Reconstruction and analysis of B cell lineage trees from single cell data using Immcantation

Human B cells play a fundamental role in the adaptive immune response to infection and vaccination, as well as the pathology of allergies and many autoimmune diseases. Central to all of these processes is the fact that B cells are an evolutionary system, and undergo rapid somatic hypermutation and antigen-driven selection as part of the adaptive immune response. The similarities between this B cell response and evolution by natural selection have made phylogenetic methods a powerful means of characterizing important processes, such as immunological memory formation. Recent methodological work has led to the development of phylogenetic methods that adjust for the unique features of B cell evolution. Further, advances in single cell sequencing can now provide an unprecedented resolution of information, including linked heavy and light chain data, as well as the associated transcriptional states of individual B cells. In this webinar, we show how single cell information can be integrated into B cell phylogenetic analysis using the Immcantation suite (Immcantation.org). Beginning with processed single cell RNA-seq (scRNA-seq) + BCR data from 10X Genomics, we show how cell type annotations can be associated with BCR sequences, how clonal clusters can be identified, and how B cell phylogenetic trees can be built and visualized using these data sources.
Speaker info:
Kenneth Hoehn is a postdoctoral associate in Steven Kleinstein’s lab at Yale University, where he works on developing computational evolutionary approaches for studying B cell biology during infection, vaccination, and autoimmune disease.
Susanna Marquez is a bioinformatician in the computational immunology lab of Steven Kleinstein at Yale University, where she develops workflows for the analysis of AIRR-seq data, and provides support to develop and maintain the Immcantation suite.

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