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A sequence-based survey of the complex structural organization of tumor genomes

Benjamin J Raphael1, Stanislav Volik2, Peng Yu3, Chunxiao Wu4, Guiqing Huang2, Elena V Linardopoulou5, Barbara J Trask5, Frederic Waldman2, Joseph Costello2, Kenneth J Pienta6, Gordon B Mills7, Krystyna Bajsarowicz2, Yasuko Kobayashi2, Shivaranjani Sridharan2, Pamela L Paris2, Quanzhou Tao8, Sarah J Aerni9, Raymond P Brown10, Ali Bashir10, Joe W Gray11, Jan-Fang Cheng12, Pieter de Jong13, Mikhail Nefedov13, Thomas Ried14, Hesed M Padilla-Nash14 and Colin C Collins2*

Author Affiliations

1 Department of Computer Science & Center for Computational Molecular Biology, Brown University, Waterman Street, Providence, RI 02912-1910, USA

2 Cancer Research Institute, UCSF Comprehensive Cancer Center, Sutter Street, San Francisco, CA 94115, USA

3 Chinese National Human Genome Center, North Yongchang Road, BDA, Beijing, P.R.C. 100016

4 Shandong Provincial Hospital, JingWuWeiQi Road, Jinan, P.R.C. 250021

5 Division of Human Biology, Fred Hutchinson Cancer Research Center, Fairview Avenue N, Seattle, WA 98109, USA

6 The University of Michigan, Departments of Internal Medicine and Urology, E Medical Center Drive, Ann Arbor, MI 48109-0330, USA

7 MD Anderson Cancer Center, University of Texas, Holcombe Blvd, Houston, TX 77030, USA

8 Amplicon Express, NE Eastgate Blvd, Pullman, WA 99163, USA

9 BioMedical Informatics Program, Stanford University, Stanford, CA 94305, USA

10 Bioinformatics Program, University of California, San Diego, Gilman Drive, La Jolla, CA 92093, USA

11 Lawrence Berkeley National Laboratory, Life Sciences Division, Cyclotron Road, Berkeley, CA 94720-8268, USA

12 Lawrence Berkeley National Laboratory, Genomics Division and Joint Genome Institute, Cyclotron Road, Berkeley, CA 94720, USA

13 BACPAC Resources Children's Hospital Oakland, 52nd Street, Oakland, CA 94609, USA

14 Section of Cancer Genomics, Genetics Branch, Center for Cancer Research, South Drive, Bldg. 50, MSC-8010, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA

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Genome Biology 2008, 9:R59  doi:10.1186/gb-2008-9-3-r59

Published: 25 March 2008

Additional files

Additional data file 1:

Supplemental text and tables, including a description of all supplemental tables.

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Additional data file 2:

Three supplemental figures.

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Additional data file 3:

Supplemental tables.

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