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Investigating the genetics and pharmacogenetics of bowel cancer

West, Hannah 2013. Investigating the genetics and pharmacogenetics of bowel cancer. PhD Thesis, Cardiff University.
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Abstract

In this thesis, we aimed to identify genetic factors that influence the risk of colorectal cancer (CRC). We also sought alleles that contribute to the likelihood of extreme adverse reactions to treatment. We validated five previously identified low penetrance variants using our training phase cohort, consisting of 2,186 advanced CRC (aCRC) from the COIN and COIN-B trials and 2,176 geographically matched controls. Using this cohort we also identified a variant in RAD1 that was significantly associated with risk (X2=13.51, P=2x10-4). However, we failed to replicate these findings in an aCRC validation cohort consisting of 1,053 cases and 1,397 geographically matched controls (X2=2.76, P=0.1), potentially as a result of a lack of power due to insufficient sample numbers. We identified ten patients from the COIN trial with severe peripheral neuropathy associated with oxaliplatin (PNAO) treatment. Through exome resequencing we identified a novel stop gain variant (Ser613X) in the nucleotide excision repair gene (NER), ERCC4. Following analysis of 54 additional patients from the COIN trial with PNAO, we identified three rare nonsynonymous variants (Pro379Ser, Arg576Thr and Glu875Gly) that were predicted to interfere with protein function. Consistent with the rare variant hypothesis of common disease, two of these variants were seen to collectively contribute to the risk of the phenotype (7/63 [11.11%] of patients with PNAO compared to 86/1763 [4.88%] of patients without PNAO; X2=4.89, P=0.03). Using the fission yeast, Schizosaccharomyces pombe, we sought to elucidate functional effects of these variants in ERCC4 by creating a model system. Using cre recombinase mediated cassette exchange, we introduced the variants of interest into the ERCC4 homolog, rad16. Following treatment with a range of DNA damaging agents, we observed an increased sensitivity following introduction of the novel stop gain, indicating a defect in the NER pathway. Additionally, there was a clear pattern of oxaliplatin-specific sensitivity of strains with the introduced rare nonsynonymous variants, suggesting a defect of XPF in other repair processes associated with interstrand crosslinks.

Item Type: Thesis (PhD)
Status: Unpublished
Schools: Medicine
Subjects: R Medicine > RC Internal medicine > RC0254 Neoplasms. Tumors. Oncology (including Cancer)
Date of First Compliant Deposit: 30 March 2016
Last Modified: 19 Mar 2016 23:34
URI: http://orca-mwe.cf.ac.uk/id/eprint/56820

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