ArticleScientific reports2016
Single-stranded DNA library preparation uncovers the origin and diversity of ultrashort cell-free DNA in plasma.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 119 papers.
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Who cites it
119 citing papers in PubMed.
- A scalable deep-learning framework for cancer detection using cell-free DNA shallow whole-genome sequencing.Science advances · 2026Article
- Molecular features unique to circulating tumor DNA enable the tumor-naïve liquid biopsy of glioblastoma.NPJ precision oncology · 2026Article
- mChIP-seq for Multiplex and Multifactorial Epigenomic Profiling Uncovers Cancer-specific Histone Features in Cellular and Circulating Nucleosomes.bioRxiv : the preprint server for biology · 2026Article
- Bacterial cell-free DNA profiling reveals the co-elevation of multiple bacteria in newborn foals with suspected sepsis.iScience · 2025Article
- In-matrix library preparation for metagenomic sequencing of microbial cell-free DNA.Journal of clinical microbiology · 2025Article
- Circulating tumour cells and circulating tumour DNA in head and neck cancer: from molecular insights to clinical impact.Cancer metastasis reviews · 2025Review
- Expanding the scope of non-invasive prenatal screening.Nature genetics · 2025Review
- The circulating cell-free DNA landscape in sepsis is dominated by impaired liver clearance.Cell genomics · 2025Article
- Circulating Cell-free DNA Fragmentomics Detection and Beyond.Aging and disease · 2025Review
- Characterization of Ultra-Short plasma Cell-Free DNA in maternal blood and its preliminary potential as a screening marker for preeclampsia.Molecular medicine (Cambridge, Mass.) · 2025Article
- Evaluation of variability in cell-free DNA extraction efficiency from plasma and urine and spike-in normalization.Scientific reports · 2025Article
- Role of Liquid Biopsy for Early Detection, Prognosis, and Therapeutic Monitoring of Hepatocellular Carcinoma.Diagnostics (Basel, Switzerland) · 2025Review
- Enrichment of Microbial DNA in Plasma to Improve Pathogen Detection in Sepsis: A Pilot Study.Clinical chemistry · 2025Article
- Cell-Free DNA: Features and Attributes Shaping the Next Frontier in Liquid Biopsy.Molecular diagnosis & therapy · 2025Review
- NGS-based Aspergillus detection in plasma and lung lavage of children with invasive pulmonary aspergillosis.NPJ genomic medicine · 2025Article
- Unravelling the Significance of Extracellular Vesicle-Associated DNA in Cancer Biology and Its Potential Clinical Applications.Journal of extracellular vesicles · 2025Review
- Fast and efficient method for parallel construction of targeted exome and methylome single-stranded DNA sequencing libraries.Scientific reports · 2025Article
- Cell-free DNA integrity and complement C4d as novel liquid biopsy biomarkers for paraneoplastic and non-paraneoplastic autoimmune encephalitis.Frontiers in immunology · 2025Article
- Diagnostic approach to elevated dd-cfDNA with reassuring EMB in heart transplantation.Frontiers in transplantation · 2025Review
- Analytical and clinical validation of direct detection of antimicrobial resistance markers by plasma microbial cell-free DNA sequencing.Journal of clinical microbiology · 2024Article
59 more citing papers are in PubMed but not listed here.
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7 authors.
Funding
Abstract
Circulating cell-free DNA (cfDNA) is emerging as a powerful monitoring tool in cancer, pregnancy and organ transplantation. Nucleosomal DNA, the predominant form of plasma cfDNA, can be adapted for sequencing via ligation of double-stranded DNA (dsDNA) adapters. dsDNA library preparations, however, are insensitive to ultrashort, degraded cfDNA. Drawing inspiration from advances in paleogenomics, we have applied a single-stranded DNA (ssDNA) library preparation method to sequencing of cfDNA in the plasma of lung transplant recipients (40 samples, six patients). We found that ssDNA library preparation yields a greater portion of sub-100 bp nuclear genomic cfDNA (p 10(-5), Mann-Whitney U Test), and an increased relative abundance of mitochondrial (10.7x, p 10(-5)) and microbial cfDNA (71.3x, p 10(-5)). The higher yield of microbial sequences from this method increases the sensitivity of cfDNA-based monitoring for infections following transplantation. We detail the fragmentation pattern of mitochondrial, nuclear genomic and microbial cfDNA over a broad fragment length range. We report the observation of donor-specific mitochondrial cfDNA in the circulation of lung transplant recipients. A ssDNA library preparation method provides a more informative window into understudied forms of cfDNA, including mitochondrial and microbial derived cfDNA and short nuclear genomic cfDNA, while retaining information provided by standard dsDNA library preparation methods.
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