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Series GSE30300 Query DataSets for GSE30300
Status Public on Oct 25, 2012
Title The histotype-specific copy-number landscape of ovarian cancer (copy number SNP)
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 46 archived frozen tumor samples collected from Department of Obstetrics and Gynecology, Tri-Service General Hospital, Taiwan, containing 9 clear cell, 6 mucinous, and 31 serous.
Data was pre-processed and normalized with Hapmap CHB using the Affymetric Genotyping Console.
Contributor(s) Goh L
Citation(s) 23078675
Submission date Jun 29, 2011
Last update date Nov 27, 2018
Contact name Liang Goh
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 (46)
GSM751039 Ovarian cancer tissue from Taiwan L513
GSM751040 Ovarian cancer tissue from Taiwan L553
GSM751041 Ovarian cancer tissue from Taiwan L609
This SubSeries is part of SuperSeries:
GSE30311 The histotype-specific copy-number landscape of ovarian cancer
BioProject PRJNA155145

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
GSE30300_RAW.tar 2.9 Gb (http)(custom) TAR (of CEL, CNCHP)
Processed data included within Sample table

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