Category: VDJbase_News

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).

MiAIRR metadata in VDJbase

VDJbase now provides AIRR-seq study metadata that follows the MiAIRR schema. For those studies that are listed in the iReceptor gateway, the metadata reflects that served by the gateway. For other studies, the metadata provided by VDJbase has been converted to MiAIRR attributes. This means that there are many more columns to choose from on… Continue reading MiAIRR metadata in VDJbase

Further updates to AIRR-seq IGH analysis

The IGH records are now processed with a pipeline that provides improved handling of sequences that are duplicated in the reference set: that is, multiple allele definitions having the same sequence. A bug in OGRDBstats that created incorrect full v-sequence alignments has also been fixed.

IGH Analysis updated

The analysis of the Human IGH dataset has now been updated to determine novel sequences based on the actual V length inferred by igblast, enabling greater recognition of variation at the 3′ end. To provide greater detail on the analysis, we now provide the commit id of the pipeline version used for analysis in the… Continue reading IGH Analysis updated