DNA methylation profiling in the clinic: applications and challenges

Cancer Epigenetics: From Mechanism to Therapy

(2012) Mark A. Dawson et al.   CELL

DNA methylation profiling identifies epigenetic dysregulation in pancreatic islets from type 2 diabetic patients

(2012) Michael Volkmar et al.   EMBO JOURNAL

IDH1 mutation is sufficient to establish the glioma hypermethylator phenotype

(2012) Sevin Turcan et al.   NATURE

BLUEPRINT to decode the epigenetic signature written in blood

(2012) David Adams et al.   NATURE BIOTECHNOLOGY

Functions of DNA methylation: islands, start sites, gene bodies and beyond

(2012) Peter A. Jones   NATURE REVIEWS GENETICS

TFAP2E–DKK4and Chemoresistance in Colorectal Cancer

(2012) Matthias P.A. Ebert et al.   NEW ENGLAND JOURNAL OF MEDICINE

Distinct DNA methylomes of newborns and centenarians

(2012) H. Heyn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Dynamics and Prognostic Potential of DNA Methylation Changes at Stem Cell Gene Loci in Women's Cancer

(2012) Joanna Zhuang et al.   PLoS Genetics

Septin 9 methylated DNA is a sensitive and specific blood test for colorectal cancer

(2011) Jorja D Warren et al.   BMC Medicine

Measurement of GSTP1 promoter methylation in body fluids may complement PSA screening: a meta-analysis

(2011) T Wu et al.   BRITISH JOURNAL OF CANCER

Selective Killing of Mixed Lineage Leukemia Cells by a Potent Small-Molecule DOT1L Inhibitor

(2011) Scott R. Daigle et al.   CANCER CELL

MLL-Rearranged Leukemia Is Dependent on Aberrant H3K79 Methylation by DOT1L

(2011) Kathrin M. Bernt et al.   CANCER CELL

NID2 and HOXA9 Promoter Hypermethylation as Biomarkers for Prevention and Early Detection in Oral Cavity Squamous Cell Carcinoma Tissues and Saliva

(2011) R. Guerrero-Preston et al.   Cancer Prevention Research

Polo-like Kinase Plk2 Is an Epigenetic Determinant of Chemosensitivity and Clinical Outcomes in Ovarian Cancer

(2011) N. Syed et al.   CANCER RESEARCH

Reference Maps of Human ES and iPS Cell Variation Enable High-Throughput Characterization of Pluripotent Cell Lines

(2011) Christoph Bock et al.   CELL

Tumour and serum MGMT promoter methylation and protein expression in glioblastoma patients

(2011) Carmen Balañá et al.   Clinical & Translational Oncology

Epigenetic Alteration of PRKCDBP in Colorectal Cancers and Its Implication in Tumor Cell Resistance to TNF -Induced Apoptosis

(2011) J.-H. Lee et al.   CLINICAL CANCER RESEARCH

DNA methylation profiling reveals a predominant immune component in breast cancers

(2011) Sarah Dedeurwaerder et al.   EMBO Molecular Medicine

CpG island hypermethylation ofBRCA1and loss of pRb as co-occurring events in basal/triple-negative breast cancer

(2011) Olafur Andri Stefansson et al.   Epigenetics

Validation of a DNA methylation microarray for 450,000 CpG sites in the human genome

(2011) Juan Sandoval et al.   Epigenetics

Next-Generation Stool DNA Test Accurately Detects Colorectal Cancer and Large Adenomas

(2011) David A. Ahlquist et al.   GASTROENTEROLOGY

Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer

(2011) G. C. Hon et al.   GENOME RESEARCH

A DNA methylation fingerprint of 1628 human samples

(2011) A. F. Fernandez et al.   GENOME RESEARCH

Genome-scale analysis of aberrant DNA methylation in colorectal cancer

(2011) T. Hinoue et al.   GENOME RESEARCH

Comparative methylome analysis of benign and malignant peripheral nerve sheath tumors

(2011) A. Feber et al.   GENOME RESEARCH

High density DNA methylation array with single CpG site resolution

(2011) Marina Bibikova et al.   GENOMICS

Twenty years of Alzheimer’s disease-causing mutations

(2011) Alison Goate et al.   JOURNAL OF NEUROCHEMISTRY

Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells

(2011) Ryan Lister et al.   NATURE

Inhibition of BET recruitment to chromatin as an effective treatment for MLL-fusion leukaemia

