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| Status |
Public on Jan 04, 2006 |
| Title |
Classification of neuroblastoma by integrating gene expression pattern with regional alterations in DNA copy number |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| Summary |
The specific genes that influence neuroblastoma biology and are targeted by genomic alterations remain largely unknown. We quantified mRNA expression in a highly annotated series of 101 prospectively collected diagnostic neuroblastoma primary tumors and the expression profiles were determined using Affymetrix U95Av2 arrays. Comparisons between the sample groups allow the identification of genes with localized expression patterns. This study demonstrates that the genomic data can be used to subcategorize the disease into molecular subsets and the regional copy number alterations are correlated with a broad number of transcriptional alterations genome wide. This data also suggests that multiple genes from several discrete regions of the human genome co-operate to supress neuroblastoma tumorigenesis and progression.
Keywords: Disease state analysis, genetic modification
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| Overall design |
A highly annotated series of 101 prospectively collected diagnostic neuroblastoma primary tumors were selected to quantify mRNA expression using an oligonucleotide based microarray. Genomic copy number status at the prognostically relevant loci 1p36,2p24(MYCN), 11q23 and 17q23 was determined by PCR and was aberrant in 26, 20, 40 and 38 cases, respectively. Fetal brain RNA was used as a control sample.
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| Web link |
http://stokes.chop.edu/programs/marislab/data
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| Contributor(s) |
Wang Q, Diskin S, Rappaport E, Attiyeh E, Mosse Y, Shue D, Seiser E, Jagannathan J, Shusterman S, Bansal M, Khazi D, Winter C, Okowa E, Grant G, Cnaan A, Zhao H, Cheung N, Gerald W, London W, Matthay K, Brodeur G, Maris J |
| Citation(s) |
16778177, 20233875, 21124317 |
| Submission date |
Jan 03, 2006 |
| Last update date |
Dec 13, 2018 |
| Contact name |
Jayanti Jagannathan |
| E-mail(s) |
jagannathan@email.chop.edu
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| Phone |
2674262286
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| Organization name |
Childrens Hospital of Philadelphia
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| Department |
Oncology
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| Street address |
34th & Civic center blvd
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| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
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| Platforms (1) |
| GPL8300 |
[HG_U95Av2] Affymetrix Human Genome U95 Version 2 Array |
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| Samples (102)
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| Relations |
| BioProject |
PRJNA94217 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE3960_RAW.tar |
277.6 Mb |
(http)(custom) |
TAR (of CEL) |
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