Background:Clonal heterogeneity is a major difficulty in the analysis of chromosome rearrangements within tumor tissue. Using in situ hybridization, a cell-to-cell analysis can be performed and should allow a better understanding of the genetic process. In addition, detection of pre-neoplastic lesions with only a few cells involved may improve the diagnosis of such lesions and their precocious treatment.Material/Methods: Automated analysis was performed on tissue sections with our previously described two-color fluorescence in situ hybridization-based method for quantitative determination of chromosome arm imbalance. The imbalance between the long and short arms of chromosome 3 was determined in 24 cases of non-small-cell and small-cell lung cancers in which only small snap-frozen sections were used, allowing other simultaneous molecular analyses, such as TP53 gene mutation detection.Results: Specifically developed software allowed localization of each nucleus within the section with regard to its chromosome imbalance and to reconstitute a multi-clonal panel within an apparently homogeneous sample. In some cases, discrepancies in the imbalance values were observed between the biopsy and the tumor obtained after surgery from the same patient.Conclusions: The discrepancies observed between biopsies and tumors, likely linked to the samples’ heterogeneity, demonstrate the necessity to analyze tissue sections collected at various locations. The fully automated approach developed in this study rendered such investigations possible.

Keywords: Chromosomal Instability - genetics, Chromosomes, Human, Pair 3 - genetics, Cohort Studies, Image Cytometry - methods, In Situ Hybridization, Fluorescence, Lung Neoplasms - diagnosis, Lung Neoplasms - genetics, Mutation, Mutation, Chromosomal Instability - genetics, Chromosomes, Human, Pair 3 - genetics, Cohort Studies, Image Cytometry - methods, In Situ Hybridization, Fluorescence, Lung Neoplasms - genetics, Mutation