Single Cell VDJ Sequencing of Normal and Malignant B and T Cells

Recent developments in single cell sequencing technologies enable researchers to examine heterogeneity of cell types and subclusters even deeper. First assays were only available for transcriptome analysis of up to 10,000 cells, but nowadays up to 60,000 cells or even more can be analyzed. Whereas initially only analysis of mRNA expression was possible, currently single cell methods multiplied, with extension of assays for examination of surface molecule expression, DNA accessibility (ATAC-seq), antigen specificity, and B or T cell receptor repertoires. Also, spatial transcriptomics or CRISPR screenings, augmenting classical CRISPR/Cas9 screens by combining them with transcriptomic data at single cell level, can be evaluated. The composition of B and T cell clones-of malignant cells in lymphomas and leukemia, as well as of infiltrating B or T cell clones in other types of cancer-is especially important in tumor research, as these clones may give valuable hints for tumor development and control. This chapter presents detailed methods for implementation and analysis of single cell B and/or T cell receptor repertoire sequencing on the Chromium system from 10× Genomics and the Rhapsody™ system from BD Bioscience.