@article {664756,
	title = {Multilevel Genomics-Based Taxonomy of Renal Cell Carcinoma.},
	journal = {Cell Rep},
	year = {2016},
	month = {2016 Mar 2},
	abstract = {
	On the basis of multidimensional and comprehensive molecular characterization (including DNA methalylation and copy number, RNA, and protein expression), we classified 894 renal cell carcinomas (RCCs) of various histologic types into nine major genomic subtypes. Site of origin within the nephron was one major determinant in the classification, reflecting differences among clear cell, chromophobe, and papillary RCC. Widespread molecular changes associated with TFE3 gene fusion or chromatin modifier genes were present within a specific subtype and\&nbsp;spanned multiple subtypes. Differences in patient survival and in alteration of specific pathways (including hypoxia, metabolism, MAP kinase, NRF2-ARE, Hippo, immune checkpoint, and PI3K/AKT/mTOR) could further distinguish the subtypes. Immune checkpoint markers and molecular signatures of T\&nbsp;cell infiltrates were both highest in the subtype associated with aggressive clear cell RCC. Differences between the genomic subtypes suggest that therapeutic strategies could be tailored to each RCC disease subset.

},
	issn = {2211-1247},
	doi = {10.1016/j.celrep.2016.02.024},
	author = {Chen, Fengju and Zhang, Yiqun and {\c S}enbabao{\u g}lu, Yasin and Ciriello, Giovanni and <b>Yang, Lixing</b> and Reznik, Ed and Shuch, Brian and Micevic, Goran and De Velasco, Guillermo and Shinbrot, Eve and Noble, Michael S and Lu, Yiling and Covington, Kyle R and Xi, Liu and Drummond, Jennifer A and Muzny, Donna and Kang, Hyojin and Lee, Junehawk and Tamboli, Pheroze and Reuter, Victor and Shelley, Carl Simon and Kaipparettu, Benny A and Bottaro, Donald P and Godwin, Andrew K and Gibbs, Richard A and Getz, Gad and Kucherlapati, Raju and <b>Park, Peter J</b> and Sander, Chris and Henske, Elizabeth P and Zhou, Jane H and Kwiatkowski, David J and Ho, Thai H and Choueiri, Toni K and Hsieh, James J and Akbani, Rehan and Mills, Gordon B and Hakimi, A Ari and Wheeler, David A and Creighton, Chad J}
}
