The Somatic Genomic Landscape of Chromophobe Renal Cell Carcinoma

Davis, Caleb F.; Ricketts, Christopher J.; Wang, Min; Yang, Lixing; Cherniack, Andrew D.; Shen, Hui; Buhay, Christian; Kang, Hyojin; Kim, Sang Cheol; Fahey, Catherine C.; Hacker, Kathryn E.; Bhanot, Gyan; Gordenin, Dmitry A.; Chu, Andy; Gunaratne, Preethi H.; Biehl, Michael; Seth, Sahil; Kaipparettu, Benny A.; Bristow, Christopher A.; Donehower, Lawrence A.; Wallen, Eric M.; Smith, Angela B.; Tickoo, Satish K.; Tamboli, Pheroze; Reuter, Victor; Schmidt, Laura S.; Hsieh, James J.; Choueiri, Toni K.; Hakimi, A. Ari; Chin, Lynda; Meyerson, Matthew; Kucherlapati, Raju; Park, Woong-Yang; Robertson, A. Gordon; Laird, Peter W.; Henske, Elizabeth P.; Kwiatkowski, David J.; Park, Peter J.; Morgan, Margaret; Shuch, Brian; Muzny, Donna; Wheeler, David A.; Linehan, W. Marston; Gibbs, Richard A.; Rathmell, W. Kimryn; Creighton, Chad J.; Creighton, Chad J.; Davis, Caleb F.; Morgan, Margaret; Gunaratne, Preethi H.

doi:10.1016/j.ccr.2014.07.014

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The Somatic Genomic Landscape of Chromophobe Renal Cell Carcinoma

