TrAC Trends in Analytical Chemistry, Journal Year: 2025, Volume and Issue: unknown, P. 118299 - 118299
Published: May 1, 2025
Language: Английский
Briefings in Bioinformatics, Journal Year: 2024, Volume and Issue: 25(3)
Published: March 27, 2024
Abstract Digital PCR (dPCR) is a highly accurate technique for the quantification of target nucleic acid(s). It has shown great potential in clinical applications, like tumor liquid biopsy and validation biomarkers. Accurate classification partitions based on end-point fluorescence intensities crucial to avoid biased estimators concentration molecules. We have evaluated many clustering methods, from general-purpose methods specific dPCR flowcytometry, both simulated real-life data. Clustering method performance was by simulating various scenarios. Based our extensive comparison we describe limits these formulate guidelines choosing an appropriate method. In addition, developed novel realistic The mixture distribution Poisson point process skew-$t$ distribution, which enables generation irregularities cluster shapes randomness between clusters (‘rain’) as commonly observed Users can fine-tune model parameters generate labeled datasets, using their own data template. Besides, database experimental augmented with serve training testing new methods. simulation available R Shiny app.
Language: Английский
Citations
6
International Journal of Molecular Medicine, Journal Year: 2024, Volume and Issue: 53(5)
Published: March 14, 2024
DNA methylation is an epigenetic modification that plays a key role in several cellular processes mediating the fine regulation of gene expression. Aberrant observed wide range pathologies, including cancer. Since these modifications are transferred to cell progenies and stable over time, analysis status has been proposed for diagnostic prognostic purposes Currently, bisulfite conversion gold standard method high‑throughput alterations. However, treatment induces fragmentation affecting its quality downstream analyses. In this field, it mandatory identify novel methods overcome limits conventional approaches. present study, Methylation‑Sensitive Restriction Enzyme‑droplet digital PCR (MSRE‑ddPCR) assay was developed as sensitive short genomic regions, combining MSRE with high‑sensitivity ddPCR using exogenous sequence control. Setup validation experiments were performed analyzing hotspot Solute Carrier Family 22 Member 17 samples derived from melanoma lines well tissues serum obtained patients healthy controls. Compared approaches, MSRE‑ddPCR more appropriate (methDNA) low amounts (up 0.651 ng) showing greater sensitivity. These findings suggested potential clinical application paving way other methDNA hotspots different tumors.
Language: Английский
Citations
5
Dyes and Pigments, Journal Year: 2022, Volume and Issue: 204, P. 110386 - 110386
Published: May 10, 2022
Language: Английский
Citations
22
Biosensors and Bioelectronics, Journal Year: 2024, Volume and Issue: 257, P. 116339 - 116339
Published: April 26, 2024
Pairing droplet microfluidics and CRISPR/Cas12a techniques creates a powerful solution for the detection quantification of nucleic acids at single-molecule level, due to its specificity, sensitivity, simplicity. However, traditional water-in-oil (W/O) single emulsion (SE) droplets often present stability issues, affecting accuracy reproducibility assay results. As an alternative, water-in-oil-in-water (W/O/W) double (DE) offer superior uniformity digital assays. Moreover, unlike SE droplets, DE are compatible with commercially available flow cytometry instruments high-throughput analysis. Despite these advantages, no study has demonstrated use CRISPR-based acid detection. In our study, we conducted comparative analysis assess performance in quantitative human papillomavirus type 18 (HPV18) DNA based on CRISPR/Cas12a. We evaluated SEs DEs by examining size variation, merging extent, content interaction before after incubation different temperatures time points. By integrating cytometry, achieved high-accuracy CRISPR/Cas12a-based target HPV18 DNA. The platform, when paired techniques, emerges as reliable tool absolute biomarkers.
Language: Английский
Citations
4
BMC Veterinary Research, Journal Year: 2024, Volume and Issue: 20(1)
Published: Sept. 28, 2024
Language: Английский
Citations
4
International Journal of Molecular Sciences, Journal Year: 2023, Volume and Issue: 24(18), P. 13767 - 13767
Published: Sept. 6, 2023
Thyroid cancer has become more common in recent years all around the world. Many issues still need to be urgently addressed diagnosis, treatment, and prognosis of thyroid cancer. Liquid biopsy (mainly circulating tumor DNA (ctDNA), cells (CTCs), exosomes) may provide a novel ideal approach solve these issues, allows us assess features diseases comprehensively, function variety malignancies. Recently, liquid been shown critical numerous previous studies. In this review, by testing CTCs, ctDNA, exosomes, we focus on possible clinical role cancer, including diagnostic prognostic biomarkers response therapy. We briefly review how components have progressed consulting existing public information. also discuss potential reference for research. useful tool early detection, monitoring, or prediction therapies with promising applications.
