NDLI: End-sequence profiling: sequence-based analysis of aberrant genomes.

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End-sequence profiling: sequence-based analysis of aberrant genomes.

Content Provider	World Health Organization (WHO)-Global Index Medicus
Author	Lapuk, Anna Huang, Guiqing Kowbel, David Magrane, Gregg Kuo, Wen-lin Collins, Colin Chin, Koei Brebner, John H. Tao, Quanzhou Zhao, Shaying Volik, Stanislav Gray, Joe W. Herndon, David R. De Jong, Pieter
Description	Author Affiliation: Volik S ( Cancer Research Institute and Department of Laboratory Medicine, University of California Comprehensive Cancer Center, 2340 Sutter Street, San Francisco, CA 94115, USA.);
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.
ISSN	00278424
e-ISSN	10916490
Journal	Proceedings of the National Academy of Sciences of the United States of America
Issue Number	13
Volume Number	100
Language	English
Publisher	National Academy of Sciences
Publisher Date	2003-06-01
Publisher Place	United States
Access Restriction	Open
Subject Keyword	Genetic Techniques Genome Sequence Analysis, DNA Animals Chromosomes, Artificial, Bacterial Gene Library In Situ Hybridization, Fluorescence Metaphase Mice Models, Genetic Molecular Sequence Data Nucleic Acid Hybridization Sequence Tagged Sites Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S. Research Support, U.S. Gov't, P.H.S. Multidisciplinary
Content Type	Text
Resource Type	Article
Subject	Multidisciplinary

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