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Davis, Caleb F., Ricketts, Christopher J., Wang, Min, Yang, Lixing, Cherniack, Andrew D., Shen, Hui, Buhay, Christian, Kang, Hyojin, Kim, Sang Cheol, Fahey, Catherine C., Hacker, Kathryn E., Bhanot, Gyan, Gordenin, Dmitry A., Chu, Andy, Gunaratne, Preethi H., Biehl, Michael, Seth, Sahil, Kaipparettu, Benny A., Bristow, Christopher A., Donehower, Lawrence A., Wallen, Eric M., Smith, Angela B., Tickoo, Satish K., Tamboli, Pheroze, Reuter, Victor, Schmidt, Laura S., Hsieh, James J., Choueiri, Toni K., Hakimi, A. Ari, Chin, Lynda, Meyerson, Matthew, Kucherlapati, Raju, Park, Woong-Yang, Robertson, A. Gordon, Laird, Peter W., Henske, Elizabeth P., Kwiatkowski, David J., Park, Peter J., Morgan, Margaret, Shuch, Brian, Muzny, Donna, Wheeler, David A., Linehan, W. Marston, Gibbs, Richard A., Rathmell, W. Kimryn, Creighton, Chad J., Creighton, Chad J., Davis, Caleb F., Morgan, Margaret, Gunaratne, Preethi H., Donehower, Lawrence A., Kaipparettu, Benny A., Wheeler, David A., Gibbs, Richard A., Signoretti, Sabina, Cherniack, Andrew D., Robertson, A. Gordon, Chu, Andy, Choueiri, Toni K., Henske, Elizabeth P., Kwiatkowski, David J., Reuter, Victor, Hsieh, James J., Hakimi, A. Ari, Tickoo, Satish K., Ricketts, Christopher, Linehan, W. Marston, Schmidt, Laura S., Gordenin, Dmitry A., Bhanot, Gyan, Seiler, Michael, Tamboli, Pheroze, Rathmell, W. Kimryn, Fahey, Catherine C., Hacker, Kathryn E., Smith, Angela B., Wallen, Eric M., Shen, Hui, Laird, Peter W., Shuch, Brian, Muzny, Donna, Buhay, Christian, Wang, Min, Chao, Hsu, Dahdouli, Mike, Xi, Liu, Kakkar, Nipun, Reid, Jeffrey G., Downs, Brittany, Drummond, Jennifer, Morton, Donna, Doddapaneni, Harsha, Lewis, Lora, English, Adam, Meng, Qingchang, Kovar, Christie, Wang, Qiaoyan, Hale, Walker, Hawes, Alicia, Kalra, Divya, Walker, Kimberly, Murray, Bradley A., Sougnez, Carrie, Saksena, Gordon, Carter, Scott L., Schumacher, Steven E., Tabak, Barbara, Zack, Travis I., Getz, Gad, Beroukhim, Rameen, Gabriel, Stacey B., Meyerson, Matthew, Ally, Adrian, Balasundaram, Miruna, Birol, Inanc, Brooks, Denise, Butterfield, Yaron S.N., Chuah, Eric, Clarke, Amanda, Dhalla, Noreen, Guin, Ranabir, Holt, Robert A., Kasaian, Katayoon, Lee, Darlene, Li, Haiyan I., Lim, Emilia, Ma, Yussanne, Mayo, Michael, Moore, Richard A., Mungall, Andrew J., Schein, Jacqueline E., Sipahimalani, Payal, Tam, Angela, Thiessen, Nina, Wong, Tina, Jones, Steven J.M., Marra, Marco A., Auman, J. Todd, Tan, Donghui, Meng, Shaowu, Jones, Corbin D., Hoadley, Katherine A., Mieczkowski, Piotr A., Mose, Lisle E., Jefferys, Stuart R., Roach, Jeffrey, Veluvolu, Umadevi, Wilkerson, Matthew D., Waring, Scot, Buda, Elizabeth, Wu, Junyuan, Bodenheimer, Tom, Hoyle, Alan P., Simons, Janae V., Soloway, Mathew G., Balu, Saianand, Parker, Joel S., Hayes, D. Neil, Perou, Charles M., Weisenberger, Daniel J., Bootwalla, Moiz S., Triche, Timothy, Lai, Phillip H., Van Den Berg, David J., Baylin, Stephen B., Chen, Fengju, Coarfa, Cristian, Noble, Michael S., DiCara, Daniel, Zhang, Hailei, Cho, Juok, Heiman, David I., Gehlenborg, Nils, Voet, Doug, Lin, Pei, Frazer, Scott, Stojanov, Petar, Liu, Yingchun, Zou, Lihua, Kim, Jaegil, Lawrence, Michael S., Chin, Lynda, Yang, Lixing, Seth, Sahil, Bristow, Christopher A., Protopopov, Alexei, Song, Xingzhi, Zhang, Jianhua, Pantazi, Angeliki, Hadjipanayis, Angela, Lee, Eunjung, Luquette, Lovelace J., Lee, Semin, Parfenov, Michael, Santoso, Netty, Seidman, Jonathan, Xu, Andrew W., Kucherlapati, Raju, Park, Peter J., Kang, Hyojin, Lee, Junehawk, Roberts, Steven A., Klimczak, Leszek J., Fargo, David, Lang, Martin, Choi, Yoon-La, Kim, Sang Cheol, Lee, June-Koo, Park, Woong-Yang, Wang, Wenyi, Fan, Yu, Ahn, Jaeil, Akbani, Rehan, Weinstein, John N., Haussler, David, Ma, Singer, Radenbaugh, Amie, Zhul, Jingchun, Biehl, Michael, Lichtenberg, Tara M., Zmuda, Erik, Black, Aaron D., Hanf, Benjamin, Ramirez, Nilsa C., Wise, Lisa, Bowen, Jay, Leraas, Kristen M., Hall, Tracy M., Gastier-Foster, Julie M., Kaelin, William G., Thorne, Leigh, Boice, Lori, Huang, Mei, Vocke, Cathy, Peterson, James, Worrell, Robert, Merino, Maria, Czerniak, Bogdan A., Aldape, Kenneth D., Wood, Christopher G., Spellman, Paul T., Atkins, Michael B., Cheville, John, Thompson, R. Houston, Jensen, Mark A., Pihl, Todd, Wan, Yunhu, Ayala, Brenda, Baboud, Julien, Velaga, Sudhakar, Walton, Jessica, Liu, Jia, Chudamani, Sudha, Wu, Ye, Sheth, Margi, Mills Shaw, Kenna R., Demchok, John A., Davidsen, Tanja, Yang, Liming, Wang, Zhining, Tarnuzzer, Roy W., Zhang, Jiashan, Eley, Greg, Felau, Ina, Zenklusen, Jean Claude, Hutter, Carolyn M., Guyer, Mark S., Ozenberger, Bradley A., Sofia, Heidi J.·2014·Cancer Cell

