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GEO help: Mouse over screen elements for information. |
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| 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
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| 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.
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| 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.
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| 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 |
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| Submission date |
Nov 11, 2008 |
| Last update date |
May 17, 2017 |
| Contact name |
Richard Rosenquist Brandell |
| E-mail(s) |
richard.rosenquist@genpat.uu.se
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| Organization name |
Uppsala University
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| Department |
Genetics and Pathology
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| Street address |
Rudbeck Laboratory
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| City |
Uppsala |
| ZIP/Postal code |
SE-751 85 |
| Country |
Sweden |
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| Platforms (4)
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| GPL3718 |
[Mapping250K_Nsp] Affymetrix Mapping 250K Nsp SNP Array |
| GPL4723 |
SWEGENE_BAC_32K_Full |
| GPL5149 |
Agilent Homo sapiens 185K array |
| GPL6980 |
Illumina HumanHap300-Duov2 Genotyping BeadChip (HumanHap300v2_A) |
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| Samples (40)
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| Relations |
| BioProject |
PRJNA110741 |
| 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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