BIRS Workshop Lecture Videos
Combining immune cell repertoire sequencing and functional expression with applications to autoimmune disease. McDavid, Andrew
The cells of the adaptive immune system have the capacity to respond to a lifetime of diverse pathogens, in part due to somatic recombination of genes comprising the T and B cell receptors ([TB]CR). Several protocols now exist for simultaneously resolving [TB]CR identity and scRNAseq expression of all other polyadenalated mRNAs. I describe a pipeline for inferring *clonal* subpopulations of cells, that is, cells that share a [TB]CR from a common ancestor. This pipeline can scale to tens of thousands of cells. A series of statistical models are proposed for testing for expansion of specific clones in covariate groups, as well the omnibus propensity for clonal expansion. Lastly, I consider how [TB]CR identity can be combined with scRNAseq expression for unsupervised clustering using methods from multiview learning. I apply these methods to a data set of B cells isolated from the synovium of rheumatoid arthritis patients.
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