[HTML][HTML] BALDR: a computational pipeline for paired heavy and light chain immunoglobulin reconstruction in single-cell RNA-seq data
AA Upadhyay, RC Kauffman, AN Wolabaugh, A Cho… - Genome medicine, 2018 - Springer
AA Upadhyay, RC Kauffman, AN Wolabaugh, A Cho, NB Patel, SM Reiss…
Genome medicine, 2018•SpringerB cells play a critical role in the immune response by producing antibodies, which display
remarkable diversity. Here we describe a bioinformatic pipeline, BALDR (B CR A ssignment
of L ineage using D e novo R econstruction) 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 …
remarkable diversity. Here we describe a bioinformatic pipeline, BALDR (B CR A ssignment
of L ineage using D e novo R econstruction) 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 …
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 .
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