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. 2022;2453:447–476. doi: 10.1007/978-1-0716-2115-8_23

Data Sharing and Reuse: A Method by the AIRR Community.

Brian D Corrie, Scott Christley, Christian E Busse, Lindsay G Cowell, Kira C M Neller, Florian Rubelt, Nicholas Schwab; AIRR Community
PMCID: PMC9761493  PMID: 35622339

Abstract

High-throughput sequencing of adaptive immune receptor repertoires (AIRR, i.e., IG and TR ) has revolutionized the ability to study the adaptive immune response via large-scale experiments. Since 2009, AIRR sequencing (AIRR-seq) has been widely applied to survey the immune state of individuals (see "The AIRR Community Guide to Repertoire Analysis" chapter for details). One of the goals of the AIRR Community is to make the resulting AIRR-seq data FAIR (Findable, Accessible, Interoperable, and Reusable) (Wilkinson et al. Sci Data 3:1-9, 2016), with a primary goal of making it easy for the research community to reuse AIRR-seq data (Breden et al. Front Immunol 8:1418, 2017; Scott and Breden. Curr Opin Syst Biol 24:71-77, 2020). The basis for this is the MiAIRR data standard (Rubelt et al. Nat Immunol 18:1274-1278, 2017). For long-term preservation, it is recommended that researchers store their sequence read data in an INSDC repository. At the same time, the AIRR Community has established the AIRR Data Commons (Christley et al. Front Big Data 3:22, 2020), a distributed set of AIRR-compliant repositories that store the critically important annotated AIRR-seq data based on the MiAIRR standard, making the data findable, interoperable, and, because the data are annotated, more valuable in its reuse. Here, we build on the other AIRR Community chapters and illustrate how these principles and standards can be incorporated into AIRR-seq data analysis workflows. We discuss the importance of careful curation of metadata to ensure reproducibility and facilitate data sharing and reuse, and we illustrate how data can be shared via the AIRR Data Commons.

