ArticleNucleic acids research2020
A novel NGS library preparation method to characterize native termini of fragmented DNA.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 12 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
12 citing papers in PubMed, 17 citations in OpenAlex.
- Pedigree-Based comparison of short-read and long-read sequencing for forensic mitochondrial genome analysis.International journal of legal medicine · 2026Article
- Widespread DNA off-targeting confounds RNA chromatin occupancy studies.Nature biotechnology · 2026Article
- Holistic determination of ends of cfDNA molecules.Cell genomics · 2026Article
- Cell-Free DNA-Based Theranostics for Inflammatory Disorders.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Systematic biases in reference-based plasma cell-free DNA fragmentomic profiling.Cell reports methods · 2024Article
- Can novel methods replace the gold standard chimerism method after allogeneic hematopoietic stem cell transplantation?Annals of hematology · 2024Review
- Analysis of the primary factors influencing donor derived cell-free DNA testing in kidney transplantation.Frontiers in immunology · 2024Review
- Cell-Free DNA Fragmentomics in Liquid Biopsy.Diagnostics (Basel, Switzerland) · 2022Review
- High-resolution analysis for urinary DNA jagged ends.NPJ genomic medicine · 2022Article
- Msuite2: All-in-one DNA methylation data analysis toolkit with enhanced usability and performance.Computational and structural biotechnology journal · 2022Article
- Detection and characterization of jagged ends of double-stranded DNA in plasma.Genome research · 2020Article
- Detecting circulating microbial cell-free DNA by next-generation sequencing in patients withTzu chi medical journalArticle
Corrections and comments
- Erratum issued
Authors and funding
8 authors at 2 institutions in 1 country.
Funding
Abstract
Biological and chemical DNA fragmentation generates DNA molecules with a variety of termini, including blunt ends and single-stranded overhangs. We have developed a Next Generation Sequencing (NGS) assay, XACTLY, to interrogate the termini of fragmented DNA, information traditionally lost in standard NGS library preparation methods. Here we describe the XACTLY method, showcase its sensitivity and specificity, and demonstrate its utility in in vitro experiments. The XACTLY assay is able to report relative abundances of all lengths and types (5' and 3') of single-stranded overhangs, if present, on each DNA fragment with an overall accuracy between 80-90%. In addition, XACTLY retains the sequence of each native DNA molecule after fragmentation and can capture the genomic landscape of cleavage events at single nucleotide resolution. The XACTLY assay can be applied as a novel research and discovery tool for fragmentation analyses and in cell-free DNA.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.