Chapter 2 - University of British Columbia

quantitative PCR experiments as well as microarray experiments where relative quantifications
are typically used. To address this, using SAGE, where quantification of expression is absolute,
genes whose expression was constant across both malignant and non-malignant samples were
identified [103]. Those genes demonstrated better constancy than some genes which are
typically used as controls for gene expression analysis.
1.12.4 Integration of gene dosage and gene expression in lung cancer
The first level of genomic integration that needed to be accomplished was the integration of
gene dosage and gene expression. In one study using cancer cell lines, hot spots of DNA
amplification were identified throughout the genome. When specifically examining lung cancer
cell lines and subsequently coupling this with gene expression data, it was found that 50% of
genes in these frequently amplified regions show correlation between gene dosage and gene
expression [52]. Moreover, it was also observed that different components of the EGFR
signaling pathway were amplified in different cell lines illustrating that for a given pathway, one
can underestimate the frequency of pathway disruption when only well known genes in the
pathway are assessed.
In a second study involving clinical lung tumors, a genomic region which was preferentially
amplified in squamous cell carcinomas as compared to adenocarcinomas was identified.
Further integration with gene expression data allowed for the identification of the target gene,
BRF2, in this amplified region [104]. Moreover, gene dosage and protein expression level
assessment of CIS samples for BRF2 showed that amplification and overexpression were
present, suggesting that this event is occurring at an early stage of tumorigenesis.
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