Unknown,Transcriptomics,Genomics,Proteomics

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Affymetrix SNP array data for breast cancer formation in mouse


ABSTRACT: We investigated the CNAs in a four stage tumorigenesis model. This model included copy number analyses in non-transgenic NMRI mice (normal) and in transgenic SVT/t mice: non-malignant hyperplastic mammary glands and breast cancers, as well as breast cancer derived cell lines. We focused our research on copy number analyses to compare the genomic alterations that occur during tumorigenesis. We addressed the question, whether common predisposed chromosomal breakpoints could be seen to promote malignant transformation. We can report a characteristic increase of copy number alterations from normal to tumor stage in our model. Furthermore, we have identified chromosomal segments and found characteristic fragmentations. Affymetrix SNP array analysis was performed with Mouse Diversity Genotyping Arrays (Affymetrix). DNA was extracted from frozen biopsies of mammary tumor samples of six mice and two cell lines. Normalization and allele summarization were performed with the BRLMM-P algorithm provided and copy number analysis was performed for the each sample using the average signal intensity of both normal samples as the reference for copy number inference.

ORGANISM(S): Mus musculus

SUBMITTER: Christoph Standfuß 

PROVIDER: E-GEOD-35873 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

SNP microarray analyses reveal copy number alterations and progressive genome reorganization during tumor development in SVT/t driven mice breast cancer.

Standfuss Christoph C   Pospisil Heike H   Klein Andreas A  

BMC cancer 20120831


<h4>Background</h4>Tumor development is known to be a stepwise process involving dynamic changes that affect cellular integrity and cellular behavior. This complex interaction between genomic organization and gene, as well as protein expression is not yet fully understood. Tumor characterization by gene expression analyses is not sufficient, since expression levels are only available as a snapshot of the cell status. So far, research has mainly focused on gene expression profiling or alterations  ...[more]

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