width of the split varies from zero to one and LRR varies from 0 to a theoretical value of log2(1/2). In biparental-uniparental disomic mosaics, the width of the split varies from zero to one, while LRR remains constant at zero. These transitions are shown in Figure 2 as deviations from expected. In chromosomal regions containing heterozygous SNPs, use of BAF alone can detect duplications (both mosaic and non-mosaic), mosaic deletions, mosaic uniparental disomy and homozygous deletions. LRR is required to detect monosomic regions and duplications in regions lacking heterozygosity. Therefore, we implemented two separate but complementary methods, called ‘BAF’ and ‘LOH’ (the latter for LRR change detection in regions lacking heterozygosity). Anomalies detected by the BAF method were classified as mosaic or non-mosaic. Anomalies detected by the LOH method were used here only to define the BAF/LRR position of heterozygous deletions and not for mosaic detection. We did not attempt to identify non-mosaic segments of uniparental isodisomy, which have no heterozygosity and normal LRR.
