ArticlePloS one2017
Stratification of clear cell renal cell carcinoma (ccRCC) genomes by gene-directed copy number alteration (CNA) analysis.
Article in PloS one, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Epigenomic subtypes and prognostic methylation signatures in clear cell renal cell carcinoma.Clinical epigenetics · 2026Article
- Unraveling the role of LINC02657 in clear cell renal cell carcinoma: insights into tumor aggression, immune modulation, and treatment response.Frontiers in immunology · 2026Article
- Computed tomography-based unsupervised clustering identifies clusters associated with progression free survival in clear cell renal cell carcinoma.Cancer imaging : the official publication of the International Cancer Imaging Society · 2025Article
- Thioredoxin 1 (Trx1) is associated with poor prognosis in clear cell renal cell carcinoma (ccRCC): an example for the crucial role of redox signaling in ccRCC.World journal of urology · 2022Article
- Expression ofFrontiers in genetics · 2021Article
- A New Survival Model Based on Cholesterol Biosynthesis-Related Genes for Prognostic Prediction in Clear Cell Renal Cell Carcinoma.BioMed research international · 2021Article
- Role of the KEAP1-NRF2 Axis in Renal Cell Carcinoma.Cancers · 2020Review
- Comprehensive analysis of copy number variance and sensitivity to common targeted therapy in clear cell renal cell carcinoma: In silico analysis with in vitro validation.Cancer medicine · 2020Article
- Comprehensive analysis of somatic copy number alterations in clear cell renal cell carcinoma.Molecular carcinogenesis · 2020Article
- A Two-DNA Methylation Signature to Improve Prognosis Prediction of Clear Cell Renal Cell Carcinoma.Yonsei medical journal · 2019Article
- Whole-Exome Sequencing Identifies Somatic Mutations Associated With Mortality in Metastatic Clear Cell Kidney Carcinoma.Frontiers in genetics · 2019Article
- Integrative analysis of dysregulated microRNAs and mRNAs in multiple recurrent synchronized renal tumors from patients with von Hippel-Lindau disease.International journal of oncology · 2018Article
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6 authors.
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Abstract
Tumorigenic processes are understood to be driven by epi-/genetic and genomic alterations from single point mutations to chromosomal alterations such as insertions and deletions of nucleotides up to gains and losses of large chromosomal fragments including products of chromosomal rearrangements e.g. fusion genes and proteins. Overall comparisons of copy number alterations (CNAs) presented in 48 clear cell renal cell carcinoma (ccRCC) genomes resulted in ratios of gene losses versus gene gains between 26 ccRCC Fuhrman malignancy grades G1 (ratio 1.25) and 20 G3 (ratio 0.58). Gene losses and gains of 15762 CNA genes were mapped to 795 chromosomal cytoband loci including 280 KEGG pathways. CNAs were classified according to their contribution to Fuhrman tumour gradings G1 and G3. Gene gains and losses turned out to be highly structured processes in ccRCC genomes enabling the subclassification and stratification of ccRCC tumours in a genome-wide manner. CNAs of ccRCC seem to start with common tumour related gene losses flanked by CNAs specifying Fuhrman grade G1 losses and CNA gains favouring grade G3 tumours. The appearance of recurrent CNA signatures implies the presence of causal mechanisms most likely implicated in the pathogenesis and disease-outcome of ccRCC tumours distinguishing lower from higher malignant tumours. The diagnostic quality of initial 201 genes (108 genes supporting G1 and 93 genes G3 phenotypes) has been successfully validated on published Swiss data (GSE19949) leading to a restricted CNA gene set of 171 CNA genes of which 85 genes favour Fuhrman grade G1 and 86 genes Fuhrman grade G3. Regarding these gene sets overall survival decreased with the number of G3 related gene losses plus G3 related gene gains. CNA gene sets presented define an entry to a gene-directed and pathway-related functional understanding of ongoing copy number alterations within and between individual ccRCC tumours leading to CNA genes of prognostic and predictive value.
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