Identifying epigenetic biomarkers of established prognostic factors and survival in a clinical cohort of individuals with oropharyngeal cancer

[1]  S. Andrews,et al.  A KHDC3L mutation resulting in recurrent hydatidiform mole causes genome-wide DNA methylation loss in oocytes and persistent imprinting defects post-fertilisation , 2019, Genome Medicine.

[2]  K. Tilling,et al.  dmrff: identifying differentially methylated regions efficiently with power and control , 2018, bioRxiv.

[3]  Pashupati P. Mishra,et al.  Association of maternal prenatal smoking GFI1-locus and cardio-metabolic phenotypes in 18,212 adults , 2018, EBioMedicine.

[4]  R. Marioni,et al.  Investigating the relationship between DNA methylation age acceleration and risk factors for Alzheimer's disease , 2018, Alzheimer's & dementia.

[5]  M. Hashibe,et al.  Cardiovascular disease risks among head and neck cancer survivors in a large, population-based cohort study. , 2018 .

[6]  M. Pawlita,et al.  Tobacco smoking and alcohol drinking at diagnosis of head and neck cancer and all‐cause mortality: Results from head and neck 5000, a prospective observational cohort of people with head and neck cancer , 2018, International journal of cancer.

[7]  Valeriia Haberland,et al.  The MR-Base platform supports systematic causal inference across the human phenome , 2018, eLife.

[8]  Matthew C. Miller,et al.  Prevalence of High-Risk Human Papillomavirus in Tonsil Tissue in Healthy Adults and Colocalization in Biofilm of Tonsillar Crypts , 2018, JAMA otolaryngology-- head & neck surgery.

[9]  Andrew E. Teschendorff,et al.  Epigenome-based cancer risk prediction: rationale, opportunities and challenges , 2018, Nature Reviews Clinical Oncology.

[10]  Ming Chen,et al.  Gene-expression signature regulated by the KEAP1-NRF2-CUL3 axis is associated with a poor prognosis in head and neck squamous cell cancer , 2018, BMC Cancer.

[11]  R. Pfeiffer,et al.  Human papillomavirus 16 E6 antibodies are sensitive for human papillomavirus–driven oropharyngeal cancer and are associated with recurrence , 2017, Cancer.

[12]  Yulan Jin,et al.  SLC7A11, a component of cysteine/glutamate transporter, is a novel biomarker for the diagnosis and prognosis in laryngeal squamous cell carcinoma. , 2017, Oncology reports.

[13]  Frank Dudbridge,et al.  Estimation of a significance threshold for epigenome‐wide association studies , 2017, Genetic epidemiology.

[14]  A. Bychkov,et al.  Aberrant promoter methylation of the PAQR3 gene is associated with prostate cancer. , 2017, Pathology, research and practice.

[15]  H. Wen,et al.  PAQR3 overexpression suppresses the aggressive phenotype of esophageal squamous cell carcinoma cells via inhibition of ERK signaling. , 2017, Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie.

[16]  P. Visscher,et al.  Testing Two Evolutionary Theories of Human Aging with DNA Methylation Data , 2017, Genetics.

[17]  N. Freedman,et al.  Kinetics of the Human Papillomavirus Type 16 E6 Antibody Response Prior to Oropharyngeal Cancer , 2017, Journal of the National Cancer Institute.

[18]  M. Wiesenfarth,et al.  Sensitivity and specificity of antibodies against HPV16 E6 and other early proteins for the detection of HPV16‐driven oropharyngeal squamous cell carcinoma , 2017, International journal of cancer.

[19]  Fang Zhou,et al.  PAQR3 Inhibits the Proliferation and Tumorigenesis in Esophageal Cancer Cells. , 2017, Oncology research.

[20]  A. Morris,et al.  SurvivalGWAS_SV: software for the analysis of genome-wide association studies of imputed genotypes with “time-to-event” outcomes , 2017, BMC Bioinformatics.

