Custom array CGH of Oral Squamous Cell Cancer

Over last decade several studies on oral cancer patients from eastern India have identified alterations in copy numbers in many regions of the chromosome such as 3p21.3, 8q24.21, 9p21, 9p22, 11q13, 11q21-24. However, all these studies employed microsatellite markers to map these CNV regions. This resulted in large map intervals (10-12 megabases) between the adjacent markers studied. As these regions contain a large number of genes, a high resolution CNV map of these regions was necessary to precisely identify novel genes affected by the amplifications and deletions. We thus used custom made Agilent 4X44K oligonucleotide array CGH platform to map the identified CNV regions in a resolution of 3 Kb in oral cancer patients from eastern India. Twenty-nine defined genomic intervals of ten male and two female oral cancer patients were compared with a normal male and normal female sample, respectively, by Agilent's custom oligo CGH array of 4X44K format.