MAGE-TAB Version	1.1					
Investigation Title	Characterization of DNA methylation in Wilms Tumor TARGET Cohort					
Experimental Design	disease state design					
Experimental Design Term Source REF	EFO					
Experimental Factor Name						
Experimental Factor Type						
Experimental Factor Term Source REF						
Person Last Name	NCI Office of Cancer Genomics (OCG)	NCI Center for Biomedical Informatics and Information Technology (CBIIT)	Gadd	Perlman		
Person First Name			Samantha	Elizabeth		
Person Mid Initials			L	J		
Person Email	ocg@mail.nih.gov	ncicbiit@mail.nih.gov	sgadd@luriechildrens.org	eperlman@luriechildrens.org 		
Person Phone	+1 301 451 8027	+1 888 478 4423	773-755-6392	312-227-3967		
Person Fax	+1 301 480 4368					
Person Address	31 Center Dr, Rm 10A07, Bethesda, MD 20892	9609 Medical Center Dr, Rockville, MD 20850	2430 N Halsted St, Room C366, Chicago, IL 60614	225 E Chicago Avenue, Chicago, IL 60611		
Person Affiliation	National Cancer Institute	National Cancer Institute	Lurie Children's Hospital of Chicago Research Center  	Ann &amp; Robert H. Lurie Children's Hospital of Chicago		
Person Roles	funder	data coder;curator	submitter;data analyst	investigator		
Person Roles Term Source REF	EFO	EFO;EFO	EFO	EFO		
Quality Control Type						
Quality Control Term Source REF						
Replicate Type						
Replicate Term Source REF						
Normalization Type						
Normalization Term Source REF						
Date of Experiment						
Public Release Date						
PubMed ID						
Publication DOI						
Publication Author List						
Publication Title						
Publication Status						
Publication Status Term Source REF						
Experiment Description	The NCI TARGET initiative seeks to identify therapeutic targets for high-risk pediatric tumors through genomic sequencing supported by copy number, gene expression, and epigenetic analyses. The aim of this study was to use the Illumina 450K DNA methylation assay to determine the DNA methylation status of Wilms Tumor to characterize the epigenetic pattern of these tumors and for use in subsequent integrative analyses.					
Protocol Name	nationwidechildrens.org:Protocol:DNA-Extraction:01	northwestern.edu:Protocol:MethylationArray-Labeling-Illumina-450k:01	northwestern.edu:Protocol:MethylationArray-Hybridization-Illumina-450k:01	northwestern.edu:Protocol:MethylationArray-Scanning-Illumina-450k:01	northwestern.edu:Protocol:MethylationArray-DataNormalization-Illumina-450k:01	nci.nih.gov:CBIIT.OCGDCC.Protocol:MethylationArray-GeneAnnotation:01
Protocol Type	nucleic acid extraction protocol	nucleic acid labeling protocol	nucleic acid hybridization to array protocol 	array scanning and feature extraction protocol	normalization data transformation protocol	data transformation protocol
Protocol Term Source REF	EFO	EFO	EFO	EFO	EFO	EFO
Protocol Description	"DNA was extracted from tumor  samples at Nationwide Children's BioPathology Center (BPC) by using the standard BPC protocol. The DNA samples were analyzed by Pico green to verify gDNA concentration, spectrophotometry to verify DNA purity, and gel electrophoresis to verify DNA quality.  DNA samples (1.5 ug) diluted in nuclease-free water were provided to the Northwestern University Genomics Core in 96-well plate format for Illumina 450K DNA methylation analysis. Randomly selected samples were tested by NU to verify that the correct concentration had been provided. "	"See hybridization protocol description since  for Illumina Infinium 450K labeling is done after hybridization."	"Nucleic acid hybridization was performed according to the manufacturer's protocol for the Illumina 450K array at the Northwestern University Genomics Core Facility. "	"The array scanning protocol was performed according to the manufacturer's protocol for the Illumina 450K array at the Northwestern University Genomics Core Facility. "	"Raw data files (1 red and 1 green .idat file per sample and 1 .sdf file from each array, which included 12 samples per array) were processed at the Northwestern University Genomics Core Facility by BeadStudio software. The following subtables were generated by BeadStudio and were downloaded in .txt format: (1) the Sample Methylation Profile .txt, (2) the Control Profile .txt, and (3) the Control Probe Profile .txt. Several quality control steps were used for these data. Samples were subjected to the internal quality controls in the Bioconductor lumi package. Samples were subjected to a color balance check using the Bioconductor lumi package. Gender analysis was performed to increase our confidence that the data correctly corresponded to the expected sample. Because one of the X chromosomes is heavily methylated in females, the density of X-chromosome methylation is a good indicator of gender. Unsupervised hierarchical clustering based on all methylated regions on the X-chromosome was performed using average-linkage clustering with CLUSTER and the results were displayed with TREEVIEW. The tumors were assigned a gender based on their clustering in the tumor dendogram, which was checked against the known gender of the sample. The X-chromosome methylation profile corresponded to gender in the majority (~95%) of the samples; the other samples did not show gender-specific patterns."	"The Sample Methylation Profile text, which included information for all of the samples, was transformed by the DCC into a single .txt file per sample and annotated using hg19 reference genome.  The per-sample files contain the following columns: (1) the sample ID, (2) probe name, (3) AVG_Beta value, (4) gene Symbol, (5) chromosome, and (6) position."
Protocol Parameters						
Protocol Hardware						
Protocol Software						
Protocol Contact						
SDRF File	TARGET_WT_MethylationArray_20160831.sdrf.txt					
Term Source Name	NCBITaxon	NCIt	MO	EFO	OBI	
Term Source File	http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html	http://ncit.nci.nih.gov/	http://mged.sourceforge.net/ontologies/MGEDontology.php	http://www.ebi.ac.uk/efo	http://purl.obolibrary.org/obo/obi	
Term Source Version						