[21]  G. Davey Smith,et al.  Genetic epidemiology and Mendelian randomization for informing disease therapeutics: Conceptual and methodological challenges , 2017, bioRxiv.

[22]  S. Thompson,et al.  Interpreting findings from Mendelian randomization using the MR-Egger method , 2017, European Journal of Epidemiology.

[23]  Josine L. Min,et al.  Meffil: efficient normalisation and analysis of very large DNA methylation samples , 2017, bioRxiv.

[24]  Olena O Yavorska,et al.  MendelianRandomization: an R package for performing Mendelian randomization analyses using summarized data , 2017, International journal of epidemiology.

[25]  Z. Herceg,et al.  Unique DNA methylation signature in HPV-positive head and neck squamous cell carcinomas , 2017, Genome Medicine.

[26]  S. Parikh,et al.  Cardiovascular risk and prevention in patients with head and neck cancer treated with radiotherapy , 2017, Head & neck.

[27]  N. Hastie,et al.  Correction: Pedigree- and SNP-Associated Genetics and Recent Environment are the Major Contributors to Anthropometric and Cardiometabolic Trait Variation , 2017, PLoS genetics.

[28]  Jean-Philippe Fortin,et al.  Preprocessing, normalization and integration of the Illumina HumanMethylationEPIC array with minfi , 2016, bioRxiv.

[29]  R. Marioni,et al.  A DNA methylation biomarker of alcohol consumption , 2016, Molecular Psychiatry.

[30]  A. Scholten,et al.  SPEG (Striated Muscle Preferentially Expressed Protein Kinase) Is Essential for Cardiac Function by Regulating Junctional Membrane Complex Activity , 2016, Circulation research.

[31]  R. Marioni,et al.  Epigenetic Signatures of Cigarette Smoking , 2016, Circulation. Cardiovascular genetics.

[32]  A. Olshan,et al.  Genome-wide association analyses identify new susceptibility loci for oral cavity and pharyngeal cancer , 2016, Nature Genetics.

[33]  Blair H. Smith,et al.  Shared Genetics and Couple-Associated Environment Are Major Contributors to the Risk of Both Clinical and Self-Declared Depression , 2016, bioRxiv.

[34]  G. Davey Smith,et al.  Challenges and novel approaches for investigating molecular mediation , 2016, Human molecular genetics.

[35]  W. Ahrens,et al.  Combined effects of smoking and HPV16 in oropharyngeal cancer. , 2016, International journal of epidemiology.

[36]  R. Shaw,et al.  Oropharyngeal cancer: United Kingdom National Multidisciplinary Guidelines , 2016, The Journal of Laryngology & Otology.

[37]  L. Rozek,et al.  Stability of methylation markers in head and neck squamous cell carcinoma , 2016, Head & neck.

[38]  Tom R. Gaunt,et al.  Systematic identification of genetic influences on methylation across the human life course , 2016, Genome Biology.

[39]  T. Peters,et al.  Recruitment, response rates and characteristics of 5511 people enrolled in a prospective clinical cohort study: head and neck 5000 , 2016, Clinical otolaryngology : official journal of ENT-UK ; official journal of Netherlands Society for Oto-Rhino-Laryngology & Cervico-Facial Surgery.

[40]  N. Hastie,et al.  Pedigree- and SNP-Associated Genetics and Recent Environment are the Major Contributors to Anthropometric and Cardiometabolic Trait Variation , 2016, PLoS genetics.

[41]  Stephen Burgess,et al.  Combining information on multiple instrumental variables in Mendelian randomization: comparison of allele score and summarized data methods , 2015, Statistics in medicine.

[42]  Mitchell J. Machiela,et al.  LDlink: a web-based application for exploring population-specific haplotype structure and linking correlated alleles of possible functional variants , 2015, Bioinform..

[43]  Gabor T. Marth,et al.  A global reference for human genetic variation , 2015, Nature.

[44]  W. Wu,et al.  PAQR3: a novel tumor suppressor gene. , 2015, American journal of cancer research.

[45]  E. de Monès,et al.  Study of the concordance between p16 immunohistochemistry and HPV-PCR genotyping for the viral diagnosis of oropharyngeal squamous cell carcinoma. , 2015, European annals of otorhinolaryngology, head and neck diseases.

[46]  G. Davey Smith,et al.  Mendelian randomization with invalid instruments: effect estimation and bias detection through Egger regression , 2015, International journal of epidemiology.

[47]  P. Elliott,et al.  A coherent approach for analysis of the Illumina HumanMethylation450 BeadChip improves data quality and performance in epigenome-wide association studies , 2015, Genome Biology.

[48]  H. Morgenstern,et al.  Risk factors for head and neck cancer in young adults: a pooled analysis in the INHANCE consortium. , 2015, International journal of epidemiology.

[49]  W. Ahrens,et al.  Human Papillomavirus 16 E6 Antibodies in Individuals without Diagnosed Cancer: A Pooled Analysis , 2015, Cancer Epidemiology, Biomarkers & Prevention.

[50]  T. Peters,et al.  Establishing a large prospective clinical cohort in people with head and neck cancer as a biomedical resource: head and neck 5000 , 2014, BMC Cancer.

[51]  K. Michels,et al.  Epigenetic epidemiology of cancer. , 2014, Biochemical and biophysical research communications.

[52]  Nilesh J Samani,et al.  Cigarette smoking reduces DNA methylation levels at multiple genomic loci but the effect is partially reversible upon cessation , 2014, Epigenetics.

[53]  S. Shete,et al.  Survival patterns in squamous cell carcinoma of the head and neck: pain as an independent prognostic factor for survival. , 2014, The journal of pain : official journal of the American Pain Society.

[54]  S. Chiocca,et al.  HPV in oropharyngeal cancer: the basics to know in clinical practice , 2014, Acta otorhinolaryngologica Italica : organo ufficiale della Societa italiana di otorinolaringologia e chirurgia cervico-facciale.

[55]  G. Davey Smith,et al.  Mendelian randomization: genetic anchors for causal inference in epidemiological studies , 2014, Human molecular genetics.

[56]  V. Velculescu,et al.  Key tumor suppressor genes inactivated by “greater promoter” methylation and somatic mutations in head and neck cancer , 2014, Epigenetics.

[57]  Katherine E Henson,et al.  Risk of Suicide After Cancer Diagnosis in England , 2018, JAMA psychiatry.

[58]  K. Hansen,et al.  Functional normalization of 450k methylation array data improves replication in large cancer studies , 2014, Genome Biology.

[59]  J. Malicki,et al.  Oral cavity and oropharyngeal squamous cell carcinoma in young adults: a review of the literature , 2014, Radiology and oncology.

[60]  W. Koch,et al.  Cigarette Smoke Modulates Vascular Smooth Muscle Phenotype: Implications for Carotid and Cerebrovascular Disease , 2013, PloS one.

[61]  Thomas M. Harris,et al.  Unique DNA Methylation Loci Distinguish Anatomic Site and HPV Status in Head and Neck Squamous Cell Carcinoma , 2013, Clinical Cancer Research.

[62]  Paolo Vineis,et al.  Evaluation of human papillomavirus antibodies and risk of subsequent head and neck cancer. , 2013, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[63]  Archie Campbell,et al.  Cohort Profile: Generation Scotland: Scottish Family Health Study (GS:SFHS). The study, its participants and their potential for genetic research on health and illness. , 2013, International journal of epidemiology.

[64]  N. Patterson,et al.  Using Extended Genealogy to Estimate Components of Heritability for 23 Quantitative and Dichotomous Traits , 2013, PLoS genetics.

[65]  B. Christensen,et al.  Biomarkers of HPV in head and neck squamous cell carcinoma. , 2012, Cancer research.

