ArticleGenome research2006
Decoding the fine-scale structure of a breast cancer genome and transcriptome.
Article in Genome research, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
32 citing papers in PubMed, 54 citations in OpenAlex.
- Genomic copy number variation correlates with survival outcomes in WHO grade IV glioma.Scientific reports · 2020Article
- Adaptively Weighted and Robust Mathematical Programming for the Discovery of Driver Gene Sets in Cancers.Scientific reports · 2019Article
- A Novel Graph-based Algorithm to Infer Recurrent Copy Number Variations in Cancer.Cancer informatics · 2016Article
- The emerging complexity of gene fusions in cancer.Nature reviews. Cancer · 2015Review
- Expanding the computational toolbox for mining cancer genomes.Nature reviews. Genetics · 2014Review
- GAP-Seq: a method for identification of DNA palindromes.BMC genomics · 2014Article
- Copy number variation analysis based on AluScan sequences.Journal of clinical bioinformatics · 2014Article
- Assessment of palindromes as platforms for DNA amplification in breast cancer.Genome research · 2012Article
- Chapter 6: Structural variation and medical genomics.PLoS computational biology · 2012Article
- ChimeraScan: a tool for identifying chimeric transcription in sequencing data.Bioinformatics (Oxford, England) · 2011Article
- Long-range massively parallel mate pair sequencing detects distinct mutations and similar patterns of structural mutability in two breast cancer cell lines.Cancer genetics · 2011Article
- Transcriptional consequences of genomic structural aberrations in breast cancer.Genome research · 2011Article
- Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes.Genome research · 2011Article
- SNPs array karyotyping reveals a novel recurrent 20p13 amplification in primary myelofibrosis.PloS one · 2011Article
- Analysis of next-generation genomic data in cancer: accomplishments and challenges.Human molecular genetics · 2010Review
- Integrating the multiple dimensions of genomic and epigenomic landscapes of cancer.Cancer metastasis reviews · 2010Review
- Advances in translational bioinformatics: computational approaches for the hunting of disease genes.Briefings in bioinformatics · 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
- Mechanisms of change in gene copy number.Nature reviews. Genetics · 2009Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
19 authors at 7 institutions in 3 countries.
Funding
Abstract
A comprehensive understanding of cancer is predicated upon knowledge of the structure of malignant genomes underlying its many variant forms and the molecular mechanisms giving rise to them. It is well established that solid tumor genomes accumulate a large number of genome rearrangements during tumorigenesis. End Sequence Profiling (ESP) maps and clones genome breakpoints associated with all types of genome rearrangements elucidating the structural organization of tumor genomes. Here we extend the ESP methodology in several directions using the breast cancer cell line MCF-7. First, targeted ESP is applied to multiple amplified loci, revealing a complex process of rearrangement and co-amplification in these regions reminiscent of breakage/fusion/bridge cycles. Second, genome breakpoints identified by ESP are confirmed using a combination of DNA sequencing and PCR. Third, in vitro functional studies assign biological function to a rearranged tumor BAC clone, demonstrating that it encodes anti-apoptotic activity. Finally, ESP is extended to the transcriptome identifying four novel fusion transcripts and providing evidence that expression of fusion genes may be common in tumors. These results demonstrate the distinct advantages of ESP including: (1) the ability to detect all types of rearrangements and copy number changes; (2) straightforward integration of ESP data with the annotated genome sequence; (3) immortalization of the genome; (4) ability to generate tumor-specific reagents for in vitro and in vivo functional studies. Given these properties, ESP could play an important role in a tumor genome project.
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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.