Longitudinal copy number alteration analysis in plasma cell-free DNA of neuroendocrine neoplasms is a novel specific biomarker for diagnosis, prognosis and follow-up

Purpose: As noninvasive biomarkers are an important unmet need for neuroendocrine neoplasms (NEN), biomarker potential of genome-wide molecular profiling of plasma cell-free DNA (cfDNA) was prospectively studied in patients with NEN. Experimental Design: Longitudinal plasma samples were collected from patients with well-differentiated, metastatic gastroenteropancreatic and lung NEN. cfDNA was subjected to shallow whole-genome sequencing to detect genome-wide copy-number alterations (CNA) and estimate circulating tumor DNA (ctDNA) fraction, and correlated to clinicopathologic and survival data. To differentiate pancreatic NENs (PNEN) from pancreatic adenocarcinomas (PAAD) using liquid biopsies, a classification model was trained using tissue-based CNAs and validated in cfDNA. Results: One hundred and ninety-five cfDNA samples from 43 patients with NEN were compared with healthy control cfDNA (N = 100). Plasma samples from patients with PNEN (N = 21) were used for comparison with publicly available PNEN tissue (N = 98), PAM) tissue (N = 109), and PAAD cfDNA (N= 96). Thirty percent of the NEN cfDNA samples contained cLDNA and 44% of the patients had at least one ctDNA-positive (ctDNA(+)) sample. CNAs detected in cfDNA were highly specific for NENs and the dassification model could distinguish PAAD and PNEN cfDNA samples with a sensitivity, specificity, and AUC of 62%, 86%, and 79%, respectively. ctDNA-positivity was associated with higher World Health Organization (WHO) grade, primary tumor location, and higher chromogran in A and neuron-specific enolase values. Overall survival was significantly worse for ctDNA(+) patients and increased ctDNA fractions were associated with poorer progression-free survival. Conclusions: Sequential genome-wide profiling of plasma cfDNA is a novel, noninvasive biomarker with high specificity for diagnosis, prognosis, and follow-up in metastatic NENs.