Array CGH analysis of the rare laryngeal basaloid squamous cell carcinoma: a case report

The aim of this study was to define copy number alterations in a rare laryngeal type basaloid squamous cell carcinoma (laryngeal BSCC) using high throughput array comparative genomic hybridization. This is the first genome wide screening of a laryngeal BSCC describing the unique events of DNA copy number changes. By Nimble-Gen Whole Genome Tiling Array CGH (consisting of 72,000 probes) we were able to identify 3,777 genes altered by copy number changes (1,726 genes with copy number gains and 2,051 genes with copy number with losses). The resolution of the array allowed us to identify a new alteration at the 17q21.31 region covering the DUSP3 gene which encodes the dual-specific protein phosphatase. Functional studies of the altered genes (Database for Annotation, Visualization and Integrated Discovery v6.7 analysis) highlighted molecular pathways including chemokine signaling, cell cycle, adherent junction-, VEGF- and TGF-beta signaling pathways that might be disrupted by copy number alterations in laryngeal BSCC.