Comment[ArrayExpressAccession] E-GEOD-50608 MAGE-TAB Version 1.1 Public Release Date 2014-04-30 Investigation Title Global DNA methylation: Uncommon event in Oral Lichenoid Disease [Illumina HumanMethylation27 BeadChip] Comment[Submitted Name] Global DNA methylation: Uncommon event in Oral Lichenoid Disease [Illumina HumanMethylation27 BeadChip] Experiment Description Purpose Accumulating evidence indicates aberrant DNA methylation is closely related to oral carcinogenesis, and it has been shown that methylation changes might be used as prognostic biomarker in oral squamous cell carcinoma. Oral lichenoid disease (OLD) is the most common oral potentially malignant disorder in our region. In this study, we have performed a wide DNA methylation study of a series of oral lichenoid disease in order to assess the relevance of DNA methylation changes in this premalignant disorder. Experimental Design Discovery phase utilized HumanMethylation27 DNA Analysis BeadChip assay in 18 OLD and 5 control samples. The differently methylated loci and the global DNA methylation surrogate LINE-, were further validated in an independent sample set consisting in 158 OLD and 65 controls. Results DNA methylation profile of the OLD showed only minor significant differences when compared to controls. MGC40178, ADORA1 and LINE-1 were slightly hypomethylated in 23, 40 and 43 % of the OLD samples respectively, while only in 13, 18 and 15% of the controls. Conclusions In summary, our data indicates that the frequency of aberrant DNA alteration is very low in OLD, which support the low rate of malignization of this oral potentially malignant disorder. Bisulphite converted DNA from the 17 Oral lichenoid samples and 5 control samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.217 Term Source Name ArrayExpress EFO Term Source File http://www.ebi.ac.uk/arrayexpress/ http://www.ebi.ac.uk/efo/efo.owl Person Last Name Bediaga Bediaga Aguirre-Urizar Acha-Sagredo Person First Name Naiara Naiara Jose Amelia Person Mid Initials G G M Person Email geo@ncbi.nlm.nih.gov Person Affiliation University of the Basque Country Person Address University of the Basque Country, Miguel de Unamuno 3, Vitoria, Spain Person Roles submitter Protocol Name P-GSE50608-22 P-GSE50608-9 P-GSE50608-19 P-GSE50608-18 P-GSE50608-17 P-GSE50608-16 P-GSE50608-20 P-GSE50608-8 P-GSE50608-15 P-GSE50608-3 P-GSE50608-7 P-GSE50608-21 P-GSE50608-13 P-GSE50608-5 P-GSE50608-11 P-GSE50608-12 P-GSE50608-14 P-GSE50608-2 P-GSE50608-4 P-GSE50608-1 P-GSE50608-10 P-GSE50608-6 P-GSE50608-24 P-GSE50608-25 P-GSE50608-23 P-GSE50608-26 Protocol Description Quality control and data pre-processisng was performed using lumi package (Bioconductor).Samples were background adjusted, processed for the colour channel adjustement and quantile normalized. For the detection of differentially methylated CpG sites, a linear model was fitted to the data and empirical Bayes moderated t-statistics were calculated using limma package (Bioconductor). ID_REF = VALUE = background adjusted, processed for the colour channel adjustement and quantile normalized data CN-12 Detection Pval = Quality control and data pre-processisng was performed using lumi package (Bioconductor).Samples were background adjusted, processed for the colour channel adjustement and quantile normalized. For the detection of differentially methylated CpG sites, a linear model was fitted to the data and empirical Bayes moderated t-statistics were calculated using limma package (Bioconductor). ID_REF = VALUE = background adjusted, processed for the colour channel adjustement and quantile normalized data LQ-94 Detection Pval = Quality control and data pre-processisng was performed using lumi package (Bioconductor).Samples were background adjusted, processed for the colour channel adjustement and quantile normalized. For the detection of differentially methylated CpG sites, a linear model was fitted to the data and empirical Bayes moderated t-statistics were calculated using limma package (Bioconductor). ID_REF = VALUE = background adjusted, processed for the colour channel adjustement and quantile normalized data CN-08 Detection Pval = Quality control and data pre-processisng was performed using lumi package (Bioconductor).Samples were background adjusted, processed for the colour channel adjustement and quantile normalized. For the detection of differentially methylated CpG sites, a linear model was fitted to the data and empirical Bayes moderated t-statistics were calculated using limma package (Bioconductor). ID_REF = VALUE = background adjusted, processed for the colour channel adjustement and quantile normalized data CN-01 Detection Pval = Quality control and data pre-processisng was performed using lumi package (Bioconductor).Samples were background adjusted, processed for the colour channel adjustement and quantile normalized. For the detection of differentially methylated CpG sites, a linear model was fitted to the data and empirical Bayes moderated t-statistics were calculated using limma package (Bioconductor). ID_REF = VALUE = background adjusted, processed for the colour channel adjustement and quantile normalized data LQ-116 Detection Pval = Quality control and data pre-processisng was performed using lumi package (Bioconductor).Samples were background adjusted, processed for the colour channel adjustement and quantile normalized. For the detection of differentially methylated CpG sites, a linear model was fitted to the data and empirical Bayes moderated t-statistics were calculated using limma package (Bioconductor). ID_REF = VALUE = background adjusted, processed for the colour channel adjustement and quantile normalized data LQ-143 Detection Pval = Quality control and data pre-processisng was performed using lumi package (Bioconductor).Samples were background adjusted, processed for the colour channel adjustement and quantile normalized. For the detection of differentially methylated CpG sites, a linear model was fitted to the data and empirical Bayes moderated t-statistics were calculated using limma package (Bioconductor). ID_REF = VALUE = background adjusted, processed for the colour channel adjustement and quantile normalized data CN-09 Detection Pval = Quality control and data pre-processisng was performed using lumi package (Bioconductor).Samples were background adjusted, processed for the colour channel adjustement and quantile normalized. For the detection of differentially methylated CpG sites, a linear model was fitted to the data and empirical Bayes moderated t-statistics were calculated using limma package (Bioconductor). ID_REF = VALUE = background adjusted, processed for the colour channel adjustement and quantile normalized data LQ-85 Detection Pval = Quality control and data pre-processisng was performed using lumi package (Bioconductor).Samples were background adjusted, processed for the colour channel adjustement and quantile normalized. For the detection of differentially methylated CpG sites, a linear model was fitted to the data and empirical Bayes moderated t-statistics were calculated using limma package (Bioconductor). ID_REF = VALUE = background adjusted, processed for the colour channel adjustement and quantile normalized data LQ-144 Detection Pval = Quality control and data pre-processisng was performed using lumi package (Bioconductor).Samples were background adjusted, processed for the colour channel adjustement and quantile normalized. For the detection of differentially methylated CpG sites, a linear model was fitted to the data and empirical Bayes moderated t-statistics were calculated using limma package (Bioconductor). ID_REF = VALUE = background adjusted, processed for the colour channel adjustement and quantile normalized data LQ-39 Detection Pval = Quality control and data pre-processisng was performed using lumi package (Bioconductor).Samples were background adjusted, processed for the colour channel adjustement and quantile normalized. For the detection of differentially methylated CpG sites, a linear model was fitted to the data and empirical Bayes moderated t-statistics were calculated using limma package (Bioconductor). ID_REF = VALUE = background adjusted, processed for the colour channel adjustement and quantile normalized data LQ-65 Detection Pval = Quality control and data pre-processisng was performed using lumi package (Bioconductor).Samples were background adjusted, processed for the colour channel adjustement and quantile normalized. For the detection of differentially methylated CpG sites, a linear model was fitted to the data and empirical Bayes moderated t-statistics were calculated using limma package (Bioconductor). ID_REF = VALUE = background adjusted, processed for the colour channel adjustement and quantile normalized data CN-11 Detection Pval = Quality control and data pre-processisng was performed using lumi package (Bioconductor).Samples were background adjusted, processed for the colour channel adjustement and quantile normalized. For the detection of differentially methylated CpG sites, a linear model was fitted to the data and empirical Bayes moderated t-statistics were calculated using limma package (Bioconductor). ID_REF = VALUE = background adjusted, processed for the colour channel adjustement and quantile normalized data LQ-121 Detection Pval = Quality control and data pre-processisng was performed using lumi package (Bioconductor).Samples were background adjusted, processed for the colour channel adjustement and quantile normalized. For the detection of differentially methylated CpG sites, a linear model was fitted to the data and empirical Bayes moderated t-statistics were calculated using limma package (Bioconductor). ID_REF = VALUE = background adjusted, processed for the colour channel adjustement and quantile normalized data LQ-60 Detection Pval = Quality control and data pre-processisng