Molecular Stratification of Clear Cell Renal Cell Carcinoma by Consensus Clustering Reveals Distinct Subtypes and Survival Patterns.

PubWeight™: 3.78‹?› | Rank: Top 1%

🔗 View Article (PMID 20871783)

Published in Genes Cancer on February 01, 2010

Authors

A Rose Brannon1, Anupama Reddy, Michael Seiler, Alexandra Arreola, Dominic T Moore, Raj S Pruthi, Eric M Wallen, Matthew E Nielsen, Huiqing Liu, Katherine L Nathanson, Börje Ljungberg, Hongjuan Zhao, James D Brooks, Shridar Ganesan, Gyan Bhanot, W Kimryn Rathmell

Author Affiliations

1: Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA.

Articles citing this

Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. N Engl J Med (2012) 44.56

Comprehensive molecular characterization of clear cell renal cell carcinoma. Nature (2013) 13.60

Integrated molecular analysis of clear-cell renal cell carcinoma. Nat Genet (2013) 4.61

Effects on survival of BAP1 and PBRM1 mutations in sporadic clear-cell renal-cell carcinoma: a retrospective analysis with independent validation. Lancet Oncol (2013) 4.24

Meta-analysis of clear cell renal cell carcinoma gene expression defines a variant subgroup and identifies gender influences on tumor biology. Eur Urol (2011) 2.55

Identifying mRNA targets of microRNA dysregulated in cancer: with application to clear cell Renal Cell Carcinoma. BMC Syst Biol (2010) 2.49

State of the science: an update on renal cell carcinoma. Mol Cancer Res (2012) 1.58

A prognostic gene expression signature in infratentorial ependymoma. Acta Neuropathol (2012) 1.44

Tumor immune microenvironment characterization in clear cell renal cell carcinoma identifies prognostic and immunotherapeutically relevant messenger RNA signatures. Genome Biol (2016) 1.41

Systematic evaluation of the prognostic impact and intratumour heterogeneity of clear cell renal cell carcinoma biomarkers. Eur Urol (2014) 1.21

Multilevel Genomics-Based Taxonomy of Renal Cell Carcinoma. Cell Rep (2016) 1.15

Adjuvant therapy for renal cell carcinoma: past, present, and future. Oncologist (2014) 1.11

Renal cancer biomarkers: the promise of personalized care. BMC Med (2012) 1.08

Identification of genes and pathways involved in kidney renal clear cell carcinoma. BMC Bioinformatics (2014) 1.05

Classification models for clear cell renal carcinoma stage progression, based on tumor RNAseq expression trained supervised machine learning algorithms. BMC Proc (2014) 1.02

Renal cell carcinoma: where will the state-of-the-art lead us? Curr Oncol Rep (2010) 0.97

Whole-Transcriptome profiling of formalin-fixed, paraffin-embedded renal cell carcinoma by RNA-seq. BMC Genomics (2014) 0.97

Biomarkers for anti-angiogenic therapy in cancer. Int J Mol Sci (2013) 0.96

Integrative genome-wide gene expression profiling of clear cell renal cell carcinoma in Czech Republic and in the United States. PLoS One (2013) 0.94

The use of automated quantitative analysis to evaluate epithelial-to-mesenchymal transition associated proteins in clear cell renal cell carcinoma. PLoS One (2012) 0.92

Robust multi-tissue gene panel for cancer detection. BMC Cancer (2010) 0.91

Differential expression of prognostic proteomic markers in primary tumour, venous tumour thrombus and metastatic renal cell cancer tissue and correlation with patient outcome. PLoS One (2013) 0.91

Tumor subtype-specific cancer-testis antigens as potential biomarkers and immunotherapeutic targets for cancers. Cancer Immunol Res (2013) 0.90

A Molecular Model for Predicting Overall Survival in Patients with Metastatic Clear Cell Renal Carcinoma: Results from CALGB 90206 (Alliance). EBioMedicine (2015) 0.90

