End-sequence profiling: Sequence-based analysis of aberrant genomes
- Stanislav Volik*,†,
- Shaying Zhao†,‡,
- Koei Chin§,
- John H. Brebner*,
- David R. Herndon¶,
- Quanzhou Tao¶,
- David Kowbel*,
- Guiqing Huang*,
- Anna Lapuk§,
- Wen-Lin Kuo§,
- Gregg Magrane*,
- Pieter de Jong∥,
- Joe W. Gray∥, and
- Colin Collins*,**
- *Cancer Research Institute and §Department of Laboratory Medicine, University of California Comprehensive Cancer Center, 2340 Sutter Street, San Francisco, CA 94115; ‡The Institute for Genome Research, 9712 Medical Center Drive, Rockville, MD 20850; ¶Amplicon Express, 1610 NE Eastgate Boulevard, No. 880, Pullman, WA 99163; and ∥BACPAC Resources, Children's Hospital, 747 52nd Street, Oakland, CA 94609
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Communicated by James E. Cleaver, University of California, San Francisco, CA, April 23, 2003 (received for review February 24, 2003)
Abstract
Genome rearrangements are important in evolution, cancer, and other diseases. Precise mapping of the rearrangements is essential for identification of the involved genes, and many techniques have been developed for this purpose. We show here that end-sequence profiling (ESP) is particularly well suited to this purpose. ESP is accomplished by constructing a bacterial artificial chromosome (BAC) library from a test genome, measuring BAC end sequences, and mapping end-sequence pairs onto the normal genome sequence. Plots of BAC end-sequences density identify copy number abnormalities at high resolution. BACs spanning structural aberrations have end pairs that map abnormally far apart on the normal genome sequence. These pairs can then be sequenced to determine the involved genes and breakpoint sequences. ESP analysis of the breast cancer cell line MCF-7 demonstrated its utility for analysis of complex genomes. End sequencing of ≈8,000 clones (0.37-fold haploid genome clonal coverage) produced a comprehensive genome copy number map of the MCF-7 genome at better than 300-kb resolution and identified 381 genome breakpoints, a subset of which was verified by fluorescence in situ hybridization mapping and sequencing.
Footnotes
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↵ ** To whom correspondence should be addressed. E-mail: Collins{at}cc.ucsf.edu.
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↵ † S.V. and S.Z. contributed equally to this work.
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Abbreviations: ESP, end-sequence profiling; BAC, bacterial artificial chromosome; BES, BAC end sequence; CGH, comparative genomic hybridization; FISH, fluorescence in situ hybridization.
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Data deposition: The sequences reported in this paper have been deposited in the GenBank database (accession nos. BZ597614–BZ612944 and AC116668).
- Copyright © 2003, The National Academy of Sciences
