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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Oct 01, 2012 |
| Title |
Spontaneous Nf1 deletion and recurrent copy number alterations in mammary tumorigenesis |
| Organism |
Mus musculus |
| Experiment type |
Genome variation profiling by genome tiling array
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| Summary |
Breast cancer is the most prevalent cancer in women 1, and most cases are believed to have a sporadic, rather than heritable basis 2. To identify breast cancer driver genes, we exploited the C3H-Mcm4Chaos3/Chaos3 (“Chaos3”) mouse model that, by virtue of bearing a defective DNA replicative helicase subunit that causes elevated genomic instability (GIN), sustains somatic alterations ultimately causing mammary adenocarcinomas 6. Array Comparative Genomic Hybridization (aCGH) analysis of Chaos3 mammary tumors revealed recurrent copy number alterations (CNAs), most notably deletion of the Neurofibromin 1 (Nf1) tumor suppressor gene in all cases. NF1, a negative regulator of RAS, is traditionally recognized for its role in driving the development of neurofibromas in the context of the human disease Neurofibromatosis Type 1, but not breast cancer.
Genomic DNA from tumor and reference samples were hybridized to NimbleGen 3x720K mouse CGH arrays. Two reference samples were used independently. CNAs were visualized using Nimblegen, IGV, and KCsmart software 32. Select genes were validated via qPCR. Critical regions within each Chaos3 CNA were identified as the region with the greatest overlap across multiple Chaos3 tumors.
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| Overall design |
Recurring Copy Number Variations (CNVs) for 12 Chaos3 tumors and 2 MMTV-Neu mammary tumors analyzed by aCGH are indicated. Samples analyzed are primary tumors except where indicated.
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| Contributor(s) |
Wallace MD, Schimenti JC, Shen L, McNairn AJ, Cerami EG, Pfefferle AD, Fallon BL, Rinaldi VD, Perou CM |
| Citation(s) |
22851646 |
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| Submission date |
Apr 26, 2012 |
| Last update date |
Jan 02, 2013 |
| Contact name |
John Schimenti |
| E-mail(s) |
jcs92@cornell.edu
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| URL |
http://web.me.com/tcomplex/
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| Organization name |
Cornell University
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| Department |
Biomedical Sciences
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| Lab |
Schimenti
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| Street address |
T9014A
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| City |
Ithaca |
| State/province |
NY |
| ZIP/Postal code |
14853 |
| Country |
USA |
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| Platforms (1) |
| GPL10989 |
NimbleGen Mouse CGH 3x720K Whole-Genome Tiling Array (Build MM9) [080603_MM9_WG_CGH_HX3] |
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| Samples (14)
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| Relations |
| BioProject |
PRJNA162281 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE37607_RAW.tar |
381.9 Mb |
(http)(custom) |
TAR (of PAIR) |
| Processed data included within Sample table |
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