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A) YF-responding clones identified using hierarchical clustering of clonal time traces with and without biological replicates. The plot shows two first principal components (x and y-axis) of the matrix, where rows are clonotypes and columns are normalized frequencies of these clonotypes on timepoints before and after primary immunization of donor M1. The frequency of each clonotype was normalized by its peak concentration. Pink color shows expanded clonotypes identified with edgeR. Two clusters (circles and crosses) were identified using hierarchical clustering. Similar results were obtained for both TCR alpha (left column) and TCR beta (right column) sequencing, with (top row) and without (bottom row) biological replicates for every timepoint. (
B) Dynamics of YF-responding clonotypes after primary vaccination data from
Pogorelyy et al. (2018). The cumulative frequency of YF-responding clonotypes defined as significantly expanded by edgeR is shown in blue. The green line indicates the cumulative frequency of responding clonotypes identified by hierarchical clustering of individual clonal trajectories. For the clustering procedure, only frequencies of biological replicate 1 of the bulk repertoire were used. (
C) Examples of time traces for two YF-responding (purple and green) and one non-responding (blue) clonotypes in the TCR alpha repertoire (left), and their associated chain in TCR beta repertoire (right). The similarity of the alpha and beta traces of the same clone allows for computational alpha-beta pairing prediction. .