- Title
- Identification of new causative genes in inherited colorectal cancer
- Creator
- Xavier, Alexandre
- Relation
- University of Newcastle Research Higher Degree Thesis
- Resource Type
- thesis
- Date
- 2020
- Description
- Research Doctorate - Doctor of Philosophy (PhD)
- Description
- Colorectal cancer (CRC) remains a heavy burden for all national health systems. It is the third most frequently diagnosed cancer and the second leading cause of death in Australia and worldwide. Around 80% of CRC diagnosed each year are sporadic and somewhere between 7% and 8% have a clearly identified genetic predisposition (inherited CRC cancer; 5% for Lynch Syndrome (LS), 1% for Familial Adenomatous Polyposis (FAP) and 1-2% inclusive for various syndromes with very low incidences), with the remaining ~ 12%-13% being described as “familial”. For many patients with a clinical diagnosis of LS and FAP, no causative mutation has been identified in MSH6, MLH1, MSH2 or PMS2 (for LS patients) and in APC or MUTYH (for FAP patients) as a result of genetic testing. For those patients and their families, it is critical to identify the genetic cause underlying their increased CRC risk to offer early detection, tightened monitoring and, if required, suitable surgical management. Establishing an exhaustive list of known genetic risk factors for inherited CRC is essential for families burdened with a high incidence of CRC. Patients with a strong family history of CRC will usually undergo a tighten monitoring. Removing this psychological burden in individuals proven to be non-carriers of pathogenic germline variants is critical. Initial investigations focused on the Mismatch Repair (MMR) pathway in patients with LS and those with Lynch-Like Syndromes (LLS). 274 DNA samples from LLS patients were sequenced for the 22 genes involved in the MMR pathway to determine the presence of pathogenic variants. The results confirmed that LLS patients harbour pathogenic variants in genes that are not part of routine clinical screening: POLD1, EXO1, MLH3, RFC1 and RPA1. The results indicate that additional MMR genes are involved in the increased risk of CRC in LLS patients. As the technology evolved and became more cost-effective, whole exome sequencing (WES) was employed. Forty-eight patients with a clinical diagnosis of FAP were recruited based on their family history of CRC, their polyp status and their negative mutational status of APC and/or MUTYH. WES was used to interrogate all coding regions of the genome. Analysis of pathogenic variants showed that genes involved in DNA repair were frequently associated with a pathogenic variant. In addition, CNV analysis revealed the deletion of large portions of CFHR3, known to cause Atypical Haemolytic Uremic Syndrome, leading to ulcerative colitis, a known risk factor in CRC. Analysing the Polygenic Risk Score (PRS) for CRC risk-factors show an enrichment in inflammatory bowel syndrome-related markers. During the WES analysis of FAP-like patients, an absence of a precise and automated method to predict pathogenicity in cohorts sharing the same phenotype was apparent. To overcome this, we developed TAPES, a bioinformatics tool that can predict pathogenicity more precisely that can also calculate variant enrichment using only publicly available control sequences. TAPES also integrate powerful variant filtering and can generate useful reports (such as pathway analysis or calculating the total gene burden in a cohort). In conclusion, the research presented herein helps strengthen the knowledge of familial CRC. The involvement of novel MMR genes in LLS was also revealed thereby expanding the known number of genes associated with this disorder. DNA-repair related genes as well as those involved in inflammation were shown to play an important role in FPS. Finally, a refined analytical pipeline for WES sequencing interpretation was developed providing new bioinformatics tools for the rapid delivery of results.
- Subject
- cancer; sequencing; variant; colorectal cancer; lynch syndrome; familial adenomatous polyposis; thesis by publication
- Identifier
- http://hdl.handle.net/1959.13/1417893
- Identifier
- uon:37271
- Rights
- Copyright 2020 Alexandre Xavier
- Language
- eng
- Full Text
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| Thumbnail | File | Description | Size | Format | |||
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| View Details Download | ATTACHMENT01 | Thesis | 12 MB | Adobe Acrobat PDF | View Details Download | ||
| View Details Download | ATTACHMENT02 | Abstract | 610 KB | Adobe Acrobat PDF | View Details Download |