Language: Английский
Citations
11
BJOG An International Journal of Obstetrics & Gynaecology, Journal Year: 2023, Volume and Issue: 130(9), P. 999 - 1006
Published: Feb. 28, 2023
Abstract Exosomes are nano‐sized vesicles derived from the endosomal system and involved in many biological pathological processes. Emerging evidence has demonstrated that exosomes with cell‐specific constituents associated tumorigenesis progression of ovarian cancer. Therefore, cancers can be potential diagnostic biomarkers therapeutic targets. In this review, we briefly present characteristics recent advances isolating detecting exosomes. Furthermore, summarise functions cancer, hoping to provide a theoretical basis for clinical applications diagnosis treatment
Language: Английский
Citations
10
Medizinische Genetik, Journal Year: 2023, Volume and Issue: 35(4), P. 201 - 235
Published: Nov. 29, 2023
Abstract Liquid biopsies, in particular the profiling of circulating tumor DNA (ctDNA), have long held promise as transformative tools cancer precision medicine. Despite a prolonged incubation phase, ctDNA has recently experienced strong wave development and innovation, indicating its imminent integration into management toolbox. Various advancements mutation-based analysis methodologies technologies greatly improved sensitivity specificity assays, such optimized preanalytics, size-based pre-enrichment strategies, targeted sequencing, enhanced library preparation methods, sequencing error suppression, integrated bioinformatics machine learning. Moreover, research breakthroughs expanded scope beyond hotspot mutational plasma-derived apoptotic, mono-nucleosomal fragments. This broader perspective considers alternative genetic features cancer, genome-wide characterization, classical newly discovered epigenetic modifications, structural variations, diverse cellular mechanistic origins, biospecimen types. These developments maximized utility ctDNA, facilitating landmark research, clinical trials, commercialization technologies, products. Consequently, tests are increasingly recognized an important part patient guidance being implemented practice. Although reimbursement for by healthcare providers still lags behind, it is gaining greater acceptance. In this work, we provide comprehensive exploration extensive landscape methodologies, considering multitude factors that influence evolution. By illuminating aspects profiling, aim to multiple entry points understanding navigating vast rapidly evolving applications, technologies.
Language: Английский
Citations
10
Ecology and Evolution, Journal Year: 2025, Volume and Issue: 15(2)
Published: Feb. 1, 2025
ABSTRACT Evaluating field‐sourced samples with poor‐quality and low‐quantity DNA, like animal feces, presents significant challenges in the field of molecular biology. Nonetheless, recent innovations PCR technology are promoted as effective tools to overcome many these issues. Here, we evaluate efficiency droplet digital (ddPCR) a method for color vision assessment from feces white‐faced capuchins ( Cebus imitator ) report frequencies alleles genotypes wild population. The sex‐linked polymorphism monkeys Americas is driven by single nucleotide polymorphisms (SNPs) opsin genes at up three tuning sites. DNA was extracted fecal collected 211 (53.1% males) Sector Santa Rosa, Costa Rica: 56 were evaluated ddPCR, 24 both ddPCR Sanger sequencing, 141 sequencing (historical dataset). same opsins derived each monkey using ddPCR; however, latter far more sensitive required fewer reach definitive genotype. Overall, most frequent phenotypes red green/red. distribution was: Females N = 99): green/red (35.4%), red/red (33.3%), green/yellow (14.1%), yellow/red (12.1%), yellow/yellow (4.0%), green/green (1.0%); Males 112): (60.7%), yellow (23.2%), green (16.1%). reliable evaluating noninvasively advantage excellent sensitivity high‐throughput. highly robust inhibitors can be potentially used identify other disease‐related SNP mutations animals.
Language: Английский
Citations
0
International Journal of Molecular Sciences, Journal Year: 2025, Volume and Issue: 26(5), P. 2216 - 2216
Published: Feb. 28, 2025
Colorectal cancer (CRC) remains a leading cause of cancer-related mortality, with metastatic disease posing significant therapeutic challenges. While anti-EGFR therapy has improved outcomes for patients RAS and BRAF wild-type tumors, resistance major hurdle, limiting treatment efficacy. The concept negative hyperselection emerged as refinement molecular profiling, identifying additional genomic alterations-such HER2 MET amplificationsand MAP2K1 mutations-that predict to agents. Studies incorporating these expanded assessments have demonstrated that nearly half RAS/BRAF tumors harbor alternative biomarkers, underscoring the need selection criteria. Liquid biopsies, particularly circulating tumor DNA (ctDNA) analysis, revolutionized precision oncology by providing minimally invasive, real-time assessment dynamics. ctDNA-based enables detection resistance-associated alterations, guiding decisions greater accuracy than conventional tissue biopsies. Recent trials support predictive value ctDNA-defined hyperselection, revealing superior stratified through liquid biopsy. This narrative review explores evolving role in first-line therapy, emphasizing integration ctDNA refine patient selection, enhance efficacy, pave way personalized strategies CRC.
Language: Английский
Citations
0