Extended Data Fig. 1: Measuring CIN across tumour types.

a, Schematic of the analyses of allele-specific copy number alterations. Left, the SCNA profiles across the genome for the two samples of a tumour (red, A allele; blue, B allele), with raw allele-specific copy number values for heterozygous SNPs shown as points and inferred allele-specific integer copy number states as lines. The clonality of the SCNAs across the two samples is indicated by a track between the two SCNA profiles, with clonal SCNAs indicated in grey, subclonal SCNAs in yellow and both clonal and subclonal SCNAs in dashed yellow and grey. All SCNA profile plots in the figure are scaled by the number of data points per chromosome. Top right, the approach to summarise SCNA timing (clonal versus subclonal) from the tumour. Bottom right, the integer SCNA profile across the genome of the inferred MRCA based on the integer SCNA profiles of the two samples of the tumour. b, c, Multi-sample phasing (b) and SCNA calling relative to ploidy (c). b, Multi-sample phasing is the method that we used to obtain allele-specific copy number profiles. This allowed us to identify previously undetected allelic imbalance (yellow boxes), and mirrored subclonal allelic imbalance and parallel SCNAs (purple boxes). c, Chromosomal illustrations and nomenclature of various SCNAs. As SCNAs are reported relative to ploidy, illustrations are provided for the diploid, triploid and tetraploid states. AI, allelic imbalance. d, e, Pan-cancer cohort characteristics. Our pan-cancer multi-sample cohort is summarised by tumour type in these bar plots, indicating the total number of patients (d) with the bar plot coloured according to the number of samples each tumour contributes, and tumour samples (e) with the bar plot coloured according to the type of sample.