Extended Data Fig. 3: NSCLC SCNAs correlate with cell cycle gene expression and tumour cell characteristics.
From: Pervasive chromosomal instability and karyotype order in tumour evolution
a, b, Scatter plots comparing the average cell cycle gene expression in LUAD tumours (n = 36), LUSC tumours (n = 15) and NSCLC-other tumours (n = 7) with the total proportion of the genome affected by SCNAs. Each dot is coloured according to tumour type. (a) and the proportion of the genome affected by clonal SCNAs (b). c, The proportion of the genome affected by subclonal SCNAs. d, The proportion of SCNAs that are subclonal. a–d, ρ and P values are from Spearman correlation tests. Associations between tumour cell characteristics and SCNA statistics for LUAD (n = 53), LUSC (n = 27) and NSCLC-other (n = 3). e–h, Mitotic index scores for each tumour are compared against total SCNAs (e), clonal SCNAs (f), subclonal SCNAs (g) and the proportion of SCNAs that are subclonal (h) in each tumour. Each dot is coloured according to tumour type. ρ and P values are from Spearman correlation tests. i–l, Association between tumour volume and SCNA metrics. For each tumour for which both digitized slides and tumour volume information were available (n = 83), we performed Spearman correlation tests comparing the tumour volume with the total proportion of the genome affected by SCNAs (i), the proportion of the genome affected by clonal SCNAs (j), the proportion of the genome affected by subclonal SCNAs (k) and the proportion of SCNAs that are subclonal (l). Padj values reflect P values from linear regression models incorporating the number of samples as well as estimated tumour volume and SCNA measure investigated. m–p, Associations between tumour cell characteristics and SCNA statistics for LUAD (n = 53), LUSC (n = 27) and NSCLC-other (n = 3). Anisonucleosis scores for each tumour are compared with the proportion of the genome affected by SCNAs (m), clonal SCNAs (n) or subclonal SCNAs (o) and the proportion of SCNAs that are subclonal (p) in each tumour. Each dot is coloured according to tumour type. The lines represent the median of each group. es, effect size.
