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Showing "Quantitative detection fusion breakpoints plasma cell free from" PubMed Articles 1–25 of 42,000+

Quantitative detection of ALK fusion breakpoints in plasma cell-free DNA from patients with non-small cell lung cancer using PCR-based target sequencing with a tiling primer set and two-step mapping/alignment.

Tyrosine kinase inhibitors targeted to anaplastic lymphoma kinase (ALK) have been demonstrated to be effective for lung cancer patients with an ALK fusion gene. Application of liquid biopsy, i.e., detection and quantitation of the fusion product in plasma cell-free DNA (cfDNA), could improve clinical practice. To detect ALK fusions, because fusion breakpoints occur somewhere in intron 19 of the ALK gene, sequencing of the entire intron is required to locate breakpoints.

Rapid detection of chromosomal translocation and precise breakpoint characterization in acute myeloid leukemia by nanopore long-read sequencing.

Detection of chromosomal translocation is a key component in diagnosis and management of acute myeloid leukemia (AML). Targeted RNA next-generation sequencing (NGS) is emerging as a powerful and clinically practical tool, but it depends on expression of RNA transcript from the underlying DNA translocation. Here, we show the clinical utility of nanopore long-read sequencing in rapidly detecting DNA translocation with exact breakpoints. In a newly diagnosed patient with AML, conventional karyotyping showed tr...

Considerations and quality controls when analyzing cell-free tumor DNA.

Circulating cell-free tumor DNA (ctDNA) is a promising biomarker in cancer. Ultrasensitive technologies enable detection of low (< 0.1%) mutant allele frequencies, a pre-requisite to fully utilize the potential of ctDNA in cancer diagnostics. In addition, the entire liquid biopsy workflow needs to be carefully optimized to enable reliable ctDNA analysis. Here, we discuss important considerations for ctDNA detection in plasma. We show how each experimental step can easily be evaluated using simple quantitati...

Resectable lung lesions malignancy assessment and cancer detection by ultra-deep sequencing of targeted gene mutations in plasma cell-free DNA.

Early detection of lung cancer to allow curative treatment remains challenging. Cell-free circulating tumour (ct) DNA (ctDNA) analysis may aid in malignancy assessment and early cancer diagnosis of lung nodules found in screening imagery.

Quantification of peripheral whole blood, cell-free plasma and exosome encapsulated mitochondrial DNA copy numbers in patients with atrial fibrillation.

Mitochondrial DNA (mtDNA) copy number changes have been associated with various diseases. Several studies showed that mtDNA content in peripheral blood was associated with oxidative stress and cardiovascular disease. Atrial fibrillation (AF) is one of the severe cardiovascular diseases. We aimed to determine the mtDNA copy numbers in peripheral blood, in cell-free plasma and in exosomes of AF patients and healthy controls. Peripheral blood was drawn from 60 AF patients and 72 healthy controls. DNA was isola...

Preparation of cfMeDIP-seq libraries for methylome profiling of plasma cell-free DNA.

Circulating cell-free DNA (cfDNA) comprises small DNA fragments derived from normal and tumor tissue that are released into the bloodstream. Recently, methylation profiling of cfDNA as a liquid biopsy tool has been gaining prominence due to the presence of tissue-specific markers in cfDNA. We have previously reported cell-free methylated DNA immunoprecipitation and high-throughput sequencing (cfMeDIP-seq) as a sensitive, low-input, cost-efficient and bisulfite-free approach to profiling DNA methylomes of pl...

Inhibition of HIV-1 envelope-dependent membrane fusion by serum antilymphocyte autoantibodies is associated with low plasma viral load.

The HIV-1 envelope protein (Env) mediates the membrane fusion process allowing virus entry to target cells and the efficiency to induce membrane fusion is an important determinant of HIV-1 pathogenicity. In addition to virus receptors, other adhesion/signaling molecules on infected and target cells and virus particles can enhance fusion. The presence of antilymphocyte autoantibodies (ALA) in HIV patients' serum suggests that they may contribute to the inhibition of Env-mediated membrane fusion. Here, sera f...


Deuterium plasma operations using a large fusion test device have been carried out since 2017 at the National Institute for Fusion Science. A small amount of tritium was produced by the fusion reaction, d(d, p)t. Then, a part of the tritium was released into the environment. Thus, monitoring the level of tritium in the environment around the fusion test facility is important. This is done before starting the deuterium plasma experiment. The environmental tritium concentrations indicated that they are at bac...