(2011) Mark A. Dawson et al.   NATURE

Donor cell type can influence the epigenome and differentiation potential of human induced pluripotent stem cells

(2011) Kitai Kim et al.   NATURE BIOTECHNOLOGY

Increased methylation variation in epigenetic domains across cancer types

(2011) Kasper Daniel Hansen et al.   NATURE GENETICS

Regions of focal DNA hypermethylation and long-range hypomethylation in colorectal cancer coincide with nuclear lamina–associated domains

(2011) Benjamin P Berman et al.   NATURE GENETICS

Cancer epigenetics reaches mainstream oncology

(2011) Manuel Rodríguez-Paredes et al.   NATURE MEDICINE

Genome-scale epigenetic reprogramming during epithelial-to-mesenchymal transition

(2011) Oliver G McDonald et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The Epigenetic promise for prostate cancer diagnosis

(2011) Leander Van Neste et al.   PROSTATE

Breast Cancer Methylomes Establish an Epigenomic Foundation for Metastasis

(2011) F. Fang et al.   Science Translational Medicine

Evaluation of the Infinium Methylation 450K technology

(2011) Sarah Dedeurwaerder et al.   Epigenomics

Frequent Alterations and Epigenetic Silencing of Differentiation Pathway Genes in Structurally Rearranged Liposarcomas

(2011) B. S. Taylor et al.   Cancer Discovery

Identification of Type 1 Diabetes–Associated DNA Methylation Variable Positions That Precede Disease Diagnosis

(2011) Vardhman K. Rakyan et al.   PLoS Genetics

Identification of a CpG Island Methylator Phenotype that Defines a Distinct Subgroup of Glioma

(2010) Houtan Noushmehr et al.   CANCER CELL

Long interspersed nuclear element-1 hypomethylation is a potential biomarker for the prediction of response to oral fluoropyrimidines in microsatellite stable and CpG island methylator phenotype-negative colorectal cancer

(2010) Kazuyuki Kawakami et al.   CANCER SCIENCE

Aberrant Epigenetic Landscape in Cancer: How Cellular Identity Goes Awry

(2010) María Berdasco et al.   DEVELOPMENTAL CELL

Dynamic changes in the human methylome during differentiation

(2010) L. Laurent et al.   GENOME RESEARCH

BRCA1 CpG Island Hypermethylation Predicts Sensitivity to Poly(Adenosine Diphosphate)- Ribose Polymerase Inhibitors

(2010) Jurgen Veeck et al.   JOURNAL OF CLINICAL ONCOLOGY

Phase I/IIa Study of Cilengitide and Temozolomide With Concomitant Radiotherapy Followed by Cilengitide and Temozolomide Maintenance Therapy in Patients With Newly Diagnosed Glioblastoma

(2010) Roger Stupp et al.   JOURNAL OF CLINICAL ONCOLOGY

Final Results From a Multicenter, International, Pivotal Study of Romidepsin in Refractory Cutaneous T-Cell Lymphoma

(2010) Sean J. Whittaker et al.   JOURNAL OF CLINICAL ONCOLOGY

DNA methylation profiling in doxorubicin treated primary locally advanced breast tumours identifies novel genes associated with survival and treatment response

(2010) Emelyne Dejeux et al.   Molecular Cancer

Down-regulation of the Nucleotide Excision Repair gene XPG as a new mechanism of drug resistance in human and murine cancer cells

(2010) Maria Antonietta Sabatino et al.   Molecular Cancer

Epigenetic memory in induced pluripotent stem cells

(2010) K. Kim et al.   NATURE

Conserved role of intragenic DNA methylation in regulating alternative promoters

(2010) Alika K. Maunakea et al.   NATURE

Selective inhibition of BET bromodomains

(2010) Panagis Filippakopoulos et al.   NATURE

Epigenetic modifications as therapeutic targets

(2010) Theresa K Kelly et al.   NATURE BIOTECHNOLOGY

Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications

(2010) R Alan Harris et al.   NATURE BIOTECHNOLOGY

Epigenetic modifications and human disease

(2010) Anna Portela et al.   NATURE BIOTECHNOLOGY

The NIH Roadmap Epigenomics Mapping Consortium

(2010) Bradley E Bernstein et al.   NATURE BIOTECHNOLOGY

The DNA Methylome of Human Peripheral Blood Mononuclear Cells

(2010) Yingrui Li et al.   PLOS BIOLOGY

DNA methylation for subtype classification and prediction of treatment outcome in patients with childhood acute lymphoblastic leukemia

