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Genome Med. 2018 Mar 20;10(1):20. doi: 10.1186/s13073-018-0528-3.

BALDR: a computational pipeline for paired heavy and light chain immunoglobulin reconstruction in single-cell RNA-seq data.

Author information

1
Division of Microbiology and Immunology, Yerkes National Primate Research Center, Atlanta, GA, USA.
2
Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, USA.
3
Yerkes NHP Genomics Core Laboratory, Yerkes National Primate Research Center, 954 Gatewood Rd, Atlanta, GA, 30329, USA.
4
Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA.
5
Scripps Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVI-ID), La Jolla, CA, USA.
6
Division of Rheumatology, School of Medicine, Emory University, Atlanta, GA, USA.
7
Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA.
8
Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
9
Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.
10
Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA, USA.
11
Divisions of Pulmonary, Allergy and Critical Care Medicine, Emory University, Atlanta, GA, USA.
12
Division of Microbiology and Immunology, Yerkes National Primate Research Center, Atlanta, GA, USA. sbosing@emory.edu.
13
Yerkes NHP Genomics Core Laboratory, Yerkes National Primate Research Center, 954 Gatewood Rd, Atlanta, GA, 30329, USA. sbosing@emory.edu.
14
Department of Pathology & Laboratory Medicine, School of Medicine, Emory University, Atlanta, GA, USA. sbosing@emory.edu.

Abstract

B cells play a critical role in the immune response by producing antibodies, which display remarkable diversity. Here we describe a bioinformatic pipeline, BALDR (BCR Assignment of Lineage using De novo Reconstruction) that accurately reconstructs the paired heavy and light chain immunoglobulin gene sequences from Illumina single-cell RNA-seq data. BALDR was accurate for clonotype identification in human and rhesus macaque influenza vaccine and simian immunodeficiency virus vaccine induced vaccine-induced plasmablasts and naïve and antigen-specific memory B cells. BALDR enables matching of clonotype identity with single-cell transcriptional information in B cell lineages and will have broad application in the fields of vaccines, human immunodeficiency virus broadly neutralizing antibody development, and cancer.BALDR is available at https://github.com/BosingerLab/BALDR .

PMID:
29558968
PMCID:
PMC5859752
DOI:
10.1186/s13073-018-0528-3
[Indexed for MEDLINE]
Free PMC Article

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