Fig. 5

T-cell repertoire analysis reveals associations of T-cell clonal expansion with B-cell repertoire and immune microenvironment in Paediatric Inflamed. A Scatterplot depicting a linear correlation between TCRβ Shannon diversity estimated from RNA-seq and measured by capturing all TCR sequences from the same RNA-seq libraries in adult and paediatric cancer samples using CapTCR-seq. B Scatterplot showing correlation between TCRβ estimated Shannon diversity and total number of TCRβ reads. Blue line shows fitted linear regression. Red and blue dots represent polyclonal and clonal T-cell repertoires defined as residuals greater than two absolute standard deviations. Circle plots to the right illustrate two examples of polyclonal (top) and clonal (bottom) T-cell repertoires. Each circle is one T-cell clone and circle diameters are proportional to TCRβ reads. C Boxplots showing differences in log-transformed estimated TCRβ Shannon diversity across immune clusters for neuroblastoma (left) and pedCNS (right). Two-sided Student’s t test with Bonferroni correction, *p < 0.05, **p < 0.01 and ***p < 0.001. D Boxplots comparing levels of T-cells, dendritic cells or monocytes, as determined in Fig. 1C, in samples with TCRβ residuals (obtained from the linear regression in B) ≤ 25th percentile and ≥ 75th percentile of Paediatric Inflamed (left) or Myeloid Predominant (right). Two-sided Student’s t test, *p < 0.05, NS: not significant. E Boxplot showing proportion of specific immunoglobulin isotypes in B-cell repertoires across immune clusters in pedNST. Two-sided Student’s t test, *p < 0.05 and **p < 0.01. F Boxplots comparing immunoglobulin clonality (gini index) across immune clusters for neuroblastoma (left) and pedCNS (right). Two-sided Student’s t test with Bonferroni correction, *p < 0.05 and **p < 0.01. G Boxplots comparing levels of gini index or tumour-type normalized expression of IGHG1 or IGHG3 in samples with TCRβ residuals (obtained from the linear regression in B) ≤ 25th percentile and ≥ 75th percentile of Paediatric Inflamed (left) or Myeloid Predominant (right). Two-sided Student’s t test, *p < 0.05, NS: not significant. In all boxplots, boxes show median and IQR and whiskers represent 1.5 times IQR