ArticleGenome biology2008
A sequence-based survey of the complex structural organization of tumor genomes.
Article in Genome biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 39 citations in OpenAlex.
- Expanding the computational toolbox for mining cancer genomes.Nature reviews. Genetics · 2014Review
- GAP-Seq: a method for identification of DNA palindromes.BMC genomics · 2014Article
- Breakpoint profiling of 64 cancer genomes reveals numerous complex rearrangements spawned by homology-independent mechanisms.Genome research · 2013Article
- Genetic consequences of programmed genome rearrangement.Current biology : CB · 2012Article
- Reconstructing cancer genomes from paired-end sequencing data.BMC bioinformatics · 2012Article
- Chapter 6: Structural variation and medical genomics.PLoS computational biology · 2012Article
- Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes.Genome research · 2011Article
- Transcriptional consequences of genomic structural aberrations in breast cancer.Genome research · 2011Article
- Are there any differences between features of proteins expressed in malignant and benign breast cancers?Journal of research in medical sciences : the official journal of Isfahan University of Medical Sciences · 2010Article
- Analysis of next-generation genomic data in cancer: accomplishments and challenges.Human molecular genetics · 2010Review
- Challenges of sequencing human genomes.Briefings in bioinformatics · 2010Review
- Article
- Optimizing PCR assays for DNA-based cancer diagnostics.Journal of computational biology : a journal of computational molecular cell biology · 2010Article
- Cancer gene discovery in mouse and man.Biochimica et biophysica acta · 2009Review
- Statistical aspects of discerning indel-type structural variation via DNA sequence alignment.BMC genomics · 2009Article
- A geometric approach for classification and comparison of structural variants.Bioinformatics (Oxford, England) · 2009Article
- The apoptotic machinery as a biological complex system: analysis of its omics and evolution, identification of candidate genes for fourteen major types of cancer, and experimental validation in CML and neuroblastoma.BMC medical genomics · 2009Article
- PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data.Genome biology · 2009Article
- A sequence-level map of chromosomal breakpoints in the MCF-7 breast cancer cell line yields insights into the evolution of a cancer genome.Genome research · 2009Article
- Signatures of selection in fusion transcripts resulting from chromosomal translocations in human cancer.PloS one · 2009Article
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Authors and funding
26 authors at 15 institutions in 2 countries.
Funding
Abstract
backgroundThe genomes of many epithelial tumors exhibit extensive chromosomal rearrangements. All classes of genome rearrangements can be identified using end sequencing profiling, which relies on paired-end sequencing of cloned tumor genomes.
resultsIn the present study brain, breast, ovary, and prostate tumors, along with three breast cancer cell lines, were surveyed using end sequencing profiling, yielding the largest available collection of sequence-ready tumor genome breakpoints and providing evidence that some rearrangements may be recurrent. Sequencing and fluorescence in situ hybridization confirmed translocations and complex tumor genome structures that include co-amplification and packaging of disparate genomic loci with associated molecular heterogeneity. Comparison of the tumor genomes suggests recurrent rearrangements. Some are likely to be novel structural polymorphisms, whereas others may be bona fide somatic rearrangements. A recurrent fusion transcript in breast tumors and a constitutional fusion transcript resulting from a segmental duplication were identified. Analysis of end sequences for single nucleotide polymorphisms revealed candidate somatic mutations and an elevated rate of novel single nucleotide polymorphisms in an ovarian tumor.
conclusionThese results suggest that the genomes of many epithelial tumors may be far more dynamic and complex than was previously appreciated and that genomic fusions, including fusion transcripts and proteins, may be common, possibly yielding tumor-specific biomarkers and therapeutic targets.
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Registered trials
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.