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Series GSE100351 Query DataSets for GSE100351
Status Public on Jun 20, 2018
Title The DNA methylation landscape of glioblastoma disease progression shows extensive heterogeneity in time and space
Organism Homo sapiens
Experiment type Methylation profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Genome variation profiling by high throughput sequencing
Summary Glioblastoma is characterized by widespread genetic and transcriptional heterogeneity, yet little is known about the role of the epigenome in glioblastoma disease progression. Here, we present genome-scale maps of DNA methylation in matched primary and recurring glioblastoma tumors, using data from a highly annotated clinical cohort that was selected through a national patient registry. We demonstrate the feasibility of DNA methylation mapping in a large set of routinely collected FFPE samples, and we validate bisulfite sequencing as a multipurpose assay that allowed us to infer a range of different genetic, epigenetic, and transcriptional characteristics of the profiled tumor samples. On the basis of these data, we identified subtle differences between primary and recurring tumors, links between DNA methylation and the tumor microenvironment, and an association of epigenetic tumor heterogeneity with patient survival. In summary, this study establishes an open resource for dissecting DNA methylation heterogeneity in a genetically diverse and heterogeneous cancer, and it demonstrates the feasibility of integrating epigenomics, radiology, and digital pathology for a national cohort, thereby leveraging existing samples and data collected as part of routine clinical practice.
Overall design Genome-wide profiling of DNA methylation levels by RRBS in 499 samples, derived from 217 glioblastoma (IDH wildtype) patients (112 progression cohort, 105 validation cohort), 14 IDH muated brain tumor patients, and 5 normal brain controls. For each patient of the progression cohort samples from at least two and up to six tumor resections are available. For 6 patients multiple regions of each tumor were sampled. For 37 samples matched RNA-seq was performed. For 43 samples matched low-coverage whole genome sequencing was performed.
*** Raw data requires controlled access and is deposited at EGAS00001002538 (EGA: Access to raw data can be requested from submitters ***
Contributor(s) Klughammer J, Kiesel B, Roetzer T, Fortelny N, Nemc A, Datlinger P, Peter N, Nenning K, Furtner J, Nowosielski M, Augustin M, Mischkulnig M, Ströbel T, Moser P, Freyschlag CF, Kerschbaumer J, Thomé C, Grams AE, Stockhammer G, Kitzwoegerer M, Oberndorfer S, Marhold F, Weis S, Trenkler J, Buchroithner J, Pichler J, Haybaeck J, Krassnig S, Ali KM, von Campe G, Payer F, Sherif C, Preiser J, Hauser T, Winkler PA, Kleindienst W, Würtz F, Brandner-Kokalj T, Stultschnig M, Schweiger S, Dieckmann K, Preusser M, Langs G, Baumann B, Knosp E, Widhalm G, Marosi C, Hainfellner JA, Woehrer A
Citation(s) 30150718
Submission date Jun 22, 2017
Last update date Jul 25, 2021
Contact name Christoph Bock
Organization name CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences
Street address Lazarettgasse 14
City Vienna
ZIP/Postal code 1090
Country Austria
Platforms (3)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
GPL21290 Illumina HiSeq 3000 (Homo sapiens)
Samples (579)
GSM2679021 RRBS Glioblastoma patient ind_0 Surg.2 frozen [ind_0_N458_14_f]
GSM2679022 RRBS Glioblastoma patient ind_0 Surg.1 frozen [ind_0_N822_13_f]
GSM2679023 RRBS Normal white matter control ind_112 Surg.N/A FFPE [ind_112_N1471_11A]
BioProject PRJNA391429

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
GSE100351_RAW.tar 7.9 Gb (http)(custom) TAR (of BED, RPKM, TXT)
Processed data provided as supplementary file
Raw data not provided for this record

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