Design and evaluation of a custom circulating tumour DNA assay to detect endometrial cancer recurrence

Circulating tumour DNA (ctDNA) has high sensitivity to detect endometrial cancer (EC) recurrence. An EC-specific ctDNA panel (ECctDNA-panel) was designed using TCGA/CPTAC mutation profile datasets and whole exome sequencing data from primary ECs. The ECctDNA-panel was tested using commercial standards to determine the detection limit for known driver variants, before investigating the plasma cell free DNA (cfDNA) from patients with/without recurrence. The ECctDNA-panel was able to detect EC hotspot mutations at >1% AF in 100% (42/42) of primary tumours tested. The ctDNA standards confirmed detection as low as 0.74% VAF in 5 ng template DNA. The ECctDNA-panel detected hotspot variants in 10/14 patients with recurrence and in 1/25 without recurrence: sensitivity/specificity 71.4%/96% and accuracy 87.2%. Potentially actionable mutations were identified in 8/10 ctDNA positive recurrences. We report the development of an ECctDNA-panel that has a high diagnostic accuracy to detect EC recurrence and could be utilised to guide patient's further management.