ArticleClinical epigenetics2022
Technical considerations in PCR-based assay design for diagnostic DNA methylation cancer biomarkers.
Article in Clinical epigenetics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- From DNA Methylation Microarray to Digital PCR: A Stepwise Strategy for Tissue Specific cfDNA Biomarker Development.Journal of clinical laboratory analysis · 2026Article
- Impact of Heterogeneous DNA Methylation on the Accuracy of Quantitative Methylation-Specific PCR for Detecting DNA Hypermethylation in Prostate Cancer.International journal of molecular sciences · 2026Article
- The diagnostic value of the liquid biopsy in the colon cancer.Future science OA · 2025Review
- Epigenetic modulation of VEGF-A/VEGFR2 pathway genes in OC/TME axis driving genetic upregulation and tumor plasticity.Scientific reports · 2025Article
- Unlocking the potential of tumor-derived DNA in urine for cancer detection: methodological challenges and opportunities.Molecular oncology · 2025Review
- Advances in the diagnosis of colorectal cancer: the application of molecular biomarkers and imaging techniques: a literature review.Annals of medicine and surgery (2012) · 2025Review
- Effectiveness of single-target fecal DNA methylation test in regional mass screening for colorectal cancer and precancerous lesions in China.Gastroenterology report · 2025Article
- Clinical promise and applications of epigenetic biomarkers.Clinical epigenetics · 2024Article
- Interlaboratory consistency ofiScience · 2024Article
- Advances in blood DNA methylation-based assay for colorectal cancer early detection: a systematic updated review.Gastroenterology and hepatology from bed to bench · 2024Review
- Combined detection of SDC2/ADHFE1/PPP2R5C methylation in stool DNA for colorectal cancer screening.Journal of cancer research and clinical oncology · 2023Article
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundDNA methylation biomarkers for early detection, risk stratification and treatment response in cancer have been of great interest over the past decades. Nevertheless, clinical implementation of these biomarkers is limited, as only < 1% of the identified biomarkers is translated into a clinical or commercial setting. Technical factors such as a suboptimal genomic location of the assay and inefficient primer or probe design have been emphasized as important pitfalls in biomarker research. Here, we use eleven diagnostic DNA methylation biomarkers for colorectal cancer (ALX4, APC, CDKN2A, MGMT, MLH1, NDRG4, SDC2, SFRP1, SFRP2, TFPI1 and VIM), previously described in a systematic literature search, to evaluate these pitfalls.
resultsTo assess the genomic assay location, the optimal genomic locations according to TCGA data were extracted and compared to the genomic locations used in the published assays for all eleven biomarkers. In addition, all primers and probes were technically evaluated according to several criteria, based on literature and expert opinion. Both assay location and assay design quality varied widely among studies.
conclusionsLarge variation in both assay location and design hinders the development of future DNA methylation biomarkers as well as inter-study comparability.
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