Quantitative Analysis of Plasma Cell-Free DNA and Its DNA Integrity and Hypomethylation Status as Biomarkers for Tumor Burden and Disease Progression in Patients with Metastatic Neuroendocrine Neoplasias.

For discrimination of patients with metastasized NEN from presumably cured NEN patients, the combination of cfDNA concentration, hypomethylation, and cfDNA integrity revealed a highly significant AUC of 0.908 (95% CI, 0.83 to 0.99; p = 0.0001) with a positive predictive value (PPV) of 91.1% and negative predictive value (NPV) of 66.7% at the chosen classification cutoff of 0.5 ( Figure 4 B).

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When the cfDNA characteristics were correlated with the circulating Chromogranin A levels at the time of analysis, a weak but significant correlation was found for cfDNA concentration (r = 0.356; p = 0.011) and Alu hypomethylation (r = 0.310; p = 0.029), and a nonsignificant trend for LINE-1 integrity (r= −0.250; p = 0.08), as analyzed by Spearman correlation analysis.

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While the ROC analysis showed a strong and highly significant predictive power for the prediction of advanced disease with a high tumor load as compared to healthy controls and cured NEN patients, the predictive power of most cfDNA characteristics was found to be weaker and only partially significant for the prediction of moderate and especially low tumor burden in metastasized NEN patients (for sensitivities and specificities see Table S2 in the Supplement section ).

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