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Series GSE9110 Query DataSets for GSE9110
Status Public on Sep 02, 2009
Title SNP array data for 56 chronic myeloid leukemia samples.
Organism Homo sapiens
Experiment type Genome variation profiling by SNP array
SNP genotyping by SNP array
Summary Copy number and LOH analysis was performed for 56 chronic myeloid leukemia cases obtained from 23 CML cases obtained atchronic phase, accelerated phase, blast crisis, or remission. All caseswere genotyped with Affymetrix 250k Sty and Nsp arrays.
Keywords: Acute leukemia, BCR-ABL1, chronic myeloid leukemia, copy number analysis, loss-of-heterozygosity, genomics

*** Due to privacy concerns, the primary SNP array data is no longer available with unrestricted access. Individuals wishing to obtain this data for research purposes may request access using the Web links below. ***
 
Overall design All assays were performed on DNA extracted fromcryopreserved, mononuclear cell preparations of diagnostic peripheralblood or bone marrow samples. All blast crisis samples were flow sortedprior to DNA extraction. SNP calls were generated using AffymetrixGTYPE. Probe intensity data was extracted and used for DNA copy numberanalysis using dChip, a karyotype-guided normalization algorithm(Reference normalization, Mullighan et al Nature 2007;446:758), dChipand circular binary segmentation (implemented as DNAcopy in R).
 
Contributor(s) Mullighan CG, Downing JR
Citation(s) 18408710
Submission date Sep 20, 2007
Last update date May 17, 2017
Contact name Charles G Mullighan
E-mail(s) charles.mullighan@stjude.org
Phone 1-901-595-3387
Organization name St Jude Children's Research Hospital
Department Pathology
Street address 262 Danny Thomas Place
City Memphis
State/province TN
ZIP/Postal code 38105
Country USA
 
Platforms (2)
GPL3718 [Mapping250K_Nsp] Affymetrix Mapping 250K Nsp SNP Array
GPL3720 [Mapping250K_Sty] Affymetrix Mapping 250K Sty2 SNP Array
Samples (112)
GSM236454 Chronic myeloid leukemia CML-#1-CP-250ksty
GSM236455 Chronic myeloid leukemia CML-#1-BC-250ksty
GSM236456 Chronic myeloid leukemia CML-#2-CP-250ksty
This SubSeries is part of SuperSeries:
GSE9113 Affymetrix SNP array data for acute lymphoblastic leukemia samples
Relations
BioProject PRJNA105227

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