The CAIRR Pipeline for Submitting Standards-Compliant B and T Cell Receptor Repertoire Sequencing Studies to the National Center for Biotechnology Information Repositories

Frontiers in Immunology
Syed Ahmad Chan BukhariSteven H Kleinstein

Abstract

The adaptation of high-throughput sequencing to the B cell receptor and T cell receptor has made it possible to characterize the adaptive immune receptor repertoire (AIRR) at unprecedented depth. These AIRR sequencing (AIRR-seq) studies offer tremendous potential to increase the understanding of adaptive immune responses in vaccinology, infectious disease, autoimmunity, and cancer. The increasingly wide application of AIRR-seq is leading to a critical mass of studies being deposited in the public domain, offering the possibility of novel scientific insights through secondary analyses and meta-analyses. However, effective sharing of these large-scale data remains a challenge. The AIRR community has proposed minimal information about adaptive immune receptor repertoire (MiAIRR), a standard for reporting AIRR-seq studies. The MiAIRR standard has been operationalized using the National Center for Biotechnology Information (NCBI) repositories. Submissions of AIRR-seq data to the NCBI repositories typically use a combination of web-based and flat-file templates and include only a minimal amount of terminology validation. As a result, AIRR-seq studies at the NCBI are often described using inconsistent terminologies, limiting scientist...Continue Reading

References

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Jul 18, 2018·BMC Bioinformatics·Syed Ahmad Chan BukhariSteven H Kleinstein

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Citations

Jun 19, 2019·Database : the Journal of Biological Databases and Curation·Marcos Martínez-RomeroMark A Musen
Oct 17, 2018·Frontiers in Immunology·Jason Anthony Vander HeidenUri Laserson
Dec 18, 2020·Nucleic Acids Research·Ofir LindenbaumSteven H Kleinstein

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Methods Mentioned

BETA
AIRR-seq
PCR

Software Mentioned

Zenodo
CEDAR
CEDAR Workbench workspace
BioPortal
CEDAR Template Designer
iReceptor
RightField
BioSample
VDJServer
CEDAR Workspace

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