iReceptor: A platform for querying and analyzing antibody/B‐cell and T‐cell receptor repertoire data across federated repositories

Corrie, Brian; Marthandan, Nishanth; Zimonja, Bojan; Jaglale, Jerome; Zhou, Yang; Barr, Emily; Knoetze, Nicole; Breden, Frances Margaret Walker; Christley, Scott; Scott, Jamie K.; Cowell, Lindsay G.; Breden, Felix

doi:10.1111/imr.12666

Cited by 133 publications

(152 citation statements)

References 41 publications

Supporting

Mentioning

151

Contrasting

Order By: Relevance

“…Some of these issues are addressed by services that provide Ig-seq-specific data deposition and analysis pipelines such as the B-T.CR wiki (https://b-t.cr), Imm-Port (http://immport.org) (26,27), immunoSEQ Analyzer (http:// clients.adaptivebiotech.com/), iReceptor (http://ireceptor.irmacs. sfu.ca/) (28), or VDJServer (http://vdjserver.org) (29). The iReceptor and the VDJServer are the main resources that fall under the umbrella of the organized effort of the Adaptive Immune Receptor Repertoire Community to provide standardized deposition and analysis pipelines for the Ig-seq outputs (24).…”

mentioning

confidence: 99%

Observed Antibody Space: A Resource for Data Mining Next-Generation Sequencing of Antibody Repertoires

Kovaltsuk

Leem

Kelm

et al. 2018

The Journal of Immunology

177

235

View full text Add to dashboard Cite

Abs are immune system proteins that recognize noxious molecules for elimination. Their sequence diversity and binding versatility have made Abs the primary class of biopharmaceuticals. Recently, it has become possible to query their immense natural diversity using next-generation sequencing of Ig gene repertoires (Ig-seq). However, Ig-seq outputs are currently fragmented across repositories and tend to be presented as raw nucleotide reads, which means nontrivial effort is required to reuse the data for analysis. To address this issue, we have collected Ig-seq outputs from 55 studies, covering more than half a billion Ab sequences across diverse immune states, organisms (primarily human and mouse), and individuals. We have sorted, cleaned, annotated, translated, and numbered these sequences and make the data available via our Observed Antibody Space (OAS) resource at http://antibodymap.org The data within OAS will be regularly updated with newly released Ig-seq datasets. We believe OAS will facilitate data mining of immune repertoires for improved understanding of the immune system and development of better biotherapeutics.

show abstract

mentioning

confidence: 99%

Observed Antibody Space: A Resource for Data Mining Next-Generation Sequencing of Antibody Repertoires

Kovaltsuk

Leem

Kelm

et al. 2018

The Journal of Immunology

177

235

View full text Add to dashboard Cite

show abstract

“…It therefore seems more promising to drive standardization within research communities while looking out for opportunities for overall standardization. Thus, the workshop envisioned the HRIC as a distributed collection of data repositories, people, and services, which together make up a framework for sharing and operating as a federated data commons, with reproducible software, standards, and expertise based on joint policies and guidelines on conducting health research, much like the smaller frameworks used successfully in previous initiatives [2,[16][17][18][19]. The need for federation is also highlighted in the proposed EU action plan for 'Making sense of big data in health research' [3].…”

Section: Existing Standards and Guidelinesmentioning

confidence: 99%

“…We would like to thank the scientific policy officers at the European Commission Health Directorate, who developed the workshop concept, organized it, and provided input to this publication: Sasa Jenko, Katarina Krepelkova, Christina Kyriakopoulou, Jana Makedonska, Joana Namorado, Elsa Papadopoulou, Jan Van de Loo and Gregor Schaffrath (National Expert in 17 Fondazione Toscana Life Sciences, 53100 Siena, Italy. 18 27 National Cancer Institute, Vilnius, Lithuania.…”

Section: Acknowledgementsmentioning

confidence: 99%

Towards a European health research and innovation cloud (HRIC)

