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...
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
Germline sets on OGRDB are copied to Zenodo.org for long-term security and have DOIs issued by Zenodo which you will see on the Germline Sets pages. The DOI is updated with each version: you can provide the DOI for the version used in your research as a permanent link to the set.
The AIRR-C standard germline sets published in OGRDB use a new naming scheme: please see this poster for details. Because the format of these names may not be compatible with all current pipeline tools, we have released receptor-germline-tools: utilities that can convert to more compatible subgroup-identifier-allele form. We have also updated the FASTA files downloadable… Continue reading Tools for working with germline sets
We have published IGHV germline sets for laboratory mouse strains BALB/c and C75BL/6, as recently reported in preprint by Jackson et al.The sets will be curated by the AIRR Community Germline Database Working Group with the aim of maintaining sets that are tuned for use in AIRR-seq, taking advantage of the latest research. We hope… Continue reading First Germline Sets Published on OGRDB
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.
For help in using OGRDB, or if you encounter any issues, please contact us.
The site is developed and maintained by William Lees (firstname.lastname@example.org)