Chimeric mice exhibit major impact on the T-cell repertoire. (A) PCA separating between the Vα and Vβ usage of CD4 (circle) and CD8 (triangle) and between transplanted NOD (CHV, red), untreated NOD (blue), and untreated C57BL/6 (gray) mice. PC1 separates between CD4 and CD8. PC2 separates the different mouse backgrounds. Significant enrichment of specific V segments is detected in both TRBV genes (more than 9 genes; P < .05 with fdr correction) TRAV families (more than 17 genes with P < .05 with fdr correction). (B) CDR3AA sequences from transplanted NOD mice are distinct from untreated NOD or untreated C57BL/6 mice. Distances between CDR3AA repertoires of α or β chain across mice were calculated using the Jaccard index and projected on 2-dimensional panel with non-matrix multidimensional scaling (NMDS).³⁵ NMDS2 separates the untreated C57BL/6 from untreated NOD and transplanted NOD mice (Jaccard score P < .001, Wilcox test-fdr corrected). NMDS1 separates between untreated NOD and transplanted NOD mice in the α chain, and to a lesser extent in the β chain (P < .001, Wilcox test-fdr corrected).