Clear cell papillary renal cell carcinoma: A chromosomal microarray analysis of two cases using a novel Molecular Inversion Probe (MIP) technology

Alexiev, Borislav A.; Zou, Ying

doi:10.1016/j.prp.2014.10.001

Cited by 9 publications

(5 citation statements)

References 14 publications

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“…Moreover, experience with this ‘pT3a’ occurrence in clear cell tubulopapillary renal cell neoplasms is limited, given its infrequency, especially when compared to that reported in oncocytoma (in the latter, adipose tissue invasion reportedly ranges from 16% to 20% and vascular invasion ranges from 2% to 4%) 20–22 . Based on multiple studies and a subsequent meta‐analysis from nephrectomy studies of 665 clear cell tubulopapillary RCCs, only two (<1%) showed pT3a staging 1,2,4–6,8,9,17,18,23–45 . Additionally, during the initial design of this study and inquiry among a large group of uropathologists for potential study cases, some notably replied that if they had encountered a clear cell tubulopapillary renal cell neoplasm within adipose tissue or a vessel, they would have likely diagnosed it as clear cell RCC by default.…”

Section: Discussionmentioning

confidence: 99%

Vascular, adipose tissue, and/or calyceal invasion in clear cell tubulopapillary renal cell tumour: potentially problematic diagnostic scenarios

Sangoi,

Tsai,

Harik

et al. 2024

Histopathology

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AimsThe 2022 WHO classification for kidney tumours recently downgraded clear cell tubulopapillary (also known as clear cell papillary) renal cell carcinoma (RCC) to a benign neoplasm (i.e. clear cell tubulopapillary renal cell tumour) based on the overwhelmingly banal nature of this neoplasm. However, it has been recognized that some clear cell tubulopapillary renal cell tumours demonstrate vascular, adipose or pelvicalyceal invasion, raising the possibility of more aggressive behaviour. The goal of this study was to determine if these ‘high stage’ features have an effect on tumour prognosis, warranting a carcinoma designation.Methods and ResultsAfter excluding cases with tissue artefact (i.e. prior core biopsy track changes) and other RCC subtypes with next‐generation sequencing, nine clear cell tubulopapillary renal cell tumours with these so‐called ‘high stage’ features, and otherwise classic morphologic and immunophenotypic findings, including low‐grade cytology and ‘cup‐like’ CA9 expression, were evaluated. Median tumour size was 2.2 cm with a range of 0.8 to 6.7 cm. Eight cases (89%) demonstrated perinephric or hilar adipose tissue invasion, although most of these cases showed a bulging (in contrast to an infiltrative) growth pattern. One case demonstrated renal vascular invasion in addition to hilar adipose tissue invasion, and one case demonstrated extension into the pelvicalyceal system. There were no recurrences or evidence of metastatic disease.ConclusionThese overall findings continue to support the benign designation for clear cell tubulopapillary renal cell tumours, despite morphologic features that might raise the possibility of a ‘higher stage’ neoplasm.

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Section: Discussionmentioning

confidence: 99%

Vascular, adipose tissue, and/or calyceal invasion in clear cell tubulopapillary renal cell tumour: potentially problematic diagnostic scenarios

Sangoi,

Tsai,

Harik

et al. 2024

Histopathology

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“…Additionally, SNP arrays can be used for detection of loss of heterozygosity (LOH) and in some platforms, mutation detection. Furthermore, OncoScan, another genome-wide microarray platform, has been developed and is widely used for detection of chromosomal aberrations in DNA samples isolated from formalin-fixed, paraffin-embedded (FFPE) solid tumor specimens (See the Affmetrix OncoScan home page link in the Internet Resources; Alexiev et al, 2014;Chandler et al, 2012;Gray et al, 2016). Overall, microarrays have been proven to be a useful tool for detection of CNVs, LOH, and uniparental disomy (UPD) in both constitutional and neoplastic disorders (Jacobs et al, 2007;Pfeifer et al, 2006;Shaw-Smith et al, 2004).…”

