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You are here: Home / Archives for Adaptive immune receptor repertoire

Join us on June 9th for our next webinar – Registration is open!

May 26, 2022 by The Antibody Society

In this webinar, Drs. Deane, Raybould and Boyles will share examples of how structure prediction enriches antibody sequence data and provide practical guidance for getting started using Oxford Protein Informatics Group (OPIG) tools to structurally featurise your antibody sequences. In particular, they will demonstrate the added value to tasks such as antibody functional clustering, repertoire disease-response diagnosis, and virtual screening.

Speaker bios are here.

Registration is open!

Filed Under: Adaptive immune receptor repertoire Tagged With: Adaptive Immune Receptor Repertoire Community

AIRR-C Meeting VI – Registration Is Live!

March 4, 2022 by Pam Borghardt

The AIRR-C Meetings Sub-committee is excited to announce that registration is live!  Be sure to sign up soon to take advantage of the early bird discount!

AIRR Community Meeting VI “Exploring New Frontiers” will be held in La Jolla, CA from May 17-19, 2022.

REGISTER NOW

Exploring New Frontiers:  This meeting has two themed “Challenge Sessions” meant to:
(i) Initiate and implement a strategic plan for the AIRR Community that integrates the Working Groups’ activities toward the central goal of universally accepted AIRR-seq data standards;
(ii) Introduce the Community to multidimensional systems approaches for characterizing immune responses, and how AIRR-seq data can benefit such approaches.

 

Meetings and presentations will take place at the Hilton La Jolla Torrey Pines and a hotel room block has been arranged at a discounted rate. The meeting will provide opportunities for investigators and trainees to network, participate in AIRR Community Working Groups and Sub-committee meetings, enjoy world class presentations, poster sessions, and deep dive tutorials.

Sign up today!

Filed Under: Adaptive immune receptor repertoire, AIRR Community Tagged With: Adaptive Immune Receptor Repertoire Community

Register now for our webinar on computational mining of immune receptor germline gene loci variation

January 28, 2022 by Janice Reichert

Registration for our next webinar, “Computational mining of immune receptor germline gene loci variation“, is now open!

B and T cell receptors play a critical role in responding to pathogens and vaccination, and in the pathology of several diseases of the immune system. Gene segments at the T cell receptor and immunoglobulin loci serve as templates for the generation and expression of T and B cell receptors and antibodies. Defining genetic variation within these highly polymorphic loci is critical to furthering our understanding of immunological diseases, and informing the design of vaccines and therapeutics. However, at the genomic level, these loci have been difficult to analyze due to their repetitive nature, rich in segmental duplications, simple repeats and retrotransposon elements. To overcome this complexity, several sequencing technologies and algorithms have been developed to more fully define the spectrum of genetic variation in these immune loci in human populations and other species. This webinar includes demonstrations of three orthogonal and complementary methods. First, Dr. Corcoran will present IgDiscover, an IG and TR adaptive immune repertoire sequencing (AIRR-seq) germline inference tool that has been in use for several years and applied to multiple species. The IgDiscover output is highly reproducible and can facilitate the comparison of multiple individuals in disease cohorts to identify disease associated allelic or structural variants. Ayelet Peres will present on VDJbase and RAbHIT, two bioinformatics tools for germline variation detection from AIRR-seq using population analysis and chromosomal phasing. These tools have been used to discover germline variations affecting the expressed repertoires. Finally, Dr. Rodriguez will demonstrate an approach using long-read sequencing and a bioinformatics tool, IGenotyper, to fully characterize both coding and non-coding single-nucleotide variants, small insertions and deletions, and structural variants across IG and TCR loci in a haplotype-specific manner. This will also include discussion on how IGenotyper is being applied to survey immune loci in non-human species.

Register here!

Tools and Software to be discussed:

  • IgDiscover analyzes antibody repertoires and discovers new V genes from high-throughput sequencing reads. Heavy chains, kappa and lambda light chains are supported (to discover VH, VK and VL genes).
  • VDJbase.org – a database of adaptive immune receptor genes, genotypes, and haplotypes.
  • RAbHIT – R tool for haplotype inference from BCR and TCR repertoires.
  • VDJbase pipeline –  BCR and TCR repertoires downstream analysis for VDJbase reports.
  • IGenotyper (or IG) was developed for PacBio capture data to assemble the Immunoglobulin Heavy Chain locus (IGH), genotype the IGH genes, and identify SNPs, indels and SVs within the IGH locus.

Filed Under: Adaptive immune receptor repertoire

Latest AIRR Community seminar available on YouTube

November 8, 2021 by Pam Borghardt

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.

 

 

Filed Under: Adaptive immune receptor repertoire, AIRR Community Tagged With: Adaptive Immune Receptor Repertoire Community, immunotherapy, single cell

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

July 31, 2021 by Pam Borghardt

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.

Filed Under: Adaptive immune receptor repertoire, AIRR Community, Biological controls

AIRR Community News

AIRR Community Merchandise Shop Now Open!

April 28, 2022 By Pam Borghardt

The AIRR Communications Sub-committee is pleased to announce the launch of an online merchandise shop featuring AIRR Community logo’d merchandise. Shirts, hoodies, tote bags and stickers are currently available, with additional designs to be added in the future. Be sure to check out the special Immuno-Collection while you are browsing! All products are constructed from certified […]

AIRR Community 2022 Executive Sub-committee Election

April 4, 2022 By Pam Borghardt

With each major meeting interval of the AIRR Community, elections are held for leadership positions on the AIRR-C Executive Sub-committee.  This spring, per our governance, we are seeking nominations for Executive SC Chair-Elect and up to three members of the Executive SC. To nominate an individual to serve on the AIRR-C Executive SC, the nominator […]

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AIRR Community

AIRR Community

The Adaptive Immune Receptor Repertoire Community is a research-driven group organizing around the use of high-throughput sequencing technologies to study antibody/B-cell and T-cell receptor repertoires.

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  • Thanks to all who participated in Antibody Engineering & Therapeutics Europe! June 9, 2022
  • European Commission approves Lunsumio for people with relapsed or refractory follicular lymphoma June 8, 2022
  • Join us on June 9th for our next webinar – Registration is open! May 26, 2022

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