ArticleNature genetics2008
Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing.
Article in Nature genetics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It is linked to 2 registered trials, which are not on this map. Cited by 426 papers.
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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.
Randomized Phase 2 Study Comparing Pathological Responses on Colorectal Cancer Metastases After Preoperative Treatment Combining Bevacizumab With FOLFOX or FOLFIRI
Randomised Phase 2 Study Comparing Pathological Responses Observed on Colorectal Cancer Metastases Resected After Preoperative Treatment Combining Cetuximab With FOLFOX or FOLFIRI in RAS and B-RAF WT Tumors
Who cites it
426 citing papers in PubMed, 830 citations in OpenAlex.
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- A Hitchhiker Guide to Structural Variant Calling: A Comprehensive Benchmark Through Different Sequencing Technologies.Biomedicines · 2025Article
- Liquid Biopsy: The Challenges of a Revolutionary Approach in Oncology.International journal of molecular sciences · 2025Review
- Oncogenic gene fusions in cancer: from biology to therapy.Signal transduction and targeted therapy · 2025Review
- Translational and clinical comparison of whole genome and transcriptome to panel sequencing in precision oncology.NPJ precision oncology · 2025Article
- LoRA-TV: read depth profile-based clustering of tumor cells in single-cell sequencing.Briefings in bioinformatics · 2024Article
- Disentangling oncogenic amplicons in esophageal adenocarcinoma.Nature communications · 2024Article
- Breaking paradigms: Long non-coding RNAs forming gene fusions with potential implications in cancer.Genes & diseases · 2024Review
- The reckoning of chromosomal instability: past, present, future.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2024Review
- Haplotype-specific assembly of shattered chromosomes in esophageal adenocarcinomas.Cell genomics · 2024Article
- On the core segmentation algorithms of copy number variation detection tools.Briefings in bioinformatics · 2024Article
- GASOLINE: detecting germline and somatic structural variants from long-reads data.Scientific reports · 2023Article
- Toward the functional interpretation of somatic structural variations: bulk- and single-cell approaches.Briefings in bioinformatics · 2023Review
- Preleukemic Fusion Genes Induced via Ionizing Radiation.International journal of molecular sciences · 2023Review
- Identification of hub genes and biological mechanisms underlying the pathogenesis of asthenozoospermia and chronic epididymitis.Frontiers in genetics · 2023Article
- Conversion of specific lncRNAs to biomarkers in exhaled breath condensate samples of patients with advanced stage non-small-cell lung cancer.Frontiers in genetics · 2023Article
- Efficient sequencing data compression and FPGA acceleration based on a two-step framework.Frontiers in genetics · 2023Article
- Defining the origin, evolution, and immune composition of SDH-deficient renal cell carcinoma.iScience · 2022Article
366 more citing papers are in PubMed but not listed here.
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Authors and funding
24 authors at 2 institutions in 1 country.
Funding
Abstract
Human cancers often carry many somatically acquired genomic rearrangements, some of which may be implicated in cancer development. However, conventional strategies for characterizing rearrangements are laborious and low-throughput and have low sensitivity or poor resolution. We used massively parallel sequencing to generate sequence reads from both ends of short DNA fragments derived from the genomes of two individuals with lung cancer. By investigating read pairs that did not align correctly with respect to each other on the reference human genome, we characterized 306 germline structural variants and 103 somatic rearrangements to the base-pair level of resolution. The patterns of germline and somatic rearrangement were markedly different. Many somatic rearrangements were from amplicons, although rearrangements outside these regions, notably including tandem duplications, were also observed. Some somatic rearrangements led to abnormal transcripts, including two from internal tandem duplications and two fusion transcripts created by interchromosomal rearrangements. Germline variants were predominantly mediated by retrotransposition, often involving AluY and LINE elements. The results demonstrate the feasibility of systematic, genome-wide characterization of rearrangements in complex human cancer genomes, raising the prospect of a new harvest of genes associated with cancer using this strategy.
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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.