End-sequence profiling: sequence-based analysis of aberrant genomes.
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.
Volik
Stanislav
S
Cancer Research Institute and Department of Laboratory Medicine, University of California Comprehensive Cancer Center, 2340 Sutter Street, San Francisco, CA 94115, USA.
Zhao
Shaying
S
Chin
Koei
K
Brebner
John H
JH
Herndon
David R
DR
Tao
Quanzhou
Q
Kowbel
David
D
Huang
Guiqing
G
Lapuk
Anna
A
Kuo
Wen-Lin
WL
Magrane
Gregg
G
De Jong
Pieter
P
Gray
Joe W
JW
Collins
Colin
C
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