Volik Stanislav, Zhao Shaying, Chin Koei, Brebner John H, Herndon David R, Tao Quanzhou, Kowbel David, Huang Guiqing, Lapuk Anna, Kuo Wen-Lin, Magrane Gregg, De Jong Pieter, Gray Joe W, Collins Colin
Cancer Research Institute and Department of Laboratory Medicine, University of California Comprehensive Cancer Center, 2340 Sutter Street, San Francisco, CA 94115, USA.
Proc Natl Acad Sci U S A. 2003 Jun 24;100(13):7696-701. doi: 10.1073/pnas.1232418100. Epub 2003 Jun 4.
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.
基因组重排在进化、癌症及其他疾病中具有重要意义。对重排进行精确作图对于确定相关基因至关重要，为此已开发出许多技术。我们在此表明，末端序列分析（ESP）特别适合这一目的。ESP通过以下步骤完成：从测试基因组构建细菌人工染色体（BAC）文库，测量BAC末端序列，并将末端序列对定位到正常基因组序列上。BAC末端序列密度图能在高分辨率下识别拷贝数异常。跨越结构畸变的BAC在正常基因组序列上具有定位异常远的末端对。然后可以对这些对进行测序，以确定相关基因和断点序列。对乳腺癌细胞系MCF - 7进行的ESP分析证明了其在复杂基因组分析中的效用。对约8000个克隆（单倍体基因组克隆覆盖率为0.37倍）进行末端测序，生成了分辨率优于300 kb的MCF - 7基因组全面拷贝数图谱，并确定了381个基因组断点，其中一部分通过荧光原位杂交作图和测序得到了验证。
