NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE23666 Query DataSets for GSE23666
Status Public on Sep 08, 2010
Title Highly Aneuploid Zebrafish Malignant Peripheral Nerve Sheath Tumors have Genetic Alterations Similar to Human Cancers
Organism Danio rerio
Experiment type Genome variation profiling by array
Genome variation profiling by high throughput sequencing
Summary Aneuploidy is a hallmark of human cancers, but most mouse cancer models lack the extensive aneuploidy seen in many human tumors. The zebrafish is becoming an increasingly popular model for studying cancer. Here we report that malignant peripheral nerve sheath tumors (MPNSTs) that arise in zebrafish as a result of mutations in either ribosomal protein (rp) genes or in p53 are highly aneuploid. Karyotyping reveals that these tumors frequently harbor near-triploid numbers of chromosomes, and they vary in chromosome number from cell-to-cell within a single tumor. Using array CGH (aCGH) we found that, as in human cancers, certain fish chromosomes are preferentially over-represented while others are under-represented in many MPNSTs. In addition, we detected evidence for recurrent sub-chromosomal amplifications and deletions that may contain genes involved in cancer initiation or progression. One striking amplification included the c-met proto-oncogene. Our results suggest that the zebrafish may be a valuable model in which to study aneuploidy in human cancer and in which to identify candidate genes that may act as drivers in fish and potentially also in human tumors.

For GSM587250-GSM587255: This Illumina sequencing data is for validation of a larger array-CGH dataset (GSM580580-GSM580621).
 
Overall design For GSM580580-GSM580621: Two-condition (x3) experiment: (1) genomic DNA: MPNST (rp gene mutation) vs normal tail : 31 replicates; (2) MPNST (p53 mutation) vs normal tail: 5 replicates; (3) normal tail vs. normal tail (6 replicates)

For GSM587250-GSM587255: Six samples total, in three pairs of tumor (MPNST) and normal tail control
 
Contributor(s) Zhang G, Hoersch S, Amsterdam A, Whittaker CA, Lees JA, Hopkins N
Citation(s) 20837522
Submission date Aug 17, 2010
Last update date May 15, 2019
Contact name Sebastian Hoersch
Organization name Massachusetts Institute of Technology
Department David H. Koch Institute for Integrative Cancer Research at MIT
Lab Bioinformatics and Computing Core
Street address 77 Massachusetts Avenue (E18-366)
City Cambridge
State/province MA
ZIP/Postal code 02474
Country USA
 
Platforms (2)
GPL9319 Illumina Genome Analyzer II (Danio rerio)
GPL10797 MIT-KI zebrafish Zv7+8 15K CGH v1.0
Samples (48)
GSM580580 MPNST tumor (rp mutation) vs normal tail tissue, replicate 1
GSM580581 MPNST tumor (rp mutation) vs normal tail tissue, replicate 2
GSM580582 MPNST tumor (rp mutation) vs normal tail tissue, replicate 3
Relations
SRA SRP003498
BioProject PRJNA130823

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
GSE23666_RAW.tar 185.0 Mb (http)(custom) TAR (of TXT)
GSE23666_processedData-6smpls-nReadsPer100KB.txt.gz 151.6 Kb (ftp)(http) TXT
GSE23666_readme.txt 2.5 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data included within Sample table
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap