MAGE-TAB Version	1.1						
Investigation Title	Copy Number and SNP Genotyping in pediatric AML						
Experimental Design	genotyping design	disease state design					
Experimental Design Term Source REF	EFO	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)	Meshinchi	Arceci	Ries		
Person First Name			Soheil	Robert	Rhonda		
Person Mid Initials				J	E 		
Person Email	ocg@mail.nih.gov	ncicbiit@mail.nih.gov	smeshinc@fhrc.org	rarceci@phoenixchildrens.com	rries@fhcrc.org		
Person Phone	+1 301 451 8027	+1 888 478 4423	206-667-4077	602-827-2508	206-667-7104		
Person Fax	+1 301 480 4368		206-667-4310	602-271-0264			
Person Address	31 Center Dr, Rm 10A07, Bethesda, MD 20892	9609 Medical Center Dr, Rockville, MD 20850	1100 Fairview Avenue North, D5-380, POB 19024, Seattle, WA  98109	445 N. 5th St, Tgen Building Room 322, Phoenix, AZ 85004	1100 Fairview Avenue North, D2-245, Seattle, WA  98109		
Person Affiliation	National Cancer Institute	National Cancer Institute	Fred Hutchinson Cancer Research Center	University of Arizona College of Medicine	Fred Hutchinson Cancer Research Center		
Person Roles	funder	data coder;curator	investigator	investigator	submitter;data analyst		
Person Roles Term Source REF	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	Analysis of copy number and SNP genotyping in the TARGET pediatric AML cohort						
Protocol Name	fredhutch.org:Protocol:DNA-Extraction-Qiagen:01	hudsonalpha.org:Protocol:CopyNumberArray-Labeling-Affymetrix-SNP6:01	hudsonalpha.org:Protocol:CopyNumberArray-Hybridization-Affymetrix-SNP6:01	hudsonalpha.org:Protocol:CopyNumberArray-Scanning-Affymetrix-SNP6:01	fredhutch.org:Protocol:CopyNumberArray-DataNormalization-Birdseed:01	fredhutch.org:Protocol:CopyNumberArray-CnvSegment-Partek:01	fredhutch.org:Protocol:CopyNumberArray-CnvSegment-Filter:01
Protocol Type	nucleic acid extraction protocol	nucleic acid labeling protocol	nucleic acid hybridization to array protocol 	array scanning protocol	normalization data transformation protocol	data transformation protocol	data transformation protocol
Protocol Term Source REF	EFO	EFO	EFO	EFO	EFO	EFO	EFO
Protocol Description	"Starting with one vial of cryopreserved cells derived from Bone Marrow (or if Bone Marrow unavailable, Peripheral Blood), cells undergo a quick thaw and are adding to a tube containing PBS (to dilute the residual DMSO).  Cells are spun at 1000RPM and pelleted.  The pellet is vortexed and resuspended in lysis buffer from the Qiagen AllPrep DNA/RNA mini kit.  The lysate is added to an RNeasy spin column to isolate RNA while the flow through is added to the DNA spin column for subsequent DNA isolation.  After a series of washes on each column, DNA or RNA is eluted into a tube using elution buffer or RNase-free H20 respectively.  Both nucleic acids are evaluated on the NanoDrop for initial sample concentration and quality.  DNA quantification is then assessed using the Picogreen assay for better accuracy.  RNA quality and quantity is also assessed using the Agilent Bioanalyzer nanochip."	"All genotyping was performed according to manufacturer’s protocol.  Briefly, two identical aliquots containing 250ng of DNA were digested with specific restrictions enzymes in separate reactions; one reaction contained Nsp1 and the other Sty1.  Immediately following digestion, each sample was ligated with adaptors containing a complementary sequence to the overhang generated at digestion.  Following ligation, each sample was subjected to PCR amplification using standard reagents.  Following PCR, each sample was assayed on a 2% agarose gel to ensure that a DNA smear of appropriate size was produced.  The Nsp and Sty amplifications were combined, purified and quantitated.  All samples with at least 180 micrograms total DNA were allowed to continue to fragmentation using the enzymatic reaction  Affymetrix Fragmentation reagent.  The fragmented DNA was assayed on a 4% agarose gel to ensure that the size of the DNA collapsed to less than 75nt.  Following fragmentation, the DNA was end-labeled with terminal deoxy transferase and Affymetrix DNA labeling reagent.  "	"Nucleic acid hybridization was performed according to the manufacturer's protocol for the AffyMetrix 6.0 SNP array.  Each sample was then resuspended in hybridization buffer and hybridized to the Affymetrix 6.0 array for 16 hours. Following hybridization, the arrays were washed on the Affymetrix Fluidics station and scanned on the GeneChip scanner. "	"The array scanning protocol was performed according to the manufacturer's protocol for the AffyMetrix 6.0 SNP array."	"All data were processed using the standard analysis suite provided by Affymetrix.  The QC call rate is developed for each sample using a subset of SNPs and the DM algorithm.  A QC call rate of greater than 87% is a passing score for Affymetrix, the average call rate for this dataset was 99.4%. Samples passing the QC call rate are then clustered using the Birdseed algorithm.  Individual data files (CEL files) were uploaded to Partek Genomics Suite (St. Louis, MO).  Using a paired analysis (each patient’s remission samples was used as the reference), copy number was calculated for each probeset and is indicated in the level 2 file, TARGET_AML_level2_paired_CN_log2_format.txt.   "	"To find areas of the genome amplified or deleted, the Partek segmentation algorithm was applied to the level 2 dataset."	"The unfiltered copy number segmentation file, TARGET_AML_CN_level3_unfiltered_Diagnostic.txt, contains all segments for each patient, both changed and unchanged, with no filtering parameters applied.  To reduce the number of false positives and filter out segments of the genomes that are unchanged, TARGET_AML_CN_level3_filtered_Diagnostic.txt, contains only segments with &lt;1.7 or &gt;2.3 copy number, have &gt;99 markers and a p-value &lt;0.05.  In addition, segments from the Y chromosome and mitochondrial genome were removed."
Protocol Parameters							
Protocol Hardware							
Protocol Software							
Protocol Contact							
SDRF File	TARGET_AML_CopyNumberArray_20161116.sdrf.txt						
Term Source Name	NCBITaxon	NCIt	MO	EFO			
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			
Term Source Version							