Adaptive Immune Receptor Repertoire Community
The Adaptive Immune Receptor Repertoire (AIRR) Community.[1][2] is a research and industry representation group with interests in the use of next-generation sequencing technologies[3][4] with focus on B-cell and T-cell receptor repertoires[5]. The group is part of The Antibody Society[6] Inc. (TAbS) a non-profit[7] international trade association. AIRR Community members include scientists, clinicians, bioinformaticians, and industry representatives.
The AIRR Community publishes research articles proposing standards for the generation, annotation, storage and sharing of AIRR-seq data following FAIR principles[8]. The Organisation provides experts[9] for the FDA precisionFDA program and organizes meetings and workshops to report progress in the field and to promote their software standards.
Contributions and Standards
The AIRR community tries to contribute to the field of immunology by defining the AIRR data standards[10][11]. These standards aim to improve data interoperability by ensuring that the data collected on adaptive immune receptor repertoires, such as B and T cell repertoires, can be shared and analyzed in a consistent and interoperable manner. Companies and software providers such as 10X Genomics and IMGT have adopted the AIRR data standards and use them in addition to their own data formats, which helps to enable data sharing and collaboration within the broader scientific community [12][13][14]
These standards are established and documented in form of the AIRR Data Commons[15] which provides public access to more than 80 MiARR standard compliant studies and AIRR-seq data for query and download. The AIRR Data Commons has grown from just under 400 million sequence annotations in late 2018 to its current size[16] (04/2022) of seven distributed repositories with 85 studies, 7200 sample repertoires, and 5.4 billion sequence annotations and is still growing. Of the seven distributed community repositories, there are two in Canada (the iReceptor Public Archive and iReceptor COVID-19 repositories[17]), one in the US (managed by VDJServer[18]), one VDJBase repository at Bar Ilan University in Israel, two in Germany at DKFZ in Heidelberg and Muenster, one in South Africa at NICD and one at Sorbonne Universite in France.
Organization and Structure
The community is organized in seven working groups and four sub-committees:
Working Groups
- Biological Resources Working Group
- Common Repository Working Group
- Diagnostics Working Group
- Germline Database Working Group
- Legal and Ethics Working Group
- Software Working Group
- Standards Working Group
Sub-committees
- Communications Sub-committee
- Executive Sub-committee
- Inferred Allele Review Sub-committee
- Meetings Sub-committee
History and Meetings
The original AIRR Community meetings were the brainchild of Jamie Scott, Tom Kepler, and Felix Breden in 2014 resulting in the first community meeting in 2015 at Wosk Centre, Simon Fraser University. This meeting was the catalyst for creating both the AIRR-C website and for the formal creation of the AIRR-C Working Groups[19].
AIRR Community Meeting II was held 27-30 June 2016 at the National Institutes of Health (NIH)'s Fishers Lane facility, Rockville, Maryland.
AIRR Community Meeting III December 3–6, 2017, NIH Fishers Lane Conference Centre, Rockville, Maryland.
AIRR Community Meeting IV: "Bridging the Gaps" May 11–15, 2019, University of Genoa, Italy was the first meeting in Europe and further expanded the outreach of the AIRR community to European research groups.
AIRR Community Special Event: Response to COVID-19, September 8–10, 2020, Virtual
AIRR Community Pre-meeting V: Joint Pre-meeting with the AIRR Community and Tsinghua University "AIRR-seq in the Pandemic", December 5–6, 2020, Virtual
AIRR Community Meeting V: Zooming in to the AIRR Community December 8–10, 2020 was conducted as online only meeting due to event and travel restriction as reaction to the COVID-19 pandemic.
AIRR Community Meeting VI: “Exploring New Frontiers” was held in La Jolla, CA from May 17-19, 2022.
See also
https://www.antibodysociety.org/the-airr-community/
https://www.antibodysociety.org/
https://www.youtube.com/airrcommunity
References
- ↑ "The AIRR Community". The Antibody Society. Retrieved 2022-04-04.
- ↑ "About the AIRR Community". Retrieved 2023-03-16.
