Comment[ArrayExpressAccession] E-MTAB-815 Investigation Title DNA methylation profiling of human adrenocortical tumors (ACTs) Comment[Submitted Name] DNA methylation profiling of adrenocortical tumors (ACTs) Experimental Design DNA_methylation_array_design Comment[AEExperimentType] methylation profiling by array Experimental Factor Name DISEASESTATE TRANSCRIPTOME-BASED_SUBGROUPS Experimental Factor Type disease_state clinical_information Person Last Name Barreau Person First Name Olivia Person Email olivia.barreau@inserm.fr Person Affiliation Ligue Nationale Contre le Cancer, Paris, France Person Roles submitter Public Release Date 2012-10-05 Comment[ArrayExpressSubmissionDate] 2011-10-07 PubMed ID 23093492 Publication Author List Olivia Barreau, Guillaume Assie , Hortense Wilmot-Roussel, Bruno Ragazzon, Camille Baudry, Karine Perlemoine, Fernande Rene-Corail, Xavier Bertagna, Bertrand Dousset, Nadim Hamzaoui, Frederique Tissier, Aurelien de Reynies, Jerome Bertherat Publication Title Identification of a CpG Island Methylator Phenotype in Adrenocortical Carcinomas Experiment Description A Cartes d'Identite des Tumeurs (CIT) project from the french Ligue Nationale Contre le Cancer (http://cit.ligue-cancer.net) | Transcriptome analysis led to the unsupervised classification of carcinomas in two groups, associated with different outcomes {de Reynies, 2009 ; Giordano, 2009}. Subsequently, we have shown that unsupervised clustering further classified the tumors of the poor prognosis group in three different subgroups, two of them harbouring a cardinal molecular alteration {Ragazzon, 2010}. One is associated with p53 inactivation, the second with ?-catenin activation. No molecular defect has been identified in the third group so far. The aim is to describe the genome-wide methylome of adrenocortical tumors, and to assess the link with previously established molecular classifications. Experimental design: Genome-wide methylation patterns of 84 adenomas and 51 carcinomas were obtained with the Infinium HumanMethylation27 beadchip (Illumina). | Submitter : Olivia Barreau | Project leader : Jerome Bertherat Protocol Name P-MTAB-23416 P-MTAB-23417 P-MTAB-23418 P-MTAB-23419 P-MTAB-23420 P-MTAB-23421 Protocol Type treatment nucleic_acid_extraction labeling hybridization scanning bioassay_data_transformation Protocol Description The tumors were prospectively collected in the tumor bank of the COMETE network (Cortico-Medulo Tumeurs Endocrines). One hundred thirthy-five tumors, collected between 1993 and 2005 by the Cochin team, were included in this study. Samples were dissected by the pathologist immediately after tumor removal, snap frozen and kept in liquid nitrogen. Tumor samples (10 to 50 mg) were powdered under liquid nitrogen. DNA was extracted and purified by cesium chloride gradient ultracentrifugation (30) or by proteinase K digestion and ethanol extraction, followed by a clean-up step on columns (Qiagen, Courtaboeuf, France). Bisulfite-converted DNA samples were prepared and quantified using a NanoDrop ND-1000 spectrophotometer. For each sample, 500ng of whole-genome bisulfite-converted DNA was denatured, fragmented, and amplified using Illumina-supplied reagents according to manufacturer instructions. DNA samples were not labelled because after hybridization, allele-specific single-base extension incorporates fluorescent labels for detection. DNA was hybridized to Illumina Infinium HumanMethylation27 arrays, containing 50-mer oligonucleotides designed to hybridize either methylated (N-CG-N following bisulfite conversion) or unmethylated (N-TG-N following bisulfite conversion) cytosine on each CG pair interrogated, coupled to beads mounted on glass slides. Microarrays were washed under high stringency, labeled with biotin (C and G nucleotides) or dinitrophenyl (A and T nucleotides), and scanned with an Illumina iScan. The methylation data were processed using the Bioconductor lumi package. The methylation data was color balance check, background corrected, and normalized using quantile normalization, based on the assumption that the intensity distribution of the pooled methylated and unmethylated probes are similar for different samples . 89 CpG sites with more than 25% of samples having detection p-values worse than 0.05 were filtered before the analysis. Methylation values for each CpG locus are expressed as a ﾓM-valueﾔ, calculated as the log2 ratio of the intensities of methylated probe versus unmethylated probe for a given locus, Term Source Name ArrayExpress Term Source File http://www.ebi.ac.uk/arrayexpress SDRF File E-MTAB-815.sdrf.txt Publication DOI 10.1210/jc.2012-2993