Open Access Research article

Gene rearrangements in hormone receptor negative breast cancers revealed by mate pair sequencing

Xiang Jiao1, Sean D Hooper12, Tatjana Djureinovic1, Chatarina Larsson1, Fredrik Wärnberg3, Christian Tellgren-Roth1, Johan Botling1 and Tobias Sjöblom1*

Author Affiliations

1 Department of Immunology, Genetics, and Pathology, Uppsala University, Uppsala, SE 751 85, Sweden

2 Current address: The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK

3 Department of Surgical Sciences, Uppsala University, Uppsala, SE 751 85, Sweden

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BMC Genomics 2013, 14:165  doi:10.1186/1471-2164-14-165

Published: 12 March 2013

Additional files

Additional file 1:

Characteristics of the breast cancer samples.

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Additional file 2:

Summary of sequencing and numbers of rearrangements discovered in each breast cancer genome.

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Additional file 3:

Rearrangements detected in mate pair sequencing.

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Additional file 4:

Circos plots of somatic rearrangements in breast cancer genomes. Outer histogram of the Circos plot displays the number of deletions in each bin, and the inner histogram displays predicted insertions. Connections represent PCR-validated (hashed lines) and sequence-validated (solid lines) somatic translocations.

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Additional file 5:

Gene Ontology (GO) terms of affected genes.

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Additional file 6:

Insertions detected in 4 breast cancer samples. Insertions were illustrated in two samples harboring insertions at much higher prevalence (120 T and 150 T) and two samples (149 T and 116 T) representing the others. Each inversion supported by at least four independent mate-pairs is illustrated as a red bar on its chromosome.

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Additional file 7:

Numbers and sizes of deletions and insertions supported by at least three reads in breast cancer genomes.

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Additional file 8:

Numbers and sizes of deletions and insertions supported by at least four reads in breast cancer genomes.

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Additional file 9:

Flowchart of structural variants (SV) identification procedures.

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