Reproducibility and Reuse of Adaptive Immune Receptor Repertoire Data
High-throughput sequencing (HTS) of immunoglobulin (B-cell receptor, antibody) and T-cell receptor repertoires has increased dramatically since the technique was introduced in 2009 (1–3). This experimental approach explores the maturation of the adaptive immune system and its response to antigens, p...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2017-11-01
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| Series: | Frontiers in Immunology |
| Subjects: | |
| Online Access: | http://journal.frontiersin.org/article/10.3389/fimmu.2017.01418/full |
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| author | Felix Breden Eline T. Luning Prak Bjoern Peters Florian Rubelt Chaim A. Schramm Christian E. Busse Jason A. Vander Heiden Scott Christley Syed Ahmad Chan Bukhari Adrian Thorogood Frederick A. Matsen IV Yariv Wine Uri Laserson David Klatzmann Daniel C. Douek Marie-Paule Lefranc Andrew M. Collins Tania Bubela Steven H. Kleinstein Corey T. Watson Lindsay G. Cowell Jamie K. Scott Thomas B. Kepler Thomas B. Kepler |
| author_facet | Felix Breden Eline T. Luning Prak Bjoern Peters Florian Rubelt Chaim A. Schramm Christian E. Busse Jason A. Vander Heiden Scott Christley Syed Ahmad Chan Bukhari Adrian Thorogood Frederick A. Matsen IV Yariv Wine Uri Laserson David Klatzmann Daniel C. Douek Marie-Paule Lefranc Andrew M. Collins Tania Bubela Steven H. Kleinstein Corey T. Watson Lindsay G. Cowell Jamie K. Scott Thomas B. Kepler Thomas B. Kepler |
| author_sort | Felix Breden |
| collection | DOAJ |
| description | High-throughput sequencing (HTS) of immunoglobulin (B-cell receptor, antibody) and T-cell receptor repertoires has increased dramatically since the technique was introduced in 2009 (1–3). This experimental approach explores the maturation of the adaptive immune system and its response to antigens, pathogens, and disease conditions in exquisite detail. It holds significant promise for diagnostic and therapy-guiding applications. New technology often spreads rapidly, sometimes more rapidly than the understanding of how to make the products of that technology reliable, reproducible, or usable by others. As complex technologies have developed, scientific communities have come together to adopt common standards, protocols, and policies for generating and sharing data sets, such as the MIAME protocols developed for microarray experiments. The Adaptive Immune Receptor Repertoire (AIRR) Community formed in 2015 to address similar issues for HTS data of immune repertoires. The purpose of this perspective is to provide an overview of the AIRR Community’s founding principles and present the progress that the AIRR Community has made in developing standards of practice and data sharing protocols. Finally, and most important, we invite all interested parties to join this effort to facilitate sharing and use of these powerful data sets (join@airr-community.org). |
| first_indexed | 2024-12-20T18:26:03Z |
| format | Article |
| id | doaj.art-baa46033725a4e99b5a18b8f93cfffdc |
| institution | Directory Open Access Journal |
| issn | 1664-3224 |
| language | English |
| last_indexed | 2024-12-20T18:26:03Z |
| publishDate | 2017-11-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Immunology |
| spelling | doaj.art-baa46033725a4e99b5a18b8f93cfffdc2022-12-21T19:30:09ZengFrontiers Media S.A.Frontiers in Immunology1664-32242017-11-01810.3389/fimmu.2017.01418308747Reproducibility and Reuse of Adaptive Immune Receptor Repertoire DataFelix Breden0Eline T. Luning Prak1Bjoern Peters2Florian Rubelt3Chaim A. Schramm4Christian E. Busse5Jason A. Vander Heiden6Scott Christley7Syed Ahmad Chan Bukhari8Adrian Thorogood9Frederick A. Matsen IV10Yariv Wine11Uri Laserson12David Klatzmann13Daniel C. Douek14Marie-Paule Lefranc15Andrew M. Collins16Tania Bubela17Steven H. Kleinstein18Corey T. Watson19Lindsay G. Cowell20Jamie K. Scott21Thomas B. Kepler22Thomas B. Kepler23Department of Biological Sciences, Simon Fraser University, Burnaby, BC, CanadaDepartment of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United StatesLa Jolla Institute for Allergy and Immunology, La Jolla, CA, United StatesDepartment of Microbiology and Immunology, Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, United StatesVaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, United StatesDivision of B Cell