Functional normalization of 450k methylation array data improves replication in large cancer studies

doi:10.1186/s13059-014-0503-2

PMID: 25599564DOI: 10.1186/s13059-014-0503-2Jan 20, 2015

Functional normalization of 450k methylation array data improves replication in large cancer studies

Genome Biology

Jean-Philippe FortinKasper D Hansen

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Abstract

We propose an extension to quantile normalization that removes unwanted technical variation using control probes. We adapt our algorithm, functional normalization, to the Illumina 450k methylation array and address the open problem of normalizing methylation data with global epigenetic changes, such as human cancers. Using data sets from The Cancer Genome Atlas and a large case-control study, we show that our algorithm outperforms all existing normalization methods with respect to replication of results between experiments, and yields robust results even in the presence of batch effects. Functional normalization can be applied to any microarray platform, provided suitable control probes are available.

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Significant out-of-sample classification from methylation profile scoring for amyotrophic lateral sclerosis

Mar 7, 2020·NPJ Genomic Medicine·Marta F NabaisNaomi R Wray

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

Jul 1, 2020·Clinical Epigenetics·Ryan LangdonCaroline Relton

Genome-Wide DNA Methylation Patterns in Children Exposed to Nonpharmacologically Treated Prenatal Depressive Symptoms: Results From 2 Independent Cohorts

Jul 1, 2020·Epigenetics Insights·Valeska StonawskiStefan Frey

Concomitant DNA methylation and transcriptome signatures define epidermal responses to acute solar UV radiation

Aug 2, 2020·Scientific Reports·Nicholas HolzscheckKatharina Gorges

Candidate methylation sites associated with endocrine therapy resistance in ER+/HER2- breast cancer

Jul 21, 2020·BMC Cancer·Maryam Soleimani DodaranAntoine H C van Kampen

Methylation Data Processing Protocol and Comparison of Blood and Cerebral Spinal Fluid Following Aneurysmal Subarachnoid Hemorrhage

Jul 17, 2020·Frontiers in Genetics·Annie I ArockiarajYvette P Conley

Calcium Signaling Alterations Caused by Epigenetic Mechanisms in Pancreatic Cancer: From Early Markers to Prognostic Impact

Jul 8, 2020·Cancers·Cleandra GregórioLuis Felipe Ribeiro Pinto

A decade of epigenetic change in aging twins: Genetic and environmental contributions to longitudinal DNA methylation

Jul 28, 2020·Aging Cell·Chandra A ReynoldsNancy L Pedersen

Placental Epigenome-Wide Association Study Identified Loci Associated with Childhood Adiposity at 3 Years of Age

Oct 3, 2020·International Journal of Molecular Sciences·Valérie Gagné-OuelletLuigi Bouchard

Stability of the human sperm DNA methylome to folic acid fortification and short-term supplementation

Dec 21, 2016·Human Reproduction·D ChanJ M Trasler

Lifetime stress accelerates epigenetic aging in an urban, African American cohort: relevance of glucocorticoid signaling

Dec 18, 2015·Genome Biology·Anthony S ZannasDivya Mehta

Epigenome-wide cross-tissue predictive modeling and comparison of cord blood and placental methylation in a birth cohort

Feb 25, 2017·Epigenomics·Margherita M De CarliAllan C Just

Distinct DNA methylation profiles in subtypes of orofacial cleft

Jun 13, 2017·Clinical Epigenetics·Gemma C SharpCaroline Relton

DNA methylation profiling reveals the presence of population-specific signatures correlating with phenotypic characteristics

Mar 9, 2017·Molecular Genetics and Genomics : MGG·Anil K GiriDwaipayan Bharadwaj

A statistical model for the analysis of beta values in DNA methylation studies

Nov 24, 2016·BMC Bioinformatics·Leonie WeinholdMatthias Schmid

Integrative epigenetic and genetic pan-cancer somatic alteration portraits

Apr 21, 2017·Epigenetics : Official Journal of the DNA Methylation Society·Lucas A SalasBrock C Christensen