Biomarkers: the next therapeutic hurdle in metastatic renal cell carcinoma. Br J Cancer (2012) 0.88

Computational repositioning and preclinical validation of pentamidine for renal cell cancer. Mol Cancer Ther (2014) 0.87

Intrinsic Genomic Differences Between African American and White Patients With Clear Cell Renal Cell Carcinoma. JAMA Oncol (2016) 0.85

Integrative genome-wide expression profiling identifies three distinct molecular subgroups of renal cell carcinoma with different patient outcome. BMC Cancer (2012) 0.85

Preclinical trial of a new dual mTOR inhibitor, MLN0128, using renal cell carcinoma tumorgrafts. Int J Cancer (2013) 0.85

Alternate Metabolic Programs Define Regional Variation of Relevant Biological Features in Renal Cell Carcinoma Progression. Clin Cancer Res (2016) 0.85

Identification of potential serum proteomic biomarkers for clear cell renal cell carcinoma. PLoS One (2014) 0.84

Patients with ClearCode34-identified molecular subtypes of clear cell renal cell carcinoma represent unique populations with distinct comorbidities. Urol Oncol (2015) 0.82

ROTS: reproducible RNA-seq biomarker detector-prognostic markers for clear cell renal cell cancer. Nucleic Acids Res (2015) 0.82

Intratumoral morphologic and molecular heterogeneity of rhabdoid renal cell carcinoma: challenges for personalized therapy. Mod Pathol (2015) 0.81

Distinct transcriptional responses elicited by unfolded nuclear or cytoplasmic protein in mammalian cells. Elife (2015) 0.81

Expression of Ror2 mediates invasive phenotypes in renal cell carcinoma. PLoS One (2014) 0.80

Predictive models for the practical management of renal cell carcinoma. Nat Rev Urol (2012) 0.79

Tumour and patient factors in renal cell carcinoma-towards personalized therapy. Nat Rev Urol (2015) 0.78

Clear Cell Type A and B Molecular Subtypes in Metastatic Clear Cell Renal Cell Carcinoma: Tumor Heterogeneity and Aggressiveness. Eur Urol (2016) 0.78

Insights into the Genetic Basis of the Renal Cell Carcinomas from The Cancer Genome Atlas. Mol Cancer Res (2016) 0.78

Cancer subtypes classification using long non-coding RNA. Oncotarget (2016) 0.78

Prognostic gene signature identification using causal structure learning: applications in kidney cancer. Cancer Inform (2015) 0.77

Full-Length Enrich c-DNA Libraries-Clear Cell-Renal Cell Carcinoma. J Oncol (2012) 0.77

Downregulation of dystroglycan glycosyltransferases LARGE2 and ISPD associate with increased mortality in clear cell renal cell carcinoma. Mol Cancer (2015) 0.77

Combined Influence of EGF+61G>A and TGFB+869T>C Functional Polymorphisms in Renal Cell Carcinoma Progression and Overall Survival: The Link to Plasma Circulating MiR-7 and MiR-221/222 Expression. PLoS One (2015) 0.77

A study exploring critical pathways in clear cell renal cell carcinoma. Exp Ther Med (2013) 0.77

Three Dimensional Culture of Human Renal Cell Carcinoma Organoids. PLoS One (2015) 0.77

Delivering preventive, predictive and personalised cancer medicine for renal cell carcinoma: the challenge of tumour heterogeneity. EPMA J (2011) 0.76

Deep sequencing reveals microRNAs predictive of antiangiogenic drug response. JCI Insight (2016) 0.75

PPARG is central to the initiation and propagation of human angiomyolipoma, suggesting its potential as a therapeutic target. EMBO Mol Med (2017) 0.75

KDM6B induces epithelial-mesenchymal transition and enhances clear cell renal cell carcinoma metastasis through the activation of SLUG. Int J Clin Exp Pathol (2015) 0.75

Molecular profiling of renal cell carcinoma: building a bridge toward clinical impact. Curr Opin Urol (2016) 0.75