- ↑ Rubelt, Florian; Busse, Christian E.; Bukhari, Syed Ahmad Chan; Bürckert, Jean-Philippe; Mariotti-Ferrandiz, Encarnita; Cowell, Lindsay G.; Watson, Corey T.; Marthandan, Nishanth; Faison, William J.; Hershberg, Uri; Laserson, Uri (December 2017). "Adaptive Immune Receptor Repertoire Community recommendations for sharing immune-repertoire sequencing data". Nature Immunology. 18 (12): 1274–1278. doi:10.1038/ni.3873. ISSN 1529-2916. PMC 5790180. PMID 29144493.
- ↑ Eugster, Anne; Bostick, Magnolia L.; Gupta, Nidhi; Mariotti-Ferrandiz, Encarnita; Kraus, Gloria; Meng, Wenzhao; Soto, Cinque; Trück, Johannes; Stervbo, Ulrik (2022), Langerak, Anton W., ed., "AIRR Community Guide to Planning and Performing AIRR-Seq Experiments", Immunogenetics: Methods and Protocols, Methods in Molecular Biology, New York, NY: Springer US, 2453, pp. 261–278, doi:10.1007/978-1-0716-2115-8_15, ISBN 978-1-0716-2115-8, PMC 9761540 Check
|pmc=value (help), PMID 35622331 Check|pmid=value (help), retrieved 2022-07-28 - ↑ Labant, MaryAnn (February 28, 2023). "Immune Profiling: Standardizing and Accessing Immunogenetic Data".
- ↑ "Homepage of The Antibody Society". The Antibody Society. Retrieved 2022-04-04.
- ↑ "Full text of Full Filing for fiscal year for THE ANTIBODY SOCIETY INC". 9 May 2013. Retrieved 2023-03-16.
- ↑ Wilkinson, Mark D.; Dumontier, Michel; Aalbersberg, IJsbrand Jan; Appleton, Gabrielle; Axton, Myles; Baak, Arie; Blomberg, Niklas; Boiten, Jan-Willem; da Silva Santos, Luiz Bonino; Bourne, Philip E.; Bouwman, Jildau (December 2016). "The FAIR Guiding Principles for scientific data management and stewardship". Scientific Data. 3 (1): 160018. Bibcode:2016NatSD...360018W. doi:10.1038/sdata.2016.18. ISSN 2052-4463. PMC 4792175. PMID 26978244.
- ↑ "PrecisionFDA Experts". Retrieved 2023-03-16.
- ↑ "airr-standards Documentation Release 1.4". Feb 15, 2023.
- ↑ "AIRR Standards v1.4.1". GitHub. Sep 24, 2022.
- ↑ "IMGT/V-QUEST program version: 3.5.31 (29 July 2022) - IMGT/V-QUEST reference directory release: 202304-4 (26 January 2023)". 26 January 2023.
- ↑ "Understanding Cell Ranger V(D)J Output".
- ↑ "Building scientific communities - Lessons learned with AIRR".
- ↑ Christley, Scott; Aguiar, Ademar; Blanck, George; Breden, Felix; Bukhari, Syed Ahmad Chan; Busse, Christian E.; Jaglale, Jerome; Harikrishnan, Srilakshmy L.; Laserson, Uri; Peters, Bjoern; Rocha, Artur (2020-06-17). "The ADC API: A Web API for the Programmatic Query of the AIRR Data Commons". Frontiers in Big Data. 3: 22. doi:10.3389/fdata.2020.00022. ISSN 2624-909X. PMC 7931935 Check
|pmc=value (help). PMID 33693395 Check|pmid=value (help). - ↑ "AIRR Data Commons". The Antibody Society. Retrieved 2022-04-04.
- ↑ "Gateway Documentation | iReceptor". ireceptor.irmacs.sfu.ca. Retrieved 2022-04-04.
- ↑ "VDJServer Wiki". wiki.vdjserver.org. Retrieved 2022-04-04.
- ↑ Breden, Felix; Luning Prak, Eline T.; Peters, Bjoern; Rubelt, Florian; Schramm, Chaim A.; Busse, Christian E.; Vander Heiden, Jason A.; Christley, Scott; Bukhari, Syed Ahmad Chan; Thorogood, Adrian; Matsen IV, Frederick A. (2017-11-01). "Reproducibility and Reuse of Adaptive Immune Receptor Repertoire Data". Frontiers in Immunology. 8: 1418. doi:10.3389/fimmu.2017.01418. ISSN 1664-3224. PMC 5671925. PMID 29163494.
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