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Series GSE30283 Query DataSets for GSE30283
Status Public on Oct 25, 2012
Title The histotype-specific copy-number landscape of ovarian cancer (copy number Japan)
Organism Homo sapiens
Experiment type Genome variation profiling by SNP array
Summary Ovarian cancer is characterized by multiple structural aberrations; most are passenger alterations which do not confer tumor growth. Like many cancers, it is a heterogeneous disease and till date, the histotype-specific copy number landscape has been difficult to elucidate. To dissect the heterogeneity of ovarian cancer and understand the pathogenesis of its various histotypes, we developed an in silico hypothesis-driven workflow to identify histotype-specific copy number aberrations across multiple datasets of epithelial ovarian cancer. In concordance with previous studies on global copy number changes, our study showed similar alterations. However, when the landscape was de-convoluted into histotypes, distinct alterations were observed. We report here a comprehensive histotype-specific copy number landscape of ovarian cancer and showed that there is genomic diversity between the histotypes; some involving well known cancer genes and some novel potential driver genes. Besides preferential occurrence of alterations in some histotypes, opposite trends of alteration were observed; such as ERBB2 amplification in mucinous but deletion in serous tumors. The landscape highlights the need for identifying histotype-specific aberrations in ovarian cancer and present potential to tailor management of ovarian cancer based on molecular signature of histotypes.
 
Overall design 56 samples containing the 4 histotypes were used for this study. It contained 12 clear cell carcinoma, 6 endometrioid adenocarcinoma, 2 mucinous adenocarcinoma, 5 mucinous-borderline tumors, 26 serous adenocarcinoma, and 5 serous-borderline tumors.
Data was pre-processed and normalized with Hapmap JPT using the Affymetric Genotyping Console.
 
Citation(s) 23078675
Submission date Jun 28, 2011
Last update date Nov 27, 2018
Contact name Liang Goh
E-mail(s) liang.goh@duke-nus.edu.sg
Organization name Duke-NUS graduate medical school
Street address College Road
City Singapore
ZIP/Postal code 169857
Country Singapore
 
Platforms (1)
GPL6801 [GenomeWideSNP_6] Affymetrix Genome-Wide Human SNP 6.0 Array
Samples (56)
GSM750312 Ovarian cancer tissue from Japan JPKO-1
GSM750313 Ovarian cancer tissue from Japan JPKO-2
GSM750314 Ovarian cancer tissue from Japan JPKO-6
This SubSeries is part of SuperSeries:
GSE30311 The histotype-specific copy-number landscape of ovarian cancer
Relations
BioProject PRJNA154789

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
GSE30283_RAW.tar 3.5 Gb (http)(custom) TAR (of CEL, CNCHP)
Processed data included within Sample table
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