Emerging molecular classification in renal cell carcinoma: implications for drug development. Target Oncol (2010) 0.75

A Five-Gene Signature Predicts Prognosis in Patients with Kidney Renal Clear Cell Carcinoma. Comput Math Methods Med (2015) 0.75

Renal cancer subtypes: Should we be lumping or splitting for therapeutic decision making? Cancer (2016) 0.75

Study design requirements for RNA sequencing-based breast cancer diagnostics. Sci Rep (2016) 0.75

Integrative analysis of protein-coding and non-coding RNAs identifies clinically relevant subtypes of clear cell renal cell carcinoma. Oncotarget (2016) 0.75

Molecular subtypes and prognosis in RCC. Aging (Albany NY) (2015) 0.75

Recognizing the Continuous Nature of Expression Heterogeneity and Clinical Outcomes in Clear Cell Renal Cell Carcinoma. Sci Rep (2017) 0.75

Identification and validation of soluble carrier family expression signature for predicting poor outcome of renal cell carcinoma. J Cancer (2017) 0.75

Articles cited by this

Molecular portraits of human breast tumours. Nature (2000) 94.14

Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc Natl Acad Sci U S A (2001) 71.82

A gene-expression signature as a predictor of survival in breast cancer. N Engl J Med (2002) 58.15

A multigene assay to predict recurrence of tamoxifen-treated, node-negative breast cancer. N Engl J Med (2004) 41.02

Silencing of the VHL tumor-suppressor gene by DNA methylation in renal carcinoma. Proc Natl Acad Sci U S A (1994) 8.47

HIF-alpha effects on c-Myc distinguish two subtypes of sporadic VHL-deficient clear cell renal carcinoma. Cancer Cell (2008) 4.84

An outcome prediction model for patients with clear cell renal cell carcinoma treated with radical nephrectomy based on tumor stage, size, grade and necrosis: the SSIGN score. J Urol (2002) 4.59

Improved prognostication of renal cell carcinoma using an integrated staging system. J Clin Oncol (2001) 4.22

Improved identification of von Hippel-Lindau gene alterations in clear cell renal tumors. Clin Cancer Res (2008) 4.02

Genetic and epigenetic analysis of von Hippel-Lindau (VHL) gene alterations and relationship with clinical variables in sporadic renal cancer. Cancer Res (2006) 2.87

Improved detection of germline mutations in the von Hippel-Lindau disease tumor suppressor gene. Hum Mutat (1998) 2.64

Gene expression profiling predicts survival in conventional renal cell carcinoma. PLoS Med (2005) 2.56

High expression of lymphocyte-associated genes in node-negative HER2+ breast cancers correlates with lower recurrence rates. Cancer Res (2007) 2.48

A postoperative prognostic nomogram predicting recurrence for patients with conventional clear cell renal cell carcinoma. J Urol (2005) 2.30

Gene expression profiling of clear cell renal cell carcinoma: gene identification and prognostic classification. Proc Natl Acad Sci U S A (2001) 2.22

Postoperative surveillance protocol for patients with localized and locally advanced renal cell carcinoma based on a validated prognostic nomogram and risk group stratification system. J Urol (2005) 2.02

Robust classification of renal cell carcinoma based on gene expression data and predicted cytogenetic profiles. Cancer Res (2004) 1.47

Renal epithelial neoplasms: diagnostic applications of gene expression profiling. Adv Anat Pathol (2008) 1.30

ConsensusCluster: a software tool for unsupervised cluster discovery in numerical data. OMICS (2010) 1.25

Portraits of breast cancer progression. BMC Bioinformatics (2007) 1.17

Differential gene expression identifies subgroups of renal cell carcinoma. J Lab Clin Med (2006) 1.06

Molecular markers for predicting prognosis of renal cell carcinoma. Urol Oncol (2007) 1.05

Data perturbation independent diagnosis and validation of breast cancer subtypes using clustering and patterns. Cancer Inform (2007) 1.00

