Eveline Vanden Eynde

The use of blood-based extracellular RNA (cell-free RNA; exRNA) as clinical biomarker requires the implementation of a validated procedure for sample collection, processing, and profiling. So far, no study has systematically addressed the pre-analytical variables affecting transcriptome analysis of exRNAs. In the exRNAQC study, we evaluated ten blo...

Extracellular RNA (cell‐free RNA; exRNA) from blood‐derived liquid biopsies is an appealing, minimally invasive source of disease biomarkers. As pre‐analytical variables strongly influence exRNA measurements, their reporting is essential for meaningful interpretation and replication of results. The aim of this review was to chart to what extent pre...

The detection of circular RNA molecules (circRNAs) is typically based on short-read RNA sequencing data processed using computational tools. Numerous such tools have been developed, but a systematic comparison with orthogonal validation is missing. Here, we set up a circRNA detection tool benchmarking study, in which 16 tools detected almost 300,00...

Circulating nucleic acids in blood plasma form an attractive resource to study human health and disease. Here, we applied mRNA capture sequencing of blood plasma cell-free RNA from 266 cancer patients and cancer-free controls (discovery n=208, 25 cancer types; validation n=58, 3 types). We observed cancer-type specific as well as pan-cancer alterat...

Using blood-based extracellular RNA (circulating cell-free RNA; exRNA) as a clinical biomarker requires validated procedures for sample collection and processing and RNA quantification. No study to date has systematically tested pre-analytical variables affecting transcriptome-wide exRNA analysis. We evaluated and compared ten blood collection tube...

We assess the performance of mRNA capture sequencing to identify fusion transcripts in FFPE tissue of different sarcoma types, followed by RT-qPCR confirmation. To validate our workflow, six positive control tumors with a specific chromosomal rearrangement were analyzed using the TruSight RNA Pan-Cancer Panel. Fusion transcript calling by FusionCat...

Molecular phenotyping through shallow 3′‐end RNA‐sequencing workflows is increasingly applied in the context of large‐scale chemical or genetic perturbation screens to study disease biology or support drug discovery. While these workflows enable accurate quantification of the most abundant genes, they are less effective for applications that requir...

Long non-coding RNAs (lncRNAs) can exhibit cell-type and cancer-type specific expression profiles, making them highly attractive as therapeutic targets. Pan-cancer RNA sequencing data revealed broad expression of the SAMMSON lncRNA in uveal melanoma (UM), the most common primary intraocular malignancy in adults. Currently, there are no effective tr...

Molecular phenotyping through shallow 3′-end RNA-sequencing workflows is increasingly applied in the context of large-scale chemical or genetic perturbation screens to study disease biology or support drug discovery. While these workflows enable accurate quantification of the most abundant genes, they are less effective for applications that requir...

The use of blood-based extracellular RNA (exRNA) as clinical biomarker requires the implementation of a validated procedure for sample collection, processing and profiling. So far, no study has systematically addressed the pre-analytical variables affecting transcriptome analysis of exRNAs. In the exRNAQC study, we evaluated 10 blood collection tub...

Liquid biopsies offer a minimally invasive alternative to tissue biopsies for both diagnosis and monitoring of treatment response. Extracellular RNAs present in biofluids have emerged as potential biomarkers in health and disease, including cancer. While current studies typically focus on plasma or serum, other biofluids may contain more informativ...

p>Cancer biomarker studies require procedures that provide accurate and precise test results with high analytical sensitivity. Consequently, the growing use of extracellular RNA from human biofluids as clinically relevant biomarker requires the implementation of benchmarked methods for sample collection, processing, and profiling. While several sma...

Extracellular RNAs present in biofluids have emerged as potential biomarkers for disease. Where most studies focus on plasma or serum, other biofluids may contain more informative RNA molecules, depending on the type of disease. Here, we present an unprecedented atlas of messenger, circular and small RNA transcriptomes of a comprehensive collection...

Extensive cDNA analysis demonstrated that all human and mouse protocadherin-beta genes are one-exon genes. The protein sequences of these genes are highly conserved, especially the three most membrane-proximal extracellular domains. Phylogenetic analysis suggested that this unique gene family evolved by duplication of one single protocadherin-beta...