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PMID: 29144493 Published · ppublish English Journal Article

Adaptive Immune Receptor Repertoire Community recommendations for sharing immune-repertoire sequencing data.

Nature immunology ·Vol. 18 ·No. 12 ·2017-00-16 ·Pages 1274-1278

Rubelt F, Busse CE, Bukhari SAC, Bürckert JP, Mariotti-Ferrandiz E, Cowell LG, Watson CT, Marthandan N, Faison WJ, Hershberg U, Laserson U, Corrie BD, Davis MM, Peters B, Lefranc MP, Scott JK, Breden F, AIRR Community, Luning Prak ET, Kleinstein SH

Abstract

暂无摘要

MeSH Terms
Animals Datasets as Topic/standards Humans Information Dissemination Receptors, Immunologic/genetics Research Design/standards
Chemicals
Receptors, Immunologic
Authors & Affiliations
20 authors, click to expand affiliations / ORCID
Rubelt Florian
Department of Microbiology and Immunology and Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, California, USA.
Busse Christian E ORCID
Division of B Cell Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany.
Bukhari Syed Ahmad Chan
Department of Pathology, Yale School of Medicine, New Haven, Connecticut, USA.
Bürckert Jean-Philippe
Department of Infection and Immunity, Luxembourg Institute of Health, Luxembourg, Luxembourg.
Mariotti-Ferrandiz Encarnita ORCID
Sorbonne Universités, UPMC Univ Paris 06, INSERM, UMR_S 959, Immunology-Immunopathology-Immunotherapy (i3), Paris, France.
Cowell Lindsay G
Department of Clinical Sciences, UT Southwestern Medical Center, Dallas, Texas, USA.
Watson Corey T
Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, Kentucky, USA.
Marthandan Nishanth
Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada.
Faison William J
Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA.
Hershberg Uri
School of Biomedical Engineering, Science & Health Systems, and Department of Microbiology and Immunology, College of Medicine, Drexel University, Philadelphia, Pennsylvania, USA.
Laserson Uri
Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.
Corrie Brian D
iReceptor, Simon Fraser University, Burnaby, British Columbia, Canada. | Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada.
Davis Mark M
Department of Microbiology and Immunology and Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, California, USA. | Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, USA.
Peters Bjoern ORCID
La Jolla Institute for Allergy and Immunology, La Jolla, California, USA.
Lefranc Marie-Paule
IMGT, the international ImMunoGeneTics information system, LIGM, Institut de Génétique Humaine IGH, CNRS, University of Montpellier, Montpellier, France.
Scott Jamie K
Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada. | iReceptor, Simon Fraser University, Burnaby, British Columbia, Canada. | Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada.
Breden Felix
iReceptor, Simon Fraser University, Burnaby, British Columbia, Canada. | Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada.
AIRR Community
Luning Prak Eline T ORCID
Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
Kleinstein Steven H
Department of Pathology, Yale School of Medicine, New Haven, Connecticut, USA. | Department of Immunobiology, Yale School of Medicine, and Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, USA.
References (23)
23 references, click to expand
  1. Automated analysis of high-throughput B-cell sequencing data reveals a high frequency of novel immunoglobulin V gene segment alleles.
    Proc Natl Acad Sci U S A. 2015 Feb 24;112(8):E862-70 PMID: 25675496
  2. Minimum Information About a Microarray Experiment (MIAME)--successes, failures, challenges.
    ScientificWorldJournal. 2009 May 29;9:420-3 PMID: 19484163
  3. The International Nucleotide Sequence Database Collaboration.
    Nucleic Acids Res. 2013 Jan;41(Database issue):D21-4 PMID: 23180798
  4. Reconstructing immune phylogeny: new perspectives.
    Nat Rev Immunol. 2005 Nov;5(11):866-79 PMID: 16261174
  5. NIH's genomic data sharing policy: timing and tradeoffs.
    Trends Genet. 2015 Feb;31(2):55-7 PMID: 25620797
  6. Minimum information about a microarray experiment (MIAME)-toward standards for microarray data.
    Nat Genet. 2001 Dec;29(4):365-71 PMID: 11726920
  7. Change-O: a toolkit for analyzing large-scale B cell immunoglobulin repertoire sequencing data.
    Bioinformatics. 2015 Oct 15;31(20):3356-8 PMID: 26069265
  8. Novel Approaches to Analyze Immunoglobulin Repertoires.
    Trends Immunol. 2017 Jul;38(7):471-482 PMID: 28566130
  9. Bioinformatic and Statistical Analysis of Adaptive Immune Repertoires.
    Trends Immunol. 2015 Nov;36(11):738-749 PMID: 26508293
  10. The FAIR Guiding Principles for scientific data management and stewardship.
    Sci Data. 2016 Mar 15;3:160018 PMID: 26978244
  11. T-cell antigen receptor genes and T-cell recognition.
    Nature. 1988 Aug 4;334(6181):395-402 PMID: 3043226
  12. Applications of Immunogenomics to Cancer.
    Cell. 2017 Feb 9;168(4):600-612 PMID: 28187283
  13. Somatic generation of antibody diversity.
    Nature. 1983 Apr 14;302(5909):575-81 PMID: 6300689
  14. Production of individualized V gene databases reveals high levels of immunoglobulin genetic diversity.
    Nat Commun. 2016 Dec 20;7:13642 PMID: 27995928
  15. Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project.
    Nat Biotechnol. 2008 Aug;26(8):889-96 PMID: 18688244
  16. Practical guidelines for B-cell receptor repertoire sequencing analysis.
    Genome Med. 2015 Nov 20;7:121 PMID: 26589402
  17. Systems Approaches towards Molecular Profiling of Human Immunity.
    Trends Immunol. 2016 Jan;37(1):53-67 PMID: 26669258
  18. High-Throughput Sequencing-Based Immune Repertoire Study during Infectious Disease.
    Front Immunol. 2016 Aug 31;7:336 PMID: 27630639
  19. Advanced Methodologies in High-Throughput Sequencing of Immune Repertoires.
    Trends Biotechnol. 2017 Mar;35(3):203-214 PMID: 28341036
  20. Reproducibility and Reuse of Adaptive Immune Receptor Repertoire Data.
    Front Immunol. 2017 Nov 01;8:1418 PMID: 29163494
  21. ImmPort: disseminating data to the public for the future of immunology.
    Immunol Res. 2014 May;58(2-3):234-9 PMID: 24791905
  22. VDJML: a file format with tools for capturing the results of inferring immune receptor rearrangements.
    BMC Bioinformatics. 2016 Oct 6;17 (Suppl 13):333 PMID: 27766961
  23. The promise and challenge of high-throughput sequencing of the antibody repertoire.
    Nat Biotechnol. 2014 Feb;32(2):158-68 PMID: 24441474
Article Info
Journal
Nature immunology
Abbr.
Nat Immunol
ISSN
1529-2916
Published
2017-00-16
Pages
1274-1278
Language
English
Region
United States
NLM ID
100941354
PMCID
PMC5790180
Subset
IM
Grants
NIAID NIH HHS · R01 AI097403 · United States
NIAID NIH HHS · R01 AI104739 · United States
NIAID NIH HHS · R37 AI022511 · United States
NIAID NIH HHS · U19 AI057229 · United States
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