250 results on '"Etemadmoghadam, Dariush"'
Search Results
2. 19q12 amplified and non-amplified subsets of high grade serous ovarian cancer with overexpression of cyclin E1 differ in their molecular drivers and clinical outcomes
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Aziz, Diar, Etemadmoghadam, Dariush, Caldon, C. Elizabeth, Au-Yeung, George, Deng, Niantao, Hutchinson, Ryan, Bowtell, David, and Waring, Paul
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- 2018
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3. Profound MEK inhibitor response in a cutaneous melanoma harboring a GOLGA4-RAF1 fusion
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McEvoy, Christopher R., Xu, Huiling, Smith, Kortnye, Etemadmoghadam, Dariush, Leong, Huei San, Choong, David Y., Byrne, David J., Iravani, Amir, Beck, Sophie, Mileshkin, Linda, Tothill, Richard W., Bowtell, David D., Bates, Bindi M., Nastevski, Violeta, Browning, Judy, Bell, Anthony H., Khoo, Chloe, Desai, Jayesh, Fellowes, Andrew P., Fox, Stephen B., and Prall, Owen W.J.
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Medical research ,Cell death -- Analysis ,Immunotherapy -- Usage ,Melanoma -- Development and progression -- Care and treatment ,Biochemistry ,Cancer research ,Lymphocytes ,Sorafenib ,Cancer ,Apoptosis ,Cancer metastasis ,Tumors ,Health care industry - Abstract
The serine/threonine kinases BRAF and CRAF are critical components of the MAPK signaling pathway that is activated in many cancer types. In approximately 1% of melanomas, BRAF or CRAF is activated through structural arrangements. We describe a metastatic melanoma with a GOLGA4-RAF1 fusion and pathogenic variants in catenin [beta]1 (CTNNB1) and cyclin-dependent kinase inhibitor 2A (CDKN2A). Anti-cytotoxic T-lymphocyte-associated protein 4/anti-programmed cell death 1 (anti-CTLA4/anti-PD-1) combination immunotherapy failed to control tumor progression. In the absence of other actionable variants, the patient was administered MEK inhibitor therapy on the basis of its potential action against RAF1 fusions. This resulted in a profound and clinically significant response. We demonstrated that GOLGA4-RAF1 expression was associated with ERK activation, elevated expression of the RAS/RAF downstream coeffector ETV5, and a high Ki67 index. These findings provide a rationale for the dramatic response to targeted therapy. This study shows that molecular characterization of treatment-resistant cancers can identify therapeutic targets and personalize therapy management, leading to improved patient outcomes., Introduction MAPK pathway activation is a hallmark of many cancers. Many genes in this pathway, including RAS, RAF (encoding the serine/ threonine kinases BRAF and CRAF), and MEK can contain [...]
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- 2019
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4. Supplementary Table 18 from Nonequivalent Gene Expression and Copy Number Alterations in High-Grade Serous Ovarian Cancers with BRCA1 and BRCA2 Mutations
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George, Joshy, primary, Alsop, Kathryn, primary, Etemadmoghadam, Dariush, primary, Hondow, Heather, primary, Mikeska, Thomas, primary, Dobrovic, Alexander, primary, deFazio, Anna, primary, Smyth, Gordon K., primary, Levine, Douglas A., primary, Mitchell, Gillian, primary, and Bowtell, David D., primary
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- 2023
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5. Supplementary Data from Integrated Genome-Wide DNA Copy Number and Expression Analysis Identifies Distinct Mechanisms of Primary Chemoresistance in Ovarian Carcinomas
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Etemadmoghadam, Dariush, primary, deFazio, Anna, primary, Beroukhim, Rameen, primary, Mermel, Craig, primary, George, Joshy, primary, Getz, Gad, primary, Tothill, Richard, primary, Okamoto, Aikou, primary, Raeder, Maria B., primary, Harnett, Paul, primary, Lade, Stephen, primary, Akslen, Lars A., primary, Tinker, Anna V., primary, Locandro, Bianca, primary, Alsop, Kathryn, primary, Chiew, Yoke-Eng, primary, Traficante, Nadia, primary, Fereday, Sian, primary, Johnson, Daryl, primary, Fox, Stephen, primary, Sellers, William, primary, Urashima, Mitsuyoshi, primary, Salvesen, Helga B., primary, Meyerson, Matthew, primary, and Bowtell, David, primary
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- 2023
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6. Data from EIF1AX and NRAS Mutations Co-occur and Cooperate in Low-Grade Serous Ovarian Carcinomas
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Etemadmoghadam, Dariush, primary, Azar, Walid J., primary, Lei, Ying, primary, Moujaber, Tania, primary, Garsed, Dale W., primary, Kennedy, Catherine J., primary, Fereday, Sian, primary, Mitchell, Chris, primary, Chiew, Yoke-Eng, primary, Hendley, Joy, primary, Sharma, Raghwa, primary, Harnett, Paul R., primary, Li, Jason, primary, Christie, Elizabeth L., primary, Patch, Ann-Marie, primary, George, Joshy, primary, Au-Yeung, George, primary, Mir Arnau, Gisela, primary, Holloway, Timothy P., primary, Semple, Timothy, primary, Pearson, John V., primary, Waddell, Nicola, primary, Grimmond, Sean M., primary, Köbel, Martin, primary, Rizos, Helen, primary, Lomakin, Ivan B., primary, Bowtell, David D.L., primary, and deFazio, Anna, primary
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- 2023
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7. Table S4 from Homologous Recombination DNA Repair Pathway Disruption and Retinoblastoma Protein Loss Are Associated with Exceptional Survival in High-Grade Serous Ovarian Cancer
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Garsed, Dale W., primary, Alsop, Kathryn, primary, Fereday, Sian, primary, Emmanuel, Catherine, primary, Kennedy, Catherine J., primary, Etemadmoghadam, Dariush, primary, Gao, Bo, primary, Gebski, Val, primary, Garès, Valérie, primary, Christie, Elizabeth L., primary, Wouters, Maartje C.A., primary, Milne, Katy, primary, George, Joshy, primary, Patch, Ann-Marie, primary, Li, Jason, primary, Arnau, Gisela Mir, primary, Semple, Timothy, primary, Gadipally, Sreeja R., primary, Chiew, Yoke-Eng, primary, Hendley, Joy, primary, Mikeska, Thomas, primary, Zapparoli, Giada V., primary, Amarasinghe, Kaushalya, primary, Grimmond, Sean M., primary, Pearson, John V., primary, Waddell, Nicola, primary, Hung, Jillian, primary, Stewart, Colin J.R., primary, Sharma, Raghwa, primary, Allan, Prue E., primary, Rambau, Peter F., primary, McNally, Orla, primary, Mileshkin, Linda, primary, Hamilton, Anne, primary, Ananda, Sumitra, primary, Grossi, Marisa, primary, Cohen, Paul A., primary, Leung, Yee C., primary, Rome, Robert M., primary, Beale, Philip, primary, Blomfield, Penny, primary, Friedlander, Michael, primary, Brand, Alison, primary, Dobrovic, Alexander, primary, Köbel, Martin, primary, Harnett, Paul, primary, Nelson, Brad H., primary, Bowtell, David D. L., primary, and deFazio, Anna, primary
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- 2023
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8. Supplementary Figures 1 - 15 from Nonequivalent Gene Expression and Copy Number Alterations in High-Grade Serous Ovarian Cancers with BRCA1 and BRCA2 Mutations
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George, Joshy, primary, Alsop, Kathryn, primary, Etemadmoghadam, Dariush, primary, Hondow, Heather, primary, Mikeska, Thomas, primary, Dobrovic, Alexander, primary, deFazio, Anna, primary, Smyth, Gordon K., primary, Levine, Douglas A., primary, Mitchell, Gillian, primary, and Bowtell, David D., primary
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- 2023
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9. Supplementary Methods, Figures 1-5 from Genomic Classification of Serous Ovarian Cancer with Adjacent Borderline Differentiates RAS Pathway and TP53-Mutant Tumors and Identifies NRAS as an Oncogenic Driver
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Emmanuel, Catherine, primary, Chiew, Yoke-Eng, primary, George, Joshy, primary, Etemadmoghadam, Dariush, primary, Anglesio, Michael S., primary, Sharma, Raghwa, primary, Russell, Peter, primary, Kennedy, Catherine, primary, Fereday, Sian, primary, Hung, Jillian, primary, Galletta, Laura, primary, Hogg, Russell, primary, Wain, Gerard V., primary, Brand, Alison, primary, Balleine, Rosemary, primary, MacConaill, Laura, primary, Palescandolo, Emanuele, primary, Hunter, Sally M., primary, Campbell, Ian, primary, Dobrovic, Alexander, primary, Wong, Stephen Q., primary, Do, Hongdo, primary, Clarke, Christine L., primary, Harnett, Paul R., primary, Bowtell, David D.L., primary, and deFazio, Anna, primary
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- 2023
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10. Supplementary Figures S1 - S6 from Selective Targeting of Cyclin E1-Amplified High-Grade Serous Ovarian Cancer by Cyclin-Dependent Kinase 2 and AKT Inhibition
