BACR 12: DNA methylation of cell-free circulating DNA and its potential as a biomarker of high grade serous ovarian cancer

Kayleigh Davis1,Kirsty Flower1,Jane Borley1,Charlotte Wilhelm-Benartzi1,Robert Brown1

1Imperial College London, London, UK

Presenting date: Monday 2 November
Presenting time: 13.10-14.00

Background

It is estimated that 19 women per day are diagnosed with ovarian cancer in the UK. Over two thirds of these women are diagnosed with Stages III/IV where the relative 5year survival is <20%.
Due to non-specific symptoms new strategies for detection and patient stratification are urgently required. Circulating tumour DNA (ctDNA) in plasma is a potential source of tumour-specific biomarkers.
Epigenetic alterations such as gene promoter methylation can be utilised as a biomarker. However, a challenge for detecting methylation in plasma is distinguishing between white blood cell (WBC) and ctDNA methylation.
If cancer-specific biomarkers that differentiate ctDNA from WBC are identified, this would offer promise for a non-invasive way to monitor patients from diagnosis to relapse.

Method

In publically available genome-wide array-based DNA methylation datasets, regions highly methylated in high-grade serous ovarian carcinoma, HGSOC (n=342), and of low methylation in WBCs (n=276) were identified, and vice versa. These sites were then interrogated in an independent dataset to examine the methylation level in both benign and malignant ovarian tissue.
Assays were developed for these sites using bisulphite pyrosequencing and technically validated in 25 HGSOC tumour samples. In order to determine the analytical sensitivity of the method, the minimal amount of DNA needed for reproducible results was determined.

Results

A total of 12 loci were identified whose methylation status differentiated HGSOC from WBC DNA, one of which achieved 100% sensitivity and specificity. In addition one marker showed differential methylation between benign and malignant tissue with 94% sensitivity and 91% specificity.

Conclusion

We have identified methylation at loci that can be used to investigate clinical potential of methylation as a biomarker in ctDNA, and shown that bisulphite pyrosequencing is a feasible detection method. Future studies will evaluate this in patient samples and explore whether DNA derived from tumours can be routinely distinguished from WBCs.