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Series GSE13557 Query DataSets for GSE13557
Status Public on Dec 10, 2008
Title Screening for copy-number alterations and LOH in CLL - a comparative study of four microarray platforms
Organism Homo sapiens
Experiment type Genome variation profiling by SNP array
Genome variation profiling by genome tiling array
Summary Screening for gene copy-number alterations (CNAs) has improved by applying genome-wide microarrays, where SNP arrays also allow analysis of loss of heterozygozity (LOH). We here analyzed 10 chronic lymphocytic leukemia (CLL) samples using four different high-resolution platforms: BAC arrays (32K), oligonucleotide arrays (185K, Agilent), and two SNP arrays (250K, Affymetrix and 317K, Illumina). Cross-platform comparison revealed 29 concordantly detected CNAs, including known recurrent alterations, which confirmed that all platforms are powerful tools when screening for large aberrations. However, detection of 32 additional regions present in 2-3 platforms illustrated a discrepancy in detection of small CNAs, which often involved reported copy-number variations. LOH analysis revealed concordance of mainly large regions, but showed numerous, small nonoverlapping regions and LOH escaping detection. Evaluation of baseline variation and copy-number ratio response showed the best performance for the Agilent platform and confirmed the robustness of BAC arrays. Accordingly, these platforms demonstrated a higher degree of platform-specific CNAs. The SNP arrays displayed higher technical variation, although this was compensated by high density of elements. Affymetrix detected a higher degree of CNAs compared to Illumina, while the latter showed a lower noise level and higher detection rate in the LOH analysis. Large-scale studies of genomic aberrations are now feasible, but new tools for LOH analysis are requested.
Overall design 10 chronic lymphocytic leukemia (CLL) samples was analyzed using four different high-resolution platforms: 32K BAC arrays, 185K Agilent oligonucleotide arrays, 250K Affymetrix SNP arrays and 317K Illumina SNP arrays.
Contributor(s) Gunnarsson R, Staaf J, Jansson M, Ottesen A, Göransson H, Liljedahl U, Ralfkiær U, Mansouri M, Buhl A, Ekström Smedby K, Hjalgrim H, Syvänen A, Borg A, Isaksson A, Jurlander J, Juliusson G, Rosenquist R
Citation(s) 18484635
Submission date Nov 11, 2008
Last update date May 17, 2017
Contact name Richard Rosenquist Brandell
Organization name Uppsala University
Department Genetics and Pathology
Street address Rudbeck Laboratory
City Uppsala
ZIP/Postal code SE-751 85
Country Sweden
Platforms (4)
GPL3718 [Mapping250K_Nsp] Affymetrix Mapping 250K Nsp SNP Array
GPL5149 Agilent Homo sapiens 185K array
Samples (40)
GSM322209 4_BAC
GSM322210 5_BAC
GSM322211 8_BAC
BioProject PRJNA110741

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
GSE13557_Illumina_raw.txt 95.0 Mb (ftp)(http) TXT
GSE13557_RAW.tar 791.9 Mb (http)(custom) TAR (of CEL, CHP, GPR, TXT)
Processed data included within Sample table

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