(A–C) Networks of the thousand most frequent CDR3 sequences are shown for (A) a naïve mouse, (B) a mouse Immunized with a self-peptide (p277), and (C) T cells from the spleen of an immunized mouse, which were re-stimulated in vitro with the p277 peptide. (D) Mean number of clustered nodes in networks formed by the top 1000 CDR3 sequences from the following repertoires: Left: naïve mice (n = 12); p277 immunized mice, 7d post immunization (n = 5); and in-vitro re-stimulated with p277 (n = 5). Right: naïve mice (n = 12); OVA immunized mice, 7d post immunization (n = 5); in-vitro re-stimulated with OVA peptide (n = 3); and immunized mice, 2 months post-immunization (n = 5). Error bars indicate standard error. (E) Frequency of the top 1000 most frequent CDR3 sequences by sharing level, for the same repertoires as in (D). Sharing levels were calculated based on sharing in the reference dataset of 28 mice. (F) The Gini Coefficient (a measure for repertoire evenness) plotted vs. the number of clustered nodes, for the top 1000 CDR3 sequences from the repertoires from (D, E) and from aged mice (n = 3). (G) The Gini Coefficient plotted vs. the number of clustered nodes for 39 human samples (Britanova et al., 2014) divided into 4 age groups. (H) The number of clustered nodes (left) and the number of public clonotypes (right, shared by all 11 young human samples in a reference cohort [Britanova et al., 2014]) for the top 1000 most abundant CDR3 sequences in 21 paired samples of patients at baseline and 30 to 60 days after receiving CTLA4 blockade treatment with tremelimumab (data from [Robert et al., 2014]). (I) Number of public clonotypes (defined as in H) out of the top 1000 most abundant CDR3 sequences in either healthy donors (left) or Juvenile Idiopathic Arthritis patients (right). (J) A conceptual figure of the evolution of repertoire structure. In young and healthy individuals the repertoire is focused and even (top-right), with public and CS-public CDR3 sequences at the center of network clusters. Following an immune response, or with aging, the repertoire becomes more skewed and spread in sequence space (bottom-left), due to preferential expansion of private clones at the expense of more public clones.