Detection of clonal mosaic events was based on assessment of allelic imbalance and copy number changes. We used the B-allele frequency (BAF) measurement, derived from the ratio of probe values relative to the locations of the estimated genotype-specific clusters, for initial segmentation using the Mosaic Alteration Detection (MAD) algorithm implemented in GADA-R with modifications17,18. The BAF and log2 relative probe intensity ratio (LRR), which provides data on copy number, were used to classify each event as copy-altering (gain or loss) or neutral (reciprocal gain and loss resulting in loss of heterozygosity, LOH) and to assign the proportions of abnormal (p) and normal (1-p) cells. Mosaic proportions were required to deviate from levels expected from constitutional (non-mosaic) changes in order to exclude homozygous chromosomal segments inherited identical by descent and non-mosaic instances of trisomy, monosomy and uniparental disomy. A minimum event size threshold was set to detect only clonal mosaic events greater than 2 Mbps to minimize the false discovery of constitutional copy number variants. Copy-neutral LOH and copy-loss events could be detected for mosaic proportions between 7% and 95% (Figure