was performed using lumi package (Bioconductor).Samples were background adjusted, processed for the colour channel adjustement and quantile normalized. For the detection of differentially methylated CpG sites, a linear model was fitted to the data and empirical Bayes moderated t-statistics were calculated using limma package (Bioconductor). ID_REF = VALUE = background adjusted, processed for the colour channel adjustement and quantile normalized data LQ-113 Detection Pval = Quality control and data pre-processisng was performed using lumi package (Bioconductor).Samples were background adjusted, processed for the colour channel adjustement and quantile normalized. For the detection of differentially methylated CpG sites, a linear model was fitted to the data and empirical Bayes moderated t-statistics were calculated using limma package (Bioconductor). ID_REF = VALUE = background adjusted, processed for the colour channel adjustement and quantile normalized data LQ-120 Detection Pval = Quality control and data pre-processisng was performed using lumi package (Bioconductor).Samples were background adjusted, processed for the colour channel adjustement and quantile normalized. For the detection of differentially methylated CpG sites, a linear model was fitted to the data and empirical Bayes moderated t-statistics were calculated using limma package (Bioconductor). ID_REF = VALUE = background adjusted, processed for the colour channel adjustement and quantile normalized data LQ-132 Detection Pval = Quality control and data pre-processisng was performed using lumi package (Bioconductor).Samples were background adjusted, processed for the colour channel adjustement and quantile normalized. For the detection of differentially methylated CpG sites, a linear model was fitted to the data and empirical Bayes moderated t-statistics were calculated using limma package (Bioconductor). ID_REF = VALUE = background adjusted, processed for the colour channel adjustement and quantile normalized data LQ-30 Detection Pval = Quality control and data pre-processisng was performed using lumi package (Bioconductor).Samples were background adjusted, processed for the colour channel adjustement and quantile normalized. For the detection of differentially methylated CpG sites, a linear model was fitted to the data and empirical Bayes moderated t-statistics were calculated using limma package (Bioconductor). ID_REF = VALUE = background adjusted, processed for the colour channel adjustement and quantile normalized data LQ-47 Detection Pval = Quality control and data pre-processisng was performed using lumi package (Bioconductor).Samples were background adjusted, processed for the colour channel adjustement and quantile normalized. For the detection of differentially methylated CpG sites, a linear model was fitted to the data and empirical Bayes moderated t-statistics were calculated using limma package (Bioconductor). ID_REF = VALUE = background adjusted, processed for the colour channel adjustement and quantile normalized data LQ-03 Detection Pval = Quality control and data pre-processisng was performed using lumi package (Bioconductor).Samples were background adjusted, processed for the colour channel adjustement and quantile normalized. For the detection of differentially methylated CpG sites, a linear model was fitted to the data and empirical Bayes moderated t-statistics were calculated using limma package (Bioconductor). ID_REF = VALUE = background adjusted, processed for the colour channel adjustement and quantile normalized data LQ-104 Detection Pval = Quality control and data pre-processisng was performed using lumi package (Bioconductor).Samples were background adjusted, processed for the colour channel adjustement and quantile normalized. For the detection of differentially methylated CpG sites, a linear model was fitted to the data and empirical Bayes moderated t-statistics were calculated using limma package (Bioconductor). ID_REF = VALUE = background adjusted, processed for the colour channel adjustement and quantile normalized data LQ-61 Detection Pval = standard as recommended by illumina Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting genomic DNA was extracted and purified from oral rinse samples using using Gentra Puregene Buccal Cell Kit according to standard instructions Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting Protocol Type normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol labelling protocol hybridization protocol nucleic acid extraction protocol array scanning protocol Experimental Factor Name DISEASE AGE SEX Experimental Factor Type disease age sex Comment[SecondaryAccession] GSE50608 Comment[GEOReleaseDate] 2014-04-30 Comment[ArrayExpressSubmissionDate] 2013-09-05 Comment[GEOLastUpdateDate] 2014-04-30 Comment[AEExperimentType] methylation profiling by array Comment[AdditionalFile:Data1] GSE50608_non-normalized.txt SDRF File E-GEOD-50608.sdrf.txt