Fig. 4

Comparing vaccine-specific clusters to a size-matched random set of clusters and a non-size-matched random set of clusters. a–c Differences in size, number of V gene mutations, and CDR3 AA sequence length of the clusters belonging to the three datasets. Shown are the mean values ± SEM of the 312 clusters in each dataset. Comparisons were performed using a t-test. d The number of visits where at least a single sequence from each cluster was found was determined and the number of clusters present at different numbers of visits in the different datasets plotted. e Same as d but counting the number of participants where a similar cluster was found (same CDR3 cluster center sequence and V/J gene usage). f The proportion of total clusters in the three different datasets utilizing different V gene segments in each participant. Error bars show mean values ± SEM of the nine participants. g Principal component analysis of V gene segment usage of the clusters in each of the datasets. h Representative lineage trees of a vaccine-specific and size-matched cluster. Each node represents a unique sequence within the cluster, with the size indicative of the number of duplicate sequences. The number within the node indicates the visit at which the sequence is first present. Shading of the node represents whether the sequence is found in the cluster, an inferred common ancestor to sequences found in the cluster, or the germline sequence. Numbers on the edges of adjoining nodes show the number of mutations between the sequences. i, j Lineage trees were created for all clusters which contained at least 50 sequences in the dataset (N = 200). Diversity was calculated for each cluster using the Shannon index and trunk length is the number of mutations between the most recent common ancestor and germline sequence. Shown are the mean values ± SEM. Comparisons were performed using a t-test