Circulating tumour DNA as a biomarker in the monitoring of neuroendocrine neoplasms and adrenocortical carcinoma

Neuroendocrine neoplasms (NENs) and adrenocortical carcinoma (ACC) are two rare malignancies affecting the endocrine system, which both have a clinical need for novel biomarker development. This thesis assessed the role of detecting and monitoring circulating tumour DNA (ctDNA) for this purpose using a bespoke, tumour informed, personalised approach in 9 patients with metastatic NENs and a case of ACC.

Tumour DNA whole exome sequencing (WES) was undertaken to identify tumour specific somatic variants. In the patients with NENs, WES demonstrated that each patient’s tumour was genetically unique and in the patient with ACC, multi-regional WES demonstrated intra-tumoural heterogeneity. Bioinformatics pipelines were applied to filter and select patient-specific variants for targeted next generation sequencing (NGS) and a bespoke, personalised AmpliSeq™ HD assay targeting 132 variants (5-22 unique to each patient) was designed. 125/132 variants were confirmed by NGS analysis of the tumour DNA with statistical concordance of variant allele frequencies (VAFs) with the WES data.

For NENs, 35 plasma samples, 2-5 for each patient, collected serially over 2-25 months underwent targeted NGS for ctDNA detection and monitoring. ctDNA was detected in 6/9 patients. In 4 of these patients, ctDNA dynamics tracked disease progression and treatment response. ctDNA was not detected in 3 patients and was associated with their indolent disease. ctDNA therefore correlated with disease activity in 7/9 patients. ctDNA performed equally to chromogranins as a biomarker in 3/8 patients, where chromogranins were monitored, however in 4 patients, ctDNA more accurately reflected with tumour dynamics. In the patient with ACC monitored over 25 months, ctDNA was detected in 2/5 samples at times of disease progression. Fewer ctDNA variants detected in the second positive sample but at higher VAFs were suggestive of clonal evolution. Absence of ctDNA in 3/5 samples was associated with treatment response/indolent disease.

This pilot study demonstrates that ctDNA can be detected and monitored in patients with metastatic NENS and ACC and, with further development, could be used as a clinically useful biomarker.