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Series GSE248618 Query DataSets for GSE248618
Status Public on Jan 31, 2024
Title Clinically relevant molecular hallmarks of PFA ependymomas display intratumoral heterogeneity and correlate with tumor morphology
Organism Homo sapiens
Experiment type Methylation profiling by array
Summary Posterior fossa type A (PF-EPN-A, PFA) ependymoma are aggressive tumors that mainly affect children and have a poor prognosis. Histopathology shows significant intratumoral heterogeneity, ranging from loose tissue to often sharply demarcated, extremely cell dense tumor areas. To determine molecular differences between these morphologically different areas and to understand their clinical significance, we analyzed 113 PF-EPN-A samples, including 40 corresponding relapse samples. Inter alia, DNA methylation profiles were analysed for high and low cell density regions seperately in 21 cases. Tumor areas with low and high cell density showed diverging DNA methylation profiles regarding their similarity to distinct previously discovered PF-EPN-A subtypes in 9/21 cases. Prognostically relevant chromosomal changes at 1q and 6q showed spatial heterogeneity within single tumors.
 
Overall design Of 21 heterogenous PFA ependymoma, DNA methylation profiles from high and low cell density areas as well as overall DNA methylation profiles from routine diagnostics were obtained and analysed.
 
Contributor(s) Gödicke S, Schüller U
Citation(s) 38265527
Submission date Nov 26, 2023
Last update date Feb 01, 2024
Contact name Swenja Gödicke
Organization name Research Institute Children‘s Cancer Center Hamburg
Lab Schüller
Street address Martinistrasse 52
City Hamburg
ZIP/Postal code 20251
Country Germany
 
Platforms (2)
GPL13534 Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)
GPL21145 Infinium MethylationEPIC
Samples (79)
GSM7917983 genomic DNA from high cell density areas of posterior fossa type A ependymoma case 4
GSM7917984 genomic DNA from low cell density areas of posterior fossa type A ependymoma case 4
GSM7917985 genomic DNA from high cell density areas of posterior fossa type A ependymoma case 10
This SubSeries is part of SuperSeries:
GSE248811 Clinically relevant molecular hallmarks of PFA ependymomas display intratumoral heterogeneity and correlate with tumor morphology.
Relations
BioProject PRJNA1045254

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
GSE248618_Beta_DetP_450k.csv.gz 7.1 Mb (ftp)(http) CSV
GSE248618_Beta_DetP_EPIC.csv.gz 759.8 Mb (ftp)(http) CSV
GSE248618_DetP_Meth_Unmeth_450k.csv.gz 5.6 Mb (ftp)(http) CSV
GSE248618_DetP_Meth_Unmeth_EPIC.csv.gz 531.5 Mb (ftp)(http) CSV
GSE248618_RAW.tar 1.4 Gb (http)(custom) TAR (of IDAT)
GSE248618_RGSet_450k.rds.gz 6.8 Mb (ftp)(http) RDS
GSE248618_RGSet_EPIC.rds.gz 370.5 Mb (ftp)(http) RDS

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