Cytogenetic studies in squamous cell carcinoma of the head and neck (SCCHN) have identified a clustering of breakpoints in a number of chromosomes, including chromosome 3. We have undertaken a loss of heterozygosity analysis (LOH) of 36 SCCHN and six solid tumours which were not squamous cell, and their respective normal specimens, using a bank of microsatellite markers, with the aim of identifying specific sites of frequent loss on chromosome 3. The analysis was undertaken with 12 microsatellite markers, 10 of which are on the p arm of chromosome 3. Allelic loss greater than 10% was seen at four sites; D3S1269 (13%), D3S1079 (23%), D3S659 (23%) and D3S1293 (31%). None of this series of tumours showed loss of the whole chromosome, however 47% of the tumours analysed had LOH at one or more loci. The highest incidence of LOH was found at D3S1293 in the 3p24-p25 region. The second highest region with LOH was found at D3S1079 and D3S659 at 3p13. The remaining markers telomeric and centromeric to these two regions were found to have a LOH of less than 10%. Furthermore, we found a strong association between loss of one marker on chromosome 3 in these SCCHN and poor clinical prognostic indicators; such as site, pathological differentiation, positive nodes at pathology (p<0.05) and TNM status (p<0.05). This study has identified two regions in SCCHN that are most likely to be important in the development of squamous cell carcinoma of the head and neck at 3p24-p25 and 3p13 and may indicate sites of novel tumour suppressor genes in this disease.

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