A search for novel cancer susceptibility genes

Armour, Nicola Jane (2012). A search for novel cancer susceptibility genes PhD Thesis, School of Chemistry and Molecular Biosciences, The University of Queensland.

       
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Author Armour, Nicola Jane
Thesis Title A search for novel cancer susceptibility genes
School, Centre or Institute School of Chemistry and Molecular Biosciences
Institution The University of Queensland
Publication date 2012-12
Thesis type PhD Thesis
Supervisor Georgia Chenevix-Trench
Peter Simpson
David Duffy
Sunil Lakhani
Melissa Brown
Total pages 383
Total colour pages 69
Total black and white pages 314
Language eng
Subjects 060405 Gene Expression (incl. Microarray and other genome-wide approaches)
111203 Cancer Genetics
060408 Genomics
Abstract/Summary The overriding aim of this research was to identify novel cancer susceptibility genes by investigating rare families with potentially new cancer susceptibility syndromes. In selecting families suitable for the research, a number of families with an unusual clustering of different cancer types were identified that did not have a coding mutation in any plausible candidate cancer genes. In additon to these families, a large Australian family with a new Gastric Adenocarcinoma and Proximal Polyposis Syndrome (GAPPS) was identified and investigated. To investigate families with multiple different cancer types, the genetic analysis of tumour and germline DNA samples was conducted in order to determine whether a common inherited mutation exisited for each individual family. Methods for this analysis involved the analysis of multiple tumours within each family using a SNP-based arrayCGH (SNP-CGH) approach to assess the tumours for common regions of chromosome copy number loss and gain, and linkage analysis in sufficiently informative families. The SNP-CGH approach was largely uninformative due to the technical difficulties associated with analysing formalin-fixed paraffin embedded tumours. However, linkage analysis in two families identified regions with LOD scores of 2 or greater that, after additional haplotype analysis in these families, were prioritised for further investigation. The most signifanct result of the research is the description of the novel cancer syndrome, GAPPS, and mapping the causal GAPPS locus to chromosome 5q13-21 by linkage analysis of the large Australian kindred. A number of approaches were used to pinpoint the GAPPS locus and included expression analysis of gastric polyps and blood samples from the Australian family, SNP-CGH to assess fresh-frozen polyp samples for chromosome copy number changes, and targeted next generation sequencing of GAPPS cases (one case from the Australian family, one case from an additional GAPPS family identified in North American family). These approaches did not result in a clear candidate gene responsible for GAPPS that was shared by both cases but a number of candidate genes from the Australian case have been prioritised for further investigation. Furthermore, the SNP-CGH approach identified a copy number loss covering the 5q13-21 linkage region in three of eight polyps investigated, suggesting that a loss of function of a tumour suppressor gene may be the mechanism of cancer pathogenesis that underpins GAPPS progression. Overall, this research used a range of contemporary and traditional methods coupled with novel research aims to identify new cancer susceptibility genes. This work demonstrates the value of family-based studies for identifying cancer genes and in furthering our understanding of cancer development.
Keyword Cancer syndrome
Cancer predisoposition
Cancer genetics
Gastric cancer
Linkage analysis
Expression analysis
SNP-CGH
Next generation sequencing

 
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Created: Fri, 07 Dec 2012, 09:50:08 EST by Miss Nicola Wayte on behalf of Scholarly Communication and Digitisation Service