Whole genome SNP arrays as a potential diagnostic tool for the detection of characteristic chromosomal aberrations in renal epithelial tumors

Monzon, Federico A.; Hagenkord, Jill; Lyons‐Weiler, Maureen A.; Balani, Jyoti; Parwani, Anil V.; Sciulli, Christin; Li, Jia; Chandran, Uma; Bastacky, Sheldon; Dhir, Rajiv

doi:10.1038/modpathol.2008.20

Cited by 66 publications

(30 citation statements)

References 26 publications

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“…The pRCCs showed frequent amplification of the entire chromosomes 3, 7, 12, 16, 17 and 20 ( Supplementary Fig. 19 ), consistent with previous reports 66 . Although chRCCs (classic) showed frequent loss of chromosomes 1, 2, 6, 8,10, 13, 17 and 21, the chRCC eosinophilic subtype appeared to be almost completely diploid.…”

Section: Resultssupporting

confidence: 91%

Spectrum of diverse genomic alterations define non–clear cell renal carcinoma subtypes

Durinck¹,

Stawiski²,

et al. 2014

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To further understand the molecular distinctions between kidney cancer subtypes, we analyzed exome, transcriptome and copy number alteration data from 167 primary human tumors that included renal oncocytomas and non–clear cell renal cell carcinomas (nccRCCs), consisting of papillary (pRCC), chromophobe (chRCC) and translocation (tRCC) subtypes. We identified ten significantly mutated genes in pRCC, including MET, NF2, SLC5A3, PNKD and CPQ. MET mutations occurred in 15% (10/65) of pRCC samples and included previously unreported recurrent activating mutations. In chRCC, we found TP53, PTEN, FAAH2, PDHB, PDXDC1 and ZNF765 to be significantly mutated. Gene expression analysis identified a five-gene set that enabled the molecular classification of chRCC, renal oncocytoma and pRCC. Using RNA sequencing, we identified previously unreported gene fusions, including ACTG1-MITF fusion. Ectopic expression of the ACTG1-MITF fusion led to cellular transformation and induced the expression of downstream target genes. Finally, we observed upregulation of the anti-apoptotic factor BIRC7 in MiTF-high RCC tumors, suggesting a potential therapeutic role for BIRC7 inhibitors.

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Section: Resultssupporting

confidence: 91%

Spectrum of diverse genomic alterations define non–clear cell renal carcinoma subtypes

Durinck¹,

Stawiski²,

et al. 2014

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“…Recently, high throughput methods for genome-wide screening of DNA copy number alterations and loss of heterozygosity have been developed and tested in small series of renal cell cancers 204–206. If proven reliable and feasible, these powerful methods hold promise for novel discoveries in large scale investigations of gene-environment and gene-gene interactions.…”

Section: Genetic Susceptibility and Environmentmentioning

confidence: 99%

Contemporary Epidemiology of Renal Cell Cancer

2008

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We analyzed renal cell cancer incidence patterns in the United States and reviewed recent epidemiologic evidence with regard to environmental and host genetic determinants of renal cell cancer risk. Renal cell cancer incidence rates continued to rise among all racial/ethnic groups in the United States, across all age groups, and for all tumor sizes, with the most rapid increases for localized stage disease and small tumors. Recent cohort studies confirmed the association of smoking, excess body weight, and hypertension with an elevated risk of renal cell cancer, and suggested that these factors can be modified to reduce the risk. There is increasing evidence for an inverse association between renal cell cancer risk and physical activity and moderate intake of alcohol. Occupational exposure to TCE has been positively associated with renal cell cancer risk in several recent studies, but its link with somatic mutations of the VHL gene has not been confirmed. Studies of genetic polymorphisms in relation to renal cell cancer risk have produced mixed results, but genome-wide association studies with larger sample size and a more comprehensive approach are underway. Few epidemiologic studies have evaluated risk factors by subtypes of renal cell cancer defined by somatic mutations and other tumor markers. Keywords renal cell cancer; incidence trends; cohort studies; smoking; obesity; hypertension; diet; occupation; genetic polymorphism; somatic mutation Malignant tumors of the kidney account for about 4% of cancer incidence and 2% of cancer mortality in the United States, with over 54,000 new cases and 13,000 deaths having been estimated for 2008. 1 More than 85% of kidney cancers arise in the renal parenchyma, with the remainder arising in the renal pelvis. 2 Renal pelvis cancer is mostly of the transitional cell type and is not the focus of this review. Nearly all cancers originating in the renal parenchyma are adenocarcinomas (renal cell carcinoma), in which clear cell is the predominant subtype. 3 The remainder is made up of the papillary type and other rare histologic types, such as collecting duct and chromophobe carcinomas. 3,4 Distinct morphologic and genetic characteristics have also been described for renal cell carcinoma in familial cancer syndromes. [5][6][7] Descriptive and analytic epidemiologic studies in general have not distinguished the subtypes of renal cell carcinoma, except for studies involving the von Hippel-Lindau (VHL) gene mutation that is seen primarily in the clear cell type. 8 Since the clear cell type comprises 85% to 90% of renal cell carcinoma, 3 the epidemiology of renal cell carcinoma is strongly influenced by that of the clear cell type.* Correspondence: Wong-Ho Chow, National Cancer Institute, 6120 Executive Blvd, EPS 8100, Bethesda, Maryland 20892-7240, USA. choww@mail.nih.gov. NIH Public Access Author ManuscriptCancer J. Author manuscript; available in PMC 2011 April 15. DESCRIPTIVE EPIDEMIOLOGY Incidence patterns and temporal trendsIncidence rates of renal cell carcinoma h...

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“…8–10,14–16 Papillary RCC is characterized by gains in chromosomes 7 and 17. 17 An increase or decrease in the expression of specific genes within these chromosomal regions likely has prognostic implications, but these genes have yet to be elucidated. To search for additional genetic changes in clear cell RCC, Dalgliesh et al 13 sequenced the coding exons of 3544 genes in 101 clear cell RCCs (see Author Note, page S-24).…”

Section: Molecular Biology Of Rccmentioning

confidence: 99%

NCCN Task Force Report: Optimizing Treatment of Advanced Renal Cell Carcinoma With Molecular Targeted Therapy

Hudes¹,

Carducci²,

Choueiri³

et al. 2011

J Natl Compr Canc Netw

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The outcome of patients with metastatic renal cell carcinoma has been substantially improved with administration of the currently available molecularly targeted therapies. However, proper selection of therapy and management of toxicities remain challenging. NCCN convened a multidisciplinary task force panel to address the clinical issues associated with these therapies in attempt to help practicing oncologists optimize patient outcomes. This report summarizes the background data presented at the task force meeting and the ensuing discussion.

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Whole genome SNP arrays as a potential diagnostic tool for the detection of characteristic chromosomal aberrations in renal epithelial tumors

Cited by 66 publications

References 26 publications

Spectrum of diverse genomic alterations define non–clear cell renal carcinoma subtypes

Spectrum of diverse genomic alterations define non–clear cell renal carcinoma subtypes

Contemporary Epidemiology of Renal Cell Cancer

NCCN Task Force Report: Optimizing Treatment of Advanced Renal Cell Carcinoma With Molecular Targeted Therapy

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