This thesis describes work undertaken by the author between 1996 and 2014. Genomics is the
study of the genome, although it is also often used as a catchall phrase and applied to the
transcriptome (study of RNAs) and methylome (study of DNA methylation). As cancer is a
disease of the genome the rapid advances in genomic technology, specifically microarrays
and next generation sequencing, are creating a wave of change in our understanding of its
molecular pathology. Molecular pathology and personalised medicine are being driven by
discoveries in genomics, and genomics is being driven by the development of faster, better
and cheaper genome sequencing. The next decade is likely to see significant changes in the
way cancer is managed for individual cancer patients as next generation sequencing enters the
clinic.
In chapter 3 I discuss how ERBB2 amplification testing for breast cancer is currently
dominated by immunohistochemistry (a single-gene test); and present the development, by
the author, of a semi-quantitative PCR test for ERBB2 amplification. I also show that
estimating ERBB2 amplification from microarray copy-number analysis of the genome is
possible. In chapter 4 I present a review of microarray comparison studies, and outline the
case for careful and considered comparison of technologies when selecting a platform for use
in a research study. Similar, indeed more stringent, care needs to be applied when selecting a
platform for use in a clinical test. In chapter 5 I present co-authored work on the development
of amplicon and exome methods for the detection and quantitation of somatic mutations in
circulating tumour DNA, and demonstrate the impact this can have in understanding tumour
heterogeneity and evolution during treatment. I also demonstrate how next-generation
sequencing technologies may allow multiple genetic abnormalities to be analysed in a single
test, and in low cellularity tumours and/or heterogenous cancers.
Keywords: Genome, exome, transcriptome, amplicon, next-generation sequencing,
differential gene expression, RNA-seq, ChIP-seq, microarray, ERBB2, companion diagnostic
