Journal ArticleDOI
Germline and sporadic mTOR pathway mutations in low-grade oncocytic tumor of the kidney.
Payal Kapur,Payal Kapur,Joanna Zawiejska-Rataj,Ming Gao,Hua Zhong,Suneetha Chintalapati,Midori Mitui,Spencer D. Barnes,Qinbo Zhou,Jeffrey Miyata,Deyssy Carrillo,Venkat S. Malladi,Dinesh Rakheja,Ivan Pedrosa,Lin Xu,Lisa N. Kinch,James Brugarolas +16 more
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In this article, the authors describe 22 low-grade oncocytic tumor (LOT) cases corresponding to 7 patients presenting with a median age of 75 years (range 63-86 years) and male to female ratio 2:5.About:
This article is published in Modern Pathology.The article was published on 2021-09-20. It has received 23 citations till now. The article focuses on the topics: Eosinophilic & TSC1.read more
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Renal Cell Carcinoma in Tuberous Sclerosis Complex.
TL;DR: A detailed understanding of the pathologic features of these distinctive tumors, which include chromophobe-like features and eosinophilia, with some of the tumors unclassified, is provided in this paper.
Journal ArticleDOI
Renal cell carcinoma associated with tuberous sclerosis complex (TSC)/mammalian target of rapamycin (MTOR) genetic alterations
Pedram Argani,Rohit Mehra +1 more
TL;DR:
Journal ArticleDOI
Low‐grade oncocytic tumour of the kidney is characterised by genetic alterations of TSC1, TSC2, MTOR or PIK3CA and consistent GATA3 positivity
Sean R. Williamson,Ondrej Hes,Kiril Trpkov,Aditi Aggarwal,Abhishek Satapathy,Sourav Mishra,Shivani Sharma,Ankur R. Sangoi,Liang Cheng,Mahmut Akgul,Muhammad Idrees,Albert M. Levin,Sudha M. Sadasivan,Pilar San Miguel Fraile,Joanna Rogala,Eva Comperat,Daniel M. Berney,Stela Bulimbasic,Jesse K. McKenney,Shilpy Jha,Nakul Y Sampat,Sambit K. Mohanty +21 more
TL;DR: Recurrent tuberous sclerosis / MTOR pathway gene alterations in LOT supports its consideration as a distinct morphologic, immunohistochemical, and genetic entity, and PIK3CA is another pathway member that may be altered in these tumors.
Journal ArticleDOI
TSC/MTOR-associated Eosinophilic Renal Tumors Exhibit a Heterogeneous Clinicopathologic Spectrum
Qiu-Yuan Xia,Ye Shengbing,Ru Fang,Βασίλειος Κοψαχείλης,Marina Lavezzo dos Santos Vilar,Yong Yu,Francis Leneghan,Leonce Leandry,Slobodan Nikolić,Melanie J. Gregg +9 more
TL;DR: In this paper , the authors evaluated the clinicopathologic and IHC profiles of 39 eosinophilic renal tumors with targeted DNA sequencing-confirmed TSC/MTOR mutations.
Journal ArticleDOI
TSC/mTOR Pathway Mutation Associated Eosinophilic/Oncocytic Renal Neoplasms: A Heterogeneous Group of Tumors with Distinct Morphology, Immunohistochemical Profile, and Similar Genetic Background
TL;DR: Despite the common genetic background, it appears that the tumors with TSC/mTOR mutations represent a diverse group of distinct renal neoplasms.
References
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Journal ArticleDOI
ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data
TL;DR: The ANNOVAR tool to annotate single nucleotide variants and insertions/deletions, such as examining their functional consequence on genes, inferring cytogenetic bands, reporting functional importance scores, finding variants in conserved regions, or identifying variants reported in the 1000 Genomes Project and dbSNP is developed.
Journal ArticleDOI
A framework for variation discovery and genotyping using next-generation DNA sequencing data
Mark A. DePristo,Eric Banks,Ryan Poplin,Kiran V. Garimella,Jared Maguire,Christopher Hartl,Anthony A. Philippakis,Anthony A. Philippakis,Anthony A. Philippakis,Guillermo del Angel,Manuel A. Rivas,Manuel A. Rivas,Matt Hanna,Aaron McKenna,Timothy Fennell,Andrew Kernytsky,Andrey Sivachenko,Kristian Cibulskis,Stacey Gabriel,David Altshuler,David Altshuler,Mark J. Daly,Mark J. Daly +22 more
TL;DR: A unified analytic framework to discover and genotype variation among multiple samples simultaneously that achieves sensitive and specific results across five sequencing technologies and three distinct, canonical experimental designs is presented.
Journal ArticleDOI
Adjusting batch effects in microarray expression data using empirical Bayes methods
TL;DR: This paper proposed parametric and non-parametric empirical Bayes frameworks for adjusting data for batch effects that is robust to outliers in small sample sizes and performs comparable to existing methods for large samples.
Journal ArticleDOI
A scaling normalization method for differential expression analysis of RNA-seq data
TL;DR: A simple and effective method for performing normalization is outlined and dramatically improved results for inferring differential expression in simulated and publicly available data sets are shown.
Journal ArticleDOI
From FastQ Data to High‐Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline
Géraldine A. Van der Auwera,Mauricio O. Carneiro,Christopher Hartl,Ryan Poplin,Guillermo del Angel,Ami Levy-Moonshine,Tadeusz Jordan,Khalid Shakir,David Roazen,Joel Thibault,Eric Banks,Kiran V. Garimella,David Altshuler,Stacey Gabriel,Mark A. DePristo +14 more
TL;DR: This unit describes how to use BWA and the Genome Analysis Toolkit to map genome sequencing data to a reference and produce high‐quality variant calls that can be used in downstream analyses.
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