ArticleMicrobiome2020
Separating the signal from the noise in metagenomic cell-free DNA sequencing.
Article in Microbiome, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed, 51 citations in OpenAlex.
- Reappraising the topology of cell-free fetal DNA in maternal blood toward improved prenatal genetic diagnostics.Science advances · 2026Review
- Intra-amniotic infection: diagnosis, nomenclature, clinical significance, management, and microbiologic tools used for the diagnosis.Clinical microbiology reviews · 2026Review
- Characteristics, Epigenetics, and Management of Non-Infectious Preterm Birth-Sterile Intrauterine Inflammation and Idiopathic Preterm Birth.Life (Basel, Switzerland) · 2026Review
- Metagenomic Cell-free DNA Sequencing for Treatment Monitoring in Sepsis.Research square · 2025Article
- In-matrix library preparation for metagenomic sequencing of microbial cell-free DNA.Journal of clinical microbiology · 2025Article
- Fragment end motif analysis to distinguish pathogens from contaminants in enriched plasma microbial DNA.medRxiv : the preprint server for health sciences · 2025Article
- Identification of bacteriophage DNA in human umbilical cord blood.JCI insight · 2025Article
- Cell-free placental DNA: What do we really know?PLoS genetics · 2024Review
- Homeostatic Macrophages Prevent Preterm Birth and Improve Neonatal Outcomes by Mitigating In Utero Sterile Inflammation in Mice.Journal of immunology (Baltimore, Md. : 1950) · 2024Article
- Plasma cell-free RNA signatures of inflammatory syndromes in children.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Systematic biases in reference-based plasma cell-free DNA fragmentomic profiling.Cell reports methods · 2024Article
- A quantitative comparison of urine centrifugation and filtration for the isolation and analysis of urinary nucleic acid biomarkers.Scientific reports · 2024Article
- Clinical chorioamnionitis at term: definition, pathogenesis, microbiology, diagnosis, and treatment.American journal of obstetrics and gynecology · 2024Review
- Article
- Blockade of IL-6R prevents preterm birth and adverse neonatal outcomes.EBioMedicine · 2023Article
- A key role for NLRP3 signaling in preterm labor and birth driven by the alarmin S100B.Translational research : the journal of laboratory and clinical medicine · 2023Article
- Noninvasive Prenatal Testing Using Circulating DNA and RNA: Advances, Challenges, and Possibilities.Annual review of biomedical data science · 2023Review
- A single-cell atlas of murine reproductive tissues during preterm labor.Cell reports · 2023Article
- Background Filtering of Clinical Metagenomic Sequencing with a Library Concentration-Normalized Model.Microbiology spectrum · 2022Article
- Species abundance correlations carry limited information about microbial network interactions.PLoS computational biology · 2022Article
Corrections and comments
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Authors and funding
10 authors at 3 institutions in 1 country.
Funding
Abstract
backgroundCell-free DNA (cfDNA) in blood, urine, and other biofluids provides a unique window into human health. A proportion of cfDNA is derived from bacteria and viruses, creating opportunities for the diagnosis of infection via metagenomic sequencing. The total biomass of microbial-derived cfDNA in clinical isolates is low, which makes metagenomic cfDNA sequencing susceptible to contamination and alignment noise.
resultsHere, we report low biomass background correction (LBBC), a bioinformatics noise filtering tool informed by the uniformity of the coverage of microbial genomes and the batch variation in the absolute abundance of microbial cfDNA. We demonstrate that LBBC leads to a dramatic reduction in false positive rate while minimally affecting the true positive rate for a cfDNA test to screen for urinary tract infection. We next performed high-throughput sequencing of cfDNA in amniotic fluid collected from term uncomplicated pregnancies or those complicated with clinical chorioamnionitis with and without intra-amniotic infection.
conclusionsThe data provide unique insight into the properties of fetal and maternal cfDNA in amniotic fluid, demonstrate the utility of cfDNA to screen for intra-amniotic infection, support the view that the amniotic fluid is sterile during normal pregnancy, and reveal cases of intra-amniotic inflammation without infection at term. Video abstract.
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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.