[66]  H. Morgenstern,et al.  Nutrient-based dietary patterns and the risk of head and neck cancer: a pooled analysis in the International Head and Neck Cancer Epidemiology consortium. , 2012, Annals of oncology : official journal of the European Society for Medical Oncology.

[67]  Nianxiang Zhang,et al.  Abstract 5004: CpG island methylator phenotype in bladder cancer , 2012 .

[68]  G. Davey Smith,et al.  Two-step epigenetic Mendelian randomization: a strategy for establishing the causal role of epigenetic processes in pathways to disease. , 2012, International journal of epidemiology.

[69]  L. Mell,et al.  Population-based study of competing mortality in head and neck cancer. , 2011, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[70]  M. Worsham.  Identifying the risk factors for late-stage head and neck cancer , 2011, Expert review of anticancer therapy.

[71]  Joseph K. Pickrell,et al.  DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines , 2011, Genome Biology.

[72]  Xiao Zhang,et al.  Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis , 2010, BMC Bioinformatics.

[73]  Huanming Yang,et al.  The DNA Methylome of Human Peripheral Blood Mononuclear Cells , 2010, PLoS biology.

[74]  J. Jansen,et al.  Gfi1 and Gfi1b: key regulators of hematopoiesis , 2010, Leukemia.

[75]  Wolfgang Viechtbauer,et al.  Conducting Meta-Analyses in R with the metafor Package , 2010 .

[76]  Gypsyamber D'Souza,et al.  HPV-associated head and neck cancer: a virus-related cancer epidemic. , 2010, The Lancet. Oncology.

[77]  K. Ang,et al.  Human papillomavirus and survival of patients with oropharyngeal cancer. , 2010, The New England journal of medicine.

[78]  S. Cole,et al.  Illustrating bias due to conditioning on a collider. , 2010, International journal of epidemiology.

[79]  K. Raj,et al.  Epigenetic repression of E-cadherin by human papillomavirus 16 E7 protein , 2010, Carcinogenesis.

[80]  Ze-Guang Han,et al.  Epigenetic modification induced by hepatitis B virus X protein via interaction with de novo DNA methyltransferase DNMT3A. , 2009, Journal of hepatology.

[81]  A. Cmelak,et al.  Improved survival of patients with human papillomavirus-positive head and neck squamous cell carcinoma in a prospective clinical trial. , 2008, Journal of the National Cancer Institute.

[82]  E. Taioli,et al.  Survival of squamous cell carcinoma of the head and neck in relation to human papillomavirus infection: Review and meta‐analysis , 2007, International journal of cancer.

[83]  John D. Storey,et al.  Capturing Heterogeneity in Gene Expression Studies by Surrogate Variable Analysis , 2007, PLoS genetics.

[84]  Witold Zatonski,et al.  Alcohol drinking in never users of tobacco, cigarette smoking in never drinkers, and the risk of head and neck cancer: pooled analysis in the International Head and Neck Cancer Epidemiology Consortium. , 2007, Journal of the National Cancer Institute.

[85]  T. Kouzarides,et al.  Viral oncoproteins target the DNA methyltransferases , 2007, Oncogene.

[86]  Markus F Templin,et al.  Multiplex human papillomavirus serology based on in situ-purified glutathione s-transferase fusion proteins. , 2005, Clinical chemistry.

[87]  S. Hofmann,et al.  Structure of the human palmitoyl-protein thioesterase-2 gene (PPT2) in the major histocompatibility complex on chromosome 6p21.3. , 1999, Genomics.

[88]  London School of Hygiene and Tropical Medicine , 1938, Nature.

[89]  A. Hofman,et al.  Meta-analyses of genome-wide association studies identify multiple loci associated with pulmonary function , 2010, Nature Genetics.

[90]  Hilde van der Togt,et al.  Publisher's Note , 2003, J. Netw. Comput. Appl..

[91]  G. Braemer.  International statistical classification of diseases and related health problems. Tenth revision. , 1988, World health statistics quarterly. Rapport trimestriel de statistiques sanitaires mondiales.