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- Title
BALDR: a computational pipeline for paired heavy and light chain immunoglobulin reconstruction in single-cell RNA-seq data.
- Authors
Upadhyay, Amit A.; Kauffman, Robert C.; Wolabaugh, Amber N.; Cho, Alice; Patel, Nirav B.; Reiss, Samantha M.; Havenar-Daughton, Colin; Dawoud, Reem A.; Tharp, Gregory K.; Sanz, Iñaki; Pulendran, Bali; Crotty, Shane; Lee, F. Eun-Hyung; Wrammert, Jens; Bosinger, Steven E.
- Abstract
B cells play a critical role in the immune response by producing antibodies, which display remarkable diversity. Here we describe a bioinformatic pipeline, <italic>BALDR</italic> (<bold>B</bold>CR <bold>A</bold>ssignment of <bold>L</bold>ineage using <bold><italic>D</italic></bold><italic>e novo </italic><bold>R</bold>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 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 <ext-link>https://github.com/BosingerLab/BALDR</ext-link>.
- Subjects
IMMUNOGLOBULINS; B cells; NUCLEOTIDE sequence; IMMUNE response; INFLUENZA vaccines; BIOINFORMATICS
- Publication
Genome Medicine, 2018, Vol 10, p1
- ISSN
1756-994X
- Publication type
Article
- DOI
10.1186/s13073-018-0528-3