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By accurately describing cancer genomes, we may link genomic mutations to phenotypic effects and eventually treat cancer patients based on the molecular cause of their disease, rather than generalizing treatment based on cell morphology or tissue of origin. Alteration of DNA copy number is a driving mutational process in the formation and progression of cancer. Deletions and amplifications of specific chromosomal regions are important for cancer diagnosis and prognosis, and copy number analysis has become standard practice for many clinicians and researchers. In this thesis we describe the development of two computational methods, TAPS and Patchwork, for analysis of genome-wide absolute allele-specific copy number per cell in tumour samples. TAPS is used with SNP microarray data and Patchwork with whole genome sequencing data. Both are suitable for unknown average ploidy of the tumour cells, are robust to admixture of genetically normal cells, and may be used to detect genetic heterogeneity in the tumour cell population. We also present two studies where TAPS was used to find copy number alterations associated with risk of recurrence after surgery, in ovarian cancer and colon cancer. We discuss the potential of such prognostic markers and the use of allele-specific copy number analysis in research and diagnostics.

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The breast cancer susceptibility gene BRCA2 is located on chromosome 13q 12-13. Using breast and ovarian cancers from a BRCA2-linked family, loss of the wild type BRCA2 allele was demonstrated in seven out of eight informative cases (87.5%) indicating that BRCA2 was a recessive oncogene. Analysis of 73 sporadic breast tumours and 12 breast cancer cell lines revealed loss of heterozygosity (LOH) in 22 (30%) of the primary tumours and seven (58%) of the breast cancer cell lines. However, it was not clear from these studies that the target for the observed LOH was the gene BRCA2 or RBl at chromosome 13q14 as the region ofLOH included both genes in all but a single case. Despite the presence of elevated levels of LOH, several separate mutation screening studies of sporadic breast and ovarian tumours have shown that somatic mutations of BRCA2 in sporadic breast and ovarian cancer are very rare. To investigate the possibility that other mechanisms of BRCA2 allelic inactivation might be operative, the methylation status of a CpG island within the promoter region of BRCA2 was examined in 64 sporadic breast tumours and 18 breast and ovarian cancer cell lines. Three CpG dinucleotides within this island were unmethylated in all the normal tissue samples (lymphocytes) examined. These three CpG dinucleotides remained unmethylated in all the breast tumours examined. Moreover, expression of BRCA2 in breast and ovarian cancer cell lines was not obviously correlated with evidence of loss of heterozygosity. These analyses indicate that methylation of the promoter region of BRCA2 and possibly other mechanisms of transcriptional silencing are unlikely to be a common mechanism of gene inactivation in these tumours. To investigate the prevalence of BRCA2 mutations, lymphocyte DNAs from a British, population-based series of 617 breast cancers diagnosed before age 45 were screened for mutations. Mutations were detected in 14 women ( 2.3%, 6/14 43% under age 35 and 8/14 57% age 36-45). This study and a parallel study of BRCA1 demonstrate that BRCA2 and BRCA1 make approximately equal contributions to early onset breast cancer in the UK. Moreover, although BRCA1 and BRCA2 account for breast cancer susceptibility in a substantial proportion of multiple case families, they only account for a small proportion of the overall familial risk conferred by an early onset case. This indicates the existence of other susceptibility genes that are more common but confer lower risks than BRCA1 and BRCA2.

The endemic New Zealand frog, Leiopelma hochstetteri, is characterized by variable numbers of mitotically-stable B chromosomes. In order to assess whether the B chromosomes had been derived from the autosome complement, B DNA was isolated and amplified by micromanipulation in conjunction with degenerate oligonucleotide-primed PCR. Southern hybridization patterns of B DNA probes to genomic DNA from males and females characterized by differing numbers of B's demonstrated that the B chromosomes were derived from the univalent W chromosome which is specific to females. The presence of homologous B specific sequences in B chromosomes from geographically-distinct populations show that only a single univalent W to B event had occurred. Furthermore, a plesiomorphic homology shows that the B chromosomes originated soon after the univalent W had been derived from the ancestral WZ/ZZ karyotype, which is still present in frogs from Great Barrier Island. Finally, sequence analysis of the probes reveals that B DNA is composed of repeat sequences, and has the ability to form stable hairpin structures in vivo. The molecular dynamics of these structures may reflect the inherent propensity to undergo rapid change in nucleotide sequence and chromosome structure.

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