Newnham et al. BMC Cancer 2011, 11:93 http://www.biomedcentral.com/1471-2407/11/93 Page 5 of 11 1 3 5 7 9 11 13 15 17 19 21 Figure 2 Chart of average standardised copy number at each BAC location for K-Ras mutant vs. wild-type tumours. X axis: BAC location along genome. Y axis: average standardised copy number. expression between 16 SCC and 25 AC samples were identified, representing the biological processes of cell adhesion, epidermis development, keratinisation and ker- atinocyte differentiation. A significant proportion of these genes had roles in antigen processing and presenta- tion, and the phosphatidylinositol signalling pathway. Thirty of 310 genes in the differentiating gene list were located on chromosome 3 (p = 0.0098), implicating geno- mic changes at this locus in determining NSCLC pheno- type. This is consistent with the genomic data, which indicates gain of 3q is associated with SCC histology. Associations with mutation status in TP53, K-Ras and EGFR pathways Expression levels of 67 genes differed significantly between TP53 mutant (17) and wt (21) tumours. Many of the biological functions represented by these genes were also strongly represented by the genes differentially expressed between AC and SCC. In addition, 20/67 dis- criminating genes were also included in the gene list dif- ferentiating SCC from AC. Hierarchical clustering based on the expression of these 67 differentially expressed genes not only segregated TP53 mutant from wild-type tumours, but also resulted in clustering of SCC samples with the TP53 mutant tumours. Our results suggest that the gene expression signature observed for TP53 mutant tumours may be at least in part related to SCC histology rather than TP53 biology. Transcriptional profiles of AC and LCC tumours with (8) and without (31) KRAS mutation were compared. Biological processes represented by 108 differentiating genes included cell growth, second-messenger mediated signalling, chromosome organisation and biogenesis, and gene regulation (mediated via histones and their effects on biosynthesis and nucleosome assembly) (table 3). These findings are consistent with other published stu- dies linking KRAS mutation to increased translation of cancer related proteins, and chromosome instability [17,18]. The low frequency of EGFR mutant cancers precluded statistically meaningful analysis of transcrip- tional data according to EGFR genotype. Associations with metastasis, tumour recurrence and NSCLC-specific survival Transcriptional profiles identified 39 genes that differen- tiated between 19 ‘metastatic’ and 35 ‘non-metastatic’ tumours, with molecular pathways involved in protein translation most strongly represented (MRPL33, RPL12, RPL27A, RPS5, RPS9). Comparison of expression pro- files of 14 tumours recurring within 12 months of sur- gery to remaining samples identified 60 genes with differential expression between the two groups, with a