Introduction

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.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.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.

Publications

  1. Assembly-based inference of B-cell receptor repertoires from short read RNA sequencing data with V'DJer.
    Cite this
    Mose LE, Selitsky SR, Bixby LM, Marron DL, Iglesia MD, Serody JS, Perou CM, Vincent BG, Parker JS, 2016-12-01 - Bioinformatics (Oxford, England)

Credits

  1. Lisle E Mose
    Developer

  2. Sara R Selitsky
    Developer

  3. Lisa M Bixby
    Developer

  4. David L Marron
    Developer

  5. Michael D Iglesia
    Developer

  6. Jonathan S Serody
    Developer

  7. Charles M Perou
    Developer

  8. Benjamin G Vincent
    Developer

  9. Joel S Parker
    Investigator

    Departments of Genetics, University of North Carolina at Chapel Hill, United States of America

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Summary
AccessionBT000851
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC, C++
User InterfaceTerminal Command Line
Download Count0
Country/RegionUnited States of America
Submitted ByJoel S Parker