Thin section arrays for I-FISH analysis of chromosome-specific imbalances in squamous cell carcinomas of the head and neck.

Thin section arrays of 20 head and neck squamous cell carcinomas were studied by I-FISH for gains (including amplification) and losses of specific genomic segments. These arrays allow the examination not only of a number of tumor sections but also of the surrounding margins and of inconspicuous control tissue in one experiment. All tumor sections examined significantly differed from the inconspicuous control tissues by containing more or less extensive cell populations with aberrant signal constitutions. In no case, however, did the aberrant population constitute the whole area of the section. Gains of signals were strikingly more frequent than were losses. All tumors showed significant gains of the segments examined, the highest differences between tumor and control sections were found for the segments 9q34 and 8q24, followed by 5p15.3 and 11q13. Amplifications were most frequently found of 11q13: 8 of the 20 tumors showed amplifications in more than 20% of the nuclei, while no nucleus with more than four signals was found in any of the control tissues (control: 0%). Amplifications of the target sequences on chromosomes 8 (14 tumors) and 9 (8 tumors) were observed in low but significant percentages of nuclei, no significant cell population was detected with an amplification of 5p15.3. Fourteen tumors exhibited a significant loss of 13q14, and only 8 tumors a significant loss at any other site. In the tumor margin sections, in most cases, the margins apparently were also affected by the one or the other of the genomic changes of the pertinent primary tumor. Nevertheless, there were, in some cases, also large differences depending on the way of analysis, but also on the specific signal constitution considered. Tumor stages T3 and T4 tended to have higher frequency of nuclei with gains of 5p15.3, 8q24, and 11q13 as compared to T2 tumors and less gains of 9q34 and loss of 13ql4. With the exception of 8q24 and 13q14 alterations there was also a trend to higher percentages of aberrant nuclei in the margin of T3-4 tumors vs. T2 tumors.