GMPR: A robust normalization method for zero-inflated count data with application to microbiome sequencing data

Apr 10, 2018·PeerJ·Li ChenJun Chen

Integrated time course omics analysis distinguishes immediate therapeutic response from acquired resistance

May 25, 2018·Genome Medicine·Genevieve Stein-O'BrienElana J Fertig

Polymorphism in Tmem132d regulates expression and anxiety-related behavior through binding of RNA polymerase II complex

Jan 11, 2018·Translational Psychiatry·Roshan R NaikLudwig Czibere

SeSAMe: reducing artifactual detection of DNA methylation by Infinium BeadChips in genomic deletions

Aug 8, 2018·Nucleic Acids Research·Wanding ZhouHui Shen

Pan-cancer deconvolution of tumour composition using DNA methylation

Aug 15, 2018·Nature Communications·Ankur ChakravarthyTim R Fenton

DNA methylation changes that precede onset of dysplasia in advanced sessile serrated adenomas

Jun 16, 2019·Clinical Epigenetics·Cheng LiuVicki L J Whitehall

Placental epigenetic clocks: estimating gestational age using placental DNA methylation levels.

Jun 27, 2019·Aging·Yunsung LeeSteve Horvath

The role of environmental stress and DNA methylation in the longitudinal course of bipolar disorder

Feb 13, 2020·International Journal of Bipolar Disorders·Ashley L ComesUrs Heilbronner

Small extracellular vesicles deliver miR-21 and miR-217 as pro-senescence effectors to endothelial cells

Mar 12, 2020·Journal of Extracellular Vesicles·Emanuela MensàFabiola Olivieri

Multiplatform genomic profiling and magnetic resonance imaging identify mechanisms underlying intratumor heterogeneity in meningioma

Sep 25, 2020·Nature Communications·Stephen T MagillDavid R Raleigh

In utero and childhood exposure to tobacco smoke and multi-layer molecular signatures in children

Aug 20, 2020·BMC Medicine·Marta Vives-UsanoMariona Bustamante

Mitochondrial DNA copy number can influence mortality and cardiovascular disease via methylation of nuclear DNA CpGs

Sep 30, 2020·Genome Medicine·Christina A CastellaniDan E Arking

PRDM8 reveals aberrant DNA methylation in aging syndromes and is relevant for hematopoietic and neuronal differentiation

Aug 21, 2020·Clinical Epigenetics·Olivia CyprisWolfgang Wagner

Comprehensive characterization, annotation and innovative use of Infinium DNA methylation BeadChip probes

Dec 8, 2016·Nucleic Acids Research·Wanding ZhouHui Shen

Age-related accrual of methylomic variability is linked to fundamental ageing mechanisms

Sep 23, 2016·Genome Biology·Roderick C SliekerBastiaan T Heijmans

Principal components analysis and the reported low intrinsic dimensionality of gene expression microarray data

Jun 3, 2016·Scientific Reports·Michael LenzAndreas Schuppert

Preprocessing, normalization and integration of the Illumina HumanMethylationEPIC array with minfi

Dec 31, 2016·Bioinformatics·Jean-Philippe FortinKasper D Hansen

DNA methylation and transcriptional trajectories during human development and reprogramming of isogenic pluripotent stem cells

Oct 17, 2017·Nature Communications·Matthias S RoostSusana M Chuva de Sousa Lopes

Epigenome-wide association of PTSD from heterogeneous cohorts with a common multi-site analysis pipeline

Jul 12, 2017·American Journal of Medical Genetics. Part B, Neuropsychiatric Genetics : the Official Publication of the International Society of Psychiatric Genetics·Andrew RatanatharathornAlicia K Smith

Association between DNA methylation in cord blood and maternal smoking: The Hokkaido Study on Environment and Children's Health

Apr 6, 2018·Scientific Reports·Kunio MiyakeReiko Kishi

DNA methylation profiling of acute chorioamnionitis-associated placentas and fetal membranes: insights into epigenetic variation in spontaneous preterm births

