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The main subjects of my thesis can be divided into three related areas. Firstly, determination of the mechanisms of tumoriogenesis associated with a recently identified, recessively inherited syndrome, AfrTZ-associated polyposis (MAP). MAP results from defective base excision repair (BER) caused by bi-allelic germline mutations in the human Mut-Y homologue (MUTYH, MYH) and leads to the development of colorectal adenomas and cancer. My work includes: further characterisation of the MAP phenotype completion of screening for mutations in other BER enzymes (OGG1 and MTH1) in individuals with multiple colorectal adenomas determination of the genetic pathway(s) involved in MAP tumorigenesis through studying loss of heterozygosity (LOH) and chromosomal abnormalities with array comparitive genomic hybridisation. A mouse model of MAP was developed as part of this thesis in order to study the development of intestinal adenomas from their earliest stages, and to evaluate the impact of environmental modification and chemopreventative therapies. Secondly, I determined to identify novel predisposition genes for the multiple adenoma phenotype. Up to fifty percent of individuals with multiple (5-100) colorectal adenomas (MCRAs) have no germline mutation in known predisposition genes (APC and MYH), but probably have a genetic origin. In these cases I determined to identify novel predisposition genes for the MCRA phenotype utilising various techniques. These included somatic screening of the adenomas for mutational signatures, expression array analysis of lymphoblastoid cell lines from these individuals and candidate gene approaches. Finally, I investigated the clonal origins of colorectal adenomas through studying adenomas from familial adenomatous polyposis (FAP), attenuated FAP (AFAP) and sporadic cases. In this thesis I developed a novel technique which utilises somatic APC mutations as clonal markers. This approach found 100% of FAP adenomas to be polyclonal and 100% of AFAP adenomas to be clonal in their origin.

Small intestinal neuroendocrine tumours (SI NETs) are the most common malignancy of the small intestine, however they remain poorly characterised and the underlying pathogenic mechanisms driving disease development have yet to be elucidated. Whole genome and exome sequencing has suggested SI NETs to be mutationally quiet, with the most frequent mutation in Cyclin Dependent Kinase 1B occurring in only 8% of tumours, suggesting mechanisms other than genetic mutations may be responsible for driving SI NET tumourigenesis. Using integrated genomic and epigenomic analysis three distinct somatic copy number alteration (SCNA) profiles of SI NET were identified. The largest subgroup characterised by loss of heterozygosity at chromosome 18, negative CpG island methylator phenotype (CIMP) status, and the presence of CDKN1B mutations, is associated with improved clinical outcomes. A novel Multiple-SCNA signature has been described which defines a smaller subgroup of SI NETs and is characterized by significantly (p=0.04) reduced progression-free survival. A panel of 21 recurrently epigenetically dysregulated genes has been identified, and these represent putative novel pathogenic drivers for SI NET tumourigenesis and candidate novel biomarkers. Epigenetically dysregulated genes identified at a recurrence rate of 80-100% include gastric inhibitory polypeptide receptor (GIPR)(73.5%) – a target for novel imaging techniques in NETs, CDX1 (85.7%), CELSR3 (83.7%), FBP1 (83.7%), PCSK1 (67.3%) and TRIM15 (63.3%). The utility of methylated circulating tumour DNA analysis, and molecular profiling of circulating tumour cells as novel non-invasive biomarkers in SI NETs have been demonstrated. This is the first comprehensive integrated molecular analysis of SI NETs, providing evidence for epigenetic rather than mutational events in addition to SCNAs as drivers of SI NET development. These findings will facilitate improved patient management, treatment selection and prognostication.