.. _OGRDB:

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OGRDB - reference database of inferred immune receptor genes
============================================================

In recent years it has become possible to sequence immune receptor repertoires
(immunoglobulins and T cell receptors) at great depth. The accurate analysis of these
repertoires requires a comprehensive understanding of the germline genes that give rise
to the repertoire through V(D)J gene recombination.

Even for well-studied species such as humans and mice, our knowledge of allelic variation
is incomplete. Identifying new immunoglobulin and T cell receptor polymorphisms from the
genome using traditional methods is technically challenging, because of the complex sequence
architecture and repetitive nature of these loci. More recently, methods have been developed
to infer novel sequences and alleles from sequenced repertoires.

The Adaptive Immune Receptor Repertoire (AIRR) Community was formed to promote and share
good practice in adaptive immune repertoire sequencing. In 2017, it established the Inferred
Allele Review Committee (IARC) to evaluate inferred alleles for inclusion in relevant
germline databases. IARC's work is outlined in more detail in a poster, which was presented
at a Systems Immunology Workshop at the University of Surrey, England, in March 2018, and
in a recent paper. IARC has worked, together with colleagues at IMGT and the US National
Institute of Health, to establish a systematic submission and review process. OGRDB was
created and designed to support that process, and provide a real-time record of affirmed
sequences. Affirmed sequences will be listed under the Sequences tab above, and the
submissions that underpin them will be found under the Submissions tab. You can make
your own submissions by following the steps below.

How to submit your sequences
----------------------------

As a first step, IARC is now ready to review submissions of inferred human IGHV genes and
alleles. These sequences may be novel, or may extend incomplete sequences currently in the
IMGT reference directories. Researchers interested in submitting sequences should:

.. toctree::
   :maxdepth: 1
   :caption: Submit sequence and data to Genbank or ENA, following the

   The Genbank/ENA Workflow. <iarc_submission_ncbi>

Submit the inferred sequences to IARC via OGRDB, following the

+ `OGRDB Submission Guide`_

Additional information is available at the

+ `OGRDB Website`_

References
==========

.. [Ohlin_2019] Ohlin M *et al*. Inferred Allelic Variants of Immunoglobulin Receptor Genes:
   A System for Their Evaluation, Documentation, and Naming. Front Immunol 10:435 (2019)
   `DOI: 10.3389/fimmu.2019.00435`_

.. _`DOI: 10.3389/fimmu.2019.00435`: https://doi.org/10.3389/fimmu.2019.00435

.. _`OGRDB Submission Guide`: https://ogrdb.airr-community.org/render_page/ogre_guide.html

.. _`OGRDB Website`: https://ogrdb.airr-community.org