine learning

Auteurs: Victor Greiff, Gur Yaari, Lindsay Cowell
Publié dans: Current Opinion in Systems Biology, 2020, ISSN 2452-3100
Éditeur: Elsevier
DOI: 10.1016/j.coisb.2020.10.010

Extended plasma half-life of albumin-binding domain fused human IgA upon pH-dependent albumin engagement of human FcRn in vitro and in vivo

Auteurs: Simone Mester, Mitchell Evers, Saskia Meyer, Jeannette Nilsen, Victor Greiff, Inger Sandlie, Jeanette Leusen, Jan Terje Andersen
Publié dans: mAbs, Numéro 13/1, 2021, Page(s) 1893888, ISSN 1942-0870
Éditeur: Landes Bioscience
DOI: 10.1080/19420862.2021.1893888

RAbHIT: R Antibody Haplotype Inference Tool

Auteurs: Ayelet Peres, Moriah Gidoni, Pazit Polak, Gur Yaari
Publié dans: Bioinformatics, Numéro 35/22, 2019, Page(s) 4840-4842, ISSN 1367-4803
Éditeur: Oxford University Press
DOI: 10.1093/bioinformatics/btz481

VDJbase: an adaptive immune receptor genotype and haplotype database.

Auteurs: Gur Yaari; William Lees; Adrian Shepherd
Publié dans: Nucleic Acids Research, Numéro 48, 2020, ISSN 0305-1048
Éditeur: Oxford University Press
DOI: 10.1093/nar/gkz872

Using Domain Based Latent Personal Analysis of B Cell Clone Diversity Patterns to Identify Novel Relationships Between the B Cell Clone Populations in Different Tissues

Auteurs: Uri Alon, Osnat Mokryn, Uri Hershberg
Publié dans: Frontiers in Immunology, Numéro 12, 2021, ISSN 1664-3224
Éditeur: Frontiers in Immunology
DOI: 10.3389/fimmu.2021.642673

A compact vocabulary of paratope-epitope interactions enables predictability of antibody-antigen binding

Auteurs: Rahmad Akbar, Philippe A. Robert, Milena Pavlović, Jeliazko R. Jeliazkov, Igor Snapkov, Andrei Slabodkin, Cédric R. Weber, Lonneke Scheffer, Enkelejda Miho, Ingrid Hobæk Haff, Dag Trygve Tryslew Haug, Fridtjof Lund-Johansen, Yana Safonova, Geir K. Sandve, Victor Greiff
Publié dans: Cell Reports, Numéro 34/11, 2021, Page(s) 108856, ISSN 2211-1247
Éditeur: Cell Press
DOI: 10.1016/j.celrep.2021.108856

Modeling the Dynamics of T-Cell Development in the Thymus

Auteurs: Philippe A. Robert, Heike Kunze-Schumacher, Victor Greiff, Andreas Krueger
Publié dans: Entropy, Numéro 23/4, 2021, Page(s) 437, ISSN 1099-4300
Éditeur: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/e23040437

Modern Hopfield Networks and Attention for Immune Repertoire Classification.

Auteurs: Michael Widrich; Bernhard Schäfl; Hubert Ramsauer; Milena Pavlović; Lukas Gruber; Markus Holzleitner; Johannes Brandstetter; Geir Kjetil Sandve; Victor Greiff; Sepp Hochreiter; Günter Klambauer
Publié dans: NeurIPS, Numéro 8, 2020, ISBN 9780262561457
Éditeur: Neural Information Processing Systems
DOI: 10.1101/2020.04.12.038158

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