Oct 31, 2018·Epigenetics & Chromatin·Chaini KonwarWendy P Robinson

Placental DNA Methylation Adaptation to Maternal Glycemic Response in Pregnancy

May 13, 2018·Diabetes·Andres CardenasMarie-France Hivert

Autosomal genetic variation is associated with DNA methylation in regions variably escaping X-chromosome inactivation

Sep 16, 2018·Nature Communications·René LuijkBastiaan T Heijmans

Serum dioxin and DNA methylation in the sperm of operation ranch hand veterans exposed to Agent Orange

Oct 31, 2019·Environmental Health : a Global Access Science Source·Karl T KelseyKim Boekelheide

Epigenome-Wide DNA Methylation Association Analysis Identified Novel Loci in Peripheral Cells for Alcohol Consumption Among European American Male Veterans

Aug 7, 2019·Alcoholism, Clinical and Experimental Research·Ke XuJoel Gelernter

Evaluation of commonly used analysis strategies for epigenome- and transcriptome-wide association studies through replication of large-scale population studies

Nov 16, 2019·Genome Biology·Jeroen van RooijJoyce B J van Meurs

Somatic mutations and promotor methylation of the ryanodine receptor 2 is a common event in the pathogenesis of head and neck cancer

May 29, 2019·International Journal of Cancer. Journal International Du Cancer·Katrin SchmittJochen Hess

Airway epithelial cell isolation techniques affect DNA methylation profiles with consequences for analysis of asthma related perturbations to DNA methylation

Oct 9, 2019·Scientific Reports·Rachel L CliffordMichael S Kobor

Genome-wide characterization of cytosine-specific 5-hydroxymethylation in normal breast tissue

Dec 18, 2019·Epigenetics : Official Journal of the DNA Methylation Society·Owen M WilkinsBrock C Christensen

The association of DNA methylation with body mass index: distinguishing between predictors and biomarkers

Apr 2, 2020·Clinical Epigenetics·Zoe E ReedGibran Hemani

Data-Mining Approach on Transcriptomics and Methylomics Placental Analysis Highlights Genes in Fetal Growth Restriction

Jan 31, 2020·Frontiers in Genetics·Floris ChabrunGeraldine Gascoin

Age-related DNA methylation in paired normal and tumour breast tissue in Chinese breast cancer patients

Sep 25, 2020·Epigenetics : Official Journal of the DNA Methylation Society·Maeve KielyXiaohong R Yang

AML displays increased CTCF occupancy associated with aberrant gene expression and transcription factor binding.

Apr 2, 2020·Blood·Huthayfa MujahedSören Lehmann

The immunohistochemical, DNA methylation, and chromosomal copy number profile of cauda equina paraganglioma is distinct from extra-spinal paraganglioma

Sep 7, 2020·Acta Neuropathologica·Biswarathan RamaniArie Perry

Pediatric bithalamic gliomas have a distinct epigenetic signature and frequent EGFR exon 20 insertions resulting in potential sensitivity to targeted kinase inhibition.

Apr 19, 2020·Acta Neuropathologica·Gourish MondalDavid A Solomon

Widespread epigenomic, transcriptomic and proteomic differences between hip osteophytic and articular chondrocytes in osteoarthritis

May 10, 2018·Rheumatology·Julia SteinbergEleftheria Zeggini

SMCHD1 regulates a limited set of gene clusters on autosomal chromosomes

Jun 8, 2017·Skeletal Muscle·Amanda G MasonSilvère M van der Maarel

ATRX, DAXX or MEN1 mutant pancreatic neuroendocrine tumors are a distinct alpha-cell signature subgroup

Oct 14, 2018·Nature Communications·Chang S ChanLaura H Tang

Epigenetics, heritability and longitudinal analysis

Sep 27, 2018·BMC Genetics·Haakon E NustadPhillip E Melton

DNA methylation profiling reliably distinguishes pulmonary enteric adenocarcinoma from metastatic colorectal cancer

