AIRR Community Standardized Representations for Annotated Immune Repertoires.

Autor: Vander Heiden JA; Department of Neurology, Yale School of Medicine, New Haven, CT, United States., Marquez S; Department of Pathology, Yale School of Medicine, New Haven, CT, United States., Marthandan N; Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada., Bukhari SAC; Department of Pathology, Yale School of Medicine, New Haven, CT, United States., Busse CE; Division of B Cell Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany., Corrie B; Department of Biological Sciences, Simon Fraser University, Burnaby, BC, Canada., Hershberg U; School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, United States.; Department of Microbiology and Immunology, College of Medicine, Drexel University, Philadelphia, PA, United States.; Department of Human Biology, Faculty of Sciences, University of Haifa, Haifa, Israel., Kleinstein SH; Department of Pathology, Yale School of Medicine, New Haven, CT, United States.; Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, United States., Matsen Iv FA; Fred Hutchinson Cancer Research Center, Seattle, WA, United States., Ralph DK; Fred Hutchinson Cancer Research Center, Seattle, WA, United States., Rosenfeld AM; School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, United States., Schramm CA; Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States., Christley S; Department of Clinical Sciences, UT Southwestern Medical Center, Dallas, TX, United States., Laserson U; Department of Genetics and Genomic Sciences and Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States.
Jazyk: angličtina
Zdroj: Frontiers in immunology [Front Immunol] 2018 Sep 28; Vol. 9, pp. 2206. Date of Electronic Publication: 2018 Sep 28 (Print Publication: 2018).
DOI: 10.3389/fimmu.2018.02206
Abstrakt: Increased interest in the immune system's involvement in pathophysiological phenomena coupled with decreased DNA sequencing costs have led to an explosion of antibody and T cell receptor sequencing data collectively termed "adaptive immune receptor repertoire sequencing" (AIRR-seq or Rep-Seq). The AIRR Community has been actively working to standardize protocols, metadata, formats, APIs, and other guidelines to promote open and reproducible studies of the immune repertoire. In this paper, we describe the work of the AIRR Community's Data Representation Working Group to develop standardized data representations for storing and sharing annotated antibody and T cell receptor data. Our file format emphasizes ease-of-use, accessibility, scalability to large data sets, and a commitment to open and transparent science. It is composed of a tab-delimited format with a specific schema. Several popular repertoire analysis tools and data repositories already utilize this AIRR-seq data format. We hope that others will follow suit in the interest of promoting interoperable standards.
Databáze: MEDLINE