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Series GSE133556 Query DataSets for GSE133556
Status Public on Jul 01, 2019
Title Differential DNA Methylation in High Grade Serous Ovarian Cancer (HGSOC) is associated with Tumor Behavior
Organism Homo sapiens
Experiment type Methylation profiling by genome tiling array
Summary Introduction/ Background: The epigenome represents and adds another facet of complexity to cancer that needs to be understood to categorize patients into those at risk of disease, recurrence, or treatment failure. Our goal is to compare DNA methylation status between controls vs HGSOC, and relate it with clinical outcomes.
Methodology: A retrospective review of our institution’s advanced/ recurrent HGSOC patients yielded 99 cases with good quality DNA and RNA. 12 normal fallopian tubes were also collected and used as controls. Infinium Illumina methylationEPIC was used to characterize DNA methylation status and RNA seq to evaluate gene expression. T- tests were used to compare methylation patterns between controls vs HGSOC, primary vs recurrent, and optimal vs suboptimal surgical outcomes. Spearman’s rank correlation was used to evaluate association between degree of methylation and expression of identified genes. Validation of our findings used the cancer genome atlas (TCGA) database followed by C-statistics to assess degree of agreement.
Results: Out of 66,069 methylation probes that interrogate known genes, 5,852 probes were significantly different between normal and HGSOC. This includes genes that are enriched in several pathways such as the RAS signaling pathway. A similar analysis of the TCGA database showed 2,075 differentially methylated probes. 1,891 probes were significant in both datasets giving a 70.1% degree of agreement. When comparing differential DNA methylation between primary and recurrent disease, there were 57 probes which represent 17 genes that were significantly different. When comparing optimal vs suboptimal surgical outcomes, 99 probes were significantly different wherein 29 genes show expected inverse correlation between methylation status and gene expression.
Conclusions: There are significant differences in methylation patterns between HGSOC and fallopian tubes, primary vs recurrent tissues, and optimal vs sub-optimal surgical outcomes. Cataloging these phenomena in a well characterized clinical population will aid in determining groupings for precision medicine treatment cohorts in the future.
 
Overall design DNA methylation profiles of 99 HGSOC tumor samples and 12 normal fallopian tube controls were generated using Infinium Illumina methylationEPIC arrays
 
Contributor(s) Gonzalez-Bosquet J, Reyes HD, Devor E
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Submission date Jun 30, 2019
Last update date Jul 03, 2019
Contact name Henry D Reyes
E-mail(s) henrypogs@yahoo.com
Organization name University of Iowa
Department OBGYN
Street address 200 Hawkins Drive
City Iowa City
State/province Iowa
ZIP/Postal code 52242
Country USA
 
Platforms (1)
GPL21145 Infinium MethylationEPIC
Samples (111)
GSM3911862 High grade serous ovarian cancer, Patient26
GSM3911863 High grade serous ovarian cancer, Patient27
GSM3911864 High grade serous ovarian cancer, Patient28
Relations
BioProject PRJNA551882

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
GSE133556_RAW.tar 1.7 Gb (http)(custom) TAR (of IDAT)
Raw data provided as supplementary file
Processed data included within Sample table

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