Figure 4

Copy number changes in an apparent tetraploid background. (A) Allelic ratios of 0.25 and 0.75 for Chr:10 in C72 indicate an unbalanced tetrasomy (labeled as "4n") for the p-arm of this chromosome, even though the log ratio is 0 and the putative copy number is 2. A decrease in the LR suggests a loss of chromosomal material in the q-arm ("3n"), but the region produces an AR pattern characteristic for trisomy with no collinear LOH. The center of the q-arm also displays a short segment of unbalanced pentasomy ("5n") accompanied by a small increase in the LR and allelic ratios consistent with ABBBB and AAAAB allele patterns. (B) Chromosome 2 in C82 exhibits a LR with an apparent CN of 2 and an AR consistent with normal disomy. However, the small deletion at the q-terminus produces a trisomic pattern and no LOH, revealing that the majority of the chromosome is actually a balanced tetrasomy (AABB). For both examples, the overall indication is that the baseline CN of the chromosome is 4 copies rather than 2, and both samples are largely tetraploid.