The majority of women with ovarian cancer (OC) have advanced disease at diagnosis and 5-year survival rates of less than 25%. Women with stage I disease have significantly better 5-year survival rates of over 90%. Recent large studies using CA 125 and transvaginal ultrasound have failed to improve mortality in a screened population. There is therefore a pressing need for new diagnostic biomarkers in OC. The primary aim of my project, as a first step in developing a diagnostic circulating tumour DNA (ctDNA) biomarker for high grade serous ovarian cancer (HGSOC), was to investigate low-cost high-throughput next generation sequencing assays in plasma samples collected from women with newly diagnosed OC. The secondary aim was to apply these methods to other non-invasive samples including cervical liquid based cytology samples that might contribute to earlier diagnosis or screening for women with OC. ctDNA was detected in 30-49% of women with newly diagnosed OC from the UKOPS (n=54) and CTCR-OV04 (n=156) cohorts using targeted sequencing. Using the trimmed median absolute deviation (t-MAD) score, a quantitative measure of genome wide copy number aberration generated from shallow whole genome sequencing (sWGS) data, ctDNA was detected in 39-41% of the women with newly diagnosed disease. To improve sensitivity of ctDNA detection I developed an optimised method for targeted sequencing that has the potential to lower the limit of detection of ctDNA in HGSOC by 100 fold. I have also shown that the size profile of HGSOC ctDNA fragments is different to that of wildtype DNA fragments and shown that selecting for DNA fragments between 90-150 bp can increase rates of ctDNA detection in HGSOC. ctDNA detection increased to 53-67% of women with newly diagnosed OC using the size selected t-MAD score. I have evaluated the utility of cervical sampling for earlier diagnosis of OC by testing and optimising DNA extraction, library preparation and sequencing methods. I have detected tumour DNA in routine cervical cytology samples collected from women subsequently diagnosed with cervical and endometrial cancers. In summary I have developed methods for ctDNA detection in women with newly diagnosed HGSOC that can be applied and refined in larger prospective studies of women undergoing follow-up for treated HGSOC, women with symptoms suggestive of OC and women at high risk of OC.
| Identifer | oai:union.ndltd.org:bl.uk/oai:ethos.bl.uk:763647 |
| Date | January 2018 |
| Creators | Moore, Elizabeth |
| Contributors | Brenton, James ; Rosenfeld, Nitzan |
| Publisher | University of Cambridge |
| Source Sets | Ethos UK |
| Detected Language | English |
| Type | Electronic Thesis or Dissertation |
| Source | https://www.repository.cam.ac.uk/handle/1810/285405 |
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