Aarestrup

Albeyatti

Armitage³

et al. 2020

Genome Med

View full text Add to dashboard Cite

The European Union (EU) initiative on the Digital Transformation of Health and Care (Digicare) aims to provide the conditions necessary for building a secure, flexible, and decentralized digital health infrastructure. Creating a European Health Research and Innovation Cloud (HRIC) within this environment should enable data sharing and analysis for health research across the EU, in compliance with data protection legislation while preserving the full trust of the participants. Such a HRIC should learn from and build on existing data infrastructures, integrate best practices, and focus on the concrete needs of the community in terms of technologies, governance, management, regulation, and ethics requirements. Here, we describe the vision and expected benefits of digital data sharing in health research activities and present a roadmap that fosters the opportunities while answering the challenges of implementing a HRIC. For this, we put forward five specific recommendations and action points to ensure that a European HRIC: i) is built on established standards and guidelines, providing cloud technologies through an open and decentralized infrastructure; ii) is developed and certified to the highest standards of interoperability and data security that can be trusted by all stakeholders; iii) is supported by a robust ethical and legal framework that is compliant with the EU General Data Protection Regulation (GDPR); iv) establishes a proper environment for the training of new generations of data and medical scientists; and v) stimulates research and innovation in transnational collaborations through public and private initiatives and partnerships funded by the EU through Horizon 2020 and Horizon Europe.

show abstract

“…Finally, high-throughput analyses of millions of different antibody sequences require advanced bioinformatics pipelines. Several bioinformatics tools have been reported [83] and standardized protocols on reporting antibody sequences have been developed by the Adaptive Immune Receptor Repertoire (AIRR) Community [84,85]. A detailed description of the methods applied is beyond the scope of this review and they are covered in previous reviews [83,86].…”

Section: Sequencing and Bioinformaticsmentioning

confidence: 99%

Exploiting B Cell Receptor Analyses to Inform on HIV-1 Vaccination Strategies

et al. 2020

View full text Add to dashboard Cite

The human antibody repertoire is generated by the recombination of different gene segments as well as by processes of somatic mutation. Together these mechanisms result in a tremendous diversity of antibodies that are able to combat various pathogens including viruses and bacteria, or malignant cells. In this review, we summarize the opportunities and challenges that are associated with the analyses of the B cell receptor repertoire and the antigen-specific B cell response. We will discuss how recent advances have increased our understanding of the antibody response and how repertoire analyses can be exploited to inform on vaccine strategies, particularly against HIV-1.Antibodies are composed of heavy and light chains, both of which are divided into a constant and a variable region ( Figure 1a). The different isotypes for the heavy chain constant regions mediate different effector functions and are grouped into the classes IgM, IgD, and IgE [3]. The variable regions of heavy and light chains form the paratope that contacts the epitope on a particular antigen (e.g., on a bacterial or viral surface protein). Two essential steps act during the lifespan of a B cell to generate B cell receptor diversity: (i) the V(D)J recombination process that builds the naïve (i.e., antigen-inexperienced) B cell repertoire, and (ii) somatic hypermutation (SHM) during the process of affinity maturation that generates high affinity B cell receptors and antibodies (i.e., the antigen-experienced repertoire).lifespan of a B cell to generate B cell receptor diversity: i.) the V(D)J recombination process that 52 builds the naïve (i.e., antigen-inexperienced) B cell repertoire, and ii.) somatic hypermutation (SHM) 53 during the process of affinity maturation that generates high affinity B cell receptors and antibodies 54 (i.e., the antigen-experienced repertoire). 55The initial diversity of the B cell repertoire results from the assembly of the B cell receptor 56 during early B cell development in the bone marrow. The recombination-activating gene (RAG) 1/2 57 enzymes recombine variable (V), diversity (D), and joining (J) gene segments of the immunoglobulin 58 heavy (IgH) chain locus to first assemble the heavy chain variable region, followed by V and J gene 59 segment recombination within the Ig kappa (IgK) and Ig lambda (IgL) loci [4]. Junctional diversity is 60 further increased by RAG1/2 and other enzymes through the generation of palindromic (P) 61 nucleotides, as well as by the terminal deoxynuclotidyl transferase (TdT) through the addition of 62 non-template (N) nucleotides [5] (Figure 1b). Heavy and light chain V genes exclusively encode for 63 two complementarity determining regions (CDR1 and CDR2) that are usually structurally exposed 64 at the tip of the antibody and contribute to antigen recognition. A third CDR (CDR3) is generated by 65 the V(D)J recombination process and is the most variable part within B cell receptors and antibodies. 66The CDRs are interspersed and flanked with framework regions (FWR) that mainly function a...

show abstract

iReceptor: A platform for querying and analyzing antibody/B‐cell and T‐cell receptor repertoire data across federated repositories

Cited by 133 publications

References 41 publications

Observed Antibody Space: A Resource for Data Mining Next-Generation Sequencing of Antibody Repertoires

Observed Antibody Space: A Resource for Data Mining Next-Generation Sequencing of Antibody Repertoires

Towards a European health research and innovation cloud (HRIC)

Exploiting B Cell Receptor Analyses to Inform on HIV-1 Vaccination Strategies

Contact Info

Product

Resources

About