GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE58579 Query DataSets for GSE58579
Status Public on Mar 01, 2015
Title High-resolution genome-wide copy number analysis of low grade serous ovarian tumours
Organism Homo sapiens
Experiment type Genome variation profiling by SNP array
Summary Integration of genomic copy number analysis (Affymetrix SNP6.0 arrays) and oncogenic RAS/RAF mutation status with clinical features and tumour progression.
This study found that loss of the 9p and the CDKN2A locus with the most significantly enriched copy number aberration distinguishing serous border tumors from low grade serous carcinomas, suggesting this is a key step to tumor progression.
Overall design Epithelial tissue from 57 serous borderline tumors (SBTs), 19 low grade serous carcinomas (LGSC)(data for 4 of the carcinomas have previously been submitted to GEO - Series GSE19539) and 355 high grade serous carinomas (HGSC)(TCGA, 2011; GSE19539; and 8 new) were analysed for copy number aberrations using Affymetrix SNP6.0 arrays and normalised SNP6.0 data. Stromal tissue from 38 SBT and 1 HGSC were analysed for copy number aberrations using Affymetrix SNP6.0 arrays. Matching lymphocyte DNA was availabe for 54 SBT, 3 LGSC and 1 HGSC. Sanger sequencing of KRAS, BRAF, NRAS, HRAS, ERBB2 and TP53 mutational hotspots was performed on the epithelial and stromal DNA. This information was then correlated with clinical features of the tumors.
Contributor(s) Campbell IG, Hunter SM, Gorringe KL
Citation missing Has this study been published? Please login to update or notify GEO.
Submission date Jun 17, 2014
Last update date Nov 27, 2018
Contact name Sally Hunter
Organization name Peter MacCallum Cancer Centre
Department Research
Lab Cancer Genetics
Street address 7 St Andrew's Pl
City Melbourne
State/province VIC
ZIP/Postal code 3002
Country Australia
Platforms (1)
GPL6801 [GenomeWideSNP_6] Affymetrix Genome-Wide Human SNP 6.0 Array
Samples (179)
GSM1414254 10115G
GSM1414255 10115T
GSM1414256 1066G
Affiliated with GSM492513
Affiliated with GSM492522
Affiliated with GSM492527
Affiliated with GSM492559
Affiliated with GSM492495
Affiliated with GSM492496
Affiliated with GSM492503
Affiliated with GSM492507
Affiliated with GSM492510
Affiliated with GSM492511
Affiliated with GSM492514
Affiliated with GSM492516
Affiliated with GSM492517
Affiliated with GSM492523
Affiliated with GSM492524
Affiliated with GSM492530
Affiliated with GSM492533
Affiliated with GSM492534
Affiliated with GSM492536
Affiliated with GSM492538
Affiliated with GSM492539
Affiliated with GSM492543
Affiliated with GSM492547
Affiliated with GSM492549
Affiliated with GSM492552
Affiliated with GSM492554
Affiliated with GSM492555
Affiliated with GSM492557
Affiliated with GSM492558
Affiliated with GSM492560
Affiliated with GSM492561
Affiliated with GSM492562
Affiliated with GSM492563
Affiliated with GSM492564
Affiliated with GSM492566
BioProject PRJNA254778

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
GSE58579_RAW.tar 5.1 Gb (http)(custom) TAR (of CEL)
Processed data included within Sample table

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