Fig 1.
Significant regions of (A) arm-level and (B) focal somatic copy number alteration across the genome (y-axis).
The x-axis indicates frequencies (A) or significance (as FDR q-values, B). Arms considered significant (q<0.05) are marked with an asterisk; the significance levels of focal events are shown as green lines. The 35 most significant focal regions of each SCNA type are labeled by associated single genes, putative drivers, or cytoband location. Labels of known oncogenes and tumor suppressors are highlighted in gray; tyrosine kinase genes are red, cell-cycle genes are green, transcription factors are blue text and large genes are brown.
Fig 2.
Classification of patient ancestry.
(A) Distribution of projections of patient germline SNP genotypes on the principle component of SNP variation. The stacked bars of the histogram are colored by the data source and summarized in overlying proportionately sized pie charts. Outliers do not appear in the histogram. (B) Ancestries determined by genotype among patients reporting Asian, Black, and White ancestry, respectively.
Fig 3.
Genomic disruption between Eastern and Western samples.
(A) Copy number profiles of Western (top) and Eastern (bottom) samples (x-axis; decreasing genomic disruption towards the left) across the genome (y-axis). Amplifications are in red and deletions in blue. (B) Fraction of the genome disrupted and (C) purity estimates of samples (circles) in each cohort. Solid lines represent median values; the dashed line represents the minimum purity detection limit. (D) Rates of CIN in each cohorts. Single and triple asterisks indicate p≤0.05 and p≤0.001, respectively.
Fig 4.
Genomic disruption after purity correction within CIN and non-CIN subtypes.
(A) Genomic disruption using purity-corrected data within samples of each subtype. Circles represent samples and lines represent median values. (B) Purity-corrected copy-number profiles arranged by molecular subtype and East/West cohort. Data are presented as in Fig 3A. “N.S.” indicates p>0.05.
Fig 5.
Event frequencies at regions of significant focal SCNA.
A bar chart of comparative event frequencies (black scale) is overlaid with a plot of the significance of the event rate difference (green scale). Only those with FDR q<1.0 (all deletions) are shown. The arrow and dashed line indicate the significance cutoff of 0.05.