ArticleBMC research notes2015
Tools for translational epigenetic studies involving formalin-fixed paraffin-embedded human tissue: applying the Infinium HumanMethyation450 Beadchip assay to large population-based studies.
Article in BMC research notes, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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15 citing papers in PubMed.
- Quality control checkpoints for high throughput DNA methylation measurement using the human MethylationEPICv1 array: application to formalin-fixed paraffin embedded prostate tissue.BMC research notes · 2025Article
- Breast tumors from ATM pathogenic variant carriers display a specific genome-wide DNA methylation profile.Breast cancer research : BCR · 2025Article
- Evaluation of agreement between common clustering strategies for DNA methylation-based subtyping of breast tumours.Epigenomics · 2025Article
- Tumour DNA methylation markers associated with breast cancer survival: a replication study.Breast cancer research : BCR · 2025Article
- Detection of differentially methylated CpGs between tumour and adjacent benign cells in diagnostic prostate cancer samples.Scientific reports · 2024Article
- Repeatability of methylation measures using a QIAseq targeted methyl panel and comparison with the Illumina HumanMethylation450 assay.BMC research notes · 2021Article
- Article
- Association of variably methylated tumour DNA regions with overall survival for invasive lobular breast cancer.Clinical epigenetics · 2021Article
- Integrating DNA methylation measures to improve clinical risk assessment: are we there yet? The case of BRCA1 methylation marks to improve clinical risk assessment of breast cancer.British journal of cancer · 2020Review
- DNA methylation genome-wide analysis in remnant and primary gastric cancers.Gastric cancer : official journal of the International Gastric Cancer Association and the Japanese Gastric Cancer Association · 2019Article
- Genome-wide DNA methylation assessment of 'BRCA1-like' early-onset breast cancer: Data from the Australian Breast Cancer Family Registry.Experimental and molecular pathology · 2018Article
- Genetic Research Using Archival Tissue: Ethical, Social, and Legal Considerations in the United Arab Emirates.Asian bioethics review · 2018Article
- Heritable DNA methylation marks associated with susceptibility to breast cancer.Nature communications · 2018Article
- Assessment of concordance between fresh-frozen and formalin-fixed paraffin embedded tumor DNA methylation using a targeted sequencing approach.Oncotarget · 2017Article
- Methylation of Breast Cancer Predisposition Genes in Early-Onset Breast Cancer: Australian Breast Cancer Family Registry.PloS one · 2016Article
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11 authors.
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Abstract
backgroundLarge population-based translational epigenetic studies are emerging due to recent technological advances that have made molecular analyses possible. For example, the Infinium HumanMethylation450 Beadchip (HM450K) has enabled studies of genome-wide methylation on a scale not previously possible. However, application of the HM450K to DNA extracted from formalin-fixed paraffin-embedded (FFPE) tumour material has been more challenging than application to high quality DNA extracted from blood. To facilitate the application of this assay consistently across a large number of FFPE tumour-enriched DNA samples we have devised a modification to the HM450K protocol for FFPE that includes an additional quality control (QC) checkpoint.
resultsQC checkpoint 3 was designed to assess the presence of DNA after bisulfite conversion and restoration, just prior to application of the HM450K assay. DNA was extracted from 474 archival FFPE breast tumour material. Five samples did not have a detectable amount of DNA with an additional 42 failing to progress past QC checkpoint 3. Genome-wide methylation was measured for the remaining 428 tumour-enriched DNA. Of these, only 4 samples failed our stringent HM450K data criteria thus representing a 99% success rate. Using prior knowledge about methylation marks associated with breast cancer we further explored the quality of the data. Twenty probes in the BRCA1 promoter region showed increased methylation in triple-negative breast cancers compared to Luminal A, Luminal B and HER2-positive breast cancer subtypes. Validation of this observation in published data from The Cancer Genome Atlas (TCGA) Network (obtained from DNA extracted from fresh frozen tumour samples) confirms the quality of the data obtained from the improved protocol.
conclusionsThe modified protocol is suitable for the analysis of FFPE tumour-enriched DNA and can be systematically applied to hundreds of samples. This protocol will have utility in population-based translational epigenetic studies and is applicable to a wide variety of translated studies interested in analysis of methylation and its role in the predisposition to disease and disease progression.
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