ArticleEpigenetics2018
Droplet digital PCR is an accurate method to assess methylation status on FFPE samples.
Article in Epigenetics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 58 citations in OpenAlex.
- Article
- DNA Methylation in Gastric Cancer and Preneoplastic Lesions: Emerging Insights and Future Directions.Cancers · 2026Review
- Prognostic Potential of Cancer-Associated Fibroblast Surface Markers and Their Specific DNA Methylation in Prostate Cancer.Diagnostics (Basel, Switzerland) · 2025Article
- Personalized medicine for cardiovascular diseases: how next generation epigenetic technologies can contribute?Epigenomics · 2025Review
- Recent advances on gene-related DNA methylation in cancer diagnosis, prognosis, and treatment: a clinical perspective.Clinical epigenetics · 2025Review
- Heightened IDO1 levels predict Bacillus Calmette-Guèrin failure in high-risk non-muscle-invasive bladder cancer patients.Cell death discovery · 2025Article
- Plasma DNA Methylation-Based Biomarkers for MPNST Detection in Patients With Neurofibromatosis Type 1.Molecular carcinogenesis · 2025Article
- DNA Methylation in Prostate Cancer: Clinical Implications and Potential Applications.Cancer medicine · 2025Review
- Epigenetic Biomarker: Improving Estimates of Fetal Exposure to Cigarette Smoke.Environmental health perspectives · 2024Article
- Methylation‑sensitive restriction enzyme‑droplet digital PCR assay for the one‑step highly sensitive analysis of DNA methylation hotspots.International journal of molecular medicine · 2024Article
- Evaluation of DNA methylation levels ofOncology reports · 2024Article
- First-time application of droplet digital PCR for methylation testing of the 11p15.5 imprinting regions.Molecular genetics & genomic medicine · 2023Article
- Circulating NPTX2 methylation as a non-invasive biomarker for prognosis and monitoring of metastatic pancreatic cancer.Clinical epigenetics · 2023Article
- Novel DNA Methylation Biomarker Panel for Detection of Esophageal Adenocarcinoma and High-Grade Dysplasia.Clinical cancer research : an official journal of the American Association for Cancer Research · 2022Article
- AhRR methylation contributes to disease progression in urothelial bladder cancer.Cancer biomarkers : section A of Disease markers · 2022Article
- The utility of cfDNA in TGCT patient management: a systematic review.Therapeutic advances in medical oncology · 2022Review
- Application of droplet digital polymerase chain reaction of plasma methylated septin 9 on detection and early monitoring of colorectal cancer.Scientific reports · 2021Article
- Circulating tumour DNA methylation in hepatocellular carcinoma diagnosis using digital droplet PCR.The Journal of international medical research · 2021Article
- Comparison of Bisulfite Pyrosequencing and Methylation-Specific qPCR for Methylation Assessment.International journal of molecular sciences · 2020Article
- New targeted approaches for epigenetic age predictions.BMC biology · 2020Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Most tissue samples available for cancer research are archived as formalin-fixed paraffin-embedded (FFPE) samples. However, the fixation process and the long storage duration lead to DNA fragmentation and hinder epigenome analysis. The use of droplet digital PCR (ddPCR) to detect DNA methylation has recently emerged. In this study, we compare an optimized ddPCR assay with a conventional qPCR assay by targeting a dilution series of control DNA. In addition, we compare the ddPCR technology with results from Infinium arrays targeting two separate CpG sites on a set of colon adenoma FFPE samples. Our data demonstrate that qPCR and ddPCR assess methylation status equally well on dilution controls with a high DNA input. However, the methylation detection on low-input samples is more accurate using ddPCR. The proposed primer design (methylation-independent primers with amplification of solely the converted DNA target) will allow for methylation detection, independent of bisulfite conversion efficiency. Those data show that ddPCR can be used for methylation analysis on FFPE samples with a wide range of DNA input and that the precision of the assay depends largely on the total amount of amplifiable DNA fragments. Due to accessibility of the ddPCR technology and its accuracy on high- as well as low-DNA input samples, we propose the use of this approach for studies involving degraded FFPE samples.
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