An efficient method for noninvasive prenatal diagnosis of fetal trisomy 13, trisomy 18, and trisomy 21.

Molecular size determination of circulating free fetal DNA in maternal plasma is an important detection method for noninvasive prenatal testing (NIPT). The fetal DNA molecule is the primary factor determining the overall performance of NIPT and its clinical interpretation. The proportion of cell-free fetal DNA molecules is expressed as the fetal DNA fraction in the plasma of pregnant women.

Prostate Cancer Detection Rate of Free-hand versus 3D Template Mapping Biopsy Using an MRI/Ultrasound Fusion Device in Biopsy-Naïve Men.

Targeted prostate biopsy devices include a 3-dimensional digital template grid for guiding systematic biopsy locations. Following a template could better ensure uniform and well-distributed sampling of the prostate compared to the traditional free-hand biopsy approach, possibly decreasing the chance for false-negative biopsy. Thus, we determined cancer detection rates obtained by conventional free-hand systematic sampling versus template mapping sampling using an MRI/ultrasound fusion device.

Label-Free Optical Detection of Multiple Biomarkers in Sweat, Plasma, Urine, Saliva.

We report a novel label-free quantitative detection of human performance "stress" biomarkers in different body fluids based on optical absorbance of the biomarkers in the ultraviolet (UV) region. Stress biomarker (hormones and neurotransmitters) concentrations in bodily fluids (blood, sweat, urine, saliva) predict the physical and mental state of the individual. Stress biomarkers primarily focused on in this manuscript are cortisol, serotonin, dopamine, norepinephrine, and neuropeptide Y. UV spectroscopy of...

Detection of cell-free circulating BRAF by droplet digital PCR in melanoma and non-melanoma patients under dermatological surveillance.

The p.V600E mutation in the BRAF gene (BRAF ) is the most frequent mutation in cutaneous melanoma and is a recurrent alteration found in common benign naevi. The analysis of cell-free BRAF mutation (cfBRAF ) in plasma has emerged as a biomarker for monitoring prognosis and treatment response in melanoma patients.

Detection of cell-free, exosomal and whole blood mitochondrial DNA copy number in plasma or whole blood of patients with serous epithelial ovarian cancer.

Ovarian tumor is one of the leading causes of cancer among women. Patients are diagnosed at an advanced stage, usually. There is a need for new specific and sensitive biomarkers. Mitochondrial DNA copy number change was observed in various cancers. Our aim was to detect mitochondrial DNA copy number in whole blood (wb-mtDNA) and in plasma (cell-free and exosome encapsulated mtDNA) in patients with serous epithelial ovarian tumor. DNA was isolated from EDTA blood and plasma obtained from 24 patients and 24 h...

Targeted sequencing of plasma cell-free DNA to predict response to PD1 inhibitors in advanced non-small cell lung cancer.

Tumor mutational burden is an emerging biomarker of response to immune checkpoint inhibitors (ICI), whose clinical adoption is challenging. We hypothesized that targeting limited but relevant genetic alterations in plasma cell-free DNA along with early monitoring may non-invasively predict response to ICI in advanced non-small cell lung cancer (NSCLC).

Detection of inorganic ions and organic molecules with cell-free biosensing systems.

Efforts to use genetically modified cells to detect inorganic ions and organic molecules have been hindered by biosafety concerns, limitation of cell membrane barriers, cytotoxicity problems, and unfriendly operations. To address those challenges, cell-free biosensing systems were established to detect arsenic, mercury, acyl-homoserine lactone, and benzoic acid in this study. The cell-free system mimics biological transcription and translation activities in an open environment without living cells. The most...

Early Detection of Metastatic Relapse and Monitoring of Therapeutic Efficacy by Ultra-Deep Sequencing of Plasma Cell-Free DNA in Patients With Urothelial Bladder Carcinoma.

Novel sensitive methods for early detection of relapse and for monitoring therapeutic efficacy may have a huge impact on risk stratification, treatment, and ultimately outcome for patients with bladder cancer. We addressed the prognostic and predictive impact of ultra-deep sequencing of cell-free DNA in patients before and after cystectomy and during chemotherapy.

A longitudinal study on circulating miR-21 as a therapeutic effect marker in head and neck squamous cell carcinoma.