Logical Analysis of Data (LAD) model for the early diagnosis of acute ischemic stroke. BMC Med Inform Decis Mak (2008) 0.96

Articles by these authors

The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature (2012) 31.78

Clinical efficacy of a RAF inhibitor needs broad target blockade in BRAF-mutant melanoma. Nature (2010) 16.12

The tuberous sclerosis complex. N Engl J Med (2006) 13.53

Acquired resistance to BRAF inhibitors mediated by a RAF kinase switch in melanoma can be overcome by cotargeting MEK and IGF-1R/PI3K. Cancer Cell (2010) 12.50

Dicer-deficient mouse embryonic stem cells are defective in differentiation and centromeric silencing. Genes Dev (2005) 12.15

Classification, subtype discovery, and prediction of outcome in pediatric acute lymphoblastic leukemia by gene expression profiling. Cancer Cell (2002) 11.83

The triple negative paradox: primary tumor chemosensitivity of breast cancer subtypes. Clin Cancer Res (2007) 11.56

Gene expression profiling identifies clinically relevant subtypes of prostate cancer. Proc Natl Acad Sci U S A (2004) 10.99

Autophagy suppresses tumorigenesis through elimination of p62. Cell (2009) 9.95

Low-penetrance susceptibility to breast cancer due to CHEK2(*)1100delC in noncarriers of BRCA1 or BRCA2 mutations. Nat Genet (2002) 9.71

X chromosomal abnormalities in basal-like human breast cancer. Cancer Cell (2006) 7.17

Phenotypic evaluation of the basal-like subtype of invasive breast carcinoma. Mod Pathol (2006) 6.86

Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas. N Engl J Med (2015) 5.71

53BP1 loss rescues BRCA1 deficiency and is associated with triple-negative and BRCA-mutated breast cancers. Nat Struct Mol Biol (2010) 5.59

Efficacy of neoadjuvant Cisplatin in triple-negative breast cancer. J Clin Oncol (2010) 5.50

A locus on 19p13 modifies risk of breast cancer in BRCA1 mutation carriers and is associated with hormone receptor-negative breast cancer in the general population. Nat Genet (2010) 4.96

HIF-alpha effects on c-Myc distinguish two subtypes of sporadic VHL-deficient clear cell renal carcinoma. Cancer Cell (2008) 4.84

PTEN loss confers BRAF inhibitor resistance to melanoma cells through the suppression of BIM expression. Cancer Res (2011) 4.80

Gene-panel sequencing and the prediction of breast-cancer risk. N Engl J Med (2015) 4.77

Network modeling links breast cancer susceptibility and centrosome dysfunction. Nat Genet (2007) 4.69

Gene expression patterns in human embryonic stem cells and human pluripotent germ cell tumors. Proc Natl Acad Sci U S A (2003) 4.67

Multiple independent variants at the TERT locus are associated with telomere length and risks of breast and ovarian cancer. Nat Genet (2013) 4.35

Single cell profiling of circulating tumor cells: transcriptional heterogeneity and diversity from breast cancer cell lines. PLoS One (2012) 3.74

A transcriptional profile of aging in the human kidney. PLoS Biol (2004) 3.69

Cancer risk estimates for BRCA1 mutation carriers identified in a risk evaluation program. J Natl Cancer Inst (2002) 3.65

RAD51 135G-->C modifies breast cancer risk among BRCA2 mutation carriers: results from a combined analysis of 19 studies. Am J Hum Genet (2007) 3.63

Metastatic potential of melanomas defined by specific gene expression profiles with no BRAF signature. Pigment Cell Res (2006) 3.42

Common breast cancer-predisposition alleles are associated with breast cancer risk in BRCA1 and BRCA2 mutation carriers. Am J Hum Genet (2008) 3.41

Stereotactic body radiotherapy for localized prostate cancer: interim results of a prospective phase II clinical trial. Int J Radiat Oncol Biol Phys (2008) 3.22

Trends in radical prostatectomy: centralization, robotics, and access to urologic cancer care. Cancer (2011) 3.13

