VDJbase: An adaptive immune receptor genotype and haplotype database

Aviv Omer; Or Shemesh; Ayelet Peres; Pazit Polak; Adrian J. Shepherd; Corey T. Watson; Scott D. Boyd; Andrew M. Collins; William Lees; Gur Yaari

doi:10.1093/nar/gkz872

VDJbase: An adaptive immune receptor genotype and haplotype database

Aviv Omer, Or Shemesh, Ayelet Peres, Pazit Polak, Adrian J. Shepherd, Corey T. Watson, Scott D. Boyd, Andrew M. Collins, William Lees, Gur Yaari

Research output: Contribution to journal › Article › peer-review

30 Scopus citations

Abstract

VDJbase is a publicly available database that offers easy searching of data describing the complete sets of gene sequences (genotypes and haplotypes) inferred from adaptive immune receptor repertoire sequencing datasets. VDJbase is designed to act as a resource that will allow the scientific community to explore the genetic variability of the immunoglobulin (Ig) and T cell receptor (TR) gene loci. It can also assist in the investigation of Ig- A nd TR-related genetic predispositions to diseases. Our database includes web-based query and online tools to assist in visualization and analysis of the genotype and haplotype data. It enables users to detect those alleles and genes that are significantly over-represented in a particular population, in terms of genotype, haplotype and gene expression. The database website can be freely accessed at https://www.vdjbase.org/, and no login is required. The data and code use creative common licenses and are freely downloadable from https://bitbucket.org/account/user/yaarilab/projects/GPHP.

Original language	English
Pages (from-to)	D1051-D1056
Journal	Nucleic Acids Research
Volume	48
Issue number	D1
DOIs	https://doi.org/10.1093/nar/gkz872
State	Published - 1 Jan 2020
Externally published	Yes

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title = "VDJbase: An adaptive immune receptor genotype and haplotype database",

abstract = "VDJbase is a publicly available database that offers easy searching of data describing the complete sets of gene sequences (genotypes and haplotypes) inferred from adaptive immune receptor repertoire sequencing datasets. VDJbase is designed to act as a resource that will allow the scientific community to explore the genetic variability of the immunoglobulin (Ig) and T cell receptor (TR) gene loci. It can also assist in the investigation of Ig- A nd TR-related genetic predispositions to diseases. Our database includes web-based query and online tools to assist in visualization and analysis of the genotype and haplotype data. It enables users to detect those alleles and genes that are significantly over-represented in a particular population, in terms of genotype, haplotype and gene expression. The database website can be freely accessed at https://www.vdjbase.org/, and no login is required. The data and code use creative common licenses and are freely downloadable from https://bitbucket.org/account/user/yaarilab/projects/GPHP.",

author = "Aviv Omer and Or Shemesh and Ayelet Peres and Pazit Polak and Shepherd, {Adrian J.} and Watson, {Corey T.} and Boyd, {Scott D.} and Collins, {Andrew M.} and William Lees and Gur Yaari",

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doi = "10.1093/nar/gkz872",

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AU - Omer, Aviv

AU - Shemesh, Or

AU - Peres, Ayelet

AU - Polak, Pazit

AU - Shepherd, Adrian J.

AU - Watson, Corey T.

AU - Boyd, Scott D.

AU - Collins, Andrew M.

AU - Lees, William

AU - Yaari, Gur

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VDJbase: An adaptive immune receptor genotype and haplotype database

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