Feb 7, 2019·Modern Pathology : an Official Journal of the United States and Canadian Academy of Pathology, Inc·Philipp JurmeisterDavid Capper

Association of a placental Interleukin-6 genetic variant (rs1800796) with DNA methylation, gene expression and risk of acute chorioamnionitis

Feb 24, 2019·BMC Medical Genetics·Chaini KonwarWendy P Robinson

DNA methylation and hydroxymethylation patterns in acute myeloid leukemia patients with mutations in DNMT3A and IDH1/2 and their combinations

Apr 17, 2019·Cancer Biomarkers : Section a of Disease Markers·Šárka ŠestákováHana Remešová

Altered Genome-Wide DNA Methylation in Peripheral Blood of South African Women with Gestational Diabetes Mellitus

Nov 24, 2019·International Journal of Molecular Sciences·Stephanie DiasCarmen Pheiffer

A combined epigenome- and transcriptome-wide association study of the oral masticatory mucosa assigns CYP1B1 a central role for epithelial health in smokers

Jul 24, 2019·Clinical Epigenetics·Gesa M RichterArne S Schaefer

Epigenetic modifiers DNMT3A and BCOR are recurrently mutated in CYLD cutaneous syndrome

Oct 19, 2019·Nature Communications·Helen R DaviesNeil Rajan

Circadian oscillations of cytosine modification in humans contribute to epigenetic variability, aging, and complex disease

Jan 5, 2019·Genome Biology·Gabriel OhArt Petronis

Screening for genes that accelerate the epigenetic aging clock in humans reveals a role for the H3K36 methyltransferase NSD1

Aug 15, 2019·Genome Biology·Daniel E Martin-HerranzJanet M Thornton

Mediation Analysis Supports a Causal Relationship between Maternal Hyperglycemia and Placental DNA Methylation Variations at the Leptin Gene Locus and Cord Blood Leptin Levels

Jan 18, 2020·International Journal of Molecular Sciences·Valérie Gagné-OuelletLuigi Bouchard

Bayesian reassessment of the epigenetic architecture of complex traits.

Jun 10, 2020·Nature Communications·Daniel Trejo BanosMatthew R Robinson

Epigenome-wide association study of seizures in childhood and adolescence

Jan 10, 2020·Clinical Epigenetics·Doretta CaramaschiEsther Walton

The Technome - A Predictive Internal Calibration Approach for Quantitative Imaging Biomarker Research.

Jan 26, 2020·Scientific Reports·Alexander MühlbergMartine Rémy-Jardin

The genomic and epigenomic evolutionary history of papillary renal cell carcinomas

Jun 20, 2020·Nature Communications·Bin ZhuMaria Teresa Landi

Biology and grading of pleomorphic xanthoastrocytoma-what have we learned about it?

Jul 4, 2020·Brain Pathology·Rachael VaubelCaterina Giannini

Comprehensive analysis of diverse low-grade neuroepithelial tumors with FGFR1 alterations reveals a distinct molecular signature of rosette-forming glioneuronal tumor

Aug 30, 2020·Acta Neuropathologica Communications·Calixto-Hope G LucasDavid A Solomon

Maternal eating disorders affect offspring cord blood DNA methylation: a prospective study

Nov 3, 2017·Clinical Epigenetics·Nabila KazmiNadia Micali

DNA methylation signatures of educational attainment

Jan 12, 2019·NPJ Science of Learning·Jenny van DongenBIOS consortium

A panel of DNA methylation signature from peripheral blood may predict colorectal cancer susceptibility

Jul 28, 2020·BMC Cancer·Justina Ucheojor OnwukaYashuang Zhao

Successful treatment of post-traumatic stress disorder reverses DNA methylation marks

Oct 25, 2019·Molecular Psychiatry·Christiaan H VinkersMarco P Boks

IDH3α regulates one-carbon metabolism in glioblastoma

Jan 8, 2019·Science Advances·Jasmine L MayAlexander H Stegh

Integration of "omics" Data and Phenotypic Data Within a Unified Extensible Multimodal Framework