The aim of the study is to investigate plasma miR-21 for a possible therapeutic effect determination marker in head and neck squamous cell carcinoma (HNSCC). Plasma samples are obtained from 86 HNSCC patients and 29 non-cancer volunteers who had been treated at Mie University Hospital between May 2015 and December 2016, and plasma miR-21 expression was measured using real-time quantitative reverse transcription polymerase chain reaction. In addition, plasma miR-21 level of advanced HNSCC patients including ...

Detection of Circulating Tumor DNA in Plasma: A Potential Biomarker for Esophageal Adenocarcinoma.

Recent literature has demonstrated the potential of "liquid biopsy" and detection of circulating, cell-free tumor deoxyribonucleic acid (ctDNA) as a cancer biomarker. However, to date there is a lack of data specific to esophageal adenocarcinoma (EAC). The purpose of this study is to determine how detection and quantification of ctDNA changes with disease burden in patients with EAC and to evaluate its potential as a biomarker in this population.

Mutations in the DI-DII linker of the NDV fusion protein conferred hemagglutinin-neuraminidase-independent cell fusion promotion.

Newcastle disease (ND), which is caused by Newcastle disease virus (NDV), is a highly contagious disease in chickens and is a great threat to the poultry industry. Fusion of the viral and target cell membranes is a prerequisite for NDV's entry into host cells. This process is directly mediated by the fusion (F) protein. Although several domains of F are known to regulate membrane fusion activity, the roles of the DI-DII linker (residues 376-381) of the NDV F protein in membrane fusion still remain unclear. ...

Protein profiling and pseudo-parallel reaction monitoring to monitor a fusion-associated conformational change in hemagglutinin.

Influenza infection requires viral escape from early endosomes into the cytosol, which is enabled by an acid-induced irreversible conformational transformation in the viral protein hemagglutinin. Despite the direct relationship between this conformational change and infectivity, label-free methods for characterizing this and other protein conformational changes in biological mixtures are limited. While the chemical reactivity of the protein backbone and side-chain residues is a proxy for protein conformatio...

A tailored approach to fusion transcript identification increases diagnosis of rare inherited disease.

RNA sequencing has been proposed as a means of increasing diagnostic rates in studies of undiagnosed rare inherited disease. Recent studies have reported diagnostic improvements in the range of 7.5-35% by profiling splicing, gene expression quantification and allele specific expression. To-date however, no study has systematically assessed the presence of gene-fusion transcripts in cases of germline disease. Fusion transcripts are routinely identified in cancer studies and are increasingly recognized as hav...

Cancer cell fusion: a potential target to tackle drug-resistant and metastatic cancer cells.

Cell fusion is an integral, established phenomenon underlying various physiological processes in the cell cycle. Although research in cancer metastasis has hypothesised numerous molecular mechanisms and signalling pathways responsible for invasion and metastasis, the origin and progression of metastatic cells within primary tumours remains unclear. Recently, the role of cancer cell fusion in cancer metastasis and development of multidrug resistance (MDR) in tumours has gained prominence. However, evidence r...

Plasma-free amino acid profiles in dogs with hepatocellular carcinoma.

Metabolomic analysis using blood samples has been suggested to be useful for the early detection of cancer. Among metabolites, plasma-free amino acid (PFAA) profiles are potential diagnostic biomarkers for several diseases including cancer. However, the relationship between PFAA concentrations and liver tumors in dogs remains unknown.

Inductively coupled plasma mass spectrometry assay for quantification of free infliximab in serum.

TNF antagonists such as infliximab are effective for the treatment of several inflammatory and autoimmune diseases. Recent clinical studies have advocated the importance of measuring trough infliximab levels to guide treatment decisions. We have developed a novel assay for measuring serum free infliximab levels using inductively coupled plasma-mass spectrometry (ICP-MS). The method involves the incubation of patient serum in wells coated with recombinant TNF, followed by detection with lanthanide-labeled mo...

Analytical Methods for Quantitative Plasma Carnitine Determination.

Carnitine is an essential molecule for mitochondrial beta-oxidation of long-chain fatty acids and other cellular functions. Several rare, inherited disorders of carnitine metabolism occur in humans, and secondary carnitine deficiency is an important feature in a variety of clinical settings. Many of these conditions can be detected via quantitative analysis of free and esterified carnitine in plasma or urine, which thus offers an effective means for assessing the transport and initial processing of fatty ac...

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