Laryngeal squamous cell carcinoma (LSCC) is a common cancer of the upper respiratory tract. The cytogenetic and molecular events involved in the pathogenesis of LSCC are not well understood. In this study, a combined strategy of conventional cytogenetics, fluorescent in situ hybridization (FISH) and microsatellite polymerase chain reaction was performed to analyze the deletion of chromosome 6 in LSCC. Karyotype analysis indicated that the deletions of 6q were marker chromosomes potentially specific to LSCC. To further characterize the loss of 6q, metaphase cells derived from both solid tumors and the Hep-2 cell line were investigated using FISH, with results consistent with those of conventional cytogenetics. Moreover, tumor-adjacent normal tissue DNA pairs from 70 LSCC in China were analyzed for loss of heterozygosity (LOH) and microsatellite instability (MI) on chromosome 6q in the region 6q25 by polymerase chain reaction (PCR) and three microsatellite markers. Overall, the highest frequency of microsatellite alteration (68.2%) was located at D6S980, which revealed that the region around D6S980 in 6q25 might harbor some important genes related to the pathogenesis of LSCC in Chinese patients. The pattern of chromosomal changes detected using the combined strategy suggests that it will become the most suitable way to find novel cancer-related genes and discover the relationship between the aberration of genetics and their tumorigenic mechanism.

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