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View article: Adapting Clinical Chemistry Plasma as a Source for Liquid Biopsies
Adapting Clinical Chemistry Plasma as a Source for Liquid Biopsies Open
Background Circulating cell-free DNA (cfDNA) has become a valuable analyte for molecular testing but requires specialized collection tubes or immediate processing. We investigated the feasibility of using residual plasma from heparin separ…
View article: Artificial intelligence and machine learning in cell-free-DNA-based diagnostics
Artificial intelligence and machine learning in cell-free-DNA-based diagnostics Open
The discovery of circulating fetal and tumor cell-free DNA (cfDNA) molecules in plasma has opened up tremendous opportunities in noninvasive diagnostics such as the detection of fetal chromosomal aneuploidies and cancers and in posttranspl…
View article: Histone modifications of circulating nucleosomes are associated with changes in cell-free DNA fragmentation patterns
Histone modifications of circulating nucleosomes are associated with changes in cell-free DNA fragmentation patterns Open
The analysis of tissues of origin of cell-free DNA (cfDNA) is of research and diagnostic interest. Many studies focused on bisulfite treatment or immunoprecipitation protocols to assess the tissues of origin of cfDNA. DNA loss often occurs…
View article: Methylation-Associated Nucleosomal Patterns of Cell-Free DNA in Cancer Patients and Pregnant Women
Methylation-Associated Nucleosomal Patterns of Cell-Free DNA in Cancer Patients and Pregnant Women Open
Background Cell-free DNA (cfDNA) analysis offers an attractive noninvasive means of detecting and monitoring diseases. cfDNA cleavage patterns within a short range (e.g., 11 nucleotides) have been reported to correlate with cytosine-phosph…
View article: Fragmentation landscape of cell-free DNA revealed by deconvolutional analysis of end motifs
Fragmentation landscape of cell-free DNA revealed by deconvolutional analysis of end motifs Open
Cell-free DNA (cfDNA) fragmentation is nonrandom, at least partially mediated by various DNA nucleases, forming characteristic cfDNA end motifs. However, there is a paucity of tools for deciphering the relative contributions of cfDNA cleav…
View article: Cell-Free DNA Fragmentomics in Liquid Biopsy
Cell-Free DNA Fragmentomics in Liquid Biopsy Open
Cell-free DNA (cfDNA) in bodily fluids has rapidly transformed the development of noninvasive prenatal testing, cancer liquid biopsy, and transplantation monitoring. Plasma cfDNA consists of a mixture of molecules originating from various …
View article: Jagged Ends on Multinucleosomal Cell-Free DNA Serve as a Biomarker for Nuclease Activity and Systemic Lupus Erythematosus
Jagged Ends on Multinucleosomal Cell-Free DNA Serve as a Biomarker for Nuclease Activity and Systemic Lupus Erythematosus Open
Background Jagged ends of plasma DNA are a recently recognized class of fragmentomic markers for cell-free DNA, reflecting the activity of nucleases. A number of recent studies have also highlighted the importance of jagged ends in the con…
View article: High-resolution analysis for urinary DNA jagged ends
High-resolution analysis for urinary DNA jagged ends Open
Single-stranded ends of double-stranded DNA (jagged ends) are more abundant in urinary DNA than in plasma DNA. However, the lengths of jagged ends in urinary DNA remained undetermined, as a previous method used for urinary DNA jagged end s…
View article: Emerging frontiers of cell-free DNA fragmentomics
Emerging frontiers of cell-free DNA fragmentomics Open
Analysis of cell-free DNA (cfDNA) in the blood has shown promise for monitoring a variety of biological processes. Plasma cfDNA is a mixture comprising DNA molecules released from various bodily tissues, mediated by characteristic DNA frag…
View article: Jagged Ends of Urinary Cell-Free DNA: Characterization and Feasibility Assessment in Bladder Cancer Detection
Jagged Ends of Urinary Cell-Free DNA: Characterization and Feasibility Assessment in Bladder Cancer Detection Open
Background Double-stranded DNA in plasma is known to carry single-stranded ends, called jagged ends. Plasma DNA jagged ends are biomarkers for pathophysiologic states such as pregnancy and cancer. It remains unknown whether urinary cell-fr…
View article: Detection and characterization of jagged ends of double-stranded DNA in plasma
Detection and characterization of jagged ends of double-stranded DNA in plasma Open
Cell-free DNA in plasma has been used for noninvasive prenatal testing and cancer liquid biopsy. The physical properties of cell-free DNA fragments in plasma, such as fragment sizes and ends, have attracted much recent interest, leading to…