ArticleBioinformatics (Oxford, England)2016
Assembly-based inference of B-cell receptor repertoires from short read RNA sequencing data with V'DJer.
Article in Bioinformatics (Oxford, England), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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Who cites it
42 citing papers in PubMed.
- Article
- The multifaceted roles of tumor-infiltrating plasma cells in cancer immunology.Fundamental research · 2026Review
- A reproducible pipeline for TCR β-chain repertoire analysis from thoracic tumour RNA-seq and ICI-associated cardiac immunotoxicity.Frontiers in immunology · 2026Article
- Identification, assembly and characterization of tumor immunoglobulin transcripts from RNA sequencing data using IgSeqR.Nature protocols · 2025Review
- Article
- Evaluation of T Cell Receptor Construction Methods from scRNA-Seq Data.Genomics, proteomics & bioinformatics · 2025Article
- Historical perspective and future directions: computational science in immuno-oncology.Journal for immunotherapy of cancer · 2024Review
- Fast clonal family inference from large-scale B cell repertoire sequencing data.Cell reports methods · 2023Article
- Multi-omics indicators of long-term survival benefits after immune checkpoint inhibitor therapy.Cell reports methods · 2023Article
- B cell profiles, antibody repertoire and reactivity reveal dysregulated responses with autoimmune features in melanoma.Nature communications · 2023Article
- The combined signatures of telomere and immune cell landscape provide a prognostic and therapeutic biomarker in glioma.Frontiers in immunology · 2023Article
- RNA-seq data science: From raw data to effective interpretation.Frontiers in genetics · 2023Review
- Antigen-specificity measurements are the key to understanding T cell responses.Frontiers in immunology · 2023Review
- Benchmarking computational methods for B-cell receptor reconstruction from single-cell RNA-seq data.NAR genomics and bioinformatics · 2022Article
- Comprehensive Characterizations of Immune Receptor Repertoire in Tumors and Cancer Immunotherapy Studies.Cancer immunology research · 2022Article
- The role of B cells in the development, progression, and treatment of lymphomas and solid tumors.Advances in immunology · 2022Review
- Comprehensive Analysis of the Immunogenomics of Triple-Negative Breast Cancer Brain Metastases From LCCC1419.Frontiers in oncology · 2022Article
- Identification of NOTCH4 mutation as a response biomarker for immune checkpoint inhibitor therapy.BMC medicine · 2021Article
- TRUST4: immune repertoire reconstruction from bulk and single-cell RNA-seq data.Nature methods · 2021Article
- Tertiary lymphoid structures and B lymphocytes in cancer prognosis and response to immunotherapies.Oncoimmunology · 2021Review
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9 authors.
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Abstract
motivationB-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.
resultsWe 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.
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