1. ¹Centre for Molecular Oncology, Cancer Research UK, Institute of Cancer, Barts and The London School of Medicine and Dentistry, Queen Mary, University of London, London, UK
2. ²Centre for Medical Oncology, Cancer Research UK, Institute of Cancer, Barts and The London School of Medicine and Dentistry, Queen Mary, University of London, London, UK

Correspondence: Professor NR Lemoine, Centre for Molecular Oncology, Cancer Research UK, Institute of Cancer, Barts and The London School of Medicine and Dentistry, Queen Mary, University of London, Charterhouse Square, London, EC1M 6BQ, UK. E-mail: nick.lemoine@cancer.org.uk

Received 13 June 2007; Revised 29 August 2007; Accepted 6 September 2007; Published online 22 October 2007.

Abstract

To identify genomic abnormalities characteristic of pancreatic ductal adenocarcinoma (PDAC) in vivo, a panel of 27 microdissected PDAC specimens were analysed using high-density microarrays representing 116 000 single nucleotide polymorphism (SNP) loci. We detected frequent gains of 1q, 2, 3, 5, 7p, 8q, 11, 14q and 17q (78% of cases), and losses of 1p, 3p, 6, 9p, 13q, 14q, 17p and 18q (44%). Although the results were comparable with those from array CGH, regions of those genetic changes were defined more accurately by SNP arrays. Integrating the Ensembl public data, we have generated 'gene' copy number indices that facilitate the search for novel candidates involved in pancreatic carcinogenesis. Copy numbers in a subset of the genes were validated using quantitative real-time PCR. The SKAP2/SCAP2 gene (7p15.2), which belongs to the src family kinases, was most frequently (63%) amplified in our sample set and its recurrent overexpression (67%) was confirmed by reverse transcription–PCR. Furthermore, fluorescence in situ hybridization and in situ RNA hybridization analyses for this gene have demonstrated a significant correlation between DNA copy number and mRNA expression level in an independent sample set (P<0.001). These findings indicate that the dysregulation of SKAP2/SCAP2, which is mostly caused by its increased gene copy number, is likely to be associated with the development of PDAC.