ArticleOncotarget2018
Identification of copy number alterations in colon cancer from analysis of amplicon-based next generation sequencing data.
Article in Oncotarget, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 19 citations in OpenAlex.
- Distinctive chromosomal, mutational and transcriptional profiling in colon versus rectal cancers.Journal of translational medicine · 2025Article
- Validation of an AI-enabled exome/transcriptome liquid biopsy platform for early detection, MRD, disease monitoring, and therapy selection for solid tumors.Scientific reports · 2025Article
- Identification of novel diagnostic biomarkers associated with liver metastasis in colon adenocarcinoma by machine learning.Discover oncology · 2024Article
- Insights into the Clinical, Biological and Therapeutic Impact of Copy Number Alteration in Cancer.International journal of molecular sciences · 2024Review
- Multi-omics prognostic signatures of IPO11 mRNA expression and clinical outcomes in colorectal cancer using bioinformatics approaches.Health information science and systems · 2023Article
- Colorectal cancer concurrent gene signature based on coherent patterns between genomic and transcriptional alterations.BMC cancer · 2022Article
- Copy Number Alterations as Novel Biomarkers and Therapeutic Targets in Colorectal Cancer.Cancers · 2022Review
- Construction and validation of a prognostic model for gastrointestinal stromal tumors based on copy number alterations and clinicopathological characteristics.Frontiers in oncology · 2022Article
- Altered SERCA Expression in Breast Cancer.Medicina (Kaunas, Lithuania) · 2021Article
- Identification and Characterization of the Copy Number Dosage-Sensitive Genes in Colorectal Cancer.Molecular therapy. Methods & clinical development · 2020Article
- Prognostic genes of melanoma identified by weighted gene co-expression network analysis and drug repositioning using a network-based method.Oncology letters · 2019Article
- Graph Algorithms for Condensing and Consolidating Gene Set Analysis Results.Molecular & cellular proteomics : MCP · 2019Article
- Identification of Prognostic Dosage-Sensitive Genes in Colorectal Cancer Based on Multi-Omics.Frontiers in genetics · 2019Article
Corrections and comments
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Authors and funding
16 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The objective of this study was to determine the feasibility to detect copy number alterations in colon cancer samples using Next Generation Sequencing data and to elucidate the association between copy number alterations in specific genes and the development of cancer in different colon segments. We report the successful detection of somatic changes in gene copy number in 37 colon cancer patients by analysis of sequencing data through Amplicon CNA Algorithm. Overall, we have found a total of 748 significant copy number alterations in 230 significant genes, of which 143 showed CN losses and 87 showed CN gains. Validation of results was performed on 20 representative genes by quantitative qPCR and/or immunostaining. By this analysis, we have identified 4 genes that were subjected to copy number alterations in tumors arising in all colon segments (defined "common genes") and the presence of copy number alterations in 14 genes that were significantly associated to one specific site (defined "site-associated genes"). Finally, copy number alterations in ASXL1, TSC1 and IL7R turned out to be clinically relevant since the loss of TSC1 and IL7R was associated with advanced stages and/or reduced survival whereas copy number gain of ASXL1 was associated with good prognosis.
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