Affymetrix SNP array data for breast cancer formation in mouse

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.