Refphase: Multi-sample phasing reveals haplotype-specific copy number heterogeneity
Fig 5
Cohort-level analysis of cancer evolution for the Sottoriva et al. [46] and Brastianos et al. [47] cohorts.
a) Barplot showing the number of samples per tumour and colored by WGD clonality status with clonal WGD (dark orange), subclonal WGD (light orange), and non-WGD (blue). b) Barplot showing proportion of the genome classified as affected by clonal SCNA (grey) and subclonal SCNA (yellow) from the pan-cancer cohort. c) Barplot showing proportion of the genome affected by parallel evolution of SCNAs relative to ploidy or LOH (red) and parallel evolution of 2|1 copy number states (dark blue). d) BAF of heterozygous SNPs across the genome from tumour samples from colorectal adenocarcinoma U. SNPs are coloured orange and blue according to the phased haplotype they are assigned to while SNPs that could not be phased are coloured grey. Regions of the genome demonstrating parallel evolution of a 2|1 and 1|2 copy number states are highlighted with a dark blue outline. e) Schematic demonstrating whole genome doubling and independent subsequent copy number loss events revealed by MSAI.