The application of genomic technologies to cancer and companion diagnostics.
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.
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