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Bioinformatics. 2016 Dec 15;32(24):3729-3734. Epub 2016 Aug 24.

Assembly-based inference of B-cell receptor repertoires from short read RNA sequencing data with V'DJer.

Author information

1
Lineberger Comprehensive Cancer Center.
2
Division of Hematology/Oncology, Department of Internal Medicine.
3
Curriculum in Genetics and Molecular Biology.
4
Department of Microbiology/Immunology.
5
Departments of Genetics and Pathology and Laboratory Medicine.
6
Departments of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.

Abstract

MOTIVATION:

B-cell receptor (BCR) repertoire profiling is an important tool for understanding the biology of diverse immunologic processes. Current methods for analyzing adaptive immune receptor repertoires depend upon PCR amplification of VDJ rearrangements followed by long read amplicon sequencing spanning the VDJ junctions. While this approach has proven to be effective, it is frequently not feasible due to cost or limited sample material. Additionally, there are many existing datasets where short-read RNA sequencing data are available but PCR amplified BCR data are not.

RESULTS:

We present here V'DJer, an assembly-based method that reconstructs adaptive immune receptor repertoires from short-read RNA sequencing data. This method captures expressed BCR loci from a standard RNA-seq assay. We applied this method to 473 Melanoma samples from The Cancer Genome Atlas and demonstrate V'DJer's ability to accurately reconstruct BCR repertoires from short read mRNA-seq data.

AVAILABILITY AND IMPLEMENTATION:

V'DJer is implemented in C/C ++, freely available for academic use and can be downloaded from Github: https://github.com/mozack/vdjer CONTACT: benjamin_vincent@med.unc.edu or parkerjs@email.unc.eduSupplementary information: Supplementary data are available at Bioinformatics online.

PMID:
27559159
PMCID:
PMC5167060
DOI:
10.1093/bioinformatics/btw526
[Indexed for MEDLINE]
Free PMC Article

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