Fig. 6

Analysis of the Genomics England DRAGEN calls with CNAqc. a QC from simple CNAs in \(n=235\) Genomics England samples (median coverage 100 ×), using DRAGEN data. The plot is like panel a in Fig. 5 for PCAWG. b Proportion of cases that pass QC, comparing Genomics England and PCAWG, for three tumor types: BRCA (breast cancer), LAML (acute myeloid leukemia), and SARC (sarcoma). c–e QC for subclonal CNAs in ALL (acute lymphocytic leukemia), BRCA, and SARC (c), complex CNAs in BRCA, SARC, and PT (pediatric tumors) (d), and proportion of segments with unassigned CCF values against purity. Plots are as in panels c–e in Fig. 5 for PCAWG. f–h Example QC of clonal simple (g) and subclonal CNAs (h) for a SARC sample with associated segmentation (f), where DRAGEN detects aneuploidy as well as a subclonal CNA involving an LOH event associated with 410 distinct mutations (in 31% of the tumor cells). These estimates are validated by CNAqc which detects, in the data, VAF peaks