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Identification of fusion genes in breast cancer by paired-end RNA-sequencing

Henrik Edgren1, Astrid Murumagi1, Sara Kangaspeska1, Daniel Nicorici1, Vesa Hongisto2, Kristine Kleivi23, Inga H Rye3, Sandra Nyberg2, Maija Wolf1, Anne-Lise Borresen-Dale14 and Olli Kallioniemi1*

Author Affiliations

1 Institute for Molecular Medicine Finland (FIMM), Tukholmankatu 8, Helsinki, 00290, Finland

2 Medical Biotechnology, VTT Technical Research Center of Finland and Turku Center for Biotechnology, Itäinen Pitkäkatu 4C, Turku, 20520, Finland

3 Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Ullernchausseen 70, Oslo, 0310, Norway

4 Institute of Clinical Medicine, University of Oslo, PO Box 1171 Blindern, Oslo, 0318, Norway

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Genome Biology 2011, 12:R6  doi:10.1186/gb-2011-12-1-r6

Published: 19 January 2011

Additional files

Additional file 1:

Table showing paired-end RNA-seq summary statistics.

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Additional file 2:

Cell line specificity of the novel fusion genes. RT-PCR validation of fusion genes discovered in BT-474 (left), SK-BR-3 (middle) and KPL-4 (right) with a panel of breast cancer cell lines and normal breast tissue. GAPDH was used as the internal reference gene.

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Additional file 3:

Long-range genomic PCR on fusion genes. Genomic PCR across the fusion junctions of selected gene fusions in BT-474 (left), KPL-4 (middle) and SK-BR-3.

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Additional file 4:

FISH analysis of fusion genes. (a) Interphase FISH showing amplification of STARD3 and DOK5 (left), VAPB and CYTH1 (middle) and RPS6KB1 and SNF8 (right) in BT-474 cells but not in control cells. White arrows indicate fused genes. Coloring of the gene names coincides with labeling of the BAC clones used. (b) Interphase FISH showing amplified signals of BSG and NFIX (left) and NOTCH1 and NUP214 (right) in KPL-4. Normal copy number of both genes is present in control cells. (c) Interphase FISH analysis showing many copies of CYTH1 and EIF3H (left) and TATDN1 and GSDMB (right) in SK-BR-3. In contrast, only normal copy number of these genes is visible in control cells.

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Additional file 5:

Combined maximum intron sizes.

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Additional file 6:

Genomic rearrangements in KPL-4 and MCF-7. Circos plots representing chromosomal translocations in KPL-4 (bottom) and MCF-7 (top). Chromosomes are drawn to scale around the rim of the circle and data are plotted on these coordinates. Selected chromosomes involved in the fusion events are shown in higher magnification. Each intrachromosomal (red) and interchromosomal (blue) fusion is indicated by an arc. Copy number measured by aCGH is plotted in the inner circle where amplifications are shown in red and deletions in green. N denotes the number of fusion genes per cell line.

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Additional file 7:

Expression of IKZF3 and ERBB2 in breast cancer. Genesapiens.org plot showing a scatterplot comparing IKZF3 and ERBB2 expression in a set of 761 breast tumors profiled on Affymetrix gene expression microarrays.

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Additional file 8:

Fusion junction sequences.

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Additional file 9:

Primer sequences used in the study.

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Additional file 10:

FISH probes used for validation.

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