Comparative Panel Sequencing of DNA Variants in cf-, ev- and tumorDNA for Pancreatic Ductal Adenocarcinoma Patients

Waldenmaier, Mareike; Schulte, Lucas-Alexander; Schönfelder, Jonathan; Fürstberger, Axel; Kraus, Johann M.; Daiss, Nora; Seibold, Tanja; Morawe, Mareen; Ettrich, Thomas Jens; Kestler, Hans A.; Kahlert, Christoph; Seufferlein, Thomas; Eiseler, Tim

doi:10.3390/cancers14041074

Cited by 2 publications

(2 citation statements)

References 62 publications

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“…Similar studies have indicated the presence of larger DNA fragments within EVs (Mao et al, 2019;Nguyen et al, 2020;Ruhen et al, 2021). It has been reported that longer EV-DNA fragments may improve the detection of single nucleotide variations, copy number variations (San Lucas et al, 2016) and insertions/deletions during NGS sequencing performance and bioinformatic analysis (Waldenmaier et al, 2022). However, other studies reported the presence of shorter DNA fragments (152.4 bp, 160 bp) within EVs, with larger DNA fragments possibly resulting from contamination with apoptotic bodies (Sun et al, 2021;.…”

Section:  Ev-dna Fragment Size Profilementioning

confidence: 63%

“…Similar studies have indicated the presence of larger DNA fragments within EVs (Mao et al., 2019 ; Nguyen et al., 2020 ; Ruhen et al., 2021 ). It has been reported that longer EV‐DNA fragments may improve the detection of single nucleotide variations, copy number variations (San Lucas et al., 2016 ) and insertions/deletions during NGS sequencing performance and bioinformatic analysis (Waldenmaier et al., 2022 ).…”

Section: Resultsmentioning

confidence: 99%

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EV‐ADD, a database for EV‐associated DNA in human liquid biopsy samples

Tsering

Chen

et al. 2022

J of Extracellular Vesicle

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Extracellular vesicles (EVs) play a key role in cellular communication both in physiological conditions and in pathologies such as cancer. Emerging evidence has shown that EVs are active carriers of molecular cargo (e.g. protein and nucleic acids) and a powerful source of biomarkers and targets. While recent studies on EV‐associated DNA (EV‐DNA) in human biofluids have generated a large amount of data, there is currently no database that catalogues information on EV‐DNA. To fill this gap, we have manually curated a database of EV‐DNA data derived from human biofluids (liquid biopsy) and in‐vitro studies, called the Extracellular Vesicle‐Associated DNA Database (EV‐ADD). This database contains validated experimental details and data extracted from peer‐reviewed published literature. It can be easily queried to search for EV isolation methods and characterization, EV‐DNA isolation techniques, quality validation, DNA fragment size, volume of starting material, gene names and disease context. Currently, our database contains samples representing 23 diseases, with 13 different types of EV isolation techniques applied on eight different human biofluids (e.g. blood, saliva). In addition, EV‐ADD encompasses EV‐DNA data both representing the whole genome and specifically including oncogenes, such as KRAS, EGFR, BRAF, MYC, and mitochondrial DNA (mtDNA). An EV‐ADD data metric system was also integrated to assign a compliancy score to the MISEV guidelines based on experimental parameters reported in each study. While currently available databases document the presence of proteins, lipids, RNA and metabolites in EVs (e.g. Vesiclepedia, ExoCarta, ExoBCD, EVpedia, and EV‐TRACK), to the best of our knowledge, EV‐ADD is the first of its kind to compile all available EV‐DNA datasets derived from human biofluid samples. We believe that this database provides an important reference resource on EV‐DNA‐based liquid biopsy research, serving as a learning tool and to showcase the latest developments in the EV‐DNA field. EV‐ADD will be updated yearly as newly published EV‐DNA data becomes available and it is freely available at http://www.evdnadatabase.com.

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Section:  Ev-dna Fragment Size Profilementioning

confidence: 63%

Section: Resultsmentioning

confidence: 99%

EV‐ADD, a database for EV‐associated DNA in human liquid biopsy samples

Tsering

Chen

et al. 2022

J of Extracellular Vesicle

View full text Add to dashboard Cite

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Extracellular vesicle-associated DNA: ten years since its discovery in human blood

Tsering,

Nadeau,

et al. 2024

Cell Death Dis

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Extracellular vesicles (EVs) have emerged as key players in intercellular communication, facilitating the transfer of crucial cargo between cells. Liquid biopsy, particularly through the isolation of EVs, has unveiled a rich source of potential biomarkers for health and disease, encompassing proteins and nucleic acids. A milestone in this exploration occurred a decade ago with the identification of extracellular vesicle-associated DNA (EV-DNA) in the bloodstream of a patient diagnosed with pancreatic cancer. Subsequent years have witnessed substantial advancements, deepening our insights into the molecular intricacies of EV-DNA emission, detection, and analysis. Understanding the complexities surrounding the release of EV-DNA and addressing the challenges inherent in EV-DNA research are pivotal steps toward enhancing liquid biopsy-based strategies. These strategies, crucial for the detection and monitoring of various pathological conditions, particularly cancer, rely on a comprehensive understanding of why and how EV-DNA is released. In our review, we aim to provide a thorough summary of a decade’s worth of research on EV-DNA. We will delve into diverse mechanisms of EV-DNA emission, its potential as a biomarker, its functional capabilities, discordant findings in the field, and the hurdles hindering its clinical application. Looking ahead to the next decade, we envision that advancements in EV isolation and detection techniques, coupled with improved standardization and data sharing, will catalyze the development of novel strategies exploiting EV-DNA as both a source of biomarkers and therapeutic targets.

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Comparative Panel Sequencing of DNA Variants in cf-, ev- and tumorDNA for Pancreatic Ductal Adenocarcinoma Patients

Cited by 2 publications

References 62 publications

EV‐ADD, a database for EV‐associated DNA in human liquid biopsy samples

EV‐ADD, a database for EV‐associated DNA in human liquid biopsy samples

Extracellular vesicle-associated DNA: ten years since its discovery in human blood

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