Fig. 3: Somatic copy number alterations (SCNAs).

a Genome-wide sample cancer cell fraction (CCF) profiles across tumors. Samples are labeled by histology subgroup and cellularity (or called purity). (b) Size of SCNAs identified in each tumor, separated into clonal alterations (purple), which have a shared breakpoint across all samples from a tumor and subclonal alterations (yellow), which have breakpoints that are found only in a subset of samples from a tumor. Where clonal and subclonal SCNAs are both identified in a tumor, they are shown side by side. The numbers of clonal and subclonal SCNAs are included in the parentheses following the tumor ID, such as pRCC1_1472_01(n = 7,0). Vertical lines separate pRCC1 (left), pRCC2 (middle) and rare subtypes (right). In each box-and-whisker plot, the line dividing the box represents the median; the ends of the box are the lower (Q1) and upper (Q3) quartiles; the whiskers are extended to Q1-1.5xIQR and Q3 + 1.5IQR with IQR = Q3–Q1. Each circle represents a data point of SCNA size. (c) SCNAs of tumor pRCC2_1824_13. Top panel: genome-wide SCNAs on ten primary tumors (T01-T10) and three metastatic samples (M01, M02 and M03); T10 has low purity and has no SCNAs. Bottom panels: metastatic sample-specific SCNAs on chromosome 4 for total copy number log-ratio (red line: estimated total copy number log-ratio; green line: median; purple line: diploid state). DLOH: hemizygous deletion loss of heterozygosity; HET: diploid heterozygous; NLOH: copy neutral loss of heterozygosity; ALOH: amplified loss of heterozygosity; ASCNA: allele-specific copy number amplification; BCNA: balanced copy number amplification.