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Au-Yeung, George, primary, Lang, Franziska, primary, Azar, Walid J., primary, Mitchell, Chris, primary, Jarman, Kate E., primary, Lackovic, Kurt, primary, Aziz, Diar, primary, Cullinane, Carleen, primary, Pearson, Richard B., primary, Mileshkin, Linda, primary, Rischin, Danny, primary, Karst, Alison M., primary, Drapkin, Ronny, primary, Etemadmoghadam, Dariush, primary, and Bowtell, David D.L., primary
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- 2023
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11. Supplementary Data from Survival Following Chemotherapy in Ovarian Clear Cell Carcinoma Is Not Associated with Pathological Misclassification of Tumor Histotype
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Takenaka, Masataka, primary, Köbel, Martin, primary, Garsed, Dale W., primary, Fereday, Sian, primary, Pandey, Ahwan, primary, Etemadmoghadam, Dariush, primary, Hendley, Joy, primary, Kawabata, Ayako, primary, Noguchi, Daito, primary, Yanaihara, Nozomu, primary, Takahashi, Hiroyuki, primary, Kiyokawa, Takako, primary, Ikegami, Masahiro, primary, Takano, Hirokuni, primary, Isonishi, Seiji, primary, Ochiai, Kazuhiko, primary, Traficante, Nadia, primary, Gadipally, Sreeja, primary, Semple, Timothy, primary, Vassiliadis, Dane, primary, Amarasinghe, Kausyalya, primary, Li, Jason, primary, Mir Arnau, Gisela, primary, Okamoto, Aikou, primary, Friedlander, Michael, primary, and Bowtell, David D. L., primary
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- 2023
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12. Supplementary Figures S1-S9 from Resistance to CDK2 Inhibitors Is Associated with Selection of Polyploid Cells in CCNE1-Amplified Ovarian Cancer
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Etemadmoghadam, Dariush, primary, Au-Yeung, George, primary, Wall, Meaghan, primary, Mitchell, Chris, primary, Kansara, Maya, primary, Loehrer, Elizabeth, primary, Batzios, Crisoula, primary, George, Joshy, primary, Ftouni, Sarah, primary, Weir, Barbara A., primary, Carter, Scott, primary, Gresshoff, Irma, primary, Mileshkin, Linda, primary, Rischin, Danny, primary, Hahn, William C., primary, Waring, Paul M., primary, Getz, Gad, primary, Cullinane, Carleen, primary, Campbell, Lynda J., primary, and Bowtell, David D., primary
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- 2023
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13. Supplementary Data from Homologous Recombination DNA Repair Pathway Disruption and Retinoblastoma Protein Loss Are Associated with Exceptional Survival in High-Grade Serous Ovarian Cancer
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Garsed, Dale W., primary, Alsop, Kathryn, primary, Fereday, Sian, primary, Emmanuel, Catherine, primary, Kennedy, Catherine J., primary, Etemadmoghadam, Dariush, primary, Gao, Bo, primary, Gebski, Val, primary, Garès, Valérie, primary, Christie, Elizabeth L., primary, Wouters, Maartje C.A., primary, Milne, Katy, primary, George, Joshy, primary, Patch, Ann-Marie, primary, Li, Jason, primary, Arnau, Gisela Mir, primary, Semple, Timothy, primary, Gadipally, Sreeja R., primary, Chiew, Yoke-Eng, primary, Hendley, Joy, primary, Mikeska, Thomas, primary, Zapparoli, Giada V., primary, Amarasinghe, Kaushalya, primary, Grimmond, Sean M., primary, Pearson, John V., primary, Waddell, Nicola, primary, Hung, Jillian, primary, Stewart, Colin J.R., primary, Sharma, Raghwa, primary, Allan, Prue E., primary, Rambau, Peter F., primary, McNally, Orla, primary, Mileshkin, Linda, primary, Hamilton, Anne, primary, Ananda, Sumitra, primary, Grossi, Marisa, primary, Cohen, Paul A., primary, Leung, Yee C., primary, Rome, Robert M., primary, Beale, Philip, primary, Blomfield, Penny, primary, Friedlander, Michael, primary, Brand, Alison, primary, Dobrovic, Alexander, primary, Köbel, Martin, primary, Harnett, Paul, primary, Nelson, Brad H., primary, Bowtell, David D. L., primary, and deFazio, Anna, primary
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- 2023
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14. Supplementary Highlighted Methods from Genomic Classification of Serous Ovarian Cancer with Adjacent Borderline Differentiates RAS Pathway and TP53-Mutant Tumors and Identifies NRAS as an Oncogenic Driver