DOI 10.1016/j.ccr.2014.07.014

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Abstract

Summary We describe the landscape of somatic genomic alterations of 66 chromophobe renal cell carcinomas (ChRCCs) based on multidimensional and comprehensive characterization, including mitochondrial DNA (mtDNA) and whole genome sequencing. The result is consistent that ChRCC originates from the distal nephron compared to other kidney cancers with more proximal origins. Combined mtDNA and gene expression analysis implicates changes in mitochondrial function as a component of the disease biology, while suggesting alternative roles for mtDNA mutations in cancers relying on oxidative phosphorylation. Genomic rearrangements lead to recurrent structural breakpoints within TERT promoter region, which correlates with highly elevated TERT expression and manifestation of kataegis, representing a mechanism of TERT up-regulation in cancer distinct from previously-observed amplifications and point mutations.

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Authors: Davis, C. F., Ricketts, C. J., Wang, M., Yang, L., Cherniack, A. D., Shen, H., Buhay, C., Kang, H., Kim, S. C., Fahey, C. C., Hacker, K. E., Bhanot, G., Gordenin, D. A., Chu, A., Gunaratne, P. H., Biehl, M., Seth, S., Kaipparettu, B. A., Bristow, C. A., Donehower, L. A., Wallen, E. M., Smith, A. B., Tickoo, S. K., Tamboli, P., Reuter, V., Schmidt, L. S., Hsieh, J. J., Choueiri, T. K., Hakimi, A. A., Chin, L., Meyerson, M., Kucherlapati, R., Park, W.-Y., Robertson, A. G., Laird, P. W., Henske, E. P., Kwiatkowski, D. J., Park, P. J., Morgan, M., Shuch, B., Muzny, D., Wheeler, D. A., Linehan, W. M., Gibbs, R. A., Rathmell, W. K., Creighton, C. J., Creighton, C. J., Davis, C. F., Morgan, M., Gunaratne, P. H., Donehower, L. A., Kaipparettu, B. A., Wheeler, D. A., Gibbs, R. A., Signoretti, S., Cherniack, A. D., Robertson, A. G., Chu, A., Choueiri, T. K., Henske, E. P., Kwiatkowski, D. J., Reuter, V., Hsieh, J. J., Hakimi, A. A., Tickoo, S. K., Ricketts, C., Linehan, W. M., Schmidt, L. S., Gordenin, D. A., Bhanot, G., Seiler, M., Tamboli, P., Rathmell, W. K., Fahey, C. C., Hacker, K. E., Smith, A. B., Wallen, E. M., Shen, H., Laird, P. W., Shuch, B., Muzny, D., Buhay, C., Wang, M., Chao, H., Dahdouli, M., Xi, L., Kakkar, N., Reid, J. G., Downs, B., Drummond, J., Morton, D., Doddapaneni, H., Lewis, L., English, A., Meng, Q., Kovar, C., Wang, Q., Hale, W., Hawes, A., Kalra, D., Walker, K., Murray, B. A., Sougnez, C., Saksena, G., Carter, S. L., Schumacher, S. E., Tabak, B., Zack, T. I., Getz, G., Beroukhim, R., Gabriel, S. B., Meyerson, M., Ally, A., Balasundaram, M., Birol, I., Brooks, D., Butterfield, Y. S. N., Chuah, E., Clarke, A., Dhalla, N., Guin, R., Holt, R. A., Kasaian, K., Lee, D., Li, H. I., Lim, E., Ma, Y., Mayo, M., Moore, R. A., Mungall, A. J., Schein, J. E., Sipahimalani, P., Tam, A., Thiessen, N., Wong, T., Jones, S. J. M., Marra, M. A., Auman, J. T., Tan, D., Meng, S., Jones, C. D., Hoadley, K. A., Mieczkowski, P. A., Mose, L. E., Jefferys, S. R., Roach, J., Veluvolu, U., Wilkerson, M. D., Waring, S., Buda, E., Wu, J., Bodenheimer, T., Hoyle, A. P., Simons, J. V., Soloway, M. G., Balu, S., Parker, J. S., Hayes, D. N., Perou, C. M., Weisenberger, D. J., Bootwalla, M. S., Triche, T., Lai, P. H., Van Den Berg, D. J., Baylin, S. B., Chen, F., Coarfa, C., Noble, M. S., DiCara, D., Zhang, H., Cho, J., Heiman, D. I., Gehlenborg, N., Voet, D., Lin, P., Frazer, S., Stojanov, P., Liu, Y., Zou, L., Kim, J., Lawrence, M. S., Chin, L., Yang, L., Seth, S., Bristow, C. A., Protopopov, A., Song, X., Zhang, J., Pantazi, A., Hadjipanayis, A., Lee, E., Luquette, L. J., Lee, S., Parfenov, M., Santoso, N., Seidman, J., Xu, A. W., Kucherlapati, R., Park, P. J., Kang, H., Lee, J., Roberts, S. A., Klimczak, L. J., Fargo, D., Lang, M., Choi, Y.-L., Kim, S. C., Lee, J.-K., Park, W.-Y., Wang, W., Fan, Y., Ahn, J., Akbani, R., Weinstein, J. N., Haussler, D., Ma, S., Radenbaugh, A., Zhul, J., Biehl, M., Lichtenberg, T. M., Zmuda, E., Black, A. D., Hanf, B., Ramirez, N. C., Wise, L., Bowen, J., Leraas, K. M., Hall, T. M., Gastier-Foster, J. M., Kaelin, W. G., Thorne, L., Boice, L., Huang, M., Vocke, C., Peterson, J., Worrell, R., Merino, M., Czerniak, B. A., Aldape, K. D., Wood, C. G., Spellman, P. T., Atkins, M. B., Cheville, J., Thompson, R. H., Jensen, M. A., Pihl, T., Wan, Y., Ayala, B., Baboud, J., Velaga, S., Walton, J., Liu, J., Chudamani, S., Wu, Y., Sheth, M., Mills Shaw, K. R., Demchok, J. A., Davidsen, T., Yang, L., Wang, Z., Tarnuzzer, R. W., Zhang, J., Eley, G., Felau, I., Zenklusen, J. C., Hutter, C. M., Guyer, M. S., Ozenberger, B. A., & Sofia, H. J.
Venue: Cancer Cell
Publisher: Elsevier BV
Published: 2014-09
Volume: 26
Issue: 3
Pages: 319-330
ISSN: 1535-6108 (ISSN-L)
DOI: 10.1016/j.ccr.2014.07.014
OpenAlex: W2010991736
Cited by: 842
References: 9
FWCI: 55.73
Type: journal article
Language: en
Open access: bronze

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The paper: Davis, C. F., Ricketts, C. J., Wang, M., Yang, L., Cherniack, A. D., Shen, H., Buhay, C., Kang, H., Kim, S. C., Fahey, C. C., Hacker, K. E., Bhanot, G., Gordenin, D. A., Chu, A., Gunaratne, P. H., Biehl, M., Seth, S., Kaipparettu, B. A., Bristow, C. A., . . . Sofia, H. J. (2014). The Somatic Genomic Landscape of Chromophobe Renal Cell Carcinoma. Cancer Cell. https://doi.org/10.1016/j.ccr.2014.07.014

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The Somatic Genomic Landscape of Chromophobe Renal Cell Carcinoma

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