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

作者：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 Inaki; Pulendran Bali; Crotty Shane; Lee F Eun Hyung; Wrammert Jens; Bosinger Steven E^*

来源：Genome Medicine, 2018, 10(1): 20.

DOI：10.1186/s13073-018-0528-3

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 naive 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.

• 出版日期2018-3-20