We comment on a few of the genes for which the Caucasian and AA samples showed different patterns of aberrations.
Discrepancies in aberration amplitudes between the tumors in the clustering pairs was, however, seen in some cases, e.g. chromosomes 11q and 17 in tumor pair 6, and chromosomes 5 and 8q in tumor pair 8; but since the assessment of genomic similarity is based on patterns of aberrations, the amplitude does not affect the outcome of the clustering analysis.
Unsupervised hierarchical clustering with adjustment for false-discovery rate revealed clusters differing by the level and pattern of aberrations and displaying particular tumor characteristics.
Furthermore, unsupervised hierarchical clustering showed that tumors could be classified into clusters exhibiting different levels and pattern of aberrations, which contained cancer genes.
Overall, CGH identified a complex pattern of aberrations; however, several frequent chromosomal loci of copy number change were seen.
The problem of determining whether a module (subset of genes) contains a significant RME pattern of aberrations can be addressed using probabilistic models or heuristic scores.
In general, the 29 genes that robustly distinguish GNS from NS cells did not show a consistent pattern of aberrations: only three genes (PDE1C, NDN and SYNM) were located in regions similarly affected by genetic lesions in all lines.
The similarity in the temporal pattern of aberrations in hESCs and hiPSCs suggests that the identification of factors that protect against the occurrence of deletions/regions of homozygosity during reprogramming might be useful also in preserving genetic stability during preim-plantation embryo culture and hESC derivation.
Alternatively, a panel of FISH probes may be designed based on the most characteristic copy number abnormalities for each subgroup, and new patient samples would be tested by FISH using the probe panel developed and classified into one of the subgroups based on the pattern of aberrations observed.
The patterns of chromosome aberration in ovarian cancer are difficult to categorise into the groups described by Hicks et al. as most are a combination of sawtooth and firestorm.