(2009) L. Milani et al.   BLOOD

Methylation of TFPI2 in Stool DNA: A Potential Novel Biomarker for the Detection of Colorectal Cancer

(2009) S. C. Glockner et al.   CANCER RESEARCH

Aberrant Methylation of APC, MGMT, RASSF2A, and Wif-1 Genes in Plasma as a Biomarker for Early Detection of Colorectal Cancer

(2009) B. B. Lee et al.   CLINICAL CANCER RESEARCH

Multimarker Circulating DNA Assay for Assessing Blood of Prostate Cancer Patients

(2009) E. Sunami et al.   CLINICAL CHEMISTRY

Changes in the pattern of DNA methylation associate with twin discordance in systemic lupus erythematosus

(2009) B. M. Javierre et al.   GENOME RESEARCH

Recent Advances in the Detection of Prostate Cancer Using Epigenetic Markers in Commonly Collected Laboratory Samples

(2009) Adam Maxwell et al.   Labmedicine

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells

(2009) Madeleine P Ball et al.   NATURE BIOTECHNOLOGY

Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts

(2009) Akiko Doi et al.   NATURE GENETICS

The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores

(2009) Rafael A Irizarry et al.   NATURE GENETICS

Inhibition of Poly(ADP-Ribose) Polymerase in Tumors fromBRCAMutation Carriers

(2009) Peter C. Fong et al.   NEW ENGLAND JOURNAL OF MEDICINE

MBD-isolated Genome Sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome

(2009) David Serre et al.   NUCLEIC ACIDS RESEARCH

IGFBP-3 hypermethylation-derived deficiency mediates cisplatin resistance in non-small-cell lung cancer

(2009) I Ibanez de Caceres et al.   ONCOGENE

Epigenetic Differences in Cortical Neurons from a Pair of Monozygotic Twins Discordant for Alzheimer's Disease

(2009) Diego Mastroeni et al.   PLoS One

Methyl-DNA immunoprecipitation (MeDIP): Hunting down the DNA methylome

(2008) Filipe V. Jacinto et al.   BIOTECHNIQUES

Identification of CDK10 as an Important Determinant of Resistance to Endocrine Therapy for Breast Cancer

(2008) Elizabeth Iorns et al.   CANCER CELL

H3K79 Methylation Profiles Define Murine and Human MLL-AF4 Leukemias

(2008) Andrei V. Krivtsov et al.   CANCER CELL

The transglutaminase 2 gene ( TGM2 ), a potential molecular marker for chemotherapeutic drug sensitivity, is epigenetically silenced in breast cancer

(2008) Lingbao Ai et al.   CARCINOGENESIS

Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis

(2008) Ryan Lister et al.   CELL

Comprehensive high-throughput arrays for relative methylation (CHARM)

(2008) R. A. Irizarry et al.   GENOME RESEARCH

Somatically acquired hypomethylation of IGF2 in breast and colorectal cancer

(2008) Yoko Ito et al.   HUMAN MOLECULAR GENETICS

A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis

(2008) Thomas A Down et al.   NATURE BIOTECHNOLOGY

DNA Methylation Markers and Early Recurrence in Stage I Lung Cancer

(2008) Malcolm V. Brock et al.   NEW ENGLAND JOURNAL OF MEDICINE

Epigenetics in Cancer

(2008) Manel Esteller   NEW ENGLAND JOURNAL OF MEDICINE

A microRNA DNA methylation signature for human cancer metastasis

(2008) A. Lujambio et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CpG Island Hypermethylation at Multiple Gene Sites in Diagnosis and Prognosis of Prostate Cancer

(2008) Jörg Ellinger et al.   UROLOGY

DNA Methylation Biomarkers for Blood-Based Colorectal Cancer Screening

(2007) C. Lofton-Day et al.   CLINICAL CHEMISTRY