Figure 1.

Expected signal patterns for chromosomal changes against a background of (A) diploidy or (B) tetraploidy. The cartoon summarizes the patterns of log ratio, allelic ratio and LOH that would accompany events (a single-copy gain, a single-copy loss, or copy-neutral LOH) at four hypothetical segments of either a disomic chromosome in a diploid background (Panel A) or tetrasomic chromosome in a tetraploid background (Panel B). A log ratio (red line) of 0 indicates that copy number (CN) is unchanged relative to the baseline, which equals 2 for a normal diploid sample. The allelic ratio is the proportion of total signal generated by the B allele probe (e.g., a genotype of AAB at a particular SNP produces an allelic ratio of 0.33 [B/A+A+B]). Similar ratios from many contiguous SNPs are shown as silver boxes with red letters (various combinations of A and B) indicating the inferred genotype that is responsible for the AR value. Segments expected to produce LOH are indicated by blue boxes. Note that for a balanced tetrasomic chromosome in a tetraploid sample (Panel B), the Background state is indistinguishable from diploidy (Panel A); the LR of 0 reflects the baseline copy number of the sample, which equals 4. The two cases are only distinguishable at losses or gains, which alter the pattern in divergent ways.