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Emmanuel, Catherine, primary, Chiew, Yoke-Eng, primary, George, Joshy, primary, Etemadmoghadam, Dariush, primary, Anglesio, Michael S., primary, Sharma, Raghwa, primary, Russell, Peter, primary, Kennedy, Catherine, primary, Fereday, Sian, primary, Hung, Jillian, primary, Galletta, Laura, primary, Hogg, Russell, primary, Wain, Gerard V., primary, Brand, Alison, primary, Balleine, Rosemary, primary, MacConaill, Laura, primary, Palescandolo, Emanuele, primary, Hunter, Sally M., primary, Campbell, Ian, primary, Dobrovic, Alexander, primary, Wong, Stephen Q., primary, Do, Hongdo, primary, Clarke, Christine L., primary, Harnett, Paul R., primary, Bowtell, David D.L., primary, and deFazio, Anna, primary
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- 2023
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15. Supplementary Figures 1 - 9 from Profiles of Genomic Instability in High-Grade Serous Ovarian Cancer Predict Treatment Outcome
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Wang, Zhigang C., primary, Birkbak, Nicolai Juul, primary, Culhane, Aedín C., primary, Drapkin, Ronny, primary, Fatima, Aquila, primary, Tian, Ruiyang, primary, Schwede, Matthew, primary, Alsop, Kathryn, primary, Daniels, Kathryn E., primary, Piao, Huiying, primary, Liu, Joyce, primary, Etemadmoghadam, Dariush, primary, Miron, Alexander, primary, Salvesen, Helga B., primary, Mitchell, Gillian, primary, DeFazio, Anna, primary, Quackenbush, John, primary, Berkowitz, Ross S., primary, Iglehart, J. Dirk, primary, Bowtell, David D.L., primary, and Matulonis, Ursula A., primary
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- 2023
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16. Data from Integrated Genome-Wide DNA Copy Number and Expression Analysis Identifies Distinct Mechanisms of Primary Chemoresistance in Ovarian Carcinomas
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Etemadmoghadam, Dariush, primary, deFazio, Anna, primary, Beroukhim, Rameen, primary, Mermel, Craig, primary, George, Joshy, primary, Getz, Gad, primary, Tothill, Richard, primary, Okamoto, Aikou, primary, Raeder, Maria B., primary, Harnett, Paul, primary, Lade, Stephen, primary, Akslen, Lars A., primary, Tinker, Anna V., primary, Locandro, Bianca, primary, Alsop, Kathryn, primary, Chiew, Yoke-Eng, primary, Traficante, Nadia, primary, Fereday, Sian, primary, Johnson, Daryl, primary, Fox, Stephen, primary, Sellers, William, primary, Urashima, Mitsuyoshi, primary, Salvesen, Helga B., primary, Meyerson, Matthew, primary, and Bowtell, David, primary
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- 2023
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17. Supplemental Material - Group Authorship from EIF1AX and NRAS Mutations Co-occur and Cooperate in Low-Grade Serous Ovarian Carcinomas
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Etemadmoghadam, Dariush, primary, Azar, Walid J., primary, Lei, Ying, primary, Moujaber, Tania, primary, Garsed, Dale W., primary, Kennedy, Catherine J., primary, Fereday, Sian, primary, Mitchell, Chris, primary, Chiew, Yoke-Eng, primary, Hendley, Joy, primary, Sharma, Raghwa, primary, Harnett, Paul R., primary, Li, Jason, primary, Christie, Elizabeth L., primary, Patch, Ann-Marie, primary, George, Joshy, primary, Au-Yeung, George, primary, Mir Arnau, Gisela, primary, Holloway, Timothy P., primary, Semple, Timothy, primary, Pearson, John V., primary, Waddell, Nicola, primary, Grimmond, Sean M., primary, Köbel, Martin, primary, Rizos, Helen, primary, Lomakin, Ivan B., primary, Bowtell, David D.L., primary, and deFazio, Anna, primary
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- 2023
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18. Supplementary Data from Novel Molecular Subtypes of Serous and Endometrioid Ovarian Cancer Linked to Clinical Outcome
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Tothill, Richard W., primary, Tinker, Anna V., primary, George, Joshy, primary, Brown, Robert, primary, Fox, Stephen B., primary, Lade, Stephen, primary, Johnson, Daryl S., primary, Trivett, Melanie K., primary, Etemadmoghadam, Dariush, primary, Locandro, Bianca, primary, Traficante, Nadia, primary, Fereday, Sian, primary, Hung, Jillian A., primary, Chiew, Yoke-Eng, primary, Haviv, Izhak, primary, Gertig, Dorota, primary, deFazio, Anna, primary, and Bowtell, David D.L., primary
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- 2023