Genomic profiling reveals alternative genetic pathways of prostate tumorigenesis. Cancer Res (2007) 3.13

Activin a efficiently specifies definitive endoderm from human embryonic stem cells only when phosphatidylinositol 3-kinase signaling is suppressed. Stem Cells (2007) 3.04

TP53 mutation status and gene expression profiles are powerful prognostic markers of breast cancer. Breast Cancer Res (2007) 3.01

Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma. N Engl J Med (2015) 3.00

High incidence of cetuximab-related infusion reactions in Tennessee and North Carolina and the association with atopic history. J Clin Oncol (2007) 2.99

Genome-wide association study of renal cell carcinoma identifies two susceptibility loci on 2p21 and 11q13.3. Nat Genet (2010) 2.96

Transcriptional programs activated by exposure of human prostate cancer cells to androgen. Genome Biol (2002) 2.87

Common variation in KITLG and at 5q31.3 predisposes to testicular germ cell cancer. Nat Genet (2009) 2.85

Robotic radical cystectomy for bladder cancer: surgical and pathological outcomes in 100 consecutive cases. J Urol (2009) 2.76

Loss of 53BP1 causes PARP inhibitor resistance in Brca1-mutated mouse mammary tumors. Cancer Discov (2012) 2.74

Urinary TMPRSS2:ERG and PCA3 in an active surveillance cohort: results from a baseline analysis in the Canary Prostate Active Surveillance Study. Clin Cancer Res (2013) 2.70

Phase II trial of sorafenib plus interferon alfa-2b as first- or second-line therapy in patients with metastatic renal cell cancer. J Clin Oncol (2007) 2.69

Prospective randomized controlled trial of robotic versus open radical cystectomy for bladder cancer: perioperative and pathologic results. Eur Urol (2009) 2.68

The mitogen-activated protein/extracellular signal-regulated kinase kinase inhibitor AZD6244 (ARRY-142886) induces growth arrest in melanoma cells and tumor regression when combined with docetaxel. Clin Cancer Res (2008) 2.64

Gene expression patterns in renal cell carcinoma assessed by complementary DNA microarray. Am J Pathol (2003) 2.59

Long-term outcomes from a prospective trial of stereotactic body radiotherapy for low-risk prostate cancer. Int J Radiat Oncol Biol Phys (2011) 2.57

Gene expression profiling predicts survival in conventional renal cell carcinoma. PLoS Med (2005) 2.56

Computerized image-based detection and grading of lymphocytic infiltration in HER2+ breast cancer histopathology. IEEE Trans Biomed Eng (2009) 2.56

Meta-analysis of clear cell renal cell carcinoma gene expression defines a variant subgroup and identifies gender influences on tumor biology. Eur Urol (2011) 2.55

Expectation-maximization-driven geodesic active contour with overlap resolution (EMaGACOR): application to lymphocyte segmentation on breast cancer histopathology. IEEE Trans Biomed Eng (2010) 2.52

Identifying mRNA targets of microRNA dysregulated in cancer: with application to clear cell Renal Cell Carcinoma. BMC Syst Biol (2010) 2.49

High expression of lymphocyte-associated genes in node-negative HER2+ breast cancers correlates with lower recurrence rates. Cancer Res (2007) 2.48

A variant TMPRSS2 isoform and ERG fusion product in prostate cancer with implications for molecular diagnosis. Mod Pathol (2007) 2.47

Metastatic potential in renal cell carcinomas ≤7 cm: Swedish Kidney Cancer Quality Register data. Eur Urol (2011) 2.45

Genome-wide association study in BRCA1 mutation carriers identifies novel loci associated with breast and ovarian cancer risk. PLoS Genet (2013) 2.39

Inherited mutations in pheochromocytoma and paraganglioma: why all patients should be offered genetic testing. Ann Surg Oncol (2013) 2.38

A genome wide linkage search for breast cancer susceptibility genes. Genes Chromosomes Cancer (2006) 2.35

