title: Assembly-based inference of B-cell receptor repertoires from short read RNA sequencing data with V'DJer.
abstract: 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.
authors: Lineberger Comprehensive Cancer Center.
authors: Lisle E
authors: LE
authors: Mose
authors: Lineberger Comprehensive Cancer Center.
authors: Sara R
authors: SR
authors: Selitsky
authors: Lineberger Comprehensive Cancer Center.|Division of Hematology/Oncology, Department of Internal Medicine.
authors: Lisa M
authors: LM
authors: Bixby
authors: Lineberger Comprehensive Cancer Center.
authors: David L
authors: DL
authors: Marron
authors: Curriculum in Genetics and Molecular Biology.
authors: Michael D
authors: MD
authors: Iglesia
authors: Lineberger Comprehensive Cancer Center.|Division of Hematology/Oncology, Department of Internal Medicine.|Department of Microbiology/Immunology.
authors: Jonathan S
authors: JS
authors: Serody
authors: Lineberger Comprehensive Cancer Center.|Departments of Genetics and Pathology and Laboratory Medicine.
authors: Charles M
authors: CM
authors: Perou
authors: Lineberger Comprehensive Cancer Center.|Division of Hematology/Oncology, Department of Internal Medicine.
authors: Benjamin G
authors: BG
authors: Vincent
authors: Lineberger Comprehensive Cancer Center.|Departments of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
authors: Joel S
authors: JS
authors: Parker
mesh_terms: D001402:B-Lymphocytes; D019295:Computational Biology / Q000379:methods*; D006801:Humans; D011947:Receptors, Antigen, B-Cell / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software
chemical_list: D011947:Receptors, Antigen, B-Cell