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

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 .

• Authors: Amit A Upadhyay, Robert C Kauffman, Amber N Wolabaugh, Alice Cho, Nirav B Patel, Samantha M Reiss, Colin Havenar-Daughton, Reem A Dawoud, Gregory K Tharp, Iñaki Sanz, Bali Pulendran, Shane Crotty, F Eun-Hyung Lee, Jens Wrammert, Steven E Bosinger
• Journal: Genome medicine (Genome Med) Vol. 10 Issue 1 Pg. 20 (03 20 2018) ISSN: 1756-994X [Electronic] England
• PMID: 29558968 (Publication Type: Journal Article, Research Support, N.I.H., Extramural)

Chemical References

• Antigens, CD19
• Immunoglobulin Heavy Chains
• Immunoglobulin Light Chains
• RNA, Messenger

Topics

• Animals
• Antigens, CD19 (metabolism)
• Base Sequence
• Clone Cells
• Computational Biology (methods)
• Humans
• Immunoglobulin Heavy Chains (genetics)
• Immunoglobulin Light Chains (genetics)
• Macaca mulatta
• Plasma Cells (metabolism)
• RNA, Messenger (genetics, metabolism)
• Sequence Analysis, RNA
• Single-Cell Analysis
• Software