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

32Citations
Citations of this article
88Readers
Mendeley users who have this article in their library.

This article is free to access.

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.

Cite

CITATION STYLE

APA

Upadhyay, A. A., Kauffman, R. C., Wolabaugh, A. N., Cho, A., Patel, N. B., Reiss, S. M., … Bosinger, S. E. (2018). BALDR: A computational pipeline for paired heavy and light chain immunoglobulin reconstruction in single-cell RNA-seq data. Genome Medicine, 10(1). https://doi.org/10.1186/s13073-018-0528-3

Register to see more suggestions

Mendeley helps you to discover research relevant for your work.

Already have an account?

Save time finding and organizing research with Mendeley

Sign up for free