NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE30777 Query DataSets for GSE30777
Status Public on Nov 29, 2011
Title Acquired genomic copy number aberrations and survival in chronic lymphocytic leukemia
Organism Homo sapiens
Experiment type Genome variation profiling by SNP array
Summary Genomic aberrations are of predominant importance to the biology and clinical outcome of patients with chronic lymphocytic leukemia (CLL), and FISH-based genomic risk classifications are routinely used in clinical decision making in CLL. One of the known limitations of CLL FISH is the inability to comprehensively interrogate the CLL genome for genomic changes. In an effort at overcoming the existing limitations in CLL genome analysis, we have analyzed high-purity DNA isolated from FACS-sorted CD19+ cells and paired CD3+ or buccal cells from 255 CLL patients for acquired genomic copy number aberrations (aCNA) using ultra-high-density Affymetrix SNP 6.0 arrays. Overall, two or more subchromosomal aCNA were found in 39% (100/255) of all cases analyzed, while ≥3 subchromosomal aCNA were detected in 20% (50/255) of cases. Subsequently, we have correlated genomic lesion loads (genomic complexity) with the clinical outcome measures time to first therapy (TTFT) and overall survival (OS). Using multivariate analyses incorporating the most important prognostic factors in CLL together with SNP 6.0 array-based genomic lesion loads at various thresholds, we identify elevated CLL genomic complexity as an independent and powerful marker for the identification of CLL patients with aggressive disease and short survival.
 
Overall design we have analyzed high-purity DNA isolated from FACS-sorted CD19+ cells and paired CD3+ or buccal cells from 255 CLL patients for acquired genomic copy number aberrations (aCNA) using ultra-high-density Affymetrix SNP 6.0 arrays
 
Contributor(s) Ouillette P, Collins R, Shakhan S, Li J, Peres E, Kujawski L, Talpaz M, Kaminski M, Li C, Shedden K, Malek SN
Citation(s) 21795749
Submission date Jul 19, 2011
Last update date Nov 27, 2018
Contact name Sami N Malek
E-mail(s) smalek@med.umich.edu, pouillet@med.umich.edu
Phone 734-763-1222
Organization name University of Michigan
Department Internal Medicine, Hematology-Oncology
Street address 4410 Cancer Center; 1500 E Medical Center Dr
City Ann Arbor
State/province MI
ZIP/Postal code 48109
Country USA
 
Platforms (1)
GPL6801 [GenomeWideSNP_6] Affymetrix Genome-Wide Human SNP 6.0 Array
Samples (510)
GSM764339 primary human: blood; FACS-sorted CD3+ cells (CLL001N_CD3)
GSM764340 primary human: blood; FACS-sorted CD19+ cells (CLL001T)
GSM764341 primary human: buccal swab (CLL002N)
Relations
BioProject PRJNA144311

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE30777_RAW.tar 14.6 Gb (http)(custom) TAR (of CEL)
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap