ArticleBMC medical genomics2017
A streamlined method for analysing genome-wide DNA methylation patterns from low amounts of FFPE DNA.
Article in BMC medical genomics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 28 citations in OpenAlex.
- Epigenetic Profiling for Early Detection and Treatment Response Monitoring in Non-Small Cell Lung Cancer: Protocol for a Prospective Translational Biomarker Study.JMIR research protocols · 2026Article
- Precision Medicine Study of Post-Exertional Malaise Epigenetic Changes in Myalgic Encephalomyelitis/Chronic Fatigue Patients During Exercise.International journal of molecular sciences · 2025Article
- Optimization of methylation capture sequencing workflow in formalin fixed tissue from oral squamous cell carcinoma patients.Oral oncology · 2025Article
- Comparing DNA Methylation Landscapes in Peripheral Blood from Myalgic Encephalomyelitis/Chronic Fatigue Syndrome and Long COVID Patients.International journal of molecular sciences · 2025Article
- Fast and efficient method for parallel construction of targeted exome and methylome single-stranded DNA sequencing libraries.Scientific reports · 2025Article
- Dynamic Epigenetic Changes during a Relapse and Recovery Cycle in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome.International journal of molecular sciences · 2022Article
- Heat selection enables highly scalable methylome profiling in cell-free DNA for noninvasive monitoring of cancer patients.Science advances · 2022Article
- A panel of DNA methylation markers for the classification of consensus molecular subtypes 2 and 3 in patients with colorectal cancer.Molecular oncology · 2021Article
- The Mouse Papillomavirus Epigenetic Signature Is Characterised by DNA Hypermethylation after Lesion Regression.Viruses · 2021Article
- Genome wide DNA methylation analysis of alveolar capillary dysplasia lung tissue reveals aberrant methylation of genes involved in development including the FOXF1 locus.Clinical epigenetics · 2021Article
- Comparison of Global DNA Methylation Patterns in Human Melanoma Tissues and Their Derivative Cell Lines.Cancers · 2021Article
- Evaluation of clinical formalin-fixed paraffin-embedded tissue quality for targeted-bisulfite sequencing.Pathology international · 2021Article
- Impact of DNA integrity on the success rate of tissue-based next-generation sequencing: Lessons from nationwide cancer genome screening project SCRUM-Japan GI-SCREEN.Pathology international · 2020Article
- Changes in DNA methylation profiles of myalgic encephalomyelitis/chronic fatigue syndrome patients reflect systemic dysfunctions.Clinical epigenetics · 2020Article
- Next-generation sequencing of residual cytologic fixative preserved DNA from pancreatic lesions: A pilot study.Cancer cytopathology · 2020Article
- Formalin-Fixed Paraffin-Embedded Tissues-An Untapped Biospecimen for Biomonitoring DNA Adducts by Mass Spectrometry.Toxics · 2018Review
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundFormalin fixed paraffin embedded (FFPE) tumor samples are a major source of DNA from patients in cancer research. However, FFPE is a challenging material to work with due to macromolecular fragmentation and nucleic acid crosslinking. FFPE tissue particularly possesses challenges for methylation analysis and for preparing sequencing-based libraries relying on bisulfite conversion. Successful bisulfite conversion is a key requirement for sequencing-based methylation analysis.
methodsHere we describe a complete and streamlined workflow for preparing next generation sequencing libraries for methylation analysis from FFPE tissues. This includes, counting cells from FFPE blocks and extracting DNA from FFPE slides, testing bisulfite conversion efficiency with a polymerase chain reaction (PCR) based test, preparing reduced representation bisulfite sequencing libraries and massively parallel sequencing.
resultsThe main features and advantages of this protocol are: An optimized method for extracting good quality DNA from FFPE tissues. An efficient bisulfite conversion and next generation sequencing library preparation protocol that uses 50 ng DNA from FFPE tissue. Incorporation of a PCR-based test to assess bisulfite conversion efficiency prior to sequencing.
conclusionsWe provide a complete workflow and an integrated protocol for performing DNA methylation analysis at the genome-scale and we believe this will facilitate clinical epigenetic research that involves the use of FFPE tissue.
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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.