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Cited by 610

The DOI matches its Crossref record; 8 of the 8 references it cites were found in a registry or an index.

Integrative Genomic Analysis of Cholangiocarcinoma Identifies Distinct IDH-Mutant Molecular Profiles

Open access
Farshidfar, Farshad, Zheng, Siyuan, Gingras, Marie-Claude, Newton, Yulia, Shih, Juliann, Robertson, A. Gordon, Hinoue, Toshinori, Hoadley, Katherine A., Gibb, Ewan A., Roszik, Jason, Covington, Kyle R., Wu, Chia-Chin, Shinbrot, Eve, Stransky, Nicolas, Hegde, Apurva, Yang, Ju Dong, Reznik, Ed, Sadeghi, Sara, Pedamallu, Chandra Sekhar, Ojesina, Akinyemi I., Hess, Julian M., Auman, J. Todd, Rhie, Suhn K., Bowlby, Reanne, Borad, Mitesh J., Akbani, Rehan, Allotey, Loretta K., Ally, Adrian, Alvaro, Domenico, Andersen, Jesper B., Appelbaum, Elizabeth L., Arora, Arshi, Auman, J. Todd, Balasundaram, Miruna, Balu, Saianand, Bardeesy, Nabeel, Bathe, Oliver F., Baylin, Stephen B., Beroukhim, Rameen, Berrios, Mario, Bodenheimer, Tom, Boice, Lori, Bootwalla, Moiz S., Borad, Mitesh J., Bowen, Jay, Bowlby, Reanne, Bragazzi, Maria Consiglia, Brooks, Denise, Cardinale, Vincenzo, Carlsen, Rebecca, Carpino, Guido, Carvalho, Andre L., Chaiteerakij, Roongruedee, Chandan, Vishal C., Cherniack, Andrew D., Chin, Lynda, Cho, Juok, Choe, Gina, Chuah, Eric, Chudamani, Sudha, Cibulskis, Carrie, Cordes, Matthew G., Covington, Kyle R., Crain, Daniel, Curley, Erin, De Rose, Agostino Maria, Defreitas, Timothy, Demchok, John A., Deshpande, Vikram, Dhalla, Noreen, Ding, Li, Evason, Kimberley, Farshidfar, Farshad, Felau, Ina, Ferguson, Martin L., Foo, Wai Chin, Franchitto, Antonio, Frazer, Scott, Fronick, Catrina C., Fulton, Lucinda A., Fulton, Robert S., Gabriel, Stacey B., Gardner, Johanna, Gastier-Foster, Julie M., Gaudio, Eugenio, Gehlenborg, Nils, Genovese, Giannicola, Gerken, Mark, Getz, Gad, Giama, Nasra H., Gibbs, Richard A., Gingras, Marie-Claude, Giuliante, Felice, Grazi, Gian Luca, Hayes, D. Neil, Hegde, Apurva M., Heiman, David I., Hess, Julian M., Hinoue, Toshinori, Hoadley, Katherine A., Holbrook, Andrea, Holt, Robert A., Hoyle, Alan P., Huang, Mei, Hutter, Carolyn M., Jefferys, Stuart R., Jones, Steven J.M., Jones, Corbin D., Kasaian, Katayoon, Kelley, Robin K., Kim, Jaegil, Kleiner, David E., Kocher, Jean-Pierre A., Kwong, Lawrence N., Lai, Phillip H., Laird, Peter W., Lawrence, Michael S., Leraas, Kristen M., Lichtenberg, Tara M., Lin, Pei, Liu, Wenbin, Liu, Jia, Lolla, Laxmi, Lu, Yiling, Ma, Yussanne, Mallery, David, Mardis, Elaine R., Marra, Marco A., Matsushita, Marcus M., Mayo, Michael, McLellan, Michael D., McRee, Autumn J., Meier, Sam, Meng, Shaowu, Meyerson, Matthew, Mieczkowski, Piotr A., Miller, Christopher A., Mills, Gordon B., Moore, Richard A., Morris, Scott, Mose, Lisle E., Moser, Catherine D., Mounajjed, Taofic, Mungall, Andrew J., Mungall, Karen, Murray, Bradley A., Naresh, Rashi, Newton, Yulia, Noble, Michael S., O’Brien, Daniel R., Ojesina, Akinyemi I., Parker, Joel S., Patel, Tushar C., Paulauskis, Joseph, Pedamallu, Chandra Sekhar, Penny, Robert, Perou, Charles M., Perou, Amy H., Pihl, Todd, Radenbaugh, Amie J., Ramirez, Nilsa C., Rathmell, W. Kimryn, Reznik, Ed, Rhie, Suhn K., Roach, Jeffrey, Roberts, Lewis R., Robertson, A. Gordon, Sadeghi, Sara, Saksena, Gordon, Sander, Chris, Schein, Jacqueline E., Schmidt, Heather K., Schumacher, Steven E., Shelton, Candace, Shelton, Troy, Shen, Ronglai, Sheth, Margi, Shi, Yan, Shih, Juliann, Shinbrot, Eve, Shroff, Rachna, Simons, Janae V., Sipahimalani, Payal, Skelly, Tara, Sofia, Heidi J., Soloway, Matthew G., Stoppler, Hubert, Stransky, Nicolas, Stuart, Josh, Sun, Qiang, Tam, Angela, Tan, Donghui, Tarnuzzer, Roy, Thiessen, Nina, Thorne, Leigh B., Torbenson, Michael S., Van Den Berg, David J., Veluvolu, Umadevi, Verhaak, Roel G.W., Voet, Doug, Wan, Yunhu, Wang, Zhining, Weinstein, John N., Weisenberger, Daniel J., Wheeler, David A., Wilson, Richard K., Wise, Lisa, Wong, Tina, Wu, Chia-Chin, Wu, Ye, Xi, Liu, Yang, Ju Dong, Yang, Liming, Zenklusen, Jean C., Zhang, Hailei, Zhang, Jiashan (Julia), Zheng, Siyuan, Zmuda, Erik, Zhu, Andrew X., Stuart, Josh M., Sander, Chris, Akbani, Rehan, Cherniack, Andrew D., Deshpande, Vikram, Mounajjed, Taofic, Foo, Wai Chin, Torbenson, Michael S., Kleiner, David E., Laird, Peter W., Wheeler, David A., McRee, Autumn J., Bathe, Oliver F., Andersen, Jesper B., Bardeesy, Nabeel, Roberts, Lewis R., Kwong, Lawrence N.·2017·Cell Reports
DOI 10.1016/j.celrep.2017.02.033
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Abstract