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References

  1. Wilkinson MD, Dumontier M, Aalbersberg IJ, Appleton G, Axton M, Baak A et al (2016) The FAIR guiding principles for scientific data management and stewardship. Sci Data 3:1–9. https://doi.org/10.1038/sdata.2016.18 doi: 10.1038/sdata.2016.18. [DOI] [PMC free article] [PubMed]
  2. Breden F, Luning Prak ET, Peters B, Rubelt F, Schramm CA, Busse CE et al (2017) Reproducibility and reuse of adaptive immune receptor repertoire data. Front Immunol 8:1418. https://doi.org/10.3389/fimmu.2017.01418 doi: 10.3389/fimmu.2017.01418. [DOI] [PMC free article] [PubMed]
  3. Scott JK, Breden F (2020) The adaptive immune receptor repertoire community as a model for FAIR stewardship of big immunology data. Curr Opin Syst Biol 24:71–77. https://doi.org/10.1016/j.coisb.2020.10.001 doi: 10.1016/j.coisb.2020.10.001. [DOI] [PMC free article] [PubMed]
  4. Rubelt F, Busse CE, Bukhari SAC, Bürckert J-P, Mariotti-Ferrandiz E, Cowell LG et al (2017) Adaptive immune receptor repertoire community recommendations for sharing immune-repertoire sequencing data. Nat Immunol 18:1274–1278. https://doi.org/10.1038/ni.3873 doi: 10.1038/ni.3873. [DOI] [PMC free article] [PubMed]
  5. Christley S, Aguiar A, Blanck G, Breden F, Bukhari SAC, Busse CE et al (2020) The ADC API: a web API for the programmatic query of the AIRR data commons. Front Big Data 3:22. https://doi.org/10.3389/fdata.2020.00022 doi: 10.3389/fdata.2020.00022. [DOI] [PMC free article] [PubMed]
  6. Vander Heiden JA, Marquez S, Marthandan N, Bukhari SAC, Busse CE, Corrie B et al (2018) AIRR community standardized representations for annotated immune repertoires. Front Immunol 9:2206. https://doi.org/10.3389/fimmu.2018.02206 doi: 10.3389/fimmu.2018.02206. [DOI] [PMC free article] [PubMed]
  7. Corrie BD, Marthandan N, Zimonja B, Jaglale J, Zhou Y, Barr E et al (2018) iReceptor: a platform for querying and analyzing antibody/B-cell and T-cell receptor repertoire data across federated repositories. Immunol Rev 284:24–41. https://doi.org/10.1111/imr.12666 doi: 10.1111/imr.12666. [DOI] [PMC free article] [PubMed]
  8. Christley S, Scarborough W, Salinas E, Rounds WH, Toby IT, Fonner JM et al (2018) VDJServer: a cloud-based analysis portal and data commons for immune repertoire sequences and rearrangements. Front Immunol 9:976. https://doi.org/10.3389/fimmu.2018.00976 doi: 10.3389/fimmu.2018.00976. [DOI] [PMC free article] [PubMed]
  9. Rosenfeld AM, Meng W, Luning Prak ET, Hershberg U (2018) ImmuneDB, a novel tool for the analysis, storage, and dissemination of immune repertoire sequencing data. Front Immunol 9:2107. https://doi.org/10.3389/fimmu.2018.02107 doi: 10.3389/fimmu.2018.02107. [DOI] [PMC free article] [PubMed]
  10. Imkeller K, Arndt PF, Wardemann H, Busse CE (2016) sciReptor: analysis of single-cell level immunoglobulin repertoires. BMC Bioinformatics 17:67. https://doi.org/10.1186/s12859-016-0920-1 doi: 10.1186/s12859-016-0920-1. [DOI] [PMC free article] [PubMed]
  11. Borghardt P (2020) COVID-19 Demands Increased Public Sharing of Biomedical Research Data. https://perma.cc/UC5Q-X4J2. Accessed 5 Mar 2021
  12. Arnaout RA, Prak ETL, Schwab N, Rubelt F, Arora R, Bashford-Rogers R et al (2021) The future of blood testing is the Immunome. Front Immunol 12:228. https://doi.org/10.3389/fimmu.2021.626793 doi: 10.3389/fimmu.2021.626793. [DOI] [PMC free article] [PubMed]
  13. Brüggemann M, Kotrová M, Knecht H, Bartram J, Boudjogrha M, Bystry V et al (2019) Standardized next-generation sequencing of immunoglobulin and T-cell receptor gene recombinations for MRD marker identification in acute lymphoblastic leukaemia; a EuroClonality-NGS validation study. Leukemia 33:2241–2253. https://doi.org/10.1038/s41375-019-0496-7 doi: 10.1038/s41375-019-0496-7. [DOI] [PMC free article] [PubMed]
  14. Gittelman RM, Lavezzo E, Snyder TM, Zahid HJ, Elyanow R, Dalai S et al (2020) Diagnosis and tracking of SARS-CoV-2 infection by T-cell receptor sequencing. Preprint, infectious diseases (except HIV/AIDS). MedRXiv preprint, downloaded 2022–01–15. https://doi.org/10.1101/2020.11.09.20228023 doi: 10.1101/2020.11.09.20228023. [DOI]
