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Series GSE65821 Query DataSets for GSE65821
Status Public on May 19, 2015
Title Whole genome characterisation of chemoresistant ovarian cancer
Organism Homo sapiens
Experiment type Non-coding RNA profiling by array
Methylation profiling by genome tiling array
Genome variation profiling by SNP array
Summary This SuperSeries is composed of the SubSeries listed below.

Patients with high-grade serous ovarian cancer (HGSC) have experienced little improvement in overall survival, and standard treatment has not advanced beyond platinum-based combination chemotherapy, during the past 30 years. To understand the drivers of clinical phenotypes better, here we use whole-genome sequencing of tumour and germline DNA samples from 92 patients with primary refractory, resistant, sensitive and matched acquired resistant disease. We show that gene breakage commonly inactivates the tumour suppressors RB1, NF1, RAD51B and PTEN in HGSC, and contributes to acquired chemotherapy resistance. CCNE1 amplification was common in primary resistant and refractory disease. We observed several molecular events associated with acquired resistance, including multiple independent reversions of germline BRCA1 or BRCA2 mutations in individual patients, loss of BRCA1 promoter methylation, an alteration in molecular subtype, and recurrent promoter fusion associated with overexpression of the drug efflux pump MDR1.
 
Overall design Refer to individual Series

Contributor: The Australian Ovarian Cancer Study Group
 
Contributor(s) Patch AM, Christie EL, Etemadmoghadam D, Garsed DW, George J, Fereday S, Nones K, Cowin P, Alsop K, Bailey PJ, Kassahn KS, Newell F, Quinn MC, Kazakoff S, Quek K, Wilhelm-Benartzi C, Curry E, San H, Leong S, Hamilton A, Mileshkin L, Au-Yeung G, Kennedy C, Hung J, Chiew YE, Harnett P, Friedlander M, Quinn M, Pyman J, Cordner S, O'Brien P, Leditschke J, Young G, Strachan K, Waring P, Azar W, Mitchell C, Traficante N, Hendley J, Thorne H, Shackleton M, Miller DK, Mir Arnau G, Tothill RW, Holloway TP, Semple T, Harliwong I, Nourse C, Nourbakhsh E, Manning S, Idrisoglu S, Bruxner TJ, Christ AN, Poudel B, Holmes O, Anderson M, Leonard C, Lonie A, Hall N, Wood S, Taylor DF, Xu Q, Fink JL, Waddell N, Drapkin R, Stronach E, Gabra H, Brown R, Jewell A, Nagaraj SH, Markham E, Wilson PJ, Ellul J, McNally O, Doyle MA, Vedururu R, Stewart C, Lengyel E, Pearson JV, Waddell N, deFazio A, Grimmond SM, Bowtell DD
Citation(s) 26017449
Submission date Feb 10, 2015
Last update date Nov 09, 2022
Contact name Ann-Marie Patch
E-mail(s) ann-marie.patch@qimrberghofer.edu.au
Organization name QIMR Berghofer Medical Research Institute
Street address 300 Herston Road
City Herston
State/province QLD
ZIP/Postal code 4006
Country Australia
 
Platforms (4)
GPL13534 Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)
GPL16104 Illumina HumanOmni2.5-8 BeadChip
GPL18952 Illumina HumanOmni2.5-8v1.1 beadchip
Samples (356)
GSM1508279 AOCS_061_ICGC_DBPC_20130205_023
GSM1508280 AOCS_063_ICGC_DBPC_20130205_025
GSM1508281 AOCS_097_ICGC_DBPC_20130205_074
This SuperSeries is composed of the following SubSeries:
GSE61568 Whole genome characterisation of chemoresistant ovarian cancer [Illumina_Omini 2.5-8_SNP]
GSE65819 Whole genome characterisation of chemoresistant ovarian cancer [NanoString miRNA]
GSE65820 Whole genome characterisation of chemoresistant ovarian cancer [Illumina_450K_Methylation]
Relations
BioProject PRJNA275136

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
GSE65821_GEO_to_DCC_IDs.txt.gz 1.5 Kb (ftp)(http) TXT
GSE65821_RAW.tar 16.3 Gb (http)(custom) TAR (of CSV, IDAT, TXT)

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