Open Res Eur. 2026 Apr 3;6:87. doi: 10.12688/openreseurope.23403.1. eCollection 2026.

ABSTRACT

BACKGROUND: Pancreatic cancer and ovarian cancer are very challenging to diagnose at early stages. The endoscopic retrieval of biopsy tissue from a suspected benign or malignant lesion is challenging due to the tissue's nature. Therefore, within the Instand-NGS4P framework, we developed Measurable Residual Disease (MRD) prototypes to analyze blood plasma samples, with the aim of cost-effectively supporting the differential diagnosis of suspected pancreatic or ovarian neoplasms.

METHODS: Our MRD prototypes examine blood plasma for mutations in cell-free DNA in specific genes associated with pancreatic neoplasms or ovarian neoplasms, respectively. Unique molecular identifiers (UMIs) are used to enable bioinformatic error correction. Ultra-deep sequencing is demonstrated on sequencing platforms from two different vendors (Illumina and MGI). We provide detailed information on bioinformatic processing of sequencing data to perform error-correction.

RESULTS: Using commercially available reference standards, we demonstrate stable mutation detection down to a variant allele frequency (VAF) of 0.1%. At a coverage of 4,000x duplex consensus reads, only two false positives were observed, which can be efficiently mitigated using an appropriate filtering strategy.

CONCLUSIONS: The technical usability of our MRD prototype has been clearly demonstrated for stable low-level VAF detection in commercial reference samples.

PMID:42728989 | PMC:PMC13560845 | DOI:10.12688/openreseurope.23403.1