Section: Alternative Methods For Genome-wide Cytogenetic Analysesmentioning

confidence: 99%

Multicolor Fluorescence In Situ Hybridization (FISH) Approaches for Simultaneous Analysis of the Entire Human Genome

et al. 2018

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Analysis of the organization of the human genome is vital for understanding genetic diversity, human evolution, and disease pathogenesis. A number of approaches, such as multicolor fluorescence in situ hybridization (FISH) assays, cytogenomic microarray (CMA), and next-generation sequencing (NGS) technologies, are available for simultaneous analysis of the entire human genome. Multicolor FISH-based spectral karyotyping (SKY), multiplex FISH (M-FISH), and Rx-FISH may provide rapid identification of interchromosomal and intrachromosomal rearrangements as well as the origin of unidentified extrachromosomal elements. Recent advances in molecular cytogenetics have made it possible to efficiently examine the entire human genome in a single experiment at much higher resolution and specificity using CMA and NGS technologies. Here, we present an overview of the approaches available for genome-wide analyses. © 2018 by John Wiley & Sons, Inc.

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“…Recently, in a renal carcinoma, OncoScan results showed novel detection of copy-neutral LOH that had been unavailable from previous diagnostic methods including aCGH [9]. In a breast cancer, CNV detection by OncoScan was tested as a recurrence biomarker [21].…”

Section: Clinical Applicationsmentioning

confidence: 99%

“…Among them, the OncoScan ® FFPE Assay Kit (Affymetrix, a Thermo Fisher Scientific company) is the first microarray designed specifically for use with degraded DNA as is found in FFPE tissue. The Oncoscan array utilizes SNP probes to provide copy number as well as allele frequency information [8][9][10]. Here we discuss utilization and implementation of the OncoScan microarray, including generation of targets from gDNA prepared from FFPE samples, microarray hybridization, data analysis, and quality control.…”

Section: Introductionmentioning

confidence: 99%

Utilization of the oncoscan microarray assay in cancer diagnostics

2017

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Current strategies for cancer patient management include the use of genomic and proteomic test results to help guide therapeutic selection. The need for multi-target variant analysis is highlighted by the growing number of novel therapies to treat tumors with specific profiles and the increasing recognition that cancer is an extremely heterogeneous syndrome. Microarray analysis is a powerful genomic tool that provides genome-wide genetic information that is critical for guiding cancer treatments. Unlike constitutional applications of microarray analysis which are performed on whole blood samples, microarray analysis of solid tumors is challenging because tumor tissues are typically formalin fixed and paraffin embedded (FFPE). Genomic DNA extracted from FFPE tissues can also be fragmented into small pieces and yield much lower concentrations of DNA. We validated and implemented the Affymetrix OncoScan® FFPE assay to enable genome-wide analysis from these types of samples. The Affymetrix OncoScan® assay utilizes molecular inversion probes that generate multiplexed array hybridization targets from as short as 40 base-pairs of sequence and as low as approximately 80 ng of genomic DNA. OncoScan microarray analysis provides genomic information that includes structural variations, copy number variations and SNPs in a timely and a cost-effective manner from FFPE tumor tissues.

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Clear cell papillary renal cell carcinoma: A chromosomal microarray analysis of two cases using a novel Molecular Inversion Probe (MIP) technology

Cited by 9 publications

References 14 publications

Vascular, adipose tissue, and/or calyceal invasion in clear cell tubulopapillary renal cell tumour: potentially problematic diagnostic scenarios

Vascular, adipose tissue, and/or calyceal invasion in clear cell tubulopapillary renal cell tumour: potentially problematic diagnostic scenarios

Multicolor Fluorescence In Situ Hybridization (FISH) Approaches for Simultaneous Analysis of the Entire Human Genome

Utilization of the oncoscan microarray assay in cancer diagnostics

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