Clinico-molecular study of synchronous head and neck squamous cell carcinoma (HNSCC) and esophageal squamous cell carcinoma (ESCC).

e17080Background: The prognoses of HNSCC and ESCC are poor, especially when two primary tumors occur at the same time. In an earlier study, we found 12.4% of all HNSCC patients had a synchronous ESCC at the time of diagnosis. To confirm whether these second tumors were of metastatic origin or a separate second primary tumor (SPT), we employed genome-wide SNP array analysis to analyze the differential LOH pattern of each synchronous tumor pair. The clinical information of the patients with synchronous tumors was also summarized. Methods: Twenty-one synchronous HNSCC formalin-fixed paraffin-embedded (FFPE) tissue samples and their ESCC counterparts were subjected to DNA extraction, quality assessment, and subsequent SNP array experiments using Illumina HumanCytoSNP12 FFPE BeadChip, which contains 300,000 probes. Signal intensity and B-allele frequency data of each pair were analyzed to identify Copy Number Variation (CNV) and LOH using Nexus Copy Number software suite. Results: Comparing the LOH pattern of ...