Refphase: Multi-sample phasing reveals haplotype-specific copy number heterogeneity
Fig 2
Detection of mirrored subclonal allelic imbalance and parallel evolution.
a) LogR and BAF tracks in chromosomes 1 to 6 from tumour CRUK0034. LogR tracks show LogR values in light grey points. The black line shows the median LogR within a minimum consistent segment. BAF tracks show phased BAF as either orange “A” haplotype points or blue “B” haplotype points. Unphased BAF values are shown as light grey points. b) SCNA summary tracks showing (top) gains relative to ploidy. The full height grey bar indicates that a gain is identified in every sample from tumour CRUK0034. A light yellow background indicates the presence of a subclonal gain, and the height of the stacked darker yellow bar indicates the proportion of samples in which a subclonal gain is present. (middle) Track indicates the presence of MSAI between at least two samples, shown by purple fill. (bottom) Track indicates the presence of parallel gains, shown by red fill. c) MSAI detected from tumour CRUK0034 affecting chromosome 4. d) Parallel evolution of chromosome arm 5p gain from tumour CRUK0034. e) Schematic of the copy number states related to MSAI and parallel evolution.