The Application of Circulating Tumour DNA to the Management of Gastrointestinal Cancers.
Circulating tumour DNA (ctDNA) are small fragments of DNA released by tumoursinto the circulation. These fragments contain pathogenic mutations which can bedetected and quantified by various next generation sequencing approaches to monitortumour burden. Many ctDNA analyses rely on sequencing of tumour tissue using largesequencing panels, querying hundreds of genes to find candidate ctDNA biomarkers forfollow-up. Whilst this approach has been successfully implemented to track changes intumour burden over time, it requires the sequencing of tumour tissue – which isdifficult to obtain and may not accurately represent the entire genomic landscape oftumours. Hence, this study designed a targeted DNA sequencing panel to detectpathogenic mutations directly from the plasma of gastric and colorectal cancer patients.In addition, the criteria of selecting ctDNA biomarkers was investigated in colorectalcancers by comparing the ability of mutations in tumour suppressor genes andoncogenes to track changes in tumour burden throughout chemotherapy treatment. The gastrointestinal cancer sequencing panel (GI cancer panel) designed in this studysuccessfully identified pathogenic mutations in the plasma of gastric and colorectalcancer patients. By restricting the panel to only 21 genes, and designing specialisedoligonucleotide sequencing primers, a high analytical sensitivity was reached.Mutations were successfully identified down to a frequency of 0.5%. This study alsoidentified technical challenges associated with ctDNA sequencing approaches –such asdistinguishing pathogenic mutations from sequencing errors and benign variants foundin the plasma. Finally, this study highlighted several factors that should be consideredwhen selecting ctDNA biomarkers – including the necessity to monitor multiple mutations to better represent the total tumour burden. Overall, this study has generatedevidence supporting the implementation of ctDNA technologies into the healthcaresystem to better manage gastrointestinal cancers.
Advisor: Guilford, Parry; Zou, Donghui
Degree Name: Bachelor of Medical Science with Honours
Degree Discipline: Department of Biochemistry
Publisher: University of Otago
Keywords: Cancer; Gastric; Colorectal; ctDNA
Research Type: Thesis