Extended Data Fig. 8: Phased BAF plots of chromosomes with multiple CNN-LOH subclones.

All of the plots exhibit step functions of increasing |ΔBAF| towards a telomere, which is the hallmark of multiple clonal cell populations containing distinct CNN-LOH events that affect different spans of a chromosomal arm (all extending to the telomere). Distinct |ΔBAF| values (called using an HMM) are indicated with different colours. Flips in the sign of phased BAF usually correspond to phase switch errors. Two samples exhibit high switch error rates: 14q individual 3067 (explained by non-European ancestry), and 1p individual 23 (explained by very high |ΔBAF|; extreme shifts in genotyping intensities result in poor genotyping quality). All five individuals with multiple CNN-LOH events on chr13q appear to contain switch errors over 13q14, but these switches are actually explained by overlapping 13q14 deletions; see Supplementary Note 1 for detailed discussion.