BALDR

BALDR reconstructs paired heavy and light chain immunoglobulin gene sequences from single-cell RNA-Seq data generated via Illumina sequencing, enabling analysis of B cell receptor (BCR) diversity.

Key Features:

• Paired heavy and light chain reconstruction: De novo reconstruction of paired immunoglobulin heavy and light chain gene sequences from single-cell RNA-Seq reads generated on Illumina platforms.
• Clonotype identification: Accurate identification of clonotypes in human and rhesus macaque samples, including influenza- and simian immunodeficiency virus (SIV)-vaccine-induced plasmablasts, naïve B cells, and antigen-specific memory B cells.
• Integration with transcriptional data: Matching of clonotype identity with single-cell transcriptional information to link BCR sequences to cellular phenotypes.
• Application breadth: Applicable to vaccine research, development of broadly neutralizing antibodies against HIV, and cancer immunotherapy studies.

Scientific Applications:

• B cell receptor diversity analysis: Reconstruction and lineage assignment of BCR sequences to study repertoire diversity.
• Vaccine response studies: Analysis of plasmablast and memory B cell responses induced by influenza and SIV vaccination.
• Broadly neutralizing antibody discovery: Support for identification and characterization of antibodies relevant to HIV broadly neutralizing antibody development.
• Cancer immunotherapy research: Linking BCR clonotypes to single-cell transcriptional profiles for tumor immunology investigations.

Methodology:

De novo reconstruction of immunoglobulin gene sequences from Illumina single-cell RNA-Seq reads with assignment of BCR clonotypes and matching of clonotype identity to single-cell transcriptional profiles.