title: End-sequence profiling: sequence-based analysis of aberrant genomes.
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 approximately 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.
authors.affiliation: Cancer Research Institute and Department of Laboratory Medicine, University of California Comprehensive Cancer Center, 2340 Sutter Street, San Francisco, CA 94115, USA.
authors.forename: Stanislav
authors.initials: S
authors.lastname: Volik
authors.forename: Shaying
authors.initials: S
authors.lastname: Zhao
authors.forename: Koei
authors.initials: K
authors.lastname: Chin
authors.forename: John H
authors.initials: JH
authors.lastname: Brebner
authors.forename: David R
authors.initials: DR
authors.lastname: Herndon
authors.forename: Quanzhou
authors.initials: Q
authors.lastname: Tao
authors.forename: David
authors.initials: D
authors.lastname: Kowbel
authors.forename: Guiqing
authors.initials: G
authors.lastname: Huang
authors.forename: Anna
authors.initials: A
authors.lastname: Lapuk
authors.forename: Wen-Lin
authors.initials: WL
authors.lastname: Kuo
authors.forename: Gregg
authors.initials: G
authors.lastname: Magrane
authors.forename: Pieter
authors.initials: P
authors.lastname: De Jong
authors.forename: Joe W
authors.initials: JW
authors.lastname: Gray
authors.forename: Colin
authors.initials: C
authors.lastname: Collins
mesh_terms: D000818:Animals; D001483:Base Sequence; D022202:Chromosomes, Artificial, Bacterial; D015723:Gene Library; D005821:Genetic Techniques; D016678:Genome; D006801:Humans; D017404:In Situ Hybridization, Fluorescence; D008677:Metaphase; D051379:Mice; D008957:Models, Genetic; D008969:Molecular Sequence Data; D009693:Nucleic Acid Hybridization; D017422:Sequence Analysis, DNA; D016324:Sequence Tagged Sites; D012984:Software