Immunology, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, GermanyDepartment of Neurology, Yale University School of Medicine, New Haven, CT, United StatesDepartment of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, TX, United StatesDepartment of Pathology, Yale University School of Medicine, New Haven, CT, United States0entre of Genomics and Policy, McGill University, Montreal, QC, Canada1Public Health Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, United States2Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel3Department of Genetics and Genome Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States4Immunology-Immunopathology-Immunotherapy (i3 & i2B), Sorbonne Université, Paris, FranceVaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States5IMGT, LIGM, Institut de Génétique Humaine IGH, CNRS, University of Montpellier, Montpellier, France6School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, NSW, Australia7Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, CanadaDepartment of Pathology, Yale University School of Medicine, New Haven, CT, United States8Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, United StatesDepartment of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, TX, United States9Faculty of Health Sciences, Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada0Department of Microbiology, Boston University School of Medicine, Boston, MA, United States1Department of Mathematics and Statistics, Boston University, Boston, MA, United StatesHigh-throughput sequencing (HTS) of immunoglobulin (B-cell receptor, antibody) and T-cell receptor repertoires has increased dramatically since the technique was introduced in 2009 (1–3). This experimental approach explores the maturation of the adaptive immune system and its response to antigens, pathogens, and disease conditions in exquisite detail. It holds significant promise for diagnostic and therapy-guiding applications. New technology often spreads rapidly, sometimes more rapidly than the understanding of how to make the products of that technology reliable, reproducible, or usable by others. As complex technologies have developed, scientific communities have come together to adopt common standards, protocols, and policies for generating and sharing data sets, such as the MIAME protocols developed for microarray experiments. The Adaptive Immune Receptor Repertoire (AIRR) Community formed in 2015 to address similar issues for HTS data of immune repertoires. The purpose of this perspective is to provide an overview of the AIRR Community’s founding principles and present the progress that the AIRR Community has made in developing standards of practice and data sharing protocols. Finally, and most important, we invite all interested parties to join this effort to facilitate sharing and use of these powerful data sets (join@airr-community.org).http://journal.frontiersin.org/article/10.3389/fimmu.2017.01418/fullB-cell receptorsT-cell receptorsdata sharingimmunogeneticscommunity standardshigh-throughput sequencing |
| spellingShingle | Felix Breden Eline T. Luning Prak Bjoern Peters Florian Rubelt Chaim A. Schramm Christian E. Busse Jason A. Vander Heiden Scott Christley Syed Ahmad Chan Bukhari Adrian Thorogood Frederick A. Matsen IV Yariv Wine Uri Laserson David Klatzmann Daniel C. Douek Marie-Paule Lefranc Andrew M. Collins Tania Bubela Steven H. Kleinstein Corey T. Watson Lindsay G. Cowell Jamie K. Scott Thomas B. Kepler Thomas B. Kepler Reproducibility and Reuse of Adaptive Immune Receptor Repertoire Data Frontiers in Immunology B-cell receptors T-cell receptors data sharing immunogenetics community standards high-throughput sequencing |
| title | Reproducibility and Reuse of Adaptive Immune Receptor Repertoire Data |
| title_full | Reproducibility and Reuse of Adaptive Immune Receptor Repertoire Data |
| title_fullStr | Reproducibility and Reuse of Adaptive Immune Receptor Repertoire Data |
| title_full_unstemmed | Reproducibility and Reuse of Adaptive Immune Receptor Repertoire Data |
| title_short | Reproducibility and Reuse of Adaptive Immune Receptor Repertoire Data |
| title_sort | reproducibility and reuse of adaptive immune receptor repertoire data |
| topic | B-cell receptors T-cell receptors data sharing immunogenetics community standards high-throughput sequencing |
| url | http://journal.frontiersin.org/article/10.3389/fimmu.2017.01418/full |
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