ArticleGenome research2011
Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes.
Article in Genome research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
50 citing papers in PubMed.
- Breeding and Molecular Characterization of Insect-Resistant Transgenic Cotton.Plants (Basel, Switzerland) · 2026Article
- Deciphering complex breakage-fusion-bridge genome rearrangements with Ambigram.Nature communications · 2023Article
- HiSV: A control-free method for structural variation detection from Hi-C data.PLoS computational biology · 2023Article
- A multi-platform reference for somatic structural variation detection.Cell genomics · 2022Article
- Integrative analysis of structural variations using short-reads and linked-reads yields highly specific and sensitive predictions.PLoS computational biology · 2020Article
- Mechanisms Underlying Recurrent Genomic Amplification in Human Cancers.Trends in cancer · 2020Review
- Breakage-Fusion-Bridge Events Trigger Complex Genome Rearrangements and Amplifications in Developmentally Arrested T Cell Lymphomas.Cell reports · 2019Article
- An AR-ERG transcriptional signature defined by long-range chromatin interactomes in prostate cancer cells.Genome research · 2019Article
- Integrative detection and analysis of structural variation in cancer genomes.Nature genetics · 2018Article
- The Tandem Duplicator Phenotype Is a Prevalent Genome-Wide Cancer Configuration Driven by Distinct Gene Mutations.Cancer cell · 2018Article
- Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line.Genome research · 2018Article
- A Pan-Cancer Compendium of Genes Deregulated by Somatic Genomic Rearrangement across More Than 1,400 Cases.Cell reports · 2018Article
- SVachra: a tool to identify genomic structural variation in mate pair sequencing data containing inward and outward facing reads.BMC genomics · 2017Article
- Global analysis of somatic structural genomic alterations and their impact on gene expression in diverse human cancers.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- The tandem duplicator phenotype as a distinct genomic configuration in cancer.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Many obesity-associated SNPs strongly associate with DNA methylation changes at proximal promoters and enhancers.Genome medicine · 2015Article
- The Obesity-Linked Gene Nudt3 Drosophila Homolog Aps Is Associated With Insulin Signaling.Molecular endocrinology (Baltimore, Md.) · 2015Article
- Contralateral breast cancer can represent a metastatic spread of the first primary tumor: determination of clonal relationship between contralateral breast cancers using next-generation whole genome sequencing.Breast cancer research : BCR · 2015Article
- Integrated sequence and expression analysis of ovarian cancer structural variants underscores the importance of gene fusion regulation.BMC medical genomics · 2015Article
- Comprehensive characterization of the genomic alterations in human gastric cancer.International journal of cancer · 2015Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
39 authors.
Funding
Abstract
Somatic genome rearrangements are thought to play important roles in cancer development. We optimized a long-span paired-end-tag (PET) sequencing approach using 10-Kb genomic DNA inserts to study human genome structural variations (SVs). The use of a 10-Kb insert size allows the identification of breakpoints within repetitive or homology-containing regions of a few kilobases in size and results in a higher physical coverage compared with small insert libraries with the same sequencing effort. We have applied this approach to comprehensively characterize the SVs of 15 cancer and two noncancer genomes and used a filtering approach to strongly enrich for somatic SVs in the cancer genomes. Our analyses revealed that most inversions, deletions, and insertions are germ-line SVs, whereas tandem duplications, unpaired inversions, interchromosomal translocations, and complex rearrangements are over-represented among somatic rearrangements in cancer genomes. We demonstrate that the quantitative and connective nature of DNA-PET data is precise in delineating the genealogy of complex rearrangement events, we observe signatures that are compatible with breakage-fusion-bridge cycles, and we discover that large duplications are among the initial rearrangements that trigger genome instability for extensive amplification in epithelial cancers.
Indexed as
Identifiers
What OpenQuestion holds
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.