ArticleScientific reports2016
Concordance between somatic copy number loss and down-regulated expression: A pan-cancer study of cancer predisposition genes.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed, 14 citations in OpenAlex.
- Multi-Omics Mining of lncRNAs with Biological and Clinical Relevance in Cancer.International journal of molecular sciences · 2023Review
- Copy number variants landscape of multiple cancers and clinical applications based on NGS gene panel.Annals of medicine · 2023Article
- circExp database: an online transcriptome platform for human circRNA expressions in cancers.Database : the journal of biological databases and curation · 2021Article
- Integrated genetic and epigenetic analysis of cancer-related genes in non-ampullary duodenal adenomas and intramucosal adenocarcinomas.The Journal of pathology · 2020Article
- Integrative analysis of rare copy number variants and gene expression data in alopecia areata implicates an aetiological role for autophagy.Experimental dermatology · 2020Article
- Significance of gene mutations in the Wnt signaling pathway in traditional serrated adenomas of the colon and rectum.PloS one · 2020Article
- Clinically Actionable Insights into Initial and Matched Recurrent Glioblastomas to Inform Novel Treatment Approaches.Journal of oncology · 2019Article
- Identification of novel prognosis-related genes associated with cancer using integrative network analysis.Scientific reports · 2018Article
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Cancer predisposition genes (CPGs) are a class of cancer genes in which germline variants lead to increased risk of cancer. Research has revealed that copy number variation (CNV) may be linked to cancer susceptibility in CPGs. In this pan-cancer analysis, we explored the relationship between somatic CNV and gene expression changes in CPGs. Based on curated 827 human CPGs from literature, we firstly identified 729 CPGs with precise CNV information from 5067 tumor samples using TCGA CNV data. Among them, 128 CPGs tended to have more frequent copy number losses (CNLs) compared with copy number gains (CNGs). Then by correlating these CNV data with TCGA gene expression data, we obtained 49 CPGs with concordant CNLs and gene down-regulation. Intriguingly, five CPGs showed concordance between CNL and down-regulation in 50 or more tumor samples: MTAP (216 samples), PTEN (143), MCPH1 (86), SMAD4 (63), and MINPP1 (51), which may represent the recurrent driving force for gene expression change during oncogenesis. Moreover, network analysis revealed that these 49 CPGs were tightly connected. In summary, this study provides the first observation of concordance between CNLs and down-regulation of CPGs in pan-cancer, which may help better understand the CPG biology in tumorigenesis and cancer progression.
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