Tools for translational epigenetic studies involving formalin-fixed paraffin-embedded human tissue: applying the Infinium HumanMethyation450 Beadchip assay to large population-based studies

Wong, Ee Ming; Joo, Ji Hoon Eric; McLean, Catriona; Baglietto, Laura; English, Dallas R.; Severi, Gianluca; Hopper, John L.; Milne, Roger L.; FitzGerald, Liesel M.; Giles, Graham G.; Southey, Melissa C.

doi:10.1186/s13104-015-1487-z

Cited by 17 publications

(19 citation statements)

References 24 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The identified tumor-enriched tissue was macrodissected from between two to ten Methyl Green stained sections per tumor using both a scalpel (Swann-Morton, Sheffield, England) and a 21-guage syringe needle (Terumo, Tokyo, Japan), as previously described [28]. DNA was extracted using the QIAamp DNA FFPE Tissue Kit as per the manufacturer’s protocol (Qiagen; Hilden, Germany), varied only by an extended tissue incubation time of 48 hours with 20μl of Proteinase K (20mg/ml) replenished at 0 and 24 hours.…”

Section: Methodsmentioning

confidence: 99%

Methylation of Breast Cancer Predisposition Genes in Early-Onset Breast Cancer: Australian Breast Cancer Family Registry

et al. 2016

Self Cite

View full text Add to dashboard Cite

DNA methylation can mimic the effects of both germline and somatic mutations for cancer predisposition genes such as BRCA1 and p16INK4a. Constitutional DNA methylation of the BRCA1 promoter has been well described and is associated with an increased risk of early-onset breast cancers that have BRCA1-mutation associated histological features. The role of methylation in the context of other breast cancer predisposition genes has been less well studied and often with conflicting or ambiguous outcomes. We examined the role of methylation in known breast cancer susceptibility genes in breast cancer predisposition and tumor development. We applied the Infinium HumanMethylation450 Beadchip (HM450K) array to blood and tumor-derived DNA from 43 women diagnosed with breast cancer before the age of 40 years and measured the methylation profiles across promoter regions of BRCA1, BRCA2, ATM, PALB2, CDH1, TP53, FANCM, CHEK2, MLH1, MSH2, MSH6 and PMS2. Prior genetic testing had demonstrated that these women did not carry a germline mutation in BRCA1, ATM, CHEK2, PALB2, TP53, BRCA2, CDH1 or FANCM. In addition to the BRCA1 promoter region, this work identified regions with variable methylation at multiple breast cancer susceptibility genes including PALB2 and MLH1. Methylation at the region of MLH1 in these breast cancers was not associated with microsatellite instability. This work informs future studies of the role of methylation in breast cancer susceptibility gene silencing.

show abstract

Section: Methodsmentioning

confidence: 99%

Methylation of Breast Cancer Predisposition Genes in Early-Onset Breast Cancer: Australian Breast Cancer Family Registry

et al. 2016

Self Cite

View full text Add to dashboard Cite

show abstract

“…Our training cohort consisted of 35 PGC samples and 13 RGC samples which were analyzed using the Infinium HumanMethylation450 Beadchip assay which allows the assessment of the methylation status of over 450,000 CpGs throughout the genome. The Infinium HumanMethyla-tion450 Beadchip assay (Illumina, San Diego, CA, USA) was performed in the Johns Hopkins University DNA Microarray Core according to the manufacturer's instructions specific for formalin-fixed embedded material [27]. Locus methylation was calculated as a β value using GenomeStudio software with the low to high ranging from 0 to 1, respectively.…”

Section: Infinium Humanmethylation450 Beadchip Assaymentioning

confidence: 99%

DNA methylation genome-wide analysis in remnant and primary gastric cancers

et al. 2019

View full text Add to dashboard Cite

Background Although primary (PGC) and remnant gastric cancers (RGC) both originate from the same gastrointestinal organ, they have very distinct clinicopathological behaviors. We hypothesized that there would be distinct differences in DNA methylation patterns that would occur during carcinogenesis of RGC and PGC, and that the differences in methylation patterns may help identify the primary factor contributing to chronic inflammation in patients with RGC. Methods We investigated the genome-wide DNA methylation patterns of PGC and RGC tissues from 48 patients using the Infinium HumanMethylation450 Beadchip assay. The results were validated by quantitative methylation-specific PCR (qMSP) in separate, independent cohorts. Results We found that in our training cohort of 48 patients, the most variable genes from the gastric cancer tissues identified by the Infinium HumanMethylation450 Beadchip clustered the resultant heatmap into high and low methylation groups. On multivariate analysis, PGCs contributed significantly to the high methylation group (p = 0.004, OR 12.33), which suggested that the promoter methylation status in PGC is higher than that in RGC. Supporting this conclusion was the finding that in a separate qMSP analysis in a test cohort, the EPB41L3 gene, chosen because of its high β value on microarray analysis in the gastric cancer tissues, had significantly higher DNA promoter methylation in cancer tissues in the validation PGC tissues than in RGC. Conclusions This study demonstrated that promoter methylation status in PGC is higher than in RGC. This result may reflect the effects of the absence of Helicobacter pylori on the reduced DNA methylation in the remnant stomach.

show abstract

“…39,40 Our experience with the Infinium HumanMethylation450 BeadChip array, which has been validated using TCGA data, showed that the CpG island (Chromosome17: 41278135-41278459) is highly methylated in blood-derived DNA from both affected and unaffected women and lacks variability between individuals. 41,42 Therefore, DNA methylation assessment of this invariant region is likely to be uninformative and, indeed, no differences in BRCA1 DNA methylation levels were observed in this region between cases and controls irrespective of their BRCA1 or BRCA2 mutation status. 39,40 Ziller et al 43 found that DNA methylation levels across the intermediate and low CpG density promoters and transcription start sites, rather than the CpG islands, are dynamic and variable between individuals.…”

Section: Dna Methylation: Methodology and Measurementmentioning

confidence: 99%

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

2020

Self Cite

View full text Add to dashboard Cite

Current risk prediction models estimate the probability of developing breast cancer over a defined period based on information such as family history, non-genetic breast cancer risk factors, genetic information from high and moderate risk breast cancer susceptibility genes and, over the past several years, polygenic risk scores (PRS) from more than 300 common variants. The inclusion of additional data such as PRS improves risk stratification, but it is anticipated that the inclusion of epigenetic marks could further improve model performance accuracy. Here, we present the case for including information on DNA methylation marks to improve the accuracy of these risk prediction models, and consider how this approach contrasts genetic information, as identifying DNA methylation marks associated with breast cancer risk differs inherently according to the source of DNA, approaches to the measurement of DNA methylation, and the timing of measurement. We highlight several DNA-methylation-specific challenges that should be considered when incorporating information on DNA methylation marks into risk prediction models, using BRCA1, a highly penetrant breast cancer susceptibility gene, as an example. Only after careful consideration of study design and DNA methylation measurement will prospective performance of the incorporation of information regarding DNA methylation marks into risk prediction models be valid.

show abstract

Tools for translational epigenetic studies involving formalin-fixed paraffin-embedded human tissue: applying the Infinium HumanMethyation450 Beadchip assay to large population-based studies

Cited by 17 publications

References 24 publications

Methylation of Breast Cancer Predisposition Genes in Early-Onset Breast Cancer: Australian Breast Cancer Family Registry

Methylation of Breast Cancer Predisposition Genes in Early-Onset Breast Cancer: Australian Breast Cancer Family Registry

DNA methylation genome-wide analysis in remnant and primary gastric cancers

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

Contact Info

Product

Resources

About