Repertoire Architecture

Networks of CDR3 aminoacidic sequences repertoires were constructed on the nonsubsampled repertoire as previously described¹⁸ based on the top 10,000 aminoacidic CDR3 sequences. Within each network, each node is a CDR3 aminoacidic sequence, and the Levenshtein distance (LevD) was calculated and used to define connections, connecting CDR3 sequences with LevD = 1 (=1 aminoacidic sequence change). LevD was calculated using the stringdist R package,¹⁹ while the degree of each node, namely the number of its connections, was calculated with the igraph package.²⁰ Comparisons between networks were performed according to the percentage of connected clonotypes (meaning the percentage of clonotypes showing at least 1 connection) out of the total number of clonotypes for each individual.