ArticleLaboratory investigation; a journal of technical methods and pathology2015
Formalin-fixed, paraffin-embedded (FFPE) tissue epigenomics using Infinium HumanMethylation450 BeadChip assays.
Article in Laboratory investigation; a journal of technical methods and pathology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers, 1 of them a synthesis that pooled it.
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Who cites it
29 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Different definitions of CpG island methylator phenotype and outcomes of colorectal cancer: a systematic review.Clinical epigenetics · 2016Pooled it
- DNA Quantity and Quality Comparisons between Cryopreserved and FFPE Tumors from Matched Pan-Cancer Samples.Current oncology (Toronto, Ont.) · 2024Article
- The Impact of Inherited Genetic Variation on DNA Methylation in Prostate Cancer and Benign Tissues of African American and European American Men.Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology · 2024Article
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- The Role of theBiomedicines · 2023Article
- A Guide to MethylationToActivity: A Deep Learning Framework That Reveals Promoter Activity Landscapes from DNA Methylomes in Individual Tumors.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Epigenome-Wide DNA Methylation Profiling of Normal Mucosa Reveals HLA-F Hypermethylation as a Biomarker Candidate for Serrated Polyposis Syndrome.The Journal of molecular diagnostics : JMD · 2022Article
- Genome-wide DNA methylation patterns reveal clinically relevant predictive and prognostic subtypes in human osteosarcoma.Communications biology · 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
- DNA methylation methods: Global DNA methylation and methylomic analyses.Methods (San Diego, Calif.) · 2021Review
- MethCORR infers gene expression from DNA methylation and allows molecular analysis of ten common cancer types using fresh-frozen and formalin-fixed paraffin-embedded tumor samples.Clinical epigenetics · 2021Article
- MethylationToActivity: a deep-learning framework that reveals promoter activity landscapes from DNA methylomes in individual tumors.Genome biology · 2021Article
- Genome wide methylation profiling of selected matched soft tissue sarcomas identifies methylation changes in metastatic and recurrent disease.Scientific reports · 2021Article
- High yield gold nanoparticle-based DNA isolation method for human papillomaviruses genotypes from cervical cancer tissue samples.IET nanobiotechnology · 2020Article
- Review
- MethCORR modelling of methylomes from formalin-fixed paraffin-embedded tissue enables characterization and prognostication of colorectal cancer.Nature communications · 2020Article
- Molecular Classification of Epithelial Ovarian Cancer Based on Methylation Profiling: Evidence for Survival Heterogeneity.Clinical cancer research : an official journal of the American Association for Cancer Research · 2019Article
- The frequency of promoter DNA hypermethylation is decreased in colorectal neoplasms of familial adenomatous polyposis.Oncotarget · 2018Article
- Article
- Evaluating the Feasibility of DNA Methylation Analyses Using Long-Term Archived Brain Formalin-Fixed Paraffin-Embedded Samples.Molecular neurobiology · 2018Article
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Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Current genome-wide methods to detect DNA-methylation in healthy and diseased tissue require high-quality DNA from fresh-frozen (FF) samples. However, well-annotated clinical samples are mostly available as formalin-fixed, paraffin-embedded (FFPE) tissues containing poor-quality DNA. To overcome this limitation, we here aimed to evaluate a DNA restoration protocol for usage with the genome-wide Infinium HumanMethylation450 BeadChip assay (HM-450K). Sixty-six DNA samples from normal colon (n=9) and breast cancer (n=11) were interrogated separately using HM-450K. Analyses included matched FF/FFPE samples and technical duplicates. FFPE DNA was processed with (FFPEr) or without a DNA restoration protocol (Illumina). Differentially methylated genes were finally validated in 24 additional FFPE tissues using nested methylation-specific PCR (MSP). In summary, β-values correlation between FFPEr duplicates was high (ρ=0.9927 (s.d. ±0.0015)). Matched FF/FFPEr correlation was also high (ρ=0.9590 (s.d. ±0.0184)) compared with matched FF/FFPE (ρ=0.8051 (s.d. ±0.1028). Probe detection rate in FFPEr samples (98.37%, s.d. ±0.66) was comparable to FF samples (99.98%, s.d. ±0.019) and substantially lower in FFPE samples (82.31%, s.d. ±18.65). Assay robustness was not decreased by sample archival age up to 10 years. We could also demonstrate no decrease in assay robustness when using 100 ng of DNA input only. Four out of the five selected differentially methylated genes could be validated by MSP. The gene failing validation by PCR showed high variation of CpG β-values in primer-binding sites. In conclusion, by using the FFPE DNA restoration protocol, HM-450K assays provide robust, accurate and reproducible results with FFPE tissue-derived DNA, which are comparable to those obtained with FF tissue. Most importantly, differentially methylated genes can be validated using more sensitive techniques, such as nested MSP, altogether providing an epigenomics platform for molecular pathological epidemiology research on archived samples with limited tissue amount.
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