Lymphatic metastasis represents the single most important clinical prognostic factor in head and neck squamous cell carcinoma (HNSCC), but underlying genetic mechanisms remain ill defined. Genetic differences between primary carcinomas and their corresponding metastases might form a key to understanding the metastatic phenotype. In this study we aimed to characterize such differences using a genome‐wide screening measure.

Four human cell lines (MDA‐686tu, MDA‐686Ln, MDA‐1386tu, MDA‐1386Ln) derived from primary tumor and synchronous lymph node metastasis of two cases of metastatic HNSCC were subjected to comparative genomic hybridization (CGH) by differentially labeling DNA from tumor tissue and normal tissue with fluorescent agents. The labeled DNAs were simultaneously hybridized onto normal metaphase chromosomes. In addition, modified CGH was performed by directly hybridizing labeled primary tumor DNA against differentially labeled metastatic tumor DNA, allowing the direct detection of copy number differences in individual pairs. Image analysis for fluorescence intensity along the entire length of each metaphase chromosome allowed generation of a color ratio, which was used to detect copy number changes.

In both cases, significant overlap was found between chromosomal aberrations present in the primary tumor and the corresponding nodal metastasis. However, several abnormalities differentiated primary tumors from their metastases. Modified CGH identified several genetic aberrations that were not detectable with the conventional CGH analysis. Gains at chromosomes 10p11‐12 and 11p and deletions at chromosomes 4q22‐31, 9p13‐24, and 14q differentiated nodal metastases from the corresponding primary tumors in both cases.

The combination of conventional and modified CGH analyses facilitates the identification of DNA copy number changes that might be involved in the development of a metastatic phenotype. Future research should aim at the identification of the genes involved at the identified sites of chromosomal aberration. © 2004 Wiley Periodicals, Inc. Head Neck 26: 10–15, 2004