Integrating T cell receptor sequences and transcriptional profiles by clonotype neighbor graph analysis (CoNGA)

Links between T cell clonotypes, as defined by T cell receptor (TCR) sequences, and phenotype, as reflected in gene expression profiles, surface protein expression, and peptide:MHC binding, can reveal functional relationships beyond the features shared by clonally related cells. We present clonotype neighbor-graph analysis (CoNGA), a graph-theoretic approach that identifies unbiased correlations between gene expression profile and TCR sequence through statistical analysis of gene expression and TCR similarity graphs. Using CoNGA, we uncovered associations between TCR sequence and gene expression profiles that include a previously undescribed ‘natural lymphocyte’ population of human circulating CD8+ T cells and a set of TCR sequence determinants of differentiation in thymocytes. These examples show that CoNGA may help elucidate complex relationships between TCR sequence and T cell phenotype in large, heterogeneous single-cell datasets.