Please read our update article in Nucleic Acids Research to learn about new features in OGRDB and VDJbase, and plans for the future. William D Lees, Ayelet Peres, Vered Klein, Naama Amos, Uddalok Jana, Eric Engelbrecht, Zachary Vanwinkle, Yaniv Malach, Thomas Konstantinovsky, Pazit Polak, Corey T Watson, Gur Yaari, The current landscape of adaptive immune… Continue reading New publication
Category: VDJbase_News
OGRDB Outage
OGRDB has been down since Saturday 25th October. I am very sorry for the outage, which has been caused by an issue with the Domain Naming System (DNS) record for the site. The issue is under investigation by administrators at the AIRR Community and The Antibody Society. Please be assured that we are doing everything… Continue reading OGRDB Outage
Genomic Data Upgraded
We have added additional annotated human loci, taking the overall total to 867. The new annotations are described in two studies: – Jana et al., “The human immunoglobulin heavy chain constant gene locus is enriched for large complex structural variants and coding polymorphisms that vary in frequency among human populations” (preprint). IGHC is represented in… Continue reading Genomic Data Upgraded
AIRR-Seq Data Upgraded: Repertoires downloadable!
We are pleased to announce a major upgrade to human AIRR-seq data on VDJbase. We have added approximately 1000 new repertoires, bringing the total to 2,345. For improved consistency and reproducibility, all repertoires have been processed with a new pipeline, processing from source reads wherever possible. IG AIRR-seq is now annotated with the AIRR-C Reference… Continue reading AIRR-Seq Data Upgraded: Repertoires downloadable!
Genomic data extended
Genomic data has been extended to include 36 human IGK samples from Engelbrecht, Rodriguez, Shields et al., 2024. We have replaced the 22 human IGL samples published in Gibson, Rodriguez, Shields et al., 2022 with 200 that have been processed with more accurate sequencing and pipelines than were available for that study. The IGL and… Continue reading Genomic data extended
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
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 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
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).