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19. Supplementary Tables 4 - 8 from Profiles of Genomic Instability in High-Grade Serous Ovarian Cancer Predict Treatment Outcome
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Wang, Zhigang C., primary, Birkbak, Nicolai Juul, primary, Culhane, Aedín C., primary, Drapkin, Ronny, primary, Fatima, Aquila, primary, Tian, Ruiyang, primary, Schwede, Matthew, primary, Alsop, Kathryn, primary, Daniels, Kathryn E., primary, Piao, Huiying, primary, Liu, Joyce, primary, Etemadmoghadam, Dariush, primary, Miron, Alexander, primary, Salvesen, Helga B., primary, Mitchell, Gillian, primary, DeFazio, Anna, primary, Quackenbush, John, primary, Berkowitz, Ross S., primary, Iglehart, J. Dirk, primary, Bowtell, David D.L., primary, and Matulonis, Ursula A., primary
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- 2023
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20. Supplementary Methods and Figure legends from Selective Targeting of Cyclin E1-Amplified High-Grade Serous Ovarian Cancer by Cyclin-Dependent Kinase 2 and AKT Inhibition
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Au-Yeung, George, primary, Lang, Franziska, primary, Azar, Walid J., primary, Mitchell, Chris, primary, Jarman, Kate E., primary, Lackovic, Kurt, primary, Aziz, Diar, primary, Cullinane, Carleen, primary, Pearson, Richard B., primary, Mileshkin, Linda, primary, Rischin, Danny, primary, Karst, Alison M., primary, Drapkin, Ronny, primary, Etemadmoghadam, Dariush, primary, and Bowtell, David D.L., primary
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- 2023
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21. Supplementary Tables S1-S8 from Selective Targeting of Cyclin E1-Amplified High-Grade Serous Ovarian Cancer by Cyclin-Dependent Kinase 2 and AKT Inhibition
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Au-Yeung, George, primary, Lang, Franziska, primary, Azar, Walid J., primary, Mitchell, Chris, primary, Jarman, Kate E., primary, Lackovic, Kurt, primary, Aziz, Diar, primary, Cullinane, Carleen, primary, Pearson, Richard B., primary, Mileshkin, Linda, primary, Rischin, Danny, primary, Karst, Alison M., primary, Drapkin, Ronny, primary, Etemadmoghadam, Dariush, primary, and Bowtell, David D.L., primary
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- 2023
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22. Supplementary Methods and Tables 1 - 15, 19 from Nonequivalent Gene Expression and Copy Number Alterations in High-Grade Serous Ovarian Cancers with BRCA1 and BRCA2 Mutations
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George, Joshy, primary, Alsop, Kathryn, primary, Etemadmoghadam, Dariush, primary, Hondow, Heather, primary, Mikeska, Thomas, primary, Dobrovic, Alexander, primary, deFazio, Anna, primary, Smyth, Gordon K., primary, Levine, Douglas A., primary, Mitchell, Gillian, primary, and Bowtell, David D., primary
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- 2023
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23. Supplemental Materials and Methods from EIF1AX and NRAS Mutations Co-occur and Cooperate in Low-Grade Serous Ovarian Carcinomas
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Etemadmoghadam, Dariush, primary, Azar, Walid J., primary, Lei, Ying, primary, Moujaber, Tania, primary, Garsed, Dale W., primary, Kennedy, Catherine J., primary, Fereday, Sian, primary, Mitchell, Chris, primary, Chiew, Yoke-Eng, primary, Hendley, Joy, primary, Sharma, Raghwa, primary, Harnett, Paul R., primary, Li, Jason, primary, Christie, Elizabeth L., primary, Patch, Ann-Marie, primary, George, Joshy, primary, Au-Yeung, George, primary, Mir Arnau, Gisela, primary, Holloway, Timothy P., primary, Semple, Timothy, primary, Pearson, John V., primary, Waddell, Nicola, primary, Grimmond, Sean M., primary, Köbel, Martin, primary, Rizos, Helen, primary, Lomakin, Ivan B., primary, Bowtell, David D.L., primary, and deFazio, Anna, primary
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- 2023
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24. Supplementary Data from Resistance to CDK2 Inhibitors Is Associated with Selection of Polyploid Cells in CCNE1-Amplified Ovarian Cancer
