Intratumoral regional variations in copy number of the chromosomal part revealed by microdissection and combined ploidy and comparative genomic hybridization analyses in esophageal squamous cell carcinoma.

Intratumoral regional variations in the copy number of chromosomal material were analyzed to demonstrate the time sequence of chromosomal changes in progression of individual squamous cell carcinoma of the esophagus. We applied combined DNA ploidy and comparative genomic hybridization (CGH) analyses to multiple DNA samples extracted from microdissected, formalin-fixed, paraffin-embedded tissues, and amplified and labeled according to degenerate oligonucleotide-primed polymerase chain reaction. We examined two cases: one with a deep invasive tumor and the other with a superficial spreading tumor. We found that each sample had unique aberrations in addition to the ones common to all or some of the samples in a tumor. Based on previous studies (Okada et al., Cancer Genet Cytogenet 2000;118:99-107), we classified significant shifts of the green to red (G/R) ratio into small and large ones, which were within and beyond the range of 0.65 to 1.35, respectively. Most of the large-shift aberrations were found to be common to all or some of the samples in each case. These were thought to represent earlier events in the DNA-diploid stage, while small shifts may possibly reflect one-copy changes after tetraploidization or chromosomal instability. Based on the breakpoints and on the absolute copy numbers of altered chromosomal parts inferred from DNA ploidy and the shift size of the G/R ratio, we reconstructed the sequence of accumulation and divergence of chromosomal alterations as a dendrogram in each case. This method of temporal analysis may enable us to extract important early events from numerous aberrations screened by CGH in individual tumors.