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Three newly certified AIRR-compliant software tools: ImmuneML, CompAIRR and Dandelion

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The AIRR Community is excited to announce that three tools have recently been certified as compliant with the AIRR-C v1.0 standard for AIRR-Seq software tools. These are ImmuneML – an ecosystem for machine learning analysis of adaptive immune receptor repertoires, CompAIRR – a tool for ultra-fast comparison of adaptive immune receptor repertoires by exact and approximate sequence matching, and Dandelion – a tool for analyzing single cell BCR/V(D)J 10x Genomics data. 

In an effort to enable rigorous and reproducible immune repertoire research at the largest scale possible, the AIRR-C Software Working Group has established a standard to validate software tools using the AIRR-C Standards and meeting a series of interoperability and quality criteria. Developers interested in certifying their tools should complete the checklist and submit it to the AIRR-C Software Working Group for evaluation and ratification by its members.

More details can be found at the website AIRR Software WG – Guidance for AIRR Software Tools.

All compliant tools will be issued a badge and listed on the website AIRR Software WG – List of Tools Certified as Compliant. The list includes SONAR, ImmuneDB, Immcantation, ImmuneML, CompAIRR and Dandelion.

Latest AIRR Community seminar available on YouTube

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If you are interested in understanding how to perform easy, fast and practical AIRR analysis, check out the latest video on the AIRR Community YouTube channel.

Learn about the “Exploration of single-cell and bulk immune repertoire data in R using Immunarch with application to immunotherapy” by speaker Vadim I. Nazarov, Co-Founder and CEO, ImmunoMind.

 

 

Needs and challenges of biological controls for AIRR-sequencing standardization: an AIRR-C review published in eLife

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Announcing the latest AIRR Community publication!

Adaptive Immune Receptor Repertoire (AIRR) can be deeply analyzed to study its complexity thanks to AIRR-sequencing (AIRR-seq) based on high throughput sequencing. However, like many high-throughput technologies, AIRR-seq comes with several technical challenges, notably the lack of established controls and standards, a necessity when considering current available and envisioned AIRR-seq applications. The Biological Resources Working Group within the AIRR Community, established in 2017, aims at studying, prioritizing and developing biological controls and standardization reagents for AIRR-seq studies. In this article, they review current practices, resources and considerations for using and developing AIRR-seq standards and controls.

COVID-19 AIRR-seq Vaccine Data Available!

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The first AIRR-seq dataset from people who have been vaccinated against COVID-19 is now available in the AIRR Data Commons, accessible through the iReceptor Gateway. As more vaccination studies are made available, researchers will be able to compare these antibody/B-cell and T-cell receptor (BCR/TCR) sequences to the over 1 billion such sequences from studies of COVID-19 patients. Vaccines are designed to elicit the same immune response as that caused by natural infection, and the availability of data from vaccinated individuals will enable direct comparisons between these two types of responses. Such comparisons can determine the effect of different vaccine technologies, measure level of protection against circulating variants, and identify immune pressures leading to future variants. For example, this first vaccination study (Goel et al.) that is now curated in the AIRR Data Commons presents data from five recovered donors at three time points: before vaccination and after the first and second vaccinations, and the comparison suggests that COVID-19 recovered individuals may only require a single vaccine dose to achieve peak immune response. Similar comparisons as new vaccination studies become available will help inform public health decisions such as vaccine dosing and booster schedules.

The AIRR Community encourages and supports researchers in sharing their COVID-19 AIRR-seq data from natural infection and vaccination through the AIRR Data Commons. Now more than ever, access to curated, ready-to-analyze antibody and BCR/TCR sequence data will contribute to rapid health insights and public health strategies worldwide as we work to move through and beyond the COVID-19 global pandemic.

For an overview of the AIRR Data Commons, including demos on how to find and share data, see our recent webinar, The AIRR Data Commons: 4 billion reasons to store, analyze and share antibody/B-cell and T-cell receptor repertoire data.

Join us for “Fundamentals of the Immune System”, Parts I & II

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Part I:  Organization of the immune system.
Thursday June 3, 2021, 11am – 1pm ET. 

Part II:  The immune system in action.
Tuesday June 15, 2021, 11am – 1pm ET.

In this 2-part workshop on the fundamentals of the immune system, Dr. Jamie Scott, Professor Emerita, Simon Fraser University, Canada, will first provide an overview of humoral and cellular immunity, and the basic structure of the immune system, including its cells, tissues and compartments, along with the “superhighway” of the immune system: the circulatory and lymphatic systems. In that context, innate and adaptive immune systems and their interaction, and the general timing and dynamics of immune responses will be presented.

The processes of lymphocyte development, including the various B- and T-cell subsets, positive and negative selection, and the genetic basis of B-cell and T-cell receptor diversification, will be presented to provide a clear idea of what adaptive-immune receptor repertoires (AIRRs) are, and in general terms, how they are currently assessed via high-throughput sequencing. Dr. Scott will then cover the signaling, activation, proliferation and differentiation of T-cell and B-cell clones in the context of lymphoid compartments where antigen is concentrated and presented to naïve and memory B and T cells. The role of co-stimulation in determining the type immune response generated will be emphasized.

In Part II, Dr. Scott will review the orchestration of systemic and mucosal immune responses, including the roles of tolerance and inflammation in these processes. Examples of immune responses to vaccines, chronic viral infection, and/or cancer, as well as autoimmunity, will be presented as variations on a common theme, reiterating the dynamics of the immune response. Some engineered immunotherapies, such as therapeutic antibodies, CAR-T cells and dendritic-cell vaccines, will be introduced as well.

The importance of AIRR-sequencing data to our understanding of immune responses will be emphasized throughout the latter half of this workshop.

Click here to register for Part I

Click here to register for Part II