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Series GSE37259 Query DataSets for GSE37259
Status Public on Feb 01, 2013
Title Gene copy number variations associated with patient survival in uveal melanoma
Organism Homo sapiens
Experiment type Genome variation profiling by SNP array
SNP genotyping by SNP array
Summary Analysis of DNA from fixed tissues specimens of 58 primary uveal melanomas, with known clinical outcome, to determine gene copy number variations that were associated with survival.
Abstract: Uveal melanomas can be stratified into subgroups with high or low risk of metastatic death, according to the presence of gross chromosomal abnormalities. Where a monosomy 3 uveal melanoma is detected, patient survival at three years is reduced to 50%. However, approximately 5% of patients with a disomy 3 tumour ultimately develop metastasis, and a further 5% of monosomy 3 uveal melanoma patients’ exhibit disease-free survival for more than five years. Despite extensive knowledge of the chromosomal abnormalities occurring in uveal melanoma, the genes driving metastasis are not well defined. Gene copy number variations occurring in a well-characterised cohort of 58 formalin-fixed, paraffin-embedded uveal melanoma samples were identified using the Affymetrix SNP 6.0 whole genome microarray. Four genetic sub-groups of primary uveal melanoma were represented in the patient cohort: 1) disomy 3 with long-term survival; 2) metastasizing disomy 3; 3) metastasizing monosomy 3; and 4) monosomy 3 with long-term survival. Cox regression and Kaplan-Meier survival analysis identified three genes that were associated with differences in patient survival. Patients with an amplification of CNKSR3 (6q) or RIPK1 (6p) demonstrated longer survival than those with gene deletions or no copy number change (log rank, p=0.022 and p<0.001, respectively). Conversely, those patients with an amplification of PENK (8q) showed reduced survival (log rank p<0.001). CNKSR3, RIPK1 and PENK are novel candidate metastasis regulatory genes in uveal melanoma. This is the first report of amplification of a specific gene on 6p that is associated with improved uveal melanoma patient survival and suggests that the development of uveal melanomas with a propensity to metastasise may be limited by genes on 6p.
Overall design 58 samples in total. Ten disomy 3 with long-term survival. Fifteen disomy 3 with metastasising. Seventeen monosomy 3 with long-term survival. Sixteen monosomy 3 metastasising.
Contributor(s) Lake SL, Damato BE, Taktak AF, Lloyd BH, Coupland SE
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Submission date Apr 13, 2012
Last update date Nov 27, 2018
Contact name Sarah Lake
Phone 01517064869
Fax 01517065883
Organization name University of Liverpool
Department Molecular and Clinical Cancer Medicine
Lab Liverpool Ocular Oncology Research Group
Street address 6th Floor, Duncan Building, Daulby Street
City Liverpool
ZIP/Postal code CH62 4US
Country United Kingdom
Platforms (1)
GPL6801 [GenomeWideSNP_6] Affymetrix Genome-Wide Human SNP 6.0 Array
Samples (58)
GSM914992 DS1
GSM914993 DS2
GSM914994 DS3
BioProject PRJNA159145

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
GSE37259_RAW.tar 2.2 Gb (http)(custom) TAR (of CEL, CHP)
GSE37259_Segmentation_UM_SNP6_SLL.txt.gz 582.3 Kb (ftp)(http) TXT
GSE37259_UM_SNP6_CopyNumber_SLL.txt.gz 53.4 Kb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file
Processed data are available on Series record

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