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| Status |
Public on Oct 01, 2017 |
| Title |
Detailed Longitudinal Sampling of Glioma Stem Cells In Situ Reveals Chr7 Gain and Chr10 Loss As Repeated Events in Primary Tumor Formation and Recurrence (SNP) |
| Organism |
Homo sapiens |
| Experiment type |
SNP genotyping by SNP array
Genome variation profiling by SNP array
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| Summary |
In this study, we developed an extensive dataset for a GBM case via the generation of polyclonal and monoclonal glioma stem cell lines from initial diagnosis, as well as from multiple sections of distant tumor locations of the deceased patient’s brain following tumor recurrence. Our analyses revealed the tissue-wide expansion of a new clone in the recurrent tumor as well as chromosome 7 gain and chromosome 10 loss as repeated genomic events in primary and recurrent disease. Moreover, chromosome 7 gain and chromosome 10 loss produced similar alterations in mRNA expression profiles in primary and recurrent tumors despite possessing other highly heterogeneous and divergent genomic alterations between the tumors. We identified ETV1 and CDK6 as putative candidate genes, and NFKB (complex), IL1B, IL6, Akt and VEGF as potential signaling regulators, as potentially central downstream effectors of chr7 gain and chr10 loss. Finally, the differences caused by the transcriptomic shift following gain of chromosome 7 and loss of chromosome 10 were consistent with those generally seen in GBM samples compared to normal brain in large-scale patient-tumor data sets.
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| Overall design |
Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from patient tumor and cell lines.
Copy number analysis of Affymetrix CSHD arrays was performed for 46 samples from a GBM patient
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| Contributor(s) |
Baysan M |
| Citation(s) |
28710771 |
| Submission date |
Jul 10, 2017 |
| Last update date |
Jul 25, 2021 |
| Contact name |
mehmet baysan |
| E-mail(s) |
baysan@gmail.com
|
| Organization name |
Istanbul Sehir university
|
| Department |
Department of Computer Science
|
| Street address |
Kuşbakışı Caddesi No: 27 34662 Altunizade – Üsküdar – İstanbul Office: East Campus 108
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| City |
Istanbul |
| ZIP/Postal code |
34662 |
| Country |
Turkey |
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| Platforms (1) |
| GPL16131 |
[CytoScanHD_Array] Affymetrix CytoScan HD Array |
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| Samples (46)
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| This SubSeries is part of SuperSeries: |
| GSE101114 |
Detailed Longitudinal Sampling of Glioma Stem Cells In Situ Reveals Chr7 Gain and Chr10 Loss As Repeated Events in Primary Tumor Formation and Recurrence |
|
| Relations |
| BioProject |
PRJNA393731 |
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