T-cell receptor analysis in IAA patients. (A) ISI distribution in HC and IAA patients (downsampled dataset). Violin plots showing median and interquartile ranges. Wilcoxon signed-rank test. (B) Number of unique clonotypes in HC and IAA patients (downsampled dataset). Violin plots showing median and interquartile ranges. Wilcoxon signed-rank test. (C) Mean size of expansion of each clonotype of size ≥2 templates in HC and IAA patients (down-sampled dataset). Violin plots showing median and interquartile ranges. Wilcoxon signed-rank test. (D) ISI distribution in HC and IAA patients in DRB1*15:01 carriers (downsampled dataset). Violin plots showing median and interquartile ranges. Wilcoxon signed-rank test. (E) ISI distribution in HC and IAA patients in non-DRB1*15:01 carriers (downsampled dataset). Violin plots showing median and interquartile ranges. Wilcoxon signed-rank test. (F) Linear regression analysis between ISI and mean class I HED. (G) Linear regression analysis between the number of unique clonotypes and mean class I HED. (H) Linear regression analysis between the mean size of clonotype expansion and mean class I HED. (I) Linear regression analysis between ISI and mean class II HED. (J) Linear regression analysis between the number of unique clonotypes and mean class II HED. (K) Linear regression analysis between the mean size of clonotype expansion and mean class II HED. r² goodness-of-fit are reported along with the P value in each box (F-K). (L) Proportion of known complementary determining region 3 (CDR3) specificities in IAA and HC groups (this distribution has been computed in the downsampled dataset). (M) Logarithm of mean frequency of autoreactive clonotypes present in HC and IAA patients. Violin plots showing median and interquartile ranges. Each dot represents the mean frequency/per subject (all the values refer to the nondownsampled dataset in order to capture all the possible recognizable CDR3 sequences). Wilcoxon signed-rank test. (N) Linear regression analysis between frequency of known autoreactive clonotypes in IAA patients and mean class II HED. Each dot represents 1 autoreactive clonotype. Clonotypes with overlapping frequencies are represented by the darkest dots (all the values refer to the nondownsampled dataset). Wilcoxon signed-rank test. R-squared goodness-of-fit are reported along with the P value. (O) Bubble matrix showing the mean frequency of each autoimmune disease-associated clonotype present in the nondownsampled repertoires of IAA and HCs. Each bubble represents the number of clonotypes with known autoimmune specificity (x-axis). The size of each bubble indicates the mean productive frequency (measure of clonal size). Wilcoxon signed-rank test is used to compare the mean frequencies of each specificity between IAA and HC groups. *****P < 10e-6; ****P < 10e-5; P < 10e-4; **P < .001; *P < .01. aa, amino acid; ISI, Inverse Simpson index; ns, nonsignificant.