Dietary curcumin inhibits chemotherapy-induced apoptosis in models of human breast cancer. Cancer Res (2002) 2.33

Identification of a microRNA panel for clear-cell kidney cancer. Urology (2009) 2.32

The loss of radiographic enhancement in primary renal cell carcinoma tumors following multitargeted receptor tyrosine kinase therapy is an additional indicator of response. Urology (2009) 2.25

Genome-wide linkage screen for testicular germ cell tumour susceptibility loci. Hum Mol Genet (2006) 2.23

Common variants in LSP1, 2q35 and 8q24 and breast cancer risk for BRCA1 and BRCA2 mutation carriers. Hum Mol Genet (2009) 2.13

Long-term oncologic outcome after laparoscopic radical nephroureterectomy for upper tract transitional cell carcinoma. Eur Urol (2007) 2.11

Pathological upstaging during radical cystectomy is associated with worse recurrence-free survival in patients with bacillus Calmette-Guerin-refractory bladder cancer. Urology (2009) 2.10

The role of KRAS rs61764370 in invasive epithelial ovarian cancer: implications for clinical testing. Clin Cancer Res (2011) 2.09

High-dose conformal radiotherapy for treatment of stage IIIA/IIIB non-small-cell lung cancer: technical issues and results of a phase I/II trial. Int J Radiat Oncol Biol Phys (2002) 2.09

Nationwide prevalence of lymph node metastases in Gleason score 3 + 3 = 6 prostate cancer. Pathology (2014) 2.07

Urinary bladder cancer treated with radical cystectomy: perioperative parameters and early complications prospectively registered in a national population-based database. Scand J Urol (2014) 2.07

Length of site-specific positive surgical margins as a risk factor for biochemical recurrence following radical prostatectomy. Int J Urol (2011) 2.04

Akt-mediated phosphorylation of Bmi1 modulates its oncogenic potential, E3 ligase activity, and DNA damage repair activity in mouse prostate cancer. J Clin Invest (2012) 2.03

Phase II efficacy and pharmacogenomic study of Selumetinib (AZD6244; ARRY-142886) in iodine-131 refractory papillary thyroid carcinoma with or without follicular elements. Clin Cancer Res (2012) 2.02

N-acetyltransferase 2 phenotype, occupation, and bladder cancer risk: results from the EPIC cohort. Cancer Epidemiol Biomarkers Prev (2013) 2.01

The telomerase reverse transcriptase regulates chromatin state and DNA damage responses. Proc Natl Acad Sci U S A (2005) 2.01

Patterns of evolution and host gene mimicry in influenza and other RNA viruses. PLoS Pathog (2008) 1.96

Management of ureteral obstruction due to advanced malignancy: optimizing therapeutic and palliative outcomes. J Urol (2008) 1.96

ENIGMA--evidence-based network for the interpretation of germline mutant alleles: an international initiative to evaluate risk and clinical significance associated with sequence variation in BRCA1 and BRCA2 genes. Hum Mutat (2011) 1.94

In vivo HIF-mediated reductive carboxylation is regulated by citrate levels and sensitizes VHL-deficient cells to glutamine deprivation. Cell Metab (2013) 1.93

Determination of cancer risk associated with germ line BRCA1 missense variants by functional analysis. Cancer Res (2007) 1.89

Identification of a BRCA2-specific modifier locus at 6p24 related to breast cancer risk. PLoS Genet (2013) 1.88

Increased cyclin D1 expression can mediate BRAF inhibitor resistance in BRAF V600E-mutated melanomas. Mol Cancer Ther (2008) 1.86

Application of a BRAF pyrosequencing assay for mutation detection and copy number analysis in malignant melanoma. J Mol Diagn (2007) 1.85

DNA methylation profiling reveals novel biomarkers and important roles for DNA methyltransferases in prostate cancer. Genome Res (2011) 1.85

Loss of pVHL is sufficient to cause HIF dysregulation in primary cells but does not promote tumor growth. Cancer Cell (2003) 1.85