NET-IMPRESS: A novel methylation-based assay to diagnose and monitor NET patients using liquid biopsies

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Introduction: Previously, we showed that analysing copy number alterations (CNAs) in cell-free DNA (cfDNA) of NET patients using shallow whole genome sequencing (sWGS) is a potential biomarker for diagnosis and follow-up (PMID: 34759042). We now present NET-IMPRESS, an easy, cost-effective methylation-based assay for detecting circulating tumour DNA (ctDNA) in NET samples.

Aim(s): We aimed to assess the diagnostic and follow-up potential of NET-IMPRESS in NET patients’ cfDNA and compare it to the CNA-based approach.

Materials and methods: We established a biomarker panel including 1152 NET-specific hypermethylated CpG sites and a novel, bisulfite-free DNA methylation detection method which we combined into the NET-IMPRESS assay. Using this assay, we analysed 56 cfDNA samples from 25 patients and 16 from healthy controls and calculated a relative methylation level (RML) per sample. Based on an RML cutoff, determined from healthy controls, NET samples were classified as ctDNA-positive or -negative. ctDNA status was then compared between the methylation- and CNA-based approach.

Conference:

Presenting Author:

Authors: Mariën L, Ibrahim J, de Meulenaere N, Chhajlani S, Neefs I,

Keywords: neuroendocrine tumour, liquid biopsy, DNA methylation, copy number alterations, biomarker selection, IMPRESS technology,