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Etemadmoghadam, Dariush, primary, Au-Yeung, George, primary, Wall, Meaghan, primary, Mitchell, Chris, primary, Kansara, Maya, primary, Loehrer, Elizabeth, primary, Batzios, Crisoula, primary, George, Joshy, primary, Ftouni, Sarah, primary, Weir, Barbara A., primary, Carter, Scott, primary, Gresshoff, Irma, primary, Mileshkin, Linda, primary, Rischin, Danny, primary, Hahn, William C., primary, Waring, Paul M., primary, Getz, Gad, primary, Cullinane, Carleen, primary, Campbell, Lynda J., primary, and Bowtell, David D., primary
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- 2023
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25. Supplementary Tables S1-5 from Resistance to CDK2 Inhibitors Is Associated with Selection of Polyploid Cells in CCNE1-Amplified Ovarian Cancer
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Etemadmoghadam, Dariush, primary, Au-Yeung, George, primary, Wall, Meaghan, primary, Mitchell, Chris, primary, Kansara, Maya, primary, Loehrer, Elizabeth, primary, Batzios, Crisoula, primary, George, Joshy, primary, Ftouni, Sarah, primary, Weir, Barbara A., primary, Carter, Scott, primary, Gresshoff, Irma, primary, Mileshkin, Linda, primary, Rischin, Danny, primary, Hahn, William C., primary, Waring, Paul M., primary, Getz, Gad, primary, Cullinane, Carleen, primary, Campbell, Lynda J., primary, and Bowtell, David D., primary
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- 2023
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26. Supplementary Tables from EIF1AX and NRAS Mutations Co-occur and Cooperate in Low-Grade Serous Ovarian Carcinomas
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Etemadmoghadam, Dariush, primary, Azar, Walid J., primary, Lei, Ying, primary, Moujaber, Tania, primary, Garsed, Dale W., primary, Kennedy, Catherine J., primary, Fereday, Sian, primary, Mitchell, Chris, primary, Chiew, Yoke-Eng, primary, Hendley, Joy, primary, Sharma, Raghwa, primary, Harnett, Paul R., primary, Li, Jason, primary, Christie, Elizabeth L., primary, Patch, Ann-Marie, primary, George, Joshy, primary, Au-Yeung, George, primary, Mir Arnau, Gisela, primary, Holloway, Timothy P., primary, Semple, Timothy, primary, Pearson, John V., primary, Waddell, Nicola, primary, Grimmond, Sean M., primary, Köbel, Martin, primary, Rizos, Helen, primary, Lomakin, Ivan B., primary, Bowtell, David D.L., primary, and deFazio, Anna, primary
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- 2023
- Full Text
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27. Supplementary Tables 1 - 3 from Profiles of Genomic Instability in High-Grade Serous Ovarian Cancer Predict Treatment Outcome
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Wang, Zhigang C., primary, Birkbak, Nicolai Juul, primary, Culhane, Aedín C., primary, Drapkin, Ronny, primary, Fatima, Aquila, primary, Tian, Ruiyang, primary, Schwede, Matthew, primary, Alsop, Kathryn, primary, Daniels, Kathryn E., primary, Piao, Huiying, primary, Liu, Joyce, primary, Etemadmoghadam, Dariush, primary, Miron, Alexander, primary, Salvesen, Helga B., primary, Mitchell, Gillian, primary, DeFazio, Anna, primary, Quackenbush, John, primary, Berkowitz, Ross S., primary, Iglehart, J. Dirk, primary, Bowtell, David D.L., primary, and Matulonis, Ursula A., primary
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- 2023
- Full Text
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28. Supplementary Figures from EIF1AX and NRAS Mutations Co-occur and Cooperate in Low-Grade Serous Ovarian Carcinomas
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Etemadmoghadam, Dariush, primary, Azar, Walid J., primary, Lei, Ying, primary, Moujaber, Tania, primary, Garsed, Dale W., primary, Kennedy, Catherine J., primary, Fereday, Sian, primary, Mitchell, Chris, primary, Chiew, Yoke-Eng, primary, Hendley, Joy, primary, Sharma, Raghwa, primary, Harnett, Paul R., primary, Li, Jason, primary, Christie, Elizabeth L., primary, Patch, Ann-Marie, primary, George, Joshy, primary, Au-Yeung, George, primary, Mir Arnau, Gisela, primary, Holloway, Timothy P., primary, Semple, Timothy, primary, Pearson, John V., primary, Waddell, Nicola, primary, Grimmond, Sean M., primary, Köbel, Martin, primary, Rizos, Helen, primary, Lomakin, Ivan B., primary, Bowtell, David D.L., primary, and deFazio, Anna, primary
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- 2023
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29. Supplementary Methods from Resistance to CDK2 Inhibitors Is Associated with Selection of Polyploid Cells in CCNE1-Amplified Ovarian Cancer
