The immune receptors of B and T cells are central to the body's response to pathogens, and implicated in autoimmune disease. High-throughput sequencing of receptor repertoires - AIRR-Seq - is widely used to study receptor development, however a comprehensive understanding of the genes from which development starts - the germline genes - is crucial for accurate interpretation. Our knowledge of human receptor alleles is incomplete, and that of other species at an early stage. OGRDB is an open database of newly discovered alleles, through which researchers can contribute newly discovered alleles for analysis, and download those that have been reviewed and affirmed. Read more...
Germline sets for human IGH, IGK and IGL are now available for download. They are described in a forthcoming publication, “AIRR-C Human IG Reference Sets: curated sets of immunoglobulin heavy and light chain germline genes”, currently available from Biorxiv as a preprint. Our aim with these sets is to provide high-quality, evidenced collections that are… Continue reading Human IG germline sets now available
In this post, we’re going to look briefly at the different ways that you can download germline sets from the command line, or from code. We want to make germline sets on OGRDB as easy to work with as possible, and making them available for download conveniently is an important part of that, so that… Continue reading Downloading germline sets from the command line or API
The JSON format in which germline sets are distributed has been updated (germline sets are also available from OGRDB in FASTA format, but the JSON format provides much richer information). The revised format is compliant with the latest development version of the AIRR schema, which is expected to be released as an update in the… Continue reading Germline Set format updates
The AIRR Community has recently published a preprint on the community development of IG and TR germline sets. This sets out the principles and approach being followed for the development and publication of germline sets on OGRDB, which we hope will gain wider traction in the community as a whole.
For many analyses, it is important to annotate AIRR-seq repertoires with an accurate and comprehensive germline set. As an example, determination of the overall mutation rate of a repertoire may give misleading results if frequently-expressed sequences are omitted. Likewise, many methods of clonal assignment require an accurate determination of the germline. The IG loci of… Continue reading Using the OGRDB mouse germline sets
If you use OGRDB in your research, please cite this paper:
OGRDB: a reference database of inferred immune receptor genes
Lees et al., Nucleic Acids Research, September 2019.
Acknowledgements and citations for individual sequences are provided under each sequence and submission.