Investigation Title	TCGA Characterization of Tumor Samples by Copy Number Variation analysis of Low Coverage Whole Genome Sequencing using Illumina HiSeq Platform						
Experimental Design	Low pass whole genome DNA sequencing 						
Experimental Design Term Source REF	MGED Ontology						
Experimental Factor Name	Brain Lower Grade Glioma
Experimental Factor Type	disease_state						
Experimental Factor Type Term Source REF	MGED Ontology						
							
Person Last Name	Kucherlapati	Chin	Sahil				
Person First Name	Raju	Lynda	Seth				
Person Mid Initials							
Person Email	rkucherlapati@rics.bwh.harvard.edu	lchin@mdanderson.org	sseth@mdanderson.org				
Person Phone	617-525-4445	713-792-6876	713-794-5262				
Person Address	"77 Avenue Louis Pasteur, Boston, MA 02115"	"1901 East Road, 4SCR6.1042, Houston, Texas 77054"	"1901 East Road, 4SCR6.1039, Houston, Texas 77054"				
Person Affiliation	Harvard-Partners Center for Genetics and Genomics	M. D. Anderson Cancer Center	M. D. Anderson Cancer Center				
Person Roles	investigator	investigator	submitter				
Person Roles Term Source REF	MGED Ontology	MGED Ontology	MGED Ontology				
							
Quality Control Types							
Quality Control Types Term Source REF							
Replicate Type							
Replicate Type Term Source REF							
Date of Experiment	2/20/11						
Public Release Date							
							
PubMed ID							
Experiment Description	TCGA Characterization of Tumor Samples by Copy Number Variation analysis of Low Coverage Whole Genome Sequencing using Ilumina HiSeq Platform						
Protocol Name	hms.harvard.edu:labelling:IlluminaHiSeq_DNASeqC:01	hms.harvard.edu:library_preparation:IlluminaHiSeq_DNASeqC:01	hms.harvard.edu:cluster_generation:IlluminaHiSeq_DNASeqC:01	hms.harvard.edu:sequence_alignment:IlluminaHiSeq_DNASeqC:01	hms.harvard.edu:data_transformation:IlluminaHiSeq_DNASeqC:01		
Protocol Type	Random Shearing	Library Preparation	Cluster Generation	Sequence Alignment	Data Transformation		
Protocol Description	Random DNA fragmentation	Paired-end 50 base pair DNA sequence 	DNA amplification to produce clonal clusters	Sequence alignment to hg19 using BWA	Converting counts of aligned read counts to tumor/normal log 2 ratio values 		
Protocol Parameters							
Protocol Hardware							 
Protocol Software							
Protocol Contact							
Protocol Term Source REF							
SDRF Files	hms.harvard.edu_LGG.IlluminaHiSeq_DNASeqC.sdrf	hms.harvard.edu_LGG.IlluminaHiSeq_DNASeqC.sdrf	hms.harvard.edu_LGG.IlluminaHiSeq_DNASeqC.sdrf	hms.harvard.edu_LGG.IlluminaHiSeq_DNASeqC.sdrf	hms.harvard.edu_LGG.IlluminaHiSeq_DNASeqC.sdrf		 
Term Source Name	MGED Ontology						
Term Source File	http://mged.sourceforge.net/ontologies/MGEDontology.php						
Term Source Version	1.3.1.1						
		 	 	 	 		