MAGE-TAB Version	1.1				
Investigation Title	TARGET: Kidney - Rhabdoid Tumor (RT) Mehtylation-array				
Experimental Design					
Experimental Design Term Source REF					
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)	Perlman	Ma	Novik
Person First Name			Elizabeth	Yussanne	Karen
Person Mid Initials				P	L
Person Email	ocg@mail.nih.gov	ncicbiit@mail.nih.gov	eperlman@luriechildrens.org	yma@bcgsc.ca	knovik@bcgsc.ca
Person Phone	+1 301 451 8027	+1 888 478 4423	+1 312 227 3967	+1 604 707 5800 Ext 6082	+1 604 707 8000 Ext 7983
Person Fax	+1 301 480 4368			+1 604 876 3561	+1 604 675 8178
Person Address	"31 Center Dr, Rm 10A07, Bethesda, MD 20892"	"9609 Medical Center Dr, Rockville, MD 20850"	"225 E Chicago Ave, Chicago, IL 60611"	"Suite 100-570 West 7th Ave, Vancouver, BC Canada V5Z 4S6"	"675 West 10th Ave Vancouver, BC Canada V5Z 1L3"
Person Affiliation	National Cancer Institute	National Cancer Institute	Ann & Robert H. Lurie Children's Hospital of Chicago	BC Cancer Agency Canada's Michael Smith Genome Sciences Centre	BC Cancer Agency Canada's Michael Smith Genome Sciences Centre
Person Roles	funder	data coder;curator	investigator	investigator;data analyst;submitter	investigator
Person Roles Term Source REF	EFO	EFO;EFO	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	TARGET Analysis of Methylation In RT				
Protocol Name	bcgsc.ca:Protocol:MethylationArray-DKFZ-Illumina-450K:01	bcgsc.ca:Protocol:MethylationArray-DKFZ-Illumina-450K:01	bcgsc.ca:Protocol:MethylationArray-DKFZ-Illumina-450K:01	bcgsc.ca:Protocol:MethylationArray-DKFZ-Illumina-450K:01	
Protocol Type	nucleic acid labeling protocol	nucleic acid sequencing protocol	array scanning and feature extraction protocol	normalization data transformation protocol	
Protocol Term Source REF	EFO	EFO	EFO	EFO	
Protocol Description	"DNA methylation from 150 primary ATRTs was assessed using Illumina HumanMethylation450 BeadChip arrays at the German Cancer Research Center (DKFZ) Genomics and Proteomics Core Facility according to the manufacturers instructions and as previously described (Sturm et al., 2012). Raw data files generated by the iScan array scanner were read and preprocessed using the capabilities of the Bioconductor package minfi (Aryee et al., 2014). With the minfi package the same preprocessing steps as in Illumina's Genomestudio software were performed. Additionally, a correction for batch effects was performed. Batch effects were estimated by fitting a linear model to the log2 transformed intensity values of the methylated and unmethylated channel. After removing the component due to the batch effect the residuals were back transformed to intensity scale and methylation beta values were calculated as described in Illuminas protocols. All samples were checked for expected and unexpected genotype matches by pairwise correlation of the 65 genotyping probes on the 450k array. In addition, the following filtering criteria were applied: Removal of probes targeting the X and Y chromosomes (n = 11,551), removal of probes containing a single nucleotide polymorphism (dbSNP132 Common) within five base pairs of and including the targeted CpG-site (n = 24,536), and probes not mapping uniquely to the human reference genome (hg19) allowing for one mismatch (n = 9,993). Finally, 438,370 probes were kept for analysis. Generation of copy number profiles was carried out as described (Sturm et al., 2012). Unsupervised hierarchical clustering was performed using the 10,000 most variable CG-probes over the whole cohort. Distance measure was euclidean for the CG-sites and 1-Pearson for the samples, average linkage. For consensus clustering, the R package ConsensusClusterPlus was used at the default settings. For assessment of overall methylation levels, beta values of all CG probes were averaged. Methylation data have been deposited at the NCBI Gene Expression Omnibus (GEO; http://www.ncbi.nlm.nih.gov/geo) and are accessible under accession number GSE70460."				
Protocol Parameters					
Protocol Hardware					
Protocol Software					
Protocol Contact					
SDRF File	TARGET_RT_MethylationArray_20191106.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					