Jan 12, 2019·Frontiers in Neuroinformatics·Samir DasAlan C Evans

Epigenetic mutation load is weakly correlated with epigenetic age acceleration

Sep 30, 2020·Aging·Qi YanBeate Ritz

Adolescent sleep timing and dietary patterns in relation to DNA methylation of core circadian genes: a pilot study of Mexican youth

Oct 6, 2020·Epigenetics : Official Journal of the DNA Methylation Society·Erica C JansenJaclyn M Goodrich

TWIST1 DNA methylation is a cell marker of airway and parenchymal lung fibroblasts that are differentially methylated in asthma

Oct 4, 2020·Clinical Epigenetics·Rachel L CliffordTillie-Louise Hackett

DNA methylation in infants with low and high body fatness

Nov 11, 2020·BMC Genomics·Pontus HenrikssonMarie Löf

Patched 1 expression in Merkel cell carcinoma

Nov 13, 2020·The Journal of Dermatology·Thilo GambichlerJürgen C Becker

DNA methylation differences at birth after conception through ART

Nov 24, 2020·Human Reproduction·Elmar W TobiAnastasia N Iliadou

Epigenome-wide association scan identifies methylation sites associated with HIV infection

Nov 25, 2020·Epigenomics·Chang ShuBrion S Maher

Genome-wide DNA methylation analysis of peripheral blood cells derived from patients with first-episode schizophrenia in the Chinese Han population

Dec 7, 2020·Molecular Psychiatry·Mingrui LiYin Yao

DNA methylation of insulin-like growth factor 2 and H19 cluster in cord blood and prenatal air pollution exposure to fine particulate matter.

Dec 9, 2020·Environmental Health : a Global Access Science Source·Congrong WangTim S Nawrot

Evidence for the placenta-brain axis: multi-omic kernel aggregation predicts intellectual and social impairment in children born extremely preterm.

Dec 15, 2020·Molecular Autism·Hudson P SantosRebecca C Fry

Platinum-Based Chemotherapy Induces Methylation Changes in Blood DNA Associated with Overall Survival in Patients with Ovarian Cancer

Sep 25, 2016·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·James M FlanaganRobert Brown

A Minimal DNA Methylation Signature in Oral Tongue Squamous Cell Carcinoma Links Altered Methylation with Tumor Attributes

Jun 12, 2016·Molecular Cancer Research : MCR·Neeraja M KrishnanBinay Panda

Genome-Wide DNA Methylation in Prediagnostic Blood and Bladder Cancer Risk in the Women's Health Initiative

Mar 16, 2018·Cancer Epidemiology, Biomarkers & Prevention : a Publication of the American Association for Cancer Research, Cosponsored by the American Society of Preventive Oncology·Kristina M JordahlParveen Bhatti

Methylomic Analysis of Ovarian Cancers Identifies Tumor-Specific Alterations Readily Detectable in Early Precursor Lesions

Aug 16, 2018·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Thomas R PisanicTian-Li Wang

Integrative Genomic Characterization Identifies Molecular Subtypes of Lung Carcinoids

Jul 14, 2019·Cancer Research·Saurabh V LaddhaChang S Chan

Associations of Alcohol Consumption With Epigenome-Wide DNA Methylation and Epigenetic Age Acceleration: Individual-Level and Co-twin Comparison Analyses.

Dec 6, 2020·Alcoholism, Clinical and Experimental Research·Mallory StephensonMiina Ollikainen

Epigenome-wide association study of maternal hemoglobin A1c in pregnancy and cord blood DNA methylation.

Jan 8, 2021·Epigenomics·Diana L Juvinao-QuinteroMarie-France Hivert

Genome-wide DNA methylomic differences between dorsolateral prefrontal and temporal pole cortices of bipolar disorder

Jul 7, 2019·Journal of Psychiatric Research·Ada M-C HoMarin Veldic

Proteogenomic Characterization Reveals Therapeutic Vulnerabilities in Lung Adenocarcinoma.

