Collaboration Opportunities

OGRDB and VDJbase are part of the AIRR Knowledge Commons project – bringing together immune repertoires from the AIRR Data Commons, epitopes from IEDB, receptor germline analysis from OGRDB and VDJbase with other emerging datasets. We are actively seeking collaborators whose projects will drive use cases and demonstrate the utility of bringing these various sources… Continue reading Collaboration Opportunities

Novel Allele Submission Process Simplified

Following an IARC decision in December 2023, the submission process for inferred novel alleles has been simplified. Previously, it was necessary to deposit the sequence of each inferred allele in GenBank or ENA, and it was usually necessary to accompany this with an extracted set of reads from the repertoire that provided explicit support for… Continue reading Novel Allele Submission Process Simplified

Categorised as OGRDB_News

Germline Databases, or adventures into the allelic underworld

If you are interested in receptor germlines, you might enjoy this On-AIRR podcast with Corey Watson and William Lees, hosted by Ulrik Stervbo and Zhaoqing Ding. “In this episode we talk about the recent work by the Germline Database Working Group of the AIRR-Community. The accuracy of V and J gene segment assignment improves with… Continue reading Germline Databases, or adventures into the allelic underworld

Genomic databases updated

We have updated the genomic databases to follow the same project/individual/sample structure that is used for AIRR-seq databases – previously we only structured genomic databases into project/individual. This change makes it easier to handle datasets that have more than one analysis of the same individual – as can be seen, for example, in the human… Continue reading Genomic databases updated

Human IG germline sets now available

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

Categorised as OGRDB_News

Human genomic IGH data now available

A set of ~150 human IGH loci from diverse backgrounds is now available. The data is taken from Rodriguez, Safonova, Silver, Shields, et al. 2023. ‘Genetic Variation in the Immunoglobulin Heavy Chain Locus Shapes the Human Antibody Repertoire’. The data presented here was taken from IGenotyper haplotyped assemblies, processed by the VDJbase automated pipeline. Analysis… Continue reading Human genomic IGH data now available

Germline Set format updates

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

Human genomic IGL data now available

Human IGL genomic assemblies are now available for browsing. The data is taken from Gibson, W.S., Rodriguez, O.L., Shields, K. et al. Characterization of the immunoglobulin lambda chain locus from diverse populations reveals extensive genetic variation. Genes Immun 24, 21–31 (2023).

Preprint on germline set development now available

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.

Categorised as OGRDB_News