ArticleProceedings of the National Academy of Sciences of the United States of America2016
Global analysis of somatic structural genomic alterations and their impact on gene expression in diverse human cancers.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 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
37 citing papers in PubMed, 56 citations in OpenAlex.
- Research progress on the protective effect and oxidative stress mechanism of rutin against liver injury (Review).Molecular medicine reports · 2026Review
- GCN2 in Cancer: Molecular Mechanisms to Therapeutic Potential.Current cancer drug targets · 2026Review
- Advancements in targeting tumor suppressor genes (p53 and BRCA 1/2) in breast cancer therapy.Molecular diversity · 2025Review
- Major impacts of widespread structural variation on sorghum.Genome research · 2024Article
- Accurate identification of structural variations from cancer samples.Briefings in bioinformatics · 2023Article
- Definition and Prognostic Value of Ph-like and IKZF1plus Status in Children With Down Syndrome and B-cell Precursor Acute Lymphoblastic Leukemia.HemaSphere · 2023Article
- Long-read sequencing identifies novel structural variations in colorectal cancer.PLoS genetics · 2023Article
- Targeting the PI3K/AKT/mTOR and RAF/MEK/ERK pathways for cancer therapy.Molecular biomedicine · 2022Review
- The pseudogenes of eukaryotic translation elongation factors (EEFs): Role in cancer and other human diseases.Genes & diseases · 2022Review
- Meerkat: An Algorithm to Reliably Identify Structural Variations and Predict Their Forming Mechanisms.Methods in molecular biology (Clifton, N.J.) · 2022Article
- DriverFuse: An R package for analysis of next-generation sequencing datasets to identify cancer driver fusion genes.PloS one · 2022Article
- Fusion transcripts and their genomic breakpoints in polyadenylated and ribosomal RNA-minus RNA sequencing data.GigaScience · 2021Article
- Enhancing breakpoint resolution with deep segmentation model: A general refinement method for read-depth based structural variant callers.PLoS computational biology · 2021Article
- Review
- A pediatric brain tumor atlas of genes deregulated by somatic genomic rearrangement.Nature communications · 2021Article
- Article
- Chromosome structural variation in tumorigenesis: mechanisms of formation and carcinogenesis.Epigenetics & chromatin · 2020Review
- Systematic investigation of promoter substitutions resulting from somatic intrachromosomal structural alterations in diverse human cancers.Scientific reports · 2020Article
- A Practical Guide for Structural Variation Detection in the Human Genome.Current protocols in human genetics · 2020Review
- Dysregulation of cancer genes by recurrent intergenic fusions.Genome biology · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Tumor genomes are mosaics of somatic structural variants (SVs) that may contribute to the activation of oncogenes or inactivation of tumor suppressors, for example, by altering gene copy number amplitude. However, there are multiple other ways in which SVs can modulate transcription, but the general impact of such events on tumor transcriptional output has not been systematically determined. Here we use whole-genome sequencing data to map SVs across 600 tumors and 18 cancers, and investigate the relationship between SVs, copy number alterations (CNAs), and mRNA expression. We find that 34% of CNA breakpoints can be clarified structurally and that most amplifications are due to tandem duplications. We observe frequent swapping of strong and weak promoters in the context of gene fusions, and find that this has a measurable global impact on mRNA levels. Interestingly, several long noncoding RNAs were strongly activated by this mechanism. Additionally, SVs were confirmed in telomere reverse transcriptase (TERT) upstream regions in several cancers, associated with elevated TERT mRNA levels. We also highlight high-confidence gene fusions supported by both genomic and transcriptomic evidence, including a previously undescribed paired box 8 (PAX8)-nuclear factor, erythroid 2 like 2 (NFE2L2) fusion in thyroid carcinoma. In summary, we combine SV, CNA, and expression data to provide insights into the structural basis of CNAs as well as the impact of SVs on gene expression in tumors.
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.