A Droplet Digital PCR Approach for the Quantitative Detection of Fusobacterium nucleatum in Formaldehyde-Fixed, Paraffin-Embedded Tumor Tissues.

Orsalem Kahsai, Amanda I Phipps, Polly A Newcomb, Meredith A J Hullar

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Article in Methods in molecular biology (Clifton, N.J.), 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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Authors and funding

4 authors.

Orsalem KahsaiCancer Prevention, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.

Amanda I PhippsEpidemiology, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.

Polly A NewcombCancer Prevention, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.

Meredith A J HullarCancer Prevention, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA. mhullar@fredhutch.org.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Fusobacterium nucleatum, a prevalent component of the intratumoral microbiome, has been associated with reduced survival in colorectal cancer. To enable sensitive and specific detection of F. nucleatum in tumor specimens, we developed a droplet digital PCR (ddPCR) assay targeting the transcription termination/anti-termination gene nusG, normalized to host tissue content using the solute carrier organic anion transporter family member 2A1 gene, SLCO2A1. Here, we present a ddPCR protocol optimized for quantifying F. nucleatum DNA in human genomic DNA extracted from formalin-fixed, paraffin-embedded (FFPE) tumor tissues. This methodology has been refined for high-throughput application, supporting large-scale analyses of F. nucleatum prevalence in tumor samples.

Indexed as

Colorectal NeoplasmsFusobacterium InfectionsFusobacterium nucleatumPolymerase Chain ReactionDNA, BacterialFormaldehydeHumansParaffin EmbeddingTissue FixationDNA, BacterialFormaldehydeCRCDigital droplet PCR (ddPCR) quantitationFusobacterium nucleatum animalisIntratumoral microbiomeTumor microenvironment

Identifiers

PMID42613561

DOI10.1016/j.meegid.2014.03.028

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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.