|
| Status |
Public on Dec 31, 2013 |
| Title |
The landscape of somatic alterations in epigenetic genes across 21 pediatric cancers |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
|
| Summary |
As a part of the St Jude Children’s Research Hospital-Washington University Pediatric Cancer Genome Project (PCGP), we adapted deep sequencing technologies and have sequenced 1025 tumor samples from 21 diseases covering brain, solid tumors and leukemias. We analyzed the genomic DNA sequences, copy number variations and structural rearrangements of 633 genes whose proteins are involved in epigenetic machineries, including those that covalently modify DNA and histones, and structurally reorder chromatin. To examine gene expression level of mutated histone genes, we analyzed gene expression in a group of 40 non-ETP T-lineage ALL samples using Affymetrix GeneChip HT HG-U133+ PM arrays (including 37 samples deposited in GSE28703 and 3 additional arrays not studied previously). The results provide us the knowledge of potential therapeutic targets for pediatric cancer treatment and improvement of personalized therapy.
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| Overall design |
Gene expression profiling was performed on 40 non ETP T-lineage acute lymphoblastic leukemia samples. No control or reference samples were included.
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| Contributor(s) |
Huether R, Dong L, Chen S, Holmfeldt L, Zhang J, Mullighan CG, Downing JR |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Dec 31, 2012 |
| Last update date |
Apr 20, 2018 |
| Contact name |
Shann-Ching Chen |
| E-mail(s) |
Shann-Ching.Chen@stjude.org
|
| Organization name |
St. Jude Children's Research Hospital
|
| Department |
Pathology
|
| Street address |
262 Danny Thomas Place
|
| City |
Memphis |
| State/province |
TN |
| ZIP/Postal code |
38105 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL13158 |
[HT_HG-U133_Plus_PM] Affymetrix HT HG-U133+ PM Array Plate |
|
| Samples (40)
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|
| Relations |
| BioProject |
PRJNA184931 |
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