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Article
Open AccessCritical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling
In recent years the Illumina HumanMethylation450 (HM450) BeadChip has provided a user-friendly platform to profile DNA methylation in human samples. However, HM450 lacked coverage of distal regulatory elements...
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Article
Open AccessDNA methylation profile of triple negative breast cancer-specific genes comparing lymph node positive patients to lymph node negative patients
Triple negative breast cancer (TNBC) is the most aggressive breast cancer subtype with no targeted treatment available. Our previous study identified 38 TNBC-specific genes with altered expression comparing tu...
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Article
Open AccessGenome-scale methylation assessment did not identify prognostic biomarkers in oral tongue carcinomas
DNA methylation profiling of heterogeneous head and neck squamous cell carcinoma (HNSCC) cohorts has been reported to predict patient outcome. We investigated if a prognostic DNA methylation profile could be f...
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Protocol
Nucleotide-Level Profiling of m5C RNA Methylation
Map** the position and quantifying the level of 5-methylcytosine (m5C) as a modification in different types of cellular RNA is an important objective in the emerging field of epitranscriptomics. Bisulfite conve...
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Article
Open AccessDNA methylation of oestrogen-regulated enhancers defines endocrine sensitivity in breast cancer
Expression of oestrogen receptor (ESR1) determines whether a breast cancer patient receives endocrine therapy, but does not guarantee patient response. The molecular factors that define endocrine response in E...
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Article
Open AccessMicroRNA profiling of the pubertal mouse mammary gland identifies miR-184 as a candidate breast tumour suppressor gene
The study of mammalian development has offered many insights into the molecular aetiology of cancer. We previously used analysis of mammary morphogenesis to discover a critical role for GATA-3 in mammary devel...
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Article
Open AccessCoordinated epigenetic remodelling of transcriptional networks occurs during early breast carcinogenesis
Dysregulation of the epigenome is a common event in malignancy; however, deciphering the earliest cancer-associated epigenetic events remains a challenge. Cancer epigenome studies to date have primarily utilis...
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Article
Methylome sequencing in triple-negative breast cancer reveals distinct methylation clusters with prognostic value
Epigenetic alterations in the cancer methylome are common in breast cancer and provide novel options for tumour stratification. Here, we perform whole-genome methylation capture sequencing on small amounts of ...
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Article
Open AccessDe novo identification of differentially methylated regions in the human genome
The identification and characterisation of differentially methylated regions (DMRs) between phenotypes in the human genome is of prime interest in epigenetics. We present a novel method, DMRcate, that fits replic...
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Article
Open AccessProfiling the tyrosine phosphoproteome of different mouse mammary tumour models reveals distinct, model-specific signalling networks and conserved oncogenic pathways
Although aberrant tyrosine kinase signalling characterises particular breast cancer subtypes, a global analysis of tyrosine phosphorylation in mouse models of breast cancer has not been undertaken to date. Thi...
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Article
Open AccessMethylation-capture and Next-Generation Sequencing of free circulating DNA from human plasma
Free circulating DNA (fcDNA) has many potential clinical applications, due to the non-invasive way in which it is collected. However, because of the low concentration of fcDNA in blood, genome-wide analysis ca...
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Article
Open AccessBayMeth: improved DNA methylation quantification for affinity capture sequencing data using a flexible Bayesian approach
Affinity capture of DNA methylation combined with high-throughput sequencing strikes a good balance between the high cost of whole genome bisulfite sequencing and the low coverage of methylation arrays. We pre...
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Article
Open AccessZNF300P1 Encodes a lincRNA that regulates cell polarity and is epigenetically silenced in type II epithelial ovarian cancer
We previously identified that the CpG island-associated promoter of the novel lincRNA ZNF300P1 (also known as LOC134466) is frequently hypermethylated and silenced in ovarian cancer tissues. However, the function...
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Article
Epigenome remodelling in breast cancer: insights from an early in vitro model of carcinogenesis
Epigenetic gene regulation has influence over a diverse range of cellular functions, including the maintenance of pluripotency, differentiation, and cellular identity, and is deregulated in many diseases, incl...
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Article
Open AccessAndrogen receptor expression predicts breast cancer survival: the role of genetic and epigenetic events
Breast cancer outcome, including response to therapy, risk of metastasis and survival, is difficult to predict using currently available methods, highlighting the urgent need for more informative biomarkers. A...
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Article
Open AccessDiscovery pipeline for epigenetically deregulated miRNAs in cancer: integration of primary miRNA transcription
Cancer is commonly associated with widespread disruption of DNA methylation, chromatin modification and miRNA expression. In this study, we established a robust discovery pipeline to identify epigenetically de...
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Article
Consolidation of the cancer genome into domains of repressive chromatin by long-range epigenetic silencing (LRES) reduces transcriptional plasticity
A prostate cancer epigenome map reveals that genes are suppressed in clusters through long-range epigenetic silencing (LRES). Regions of LRES contain known tumour suppressors and miRNAs, and may expand to neig...
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Article
Breast cancer epigenetics: normal human mammary epithelial cells as a model system
DNA hypermethylation and histone modifications are two critical players involved in epigenetic regulation and together play an important role in silencing tumor-suppressor genes in all cancers, including breas...
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Article
Open AccessEpigenetic and phenotypic changes result from a continuous pre and post natal dietary exposure to phytoestrogens in an experimental population of mice
Developmental effects of exposure to endocrine disruptors can influence adult characters in mammals, but could also have evolutionary consequences. The aim of this study was to simulate an environmental exposu...
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Chapter and Conference Paper
Epigenetic Markers of Ovarian Cancer
Ovarian cancer is the fourth leading cause of cancer death in women, and has the highest mortality rate of the reproductive cancers (1). Ovarian cancer is often asymptomatic in its early stages and because of ...
