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Series GSE8649 Query DataSets for GSE8649
Status Public on Mar 15, 2008
Title High-resolution genetic analysis of cancer cell lines with near normal karyotypes
Organism Homo sapiens
Experiment type Genome variation profiling by SNP array
SNP genotyping by SNP array
Summary Cancer development is associated with multiple genetic alterations and genomic instability either at the chromosomal or base pair level is generally thought to underlie these changes. However, it is still unknown whether genetic instability is absolutely required for tumorigenesis. Here we investigated the genomic instability status of four cytogenetically stable diploid cell lines CAL51, SK-UT-1B, A204 and CH1. We applied high resolution 500K single nucleotide polymorphism (SNP) array analysis and found that all the four cell lines have some sub-microscopic genomic copy number changes. Interestingly, there were many more sub-microscopic chromosome alterations in A204 and CH1 than in CAL51 and SK-UT-1B. Twenty-four-color fluorescence in situ hybridization (FISH) was used to analyse a large number of metaphases from CAL51, SK-UT-1B and CH1 cells. The rate of de novo chromosome rearrangements was significantly higher in CH1 than CAL51 and SK-UT-1B. Although this increased rate did not lead to many clonal cytogenetically apparent chromosome alterations in CH1 cells, it is consistent with a first step towards chromosomal instability. It is more striking that both cell lines CAL51 and SK-UT-1B which have a similar de novo chromosomal change rate to that of normal lymphocytes were microsatellite instability positive by BAT-26 microsatellite analysis. This study further strengths the current concept that genomic instability is associated with tumor development.
Keywords: DNA copy number changes
Overall design DNA from A204, CH1, CAL51 and SK-UT-1B were analyzed by Affymetrix Genechip Mapping 500K Set array. Data were compared with normal samples from HAPMAP database.
Contributor(s) Mao X, Young BD, Chaplin T, Shipley J, Lu Y
Citation(s) 18407410
Submission date Aug 01, 2007
Last update date May 17, 2017
Contact name Xueying Mao
Organization name Queen Mary
Street address Charterhouse Square
City London
ZIP/Postal code EC1M 6BQ
Country United Kingdom
Platforms (2)
GPL3718 [Mapping250K_Nsp] Affymetrix Mapping 250K Nsp SNP Array
GPL3720 [Mapping250K_Sty] Affymetrix Mapping 250K Sty2 SNP Array
Samples (8)
GSM214534 Human rhabdomyosarcoma cell line_A204_NSP
GSM214535 Human rhabdomyosarcoma cell line_A204_STY
GSM214536 Human ovarian carcinoma cell line_CH1_NSP
BioProject PRJNA101839

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Supplementary file Size Download File type/resource
GSE8649_RAW.tar 230.7 Mb (http)(custom) TAR (of CEL, CHP)
Processed data provided as supplementary file
Processed data included within Sample table

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