Fig. 4. WGS validates SKY-based cytogenetic markers used for phylogenetic trees.

a The WGS-based copy number (CN) ratios of four tumor samples over tail (black points) from Mouse 2 were compared to the average of chromosome copy numbers obtained from SKY analysis (solid red segments). Arrowheads indicate the t(2;4) acquisition (red) and chromosome loss (blue). b Comparison of whole-chromosome CNV estimation (log2 ratio) between WGS and SKY using Pearson correlation coefficient (r). Dots represent each chromosome in each sample (n = 13). Dotted line represents a linear regression line between WGS and SKY estimations. c WGS analysis of primary cells from four tumors in Mouse 2 shows the interchromosomal rearrangement t(2;4) (red line) and t(10;11) (green line). d, e Sanger sequencing of t(2;4) and wild-type chr2 in Mouse 2 (d), with malignant glioma from other animal as control. q-PCR analysis shows the relative ratio of t(2;4) to wild-type chr2 between SVZ^L-T (100%) and SVZ^R-T (40%), exhibiting an excellent agreement with the SKY data (e). Source data are provided as a Source data file. f Sample-wise NRT sharing matrix was built for p53^nullCKO and p53^R172HCKO gliomas. Shared NRTs between metaphases are displayed using a heatmap. Blue indicates no shared NRTs and red indicates shared NRTs. Red dashed squares indicate metaphases from a single mouse.