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Open Access Research article

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

Christoph Standfuß1, Heike Pospisil1* and Andreas Klein2

Author Affiliations

1 , Bioinformatics, Technical University of Applied Sciences Wildau, 15745 Wildau, Bahnhofstraße, Germany

2 Institute of Biochemistry, harité-Universitätsmedizin Berlin, 10117 Berlin, CCO, Charitéplatz 1, Germany

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BMC Cancer 2012, 12:380  doi:10.1186/1471-2407-12-380

Published: 31 August 2012

Additional files

Additional file 1:

Sample description. Table S1: The sample names used in this publication are listed. GEO accession numbers for each experiment can be found in this table. For the Transgenic2 (183T8) sample no gene expression data was available.

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Additional file 2:

Kaplan-Meier curve. Figure S1: This figure illustrates the Kaplan-Meier curve. The x-axis depicts the duration from the first mating and the finding of tumor formation. All mice were euthanized as soon as a tumor was found. All 64 mice developed breast cancer within less than 200 days after their first day of pregnancy. In fact, about 60% of the animals showed a tumor formation within the first 100 days.

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Additional file 5:

Log2-ratio distribution. Table S3: (A) and (B): Tables listing the alteration of single SNP log2-ratio (as shown in Figure 3A) and the alteration of segment log2-ratio values (as shown in Figure 3B).

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Additional file 3:

Number of segments computed for each sample. Table S2: This table lists the number of segments calculated for each chromosome in each of the 14 samples.

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Additional file 4:

Copy number alteration and motif position in Tumor1 sample. Figure S4: Copy number alterations are depicted in the outer cirular plot. The five inner circular plots illustrate the motif positions of motif 1 (blue), motif 2 (orange), motif 3 (green), motif 4 (red), motif 5 (purple) and motif 6 (grey). Thicker lines illustrate a short distance of two motif positions. Common breakpoints of Tumor2 and Tumor1 samples are illustrated in the most inner circular plot.

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Additional file 6:

Segmentation in different samples. Figure S3: Different segmentation results for chromosome 6 in all samples is depicted. Comparing Normal1 to Transgenic1 and to Tumor1, one can see an increase in both the fragmentation and the copy number. Comparable alterations can also be found in both SV40 cell line samples. By comparison, the Transgenic2 and Tumor2 samples show less fragmentations. Interestingly, even more segments can be identified in the Transgenic2 sample than in Tumor2.

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Additional file 7:

Plot of qPCR results. Figure S2: Barplot illustrating the qPCR results for the three previously mentioned regions of chromosome 6.

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Additional file 8:

Genotyping Protocol. Protocol of genotyping analyses.

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