Molecular cytogenetic characterization of head and neck squamous cell carcinoma and refinement of 3q amplification

We applied a combination of molecular cytogenetic methods, including compar ative genomic hybridization (CGH), spectral karyotyping (SKY), and fluoresc ence in situ hybridization, to characterize the genetic aberrations in a pa nel of II cell lines derived from head and neck squamous cell carcinoma and 1 cell line derived from premalignant oral epithelium. CGH identified recu rrent chromosomal losses at 1p, 3p, 4, 8p, 10p, and 18q; gains at 3q, 5q, 8 q, 9q, and 14q; and high-level amplification at 3q13, 3q25-q26, 5q22-q23, 7 q21, 8q24, 11q13-q14, 12p13, 14q24, and 20q13.1. Several recurrent transloc ations including t(1;13)(q10;q10), t(13;13)(q10; q10), t(14;14)(q10;q10), i (8)(q10), and i(9)(q10) and breakpoint clusters at 1p11, 1q21, 3p11, 5q11, 5q13, 6q23, 8p11 ,8q11, 13q10, 14q10, and 15q10 were identified by SKY. The re was a good correlation between the number of aberrations identified by C GH and SKY (r = 0.69), and the analyses were both confirmatory and compleme ntary in their assessment of genetic aberrations. Amplification at 3q26q27 was identified in 42% of cases. Although SKY defined the derivation of 39 g ain, the precise breakpoint remained unassigned, positional cloning efforts directed at the amplified region at 3q26-q27 identified three highly overl apping nonchimeric yeast artificial chromosome clones containing the apex o f amplification The use of these yeast artificial chromosome clones as a pr obe for fluorescence in situ hybridization analysis allowed a detailed char acterization and quantification of the 3q amplification and refinement of u nassigned SKY breakpoints.