  15. Commissioner O of the (2021) Coronavirus (COVID-19) update: FDA authorizes adaptive biotechnologies T-detect COVID test. In: FDA https://www.fda.gov/news-events/press-announcements/coronavirus-covid-19-update-fda-authorizes-adaptive-biotechnologies-t-detect-covid-test. Accessed 9 Mar 2021
  16. Zhang Y, Yang X, Zhang Y, Zhang Y, Wang M, Ou JX et al (2020) Tools for fundamental analysis functions of TCR repertoires: a systematic comparison. Brief Bioinform 21:1706–1716. https://doi.org/10.1093/bib/bbz092 doi: 10.1093/bib/bbz092. [DOI] [PMC free article] [PubMed]
  17. López-Santibáñez-Jácome L, Avendaño-Vázquez SE, Flores-Jasso CF (2019) The pipeline repertoire for Ig-Seq analysis. Front Immunol 10:899. https://doi.org/10.3389/fimmu.2019.00899 doi: 10.3389/fimmu.2019.00899. [DOI] [PMC free article] [PubMed]
  18. Lees WD (2020) Tools for adaptive immune receptor repertoire sequencing. Curr Opin Syst Biol 24:86–92. https://doi.org/10.1016/j.coisb.2020.10.003 10.1016/j.coisb.2020.10.003PMC766527033195881 [DOI]
  19. Smakaj E, Babrak L, Ohlin M, Shugay M, Briney B, Tosoni D et al (2020) Benchmarking immunoinformatic tools for the analysis of antibody repertoire sequences. Bioinformatics 36:1731–1739. https://doi.org/10.1093/bioinformatics/btz845 doi: 10.1093/bioinformatics/btz845. [DOI] [PMC free article] [PubMed]
  20. Bukhari SAC, O’Connor MJ, Martínez-Romero M, Egyedi AL, Willrett D, Graybeal J et al (2018) The CAIRR pipeline for submitting standards-compliant B and T cell receptor repertoire sequencing studies to the National Center for biotechnology information repositories. Front Immunol 9:1877. https://doi.org/10.3389/fimmu.2018.01877 doi: 10.3389/fimmu.2018.01877. [DOI] [PMC free article] [PubMed]
  21. Kovaltsuk A, Leem J, Kelm S, Snowden J, Deane CM, Krawczyk K (2018) Observed antibody space: a resource for data mining next-generation sequencing of antibody repertoires. J Immunol 201:2502–2509. https://doi.org/10.4049/jimmunol.1800708 doi: 10.4049/jimmunol.1800708. [DOI] [PubMed]
  22. Zhang W, Wang L, Liu K, Wei X, Yang K, Du W et al (2019) PIRD: pan immune repertoire database. Bioinformatics 36(3):897–903. https://doi.org/10.1093/bioinformatics/btz614 doi: 10.1093/bioinformatics/btz614. [DOI] [PubMed]
  23. Chen S-Y, Yue T, Lei Q, Guo A-Y (2021) TCRdb: a comprehensive database for T-cell receptor sequences with powerful search function. Nucleic Acids Res 49:D468–D474. https://doi.org/10.1093/nar/gkaa796 doi: 10.1093/nar/gkaa796. [DOI] [PMC free article] [PubMed]
  24. Adaptive Biotechnologies immuneACCESS Data. https://clients.adaptivebiotech.com/immuneaccess. Accessed 3 Mar 2021
  25. Heming M, Li X, Räuber S, Mausberg AK, Börsch A-L, Hartlehnert M et al (2021) Neurological manifestations of COVID-19 feature T cell exhaustion and dedifferentiated monocytes in cerebrospinal fluid. Immunity 54:164–175.e6. https://doi.org/10.1016/j.immuni.2020.12.011 doi: 10.1016/j.immuni.2020.12.011. [DOI] [PMC free article] [PubMed]
  26. Randi, Vita Swapnil, Mahajan James A, Overton Sandeep Kumar, Dhanda Sheridan, Martini Jason R, Cantrell Daniel K, Wheeler Alessandro, Sette Bjoern, Peters (2019) (2018) The Immune Epitope Database (IEDB): 2018 update. Nucleic Acids Research 47(D1) D339–D343. https://doi.org/10.1093/nar/gky1006 doi: 10.1093/nar/gky1006. [DOI] [PMC free article] [PubMed]
  27. Nili, Tickotsky Tal, Sagiv Jaime, Prilusky Eric, Shifrut Nir, Friedman Jonathan, Wren (2017) McPAS-TCR: a manually curated catalogue of pathology-associated T cell receptor sequences. Bioinformatics 33(18):2924–2929. https://doi.org/10.1093/bioinformatics/btx286 doi: 10.1093/bioinformatics/btx286. [DOI] [PubMed]
  28. Mikhail, Shugay Dmitriy V, Bagaev Ivan V, Zvyagin Renske M, Vroomans Jeremy Chase, Crawford Garry, Dolton Ekaterina A, Komech Anastasiya L, Sycheva Anna E, Koneva Evgeniy S, Egorov Alexey V, Eliseev Ewald, Van Dyk Pradyot, Dash Meriem, Attaf Cristina, Rius Kristin, Ladell James E, McLaren Katherine K, Matthews E Bridie, Clemens Daniel C, Douek Fabio, Luciani Debbie, van Baarle Katherine, Kedzierska Can, Kesmir Paul G, Thomas David A, Price Andrew K, Sewell Dmitriy M, Chudakov (2018) (2017) VDJdb: a curated database of T-cell receptor sequences with known antigen specificity. Nucleic Acids Research 46(D1):D419–D427. https://doi.org/10.1093/nar/gkx760 doi: 10.1093/nar/gkx760. [DOI] [PMC free article] [PubMed]

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