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Etemadmoghadam, Dariush, primary, Au-Yeung, George, primary, Wall, Meaghan, primary, Mitchell, Chris, primary, Kansara, Maya, primary, Loehrer, Elizabeth, primary, Batzios, Crisoula, primary, George, Joshy, primary, Ftouni, Sarah, primary, Weir, Barbara A., primary, Carter, Scott, primary, Gresshoff, Irma, primary, Mileshkin, Linda, primary, Rischin, Danny, primary, Hahn, William C., primary, Waring, Paul M., primary, Getz, Gad, primary, Cullinane, Carleen, primary, Campbell, Lynda J., primary, and Bowtell, David D., primary
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- 2023
- Full Text
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30. Supplementary Tables 1-7 from Genomic Classification of Serous Ovarian Cancer with Adjacent Borderline Differentiates RAS Pathway and TP53-Mutant Tumors and Identifies NRAS as an Oncogenic Driver
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Emmanuel, Catherine, primary, Chiew, Yoke-Eng, primary, George, Joshy, primary, Etemadmoghadam, Dariush, primary, Anglesio, Michael S., primary, Sharma, Raghwa, primary, Russell, Peter, primary, Kennedy, Catherine, primary, Fereday, Sian, primary, Hung, Jillian, primary, Galletta, Laura, primary, Hogg, Russell, primary, Wain, Gerard V., primary, Brand, Alison, primary, Balleine, Rosemary, primary, MacConaill, Laura, primary, Palescandolo, Emanuele, primary, Hunter, Sally M., primary, Campbell, Ian, primary, Dobrovic, Alexander, primary, Wong, Stephen Q., primary, Do, Hongdo, primary, Clarke, Christine L., primary, Harnett, Paul R., primary, Bowtell, David D.L., primary, and deFazio, Anna, primary
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- 2023
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31. Data from Cyclin E1 Deregulation Occurs Early in Secretory Cell Transformation to Promote Formation of Fallopian Tube–Derived High-Grade Serous Ovarian Cancers
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Karst, Alison M., primary, Jones, Paul M., primary, Vena, Natalie, primary, Ligon, Azra H., primary, Liu, Joyce F., primary, Hirsch, Michelle S., primary, Etemadmoghadam, Dariush, primary, Bowtell, David D.L., primary, and Drapkin, Ronny, primary
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- 2023
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32. Supplementary Methods from Cyclin E1 Deregulation Occurs Early in Secretory Cell Transformation to Promote Formation of Fallopian Tube–Derived High-Grade Serous Ovarian Cancers
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Karst, Alison M., primary, Jones, Paul M., primary, Vena, Natalie, primary, Ligon, Azra H., primary, Liu, Joyce F., primary, Hirsch, Michelle S., primary, Etemadmoghadam, Dariush, primary, Bowtell, David D.L., primary, and Drapkin, Ronny, primary
- Published
- 2023
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33. Supplementary Figure 1 from Cyclin E1 Deregulation Occurs Early in Secretory Cell Transformation to Promote Formation of Fallopian Tube–Derived High-Grade Serous Ovarian Cancers
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Karst, Alison M., primary, Jones, Paul M., primary, Vena, Natalie, primary, Ligon, Azra H., primary, Liu, Joyce F., primary, Hirsch, Michelle S., primary, Etemadmoghadam, Dariush, primary, Bowtell, David D.L., primary, and Drapkin, Ronny, primary
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- 2023
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34. Data from LRP1B Deletion in High-Grade Serous Ovarian Cancers Is Associated with Acquired Chemotherapy Resistance to Liposomal Doxorubicin
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Cowin, Prue A., primary, George, Joshy, primary, Fereday, Sian, primary, Loehrer, Elizabeth, primary, Van Loo, Peter, primary, Cullinane, Carleen, primary, Etemadmoghadam, Dariush, primary, Ftouni, Sarah, primary, Galletta, Laura, primary, Anglesio, Michael S., primary, Hendley, Joy, primary, Bowes, Leanne, primary, Sheppard, Karen E., primary, Christie, Elizabeth L., primary, Pearson, Richard B., primary, Harnett, Paul R., primary, Heinzelmann-Schwarz, Viola, primary, Friedlander, Michael, primary, McNally, Orla, primary, Quinn, Michael, primary, Campbell, Peter, primary, deFazio, Anna, primary, and Bowtell, David D.L., primary
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- 2023
- Full Text
- View/download PDF
35. Supplementary Table 2 from Cyclin E1 Deregulation Occurs Early in Secretory Cell Transformation to Promote Formation of Fallopian Tube–Derived High-Grade Serous Ovarian Cancers