Cholangiocarcinoma (CCA) is an aggressive malignancy of the bile ducts, with poor prognosis and limited treatment options. Here, we describe the integrated analysis of somatic mutations, RNA expression, copy number, and DNA methylation by The Cancer Genome Atlas of a set of predominantly intrahepatic CCA cases and propose a molecular classification scheme. We identified an IDH mutant-enriched subtype with distinct molecular features including low expression of chromatin modifiers, elevated expression of mitochondrial genes, and increased mitochondrial DNA copy number. Leveraging the multi-platform data, we observed that ARID1A exhibited DNA hypermethylation and decreased expression in the IDH mutant subtype. More broadly, we found that IDH mutations are associated with an expanded histological spectrum of liver tumors with molecular features that stratify with CCA. Our studies reveal insights into the molecular pathogenesis and heterogeneity of cholangiocarcinoma and provide classification information of potential therapeutic significance.

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Authors
Farshidfar, F., Zheng, S., Gingras, M.-C., Newton, Y., Shih, J., Robertson, A. G., Hinoue, T., Hoadley, K. A., Gibb, E. A., Roszik, J., Covington, K. R., Wu, C.-C., Shinbrot, E., Stransky, N., Hegde, A., Yang, J. D., Reznik, E., Sadeghi, S., Pedamallu, C. S., Ojesina, A. I., Hess, J. M., Auman, J. T., Rhie, S. K., Bowlby, R., Borad, M. J., Akbani, R., Allotey, L. K., Ally, A., Alvaro, D., Andersen, J. B., Appelbaum, E. L., Arora, A., Auman, J. T., Balasundaram, M., Balu, S., Bardeesy, N., Bathe, O. F., Baylin, S. B., Beroukhim, R., Berrios, M., Bodenheimer, T., Boice, L., Bootwalla, M. S., Borad, M. J., Bowen, J., Bowlby, R., Bragazzi, M. C., Brooks, D., Cardinale, V., Carlsen, R., Carpino, G., Carvalho, A. L., Chaiteerakij, R., Chandan, V. C., Cherniack, A. D., Chin, L., Cho, J., Choe, G., Chuah, E., Chudamani, S., Cibulskis, C., Cordes, M. G., Covington, K. R., Crain, D., Curley, E., De Rose, A. M., Defreitas, T., Demchok, J. A., Deshpande, V., Dhalla, N., Ding, L., Evason, K., Farshidfar, F., Felau, I., Ferguson, M. L., Foo, W. C., Franchitto, A., Frazer, S., Fronick, C. C., Fulton, L. A., Fulton, R. S., Gabriel, S. B., Gardner, J., Gastier-Foster, J. M., Gaudio, E., Gehlenborg, N., Genovese, G., Gerken, M., Getz, G., Giama, N. H., Gibbs, R. A., Gingras, M.-C., Giuliante, F., Grazi, G. L., Hayes, D. N., Hegde, A. M., Heiman, D. I., Hess, J. M., Hinoue, T., Hoadley, K. A., Holbrook, A., Holt, R. A., Hoyle, A. P., Huang, M., Hutter, C. M., Jefferys, S. R., Jones, S. J. M., Jones, C. D., Kasaian, K., Kelley, R. K., Kim, J., Kleiner, D. E., Kocher, J.