Comment[ArrayExpressAccession]	E-MTAB-1986
MAGE-TAB Version	1.1
Investigation Title	DNA copy number profiling of canine osteosarcoma
Comment[Submitted Name]	DNA copy number profiling of canine osteosarcoma
Experiment Description	Identification of DNA copy number imbalances in 22 spontaneous canine osteosarcoma cases using array comparative genomic hybridization (aCGH) analysis
Experimental Design	disease state design	reference_design
Comment[AEExperimentType]	comparative genomic hybridization by array
Comment[AEExperimentDisplayName]	DNA copy number profiling of canine osteosarcoma
Experimental Factor Name	organism part	disease
Experimental Factor Type	organism part	disease
Quality Control Type	technical replicate
Quality Control Term Source REF	EFO
Public Release Date	2013-11-01
Person Last Name	Thomas
Person First Name	Rachael
Person Mid Initials
Person Email	rachael_thomas@ncsu.edu
Person Phone	919-513-0922
Person Address	1060 William Moore Drive, Raleigh, NC 27607
Person Affiliation	North Carolina State University College of Veterinary Medicine
Person Roles	submitter;investigator
PubMed ID
Publication Author List	Elinor K. Karlsson, Snaevar Sigurdsson, Emma Ivansson, Rachael Thomas, Ingegerd Elvers, Jason Wright, Cedric Howald, Noriko Tonomura, Michele Perloski, Ross Swofford, Tara Biagi, Sarah Fryc, Nathan Anderson, Celine Courtay-Cahen, Lisa Youell, Sally L. Ricketts, Sarah Mandlebaum, Patricio Rivera, Henrik von Euler, Bill Kisseberth, Eric S. Lander, Guillermo Couto, Kenine Comstock, Mike P. Starkey, Jaime Modiano, Matthew Breen, Kerstin Lindblad-Toh
Publication Title	Genome-wide analyses implicate 33 loci in heritable dog osteosarcoma, including regulatory variants near CDKN2A/B (Genome Biology)
Publication Status	submitted
Protocol Name	P-MTAB-35413	P-MTAB-35414	P-MTAB-35415	P-MTAB-35416	P-MTAB-35417
Protocol Type	growth protocol	nucleic acid extraction protocol	nucleic acid labeling protocol	nucleic acid hybridization to array protocol	array scanning protocol
Protocol Description	Biopsies obtained from family owned patients during routine diagnosis	Tissue biopsies from spontaneous osteosarcoma cases were acquired under aseptic conditions at the time of diagnosis by the primary clinician with the owner's consent. The diagnosis was confirmed by routine histopathologic examination. Biopsy specimens were snap frozen in liquid nitrogen and stored at -80C prior to DNA isolation. Total genomic DNA was isolated from fresh-frozen tumor tissue using a Qiagen DNeasy Blood and Tissue Kit (Qiagen, Valencia, CA) according to the manufacturer's instructions. DNA was eluted with ultrapure water and assessed for quality and concentration by spectrophotometry and agarose gel electrophoresis. An equimolar pool of blood-derived DNA from 50 female dogs of mixed breed was used as the common reference for all OS cases (Qiagen DNeasy Blood and Tissue Kit, Valencia, CA).	Thomas R, Seiser EL, Motsinger-Reif A, Borst L, Valli V, Kelley K, Suter SE, Argyle D, Burgess K, Bell J, Lindblad-Toh K, Modiano JF and Breen M. Refining tumor-associated aneuploidy through genomic recoding of recurrent DNA copy number aberrations in 150 canine non-Hodgkins lymphomas. Leukemia and Lymphoma 52:1321-1335 (2011) 	Thomas R, Seiser EL, Motsinger-Reif A, Borst L, Valli V, Kelley K, Suter SE, Argyle D, Burgess K, Bell J, Lindblad-Toh K, Modiano JF and Breen M. Refining tumor-associated aneuploidy through Ôgenomic recoding of recurrent DNA copy number aberrations in 150 canine non-Hodgkins lymphomas. Leukemia and Lymphoma 52:1321-1335 (2011) 	Thomas R, Seiser EL, Motsinger-Reif A, Borst L, Valli V, Kelley K, Suter SE, Argyle D, Burgess K, Bell J, Lindblad-Toh K, Modiano JF and Breen M. Refining tumor-associated aneuploidy through Ôgenomic recoding of recurrent DNA copy number aberrations in 150 canine non-Hodgkins lymphomas. Leukemia and Lymphoma 52:1321-1335 (2011)
Protocol Term Source REF	EFO	EFO	EFO	EFO	EFO
Term Source Name	EFO
Term Source File	http://www.ebi.ac.uk/efo
SDRF File	E-MTAB-1986.sdrf.txt