Fig. 2

Comparing the performance of SCNA detection in low tumour purity samples and determining the limit of detection. a Left column: RCN calls by conliga, showing a selection of chromosomes, at different dilutions of sample OAC3, compared to the ASCAT RCN profile of the undiluted sample (top left), discrete copy number states are coloured with a gradient (light green to purple), highlighting regions with differing SCNAs. Middle column: RCN calls by CNVkit at different dilutions of sample OAC3, compared to ASCAT RCN profile (top middle). Right column: RCN calls by QDNAseq at different dilutions of sample OAC3, compared to ASCAT RCN profile (top right). Calls by CNVkit and QDNAseq are not coloured because they do not provide hidden state information. Purity levels are indicated as a percentage on the right-hand side. 0% purity profiles are highlighted in a red box, for which all regions of the genome should have equal RCN. b The number of copy number states detected by conliga (left) in each of eight OAC samples at differing purity levels. The limit of detection is determined by the lowest purity level in which more than one copy number state is detected. Red dashed line indicates one hidden state inferred, indicating that zero copy number changes are inferred. The number of unique RCN calls observed within each sample for CNVkit (middle) and QDNAseq (right). Note the differing y-axis ranges and that the number of unique RCN calls are always greater than one for CNVkit and QDNAseq