ArticleBMC bioinformatics2016
Identification of recurrent focal copy number variations and their putative targeted driver genes in ovarian cancer.
Article in BMC bioinformatics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 26 citations in OpenAlex.
- Benchmarking copy number alteration inference methods for spatial transcriptomics.Nature communications · 2026Article
- Replication stress increases de novo CNVs across the malaria parasite genome.Nucleic acids research · 2026Article
- Replication stress increases de novo CNVs across the malaria parasite genome.bioRxiv : the preprint server for biology · 2025Article
- Detecting copy-number alterations from single-cell chromatin sequencing data by AtaCNA.Cell reports methods · 2025Article
- A Review of Limbic System-Associated Membrane Protein in Tumorigenesis.Biomedicines · 2024Review
- DNA Copy Number Alterations and Copy Neutral Loss of Heterozygosity in Adult Ph-Negative Acute B-Lymphoblastic Leukemia: Focus on the Genes Involved.International journal of molecular sciences · 2023Article
- Identification of recurrent 3q13.31 chromosomal rearrangement indicatesInternational journal of oncology · 2023Article
- DNA copy number variation: Main characteristics, evolutionary significance, and pathological aspects.Biomedical journal · 2021Review
- CIRCNV: Detection of CNVs Based on a Circular Profile of Read Depth from Sequencing Data.Biology · 2021Article
- Association of Copy Number Variation Signature and Survival in Patients With Serous Ovarian Cancer.JAMA network open · 2021Article
- Proteome Profiling Uncovers an Autoimmune Response Signature That Reflects Ovarian Cancer Pathogenesis.Cancers · 2020Article
- CAISMOV24, a new human low-grade serous ovarian carcinoma cell line.BMC cancer · 2017Article
- Integrative analysis of copy number and transcriptional expression profiles in esophageal cancer to identify a novel driver gene for therapy.Scientific reports · 2017Article
- Copy Number Alterations in Tumor Genomes Deleting Antineoplastic Drug Targets Partially Compensated by Complementary Amplifications.Cancer genomics & proteomicsArticle
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
Abstract
backgroundGenomic regions with recurrent DNA copy number variations (CNVs) are generally believed to encode oncogenes and tumor suppressor genes (TSGs) that drive cancer growth. However, it remains a challenge to delineate the key cancer driver genes from the regions encoding a large number of genes.
resultsIn this study, we developed a new approach to CNV analysis based on spectral decomposition of CNV profiles into focal CNVs and broad CNVs. We performed an analysis of CNV data of 587 serous ovarian cancer samples on multiple platforms. We identified a number of novel focal regions, such as focal gain of ESR1, focal loss of LSAMP, prognostic site at 3q26.2 and losses of sub-telomere regions in multiple chromosomes. Furthermore, we performed network modularity analysis to examine the relationships among genes encoded in the focal CNV regions. Our results also showed that the recurrent focal gains were significantly associated with the known oncogenes and recurrent losses associated with TSGs and the CNVs had a greater effect on the mRNA expression of the driver genes than that of the non-driver genes.
conclusionsOur results demonstrate that spectral decomposition of CNV profiles offers a new way of understanding the role of CNVs in cancer.
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