AIRR Community Standardized Representations for Annotated Immune Repertoires

Front Immunol. 2018 Sep 28;9:2206. doi: 10.3389/fimmu.2018.02206. eCollection 2018.

Abstract

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.

Keywords: AIRR-seq; B cell; Rep-Seq; T cell; antibody; immunoglobulin; immunology; repertoire.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adaptive Immunity / genetics
  • Antibodies / genetics*
  • Base Sequence*
  • Database Management Systems*
  • Databases, Genetic
  • Datasets as Topic
  • High-Throughput Nucleotide Sequencing / economics
  • Humans
  • Information Dissemination / methods*
  • Receptors, Antigen, T-Cell / genetics*
  • Receptors, Immunologic / genetics
  • Research Design

Substances

  • Antibodies
  • Receptors, Antigen, T-Cell
  • Receptors, Immunologic