-P. A., Kwong, L. N., Lai, P. H., Laird, P. W., Lawrence, M. S., Leraas, K. M., Lichtenberg, T. M., Lin, P., Liu, W., Liu, J., Lolla, L., Lu, Y., Ma, Y., Mallery, D., Mardis, E. R., Marra, M. A., Matsushita, M. M., Mayo, M., McLellan, M. D., McRee, A. J., Meier, S., Meng, S., Meyerson, M., Mieczkowski, P. A., Miller, C. A., Mills, G. B., Moore, R. A., Morris, S., Mose, L. E., Moser, C. D., Mounajjed, T., Mungall, A. J., Mungall, K., Murray, B. A., Naresh, R., Newton, Y., Noble, M. S., O’Brien, D. R., Ojesina, A. I., Parker, J. S., Patel, T. C., Paulauskis, J., Pedamallu, C. S., Penny, R., Perou, C. M., Perou, A. H., Pihl, T., Radenbaugh, A. J., Ramirez, N. C., Rathmell, W. K., Reznik, E., Rhie, S. K., Roach, J., Roberts, L. R., Robertson, A. G., Sadeghi, S., Saksena, G., Sander, C., Schein, J. E., Schmidt, H. K., Schumacher, S. E., Shelton, C., Shelton, T., Shen, R., Sheth, M., Shi, Y., Shih, J., Shinbrot, E., Shroff, R., Simons, J. V., Sipahimalani, P., Skelly, T., Sofia, H. J., Soloway, M. G., Stoppler, H., Stransky, N., Stuart, J., Sun, Q., Tam, A., Tan, D., Tarnuzzer, R., Thiessen, N., Thorne, L. B., Torbenson, M. S., Van Den Berg, D. J., Veluvolu, U., Verhaak, R. G. W., Voet, D., Wan, Y., Wang, Z., Weinstein, J. N., Weisenberger, D. J., Wheeler, D. A., Wilson, R. K., Wise, L., Wong, T., Wu, C.-C., Wu, Y., Xi, L., Yang, J. D., Yang, L., Zenklusen, J. C., Zhang, H., Zhang, J. (., Zheng, S., Zmuda, E., Zhu, A. X., Stuart, J. M., Sander, C., Akbani, R., Cherniack, A. D., Deshpande, V., Mounajjed, T., Foo, W. C., Torbenson, M. S., Kleiner, D. E., Laird, P. W., Wheeler, D. A., McRee, A. J., Bathe, O. F., Andersen, J. B., Bardeesy, N., Roberts, L. R., & Kwong, L. N.
Venue
Cell Reports
Publisher
Elsevier BV
Published
2017-03
Volume
18
Issue
11
Pages
2780-2794
ISSN
2211-1247 (ISSN-L)
DOI
10.1016/j.celrep.2017.02.033
OpenAlex
W2603204749
Cited by
610
References
8
FWCI
58.12
Type
journal article
Language
en
Open access
gold

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The paper
Farshidfar, F., Zheng, S., Gingras, M.-C., Newton, Y., Shih, J., Robertson, A. G., Hinoue, T., Hoadley, K. A., Gibb, E. A., Roszik, J., Covington, K. R., Wu, C.-C., Shinbrot, E., Stransky, N., Hegde, A., Yang, J. D., Reznik, E., Sadeghi, S., Pedamallu, C. S., . . . Kwong, L. N. (2017). Integrative Genomic Analysis of Cholangiocarcinoma Identifies Distinct IDH-Mutant Molecular Profiles. Cell Reports. https://doi.org/10.1016/j.celrep.2017.02.033

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Bibliographic data: Semantic Scholar, OpenAlex, Crossref.

Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).

Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.