Jul 11, 2020·Cell·Michael A GilletteClinical Proteomic Tumor Analysis Consortium

Proteogenomic insights into the biology and treatment of HPV-negative head and neck squamous cell carcinoma.

Jan 9, 2021·Cancer Cell·Chen HuangClinical Proteomic Tumor Analysis Consortium

Pangenomic Classification of Pituitary Neuroendocrine Tumors

Dec 31, 2019·Cancer Cell·Mario NeouGuillaume Assié

Association of variably methylated tumour DNA regions with overall survival for invasive lobular breast cancer.

Jan 20, 2021·Clinical Epigenetics·Medha SumanMelissa C Southey

Differential DNA Methylation in Prostate Tumors from Puerto Rican Men.

Jan 17, 2021·International Journal of Molecular Sciences·Gilberto Ruiz-DeyaJong Y Park

Investigation of MORC1 DNA methylation as biomarker of early life stress and depressive symptoms

Nov 5, 2019·Journal of Psychiatric Research·Mara ThomasVanessa Nieratschker

Genome-Wide Identification and Analysis of the Methylation of lncRNAs and Prognostic Implications in the Glioma.

Jan 26, 2021·Frontiers in Oncology·Yijie HeZhijie Han

Novel DNA methylation marker discovery by assumption-free genome-wide association analysis of cognitive function in twins.

Feb 3, 2021·Aging Cell·Afsaneh MohammadnejadQihua Tan

A Longitudinal Epigenetic Aging and Leukocyte Analysis of Simulated Space Travel: The Mars-500 Mission

Nov 27, 2020·Cell Reports·Jamaji C Nwanaji-EnweremAndres Cardenas

Epigenome-wide DNA methylation and risk of breast cancer: a systematic review

Nov 2, 2020·BMC Cancer·Kaoutar Ennour-IdrissiCaroline Diorio

Hypermethylation and global remodelling of DNA methylation is associated with acquired cisplatin resistance in testicular germ cell tumours

Nov 1, 2020·Epigenetics : Official Journal of the DNA Methylation Society·Zeeshan FazalMichael J Spinella

Combined effects of genotype and childhood adversity shape variability of DNA methylation across age.

Feb 3, 2021·Translational Psychiatry·Darina CzamaraElisabeth B Binder

Maternal environmental exposure to bisphenols and epigenome-wide DNA methylation in infant cord blood

Jan 5, 2021·Environmental Epigenetics·Carolyn F McCabeJaclyn M Goodrich

Integrated digital pathology and transcriptome analysis identifies molecular mediators of T-cell exclusion in ovarian cancer

Nov 6, 2020·Nature Communications·Mélanie DesboisYulei Wang

Unsupervised subtyping and methylation landscape of pancreatic ductal adenocarcinoma.

Feb 2, 2021·Heliyon·Shikha RoyDinesh Gupta

Blood-based epigenetic estimators of chronological age in human adults using DNA methylation data from the Illumina MethylationEPIC array

Oct 29, 2020·BMC Genomics·Yunsung LeeJon Bohlin

MADA: a web service for analysing DNA methylation array data.

Nov 19, 2020·BMC Bioinformatics·Xinyu HuMin Li

EWASex: an efficient R-package to predict sex in epigenome-wide association studies

Dec 15, 2020·Bioinformatics·Jesper Beltoft LundQihua Tan

DNA Methylation in LIME1 and SPTBN2 Genes Is Associated with Attention Deficit in Children.

Feb 13, 2021·Children·Sung-Chou LiLiang-Jen Wang

Lymphocyte DNA methylation mediates genetic risk at shared immune-mediated disease loci.

Jan 17, 2020·The Journal of Allergy and Clinical Immunology·Alexander D ClarkLouise N Reynard

Related Concepts

Malignant Neoplasms

Whole Genomic DNA Probes

DNA Methylation

Computational Molecular Biology

Cdna Microarrays

Epigenesis, Genetic

Malignant Neoplasms

Case-Control Studies

Genome

Methylation

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