ArticleProceedings of the National Academy of Sciences of the United States of America2003
End-sequence profiling: sequence-based analysis of aberrant genomes.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 79 papers.
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Who cites it
79 citing papers in PubMed, 118 citations in OpenAlex.
- Article
- Quantitative, in situ analysis of mRNAs and proteins with subcellular resolution.Scientific reports · 2017Article
- SVachra: a tool to identify genomic structural variation in mate pair sequencing data containing inward and outward facing reads.BMC genomics · 2017Article
- Genomic Comparison of Two O111:H- Enterohemorrhagic Escherichia coli Isolates from a Historic Hemolytic-Uremic Syndrome Outbreak in Australia.Infection and immunity · 2016Article
- The emerging complexity of gene fusions in cancer.Nature reviews. Cancer · 2015Review
- PacBio-LITS: a large-insert targeted sequencing method for characterization of human disease-associated chromosomal structural variations.BMC genomics · 2015Article
- Molecular homology and difference between spontaneous canine mammary cancer and human breast cancer.Cancer research · 2014Article
- Expanding the computational toolbox for mining cancer genomes.Nature reviews. Genetics · 2014Review
- GAP-Seq: a method for identification of DNA palindromes.BMC genomics · 2014Article
- Identification of cancer gene fusions based on advanced analysis of the human genome or transcriptome.Frontiers of medicine · 2013Review
- Structural analysis of the genome of breast cancer cell line ZR-75-30 identifies twelve expressed fusion genes.BMC genomics · 2012Article
- nFuse: discovery of complex genomic rearrangements in cancer using high-throughput sequencing.Genome research · 2012Article
- Reconstructing cancer genomes from paired-end sequencing data.BMC bioinformatics · 2012Article
- Massively parallel sequencing approaches for characterization of structural variation.Methods in molecular biology (Clifton, N.J.) · 2012Review
- Chapter 6: Structural variation and medical genomics.PLoS computational biology · 2012Article
- Article
- PAR6B is required for tight junction formation and activated PKCζ localization in breast cancer.American journal of cancer research · 2012Article
- Advances in BAC-based physical mapping and map integration strategies in plants.Journal of biomedicine & biotechnology · 2012Review
- An integrative probabilistic model for identification of structural variation in sequencing data.Genome biology · 2012Article
- Simultaneous structural variation discovery among multiple paired-end sequenced genomes.Genome research · 2011Article
19 more citing papers are in PubMed but not listed here.
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Authors and funding
14 authors at 1 institution in 1 country.
Funding
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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.