Inferred allelic variants of immunoglobulin receptor genes: A system for their evaluation, documentation, and naming

Mats Ohlin, Cathrine Scheepers, Martin Corcoran, William D. Lees, Christian E. Busse, Davide Bagnara, Linnea Thörnqvist, Jean Philippe Bürckert, Katherine J.L. Jackson, Duncan Ralph, Chaim A. Schramm, Nishanth Marthandan, Felix Breden, Jamie Scott, Frederick A. Matsen, Victor Greiff, Gur Yaari, Steven H. Kleinstein, Scott Christley, Jacob S. SherkowSofia Kossida, Marie Paule Lefranc, Menno C. Van Zelm, Corey T. Watson, Andrew M. Collins

Research output: Contribution to journalReview article

Abstract

Immunoglobulins or antibodies are the main effector molecules of the B-cell lineage and are encoded by hundreds of variable (V), diversity (D), and joining (J) germline genes, which recombine to generate enormous IG diversity. Recently, high-throughput adaptive immune receptor repertoire sequencing (AIRR-seq) of recombined V-(D)-J genes has offered unprecedented insights into the dynamics of IG repertoires in health and disease. Faithful biological interpretation of AIRR-seq studies depends upon the annotation of raw AIRR-seq data, using reference germline gene databases to identify the germline genes within each rearrangement. Existing reference databases are incomplete, as shown by recent AIRR-seq studies that have inferred the existence of many previously unreported polymorphisms. Completing the documentation of genetic variation in germline gene databases is therefore of crucial importance. Lymphocyte receptor genes and alleles are currently assigned by the Immunoglobulins, T cell Receptors and Major Histocompatibility Nomenclature Subcommittee of the International Union of Immunological Societies (IUIS) and managed in IMGT®, the international ImMunoGeneTics information system® (IMGT). In 2017, the IMGT Group reached agreement with a group of AIRR-seq researchers on the principles of a streamlined process for identifying and naming inferred allelic sequences, for their incorporation into IMGT®. These researchers represented the AIRR Community, a network of over 300 researchers whose objective is to promote all aspects of immunoglobulin and T-cell receptor repertoire studies, including the standardization of experimental and computational aspects of AIRR-seq data generation and analysis. The Inferred Allele Review Committee (IARC) was established by the AIRR Community to devise policies, criteria, and procedures to perform this function. Formalized evaluations of novel inferred sequences have now begun and submissions are invited via a new dedicated portal (https://ogrdb.airr-community.org). Here, we summarize recommendations developed by the IARC—focusing, to begin with, on human IGHV genes—with the goal of facilitating the acceptance of inferred allelic variants of germline IGHV genes. We believe that this initiative will improve the quality of AIRR-seq studies by facilitating the description of human IG germline gene variation, and that in time, it will expand to the documentation of TR and IG genes in many vertebrate species.

Original languageEnglish (US)
Article number435
JournalFrontiers in immunology
Volume10
Issue numberMAR
DOIs
StatePublished - 2019
Externally publishedYes

Keywords

  • AIRR-seq
  • Allelic variation
  • IGHV
  • Immunoglobulin
  • Inference
  • V(D)J rearrangement

ASJC Scopus subject areas

  • Immunology and Allergy
  • Immunology

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  • Cite this

    Ohlin, M., Scheepers, C., Corcoran, M., Lees, W. D., Busse, C. E., Bagnara, D., Thörnqvist, L., Bürckert, J. P., Jackson, K. J. L., Ralph, D., Schramm, C. A., Marthandan, N., Breden, F., Scott, J., Matsen, F. A., Greiff, V., Yaari, G., Kleinstein, S. H., Christley, S., ... Collins, A. M. (2019). Inferred allelic variants of immunoglobulin receptor genes: A system for their evaluation, documentation, and naming. Frontiers in immunology, 10(MAR), [435]. https://doi.org/10.3389/fimmu.2019.00435