Biology subjects

Vynck, M.

Publications and source records attributed to Vynck, M..

3 recordsLinked to original sources

bioRxiv2026

Introducing the digital PCR data essentials standard to harmonize data structure for clinical and research use

Digital PCR (dPCR) is a powerful technology for absolute quantification of nucleic acids, valued for its accuracy, sensitivity, and repeatability. Yet, the commercialization of different instruments with proprietary software has introduced challenges to data analysis, interoperability, and comparability. Therefore, we present the Digital PCR Data Essentials Standard (DDES) - a lightweight, human- and machine-readable, and cross-platform data standard developed in collaboration with the dPCR community. The standard consists of three file types designed to enable both manual inspection and automated analysis: (i) a main file summarizing experiment and reaction-level (meta-)data; (ii) an assay file describing targets and detection chemistry, and (iii) intensity files capturing partition-level raw fluorescence data per reaction. DDES supports a wide range of current dPCR applications, including singleplex and multiplex assays, endpoint and real-time readouts, and will be curated to implement future dPCR developments. By harmonizing the data structure, DDES lays out the foundation for FAIR dPCR data practices and supports improved software compatibility, collaborative and reproducible research, and future dPCR data repositories.

bioinformatics↗

bioRxiv2025

Robust metabolomics data normalization across scales and experimental designs

Metabolomics studies employing liquid chromatography-mass spectrometry are affected by signal drift and batch effects, introducing technical variance that impedes biological knowledge discovery. Quality control (QC) sample-based normalization strategies are widely implemented but remain vulnerable to outliers, thereby reducing normalization performance. We introduce rLOESS, rGAM and tGAM, three robust normalization methods that improve resistance to outliers by downweighting or accommodating them. Leveraging additive models, the rGAM and tGAM methods allow flexible non-linear modeling, differential sample weighting, and data-driven QC representativeness evaluation. Implementations of these methods are gathered in the Metanorm R package, integrating robust normalization with visualization for performance verification, while supporting efficient parallel processing. In in silico and/or experimental datasets, the robust methods, relative to several popular existing strategies, improved replicate concordance, and reduced drift and batch effects. The robust methods, with improved recovery of the underlying signal demonstrated in simulation, produced distinct differential abundance results, highlighting the impact of normalization on downstream statistical inference. Overall, tGAM-based normalization suggested the best performance across scenarios and is proposed as default choice. Metanorm is versatile, supporting normalization in metabolomics studies across scales and experimental setups.

bioinformatics↗

bioRxiv2025

Cross-platform digital PCR evaluation of bovine papilloma virus quantification: introducing PCR-ValiPal for Standardized guided assay validation

Digital Polymerase chain reaction (dPCR) enables precise and absolute quantification of nucleic acids by partitioning samples into thousands of individual PCR micro-reactions. While it minimizes the need for standard curves and enhances reproducibility compared to qPCR, thorough assay validation remains crucial. We introduce PCR-ValiPal, a user-friendly web application that standardizes dPCR assay validation steps and streamlines calculations of limit of blank (LOB), limit of detection (LOD), limit of quantification (LOQ), precision, trueness, and linearity in accordance with International Organization for Standardization (ISO) 20395:2019. To demonstrate PCR-ValiPals capabilities and the value of method-specific optimization, we use it to validate a novel three-color PCR assay for Bovine Papillomavirus (BPV) types 1 and 2, comparing four platforms: Naica (droplet dPCR), QIAcuity (microwell dPCR), LOAA (real-time dPCR), and CFX96 (qPCR). Using synthetic standards, we assess the platforms performance under identical assay conditions. Naica and QIAcuity showed lower LOB and LOQ values, along with minimal bias for BPV-1, while LOAA demonstrated stable but negative bias. Although qPCR exhibited the highest sensitivity for BPV-2, it was less sensitive at low concentrations for BPV-1. These results underscore the value of method-specific optimization and the usefulness of PCR-ValiPal.

molecular biology↗