ArticleScientific reports2019
A Pipeline for Faecal Host DNA Analysis by Absolute Quantification of LINE-1 and Mitochondrial Genomic Elements Using ddPCR.
Article in Scientific reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed, 17 citations in OpenAlex.
- Diagnostic performance of LINE-1 repetitive elements in stool DNA for non-invasive detection of colorectal cancer.Clinical & translational oncology : official publication of the Federation of Spanish Oncology Societies and of the National Cancer Institute of Mexico · 2026Article
- Beyond colonoscopy, faecal DNA mutation screening provides a potential and viable path to early colorectal cancer detection.Scientific reports · 2025Article
- Hologenomic analysis of rectal mucus sampling for detection of adenomatous polyps and colorectal cancer.Nature communications · 2025Article
- Comparison of Fecal DNA Extraction Kits for the Giant Panda (Ecology and evolution · 2025Article
- Temporary dietary fiber depletion prompts rapid and lasting gut microbiota restructuring in mice.Microbiology spectrum · 2025Article
- High-throughput, pan-leukocyte biomarkers for the detection of inflammation in human breastmilk and stool.Frontiers in epigenetics and epigenomics · 2025Article
- The standardisation of the approach to metagenomic human gut analysis: from sample collection to microbiome profiling.Scientific reports · 2022Article
- Impact of Preanalytical and Analytical Methods on Cell-Free DNA Diagnostics.Frontiers in cell and developmental biology · 2021Article
- Technical and Methodological Aspects of Cell-Free Nucleic Acids Analyzes.International journal of molecular sciences · 2020Review
Corrections and comments
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Authors and funding
7 authors at 1 institution in 1 country.
Funding
Abstract
Stool contains DNA shed from cells of the gastrointestinal (GI) tract and has great potential as a bio-specimen for non-invasive, nucleic acid-based detection of GI diseases. Whereas methods for studying faecal microbiome DNA are plentiful, there is a lack of well-characterised procedures for stabilisation, isolation, and quantitative analysis of faecal host DNA. We report an optimised pipeline for faecal host DNA analysis from the point-of-collection to droplet digital PCR (ddPCR) absolute quantification of host-specific gene targets. We evaluated multiple methods for preservation and isolation of host DNA from stool to identify the highest performing methods. To quantify host DNA even if present in partially degraded form, we developed sensitive, human-specific short-amplicon ddPCR assays targeting repetitive nuclear genomic elements (LINE-1) and mitochondrial genes. We validated the ability of these optimised methods to perform absolute quantification of host DNA in 200 stool DNA extracts from samples that were serially collected from three healthy individuals and three hospitalised patients. These specimens allowed assessment of host DNA day-to-day variability in stool specimens with widely varying physical characteristics (i.e., Bristol scores). We further extended this approach to mouse stool analysis, to enable faecal host DNA studies in animal disease models as well.
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