- Author
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Karst, Alison M., primary, Jones, Paul M., primary, Vena, Natalie, primary, Ligon, Azra H., primary, Liu, Joyce F., primary, Hirsch, Michelle S., primary, Etemadmoghadam, Dariush, primary, Bowtell, David D.L., primary, and Drapkin, Ronny, primary
- Published
- 2023
- Full Text
- View/download PDF
36. Supplementary Table 1 from Cyclin E1 Deregulation Occurs Early in Secretory Cell Transformation to Promote Formation of Fallopian Tube–Derived High-Grade Serous Ovarian Cancers
- Author
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Karst, Alison M., primary, Jones, Paul M., primary, Vena, Natalie, primary, Ligon, Azra H., primary, Liu, Joyce F., primary, Hirsch, Michelle S., primary, Etemadmoghadam, Dariush, primary, Bowtell, David D.L., primary, and Drapkin, Ronny, primary
- Published
- 2023
- Full Text
- View/download PDF
37. Supplementary Figures 1-10 from LRP1B Deletion in High-Grade Serous Ovarian Cancers Is Associated with Acquired Chemotherapy Resistance to Liposomal Doxorubicin
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Cowin, Prue A., primary, George, Joshy, primary, Fereday, Sian, primary, Loehrer, Elizabeth, primary, Van Loo, Peter, primary, Cullinane, Carleen, primary, Etemadmoghadam, Dariush, primary, Ftouni, Sarah, primary, Galletta, Laura, primary, Anglesio, Michael S., primary, Hendley, Joy, primary, Bowes, Leanne, primary, Sheppard, Karen E., primary, Christie, Elizabeth L., primary, Pearson, Richard B., primary, Harnett, Paul R., primary, Heinzelmann-Schwarz, Viola, primary, Friedlander, Michael, primary, McNally, Orla, primary, Quinn, Michael, primary, Campbell, Peter, primary, deFazio, Anna, primary, and Bowtell, David D.L., primary
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- 2023
- Full Text
- View/download PDF
38. Supplementary Methods from LRP1B Deletion in High-Grade Serous Ovarian Cancers Is Associated with Acquired Chemotherapy Resistance to Liposomal Doxorubicin
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Cowin, Prue A., primary, George, Joshy, primary, Fereday, Sian, primary, Loehrer, Elizabeth, primary, Van Loo, Peter, primary, Cullinane, Carleen, primary, Etemadmoghadam, Dariush, primary, Ftouni, Sarah, primary, Galletta, Laura, primary, Anglesio, Michael S., primary, Hendley, Joy, primary, Bowes, Leanne, primary, Sheppard, Karen E., primary, Christie, Elizabeth L., primary, Pearson, Richard B., primary, Harnett, Paul R., primary, Heinzelmann-Schwarz, Viola, primary, Friedlander, Michael, primary, McNally, Orla, primary, Quinn, Michael, primary, Campbell, Peter, primary, deFazio, Anna, primary, and Bowtell, David D.L., primary
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- 2023
- Full Text
- View/download PDF
39. Supplementary Tables 1-6 from LRP1B Deletion in High-Grade Serous Ovarian Cancers Is Associated with Acquired Chemotherapy Resistance to Liposomal Doxorubicin
- Author
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Cowin, Prue A., primary, George, Joshy, primary, Fereday, Sian, primary, Loehrer, Elizabeth, primary, Van Loo, Peter, primary, Cullinane, Carleen, primary, Etemadmoghadam, Dariush, primary, Ftouni, Sarah, primary, Galletta, Laura, primary, Anglesio, Michael S., primary, Hendley, Joy, primary, Bowes, Leanne, primary, Sheppard, Karen E., primary, Christie, Elizabeth L., primary, Pearson, Richard B., primary, Harnett, Paul R., primary, Heinzelmann-Schwarz, Viola, primary, Friedlander, Michael, primary, McNally, Orla, primary, Quinn, Michael, primary, Campbell, Peter, primary, deFazio, Anna, primary, and Bowtell, David D.L., primary
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- 2023
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40. The Colorectal cancer RISk Prediction (CRISP) trial: a randomised controlled trial of a decision support tool for risk-stratified colorectal cancer screening
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Emery, Jon D, primary, Jenkins, Mark A, additional, Saya, Sibel, additional, Chondros, Patty, additional, Oberoi, Jasmeen, additional, Milton, Shakira, additional, Novy, Kitty, additional, Habgood, Emily, additional, Karnchanachari, Napin, additional, Pirotta, Marie, additional, Trevena, Lyndal, additional, Bickerstaffe, Adrian, additional, De Abreu Lourenço, Richard, additional, Crothers, Anna, additional, Ouakrim, Driss Ait, additional, Flander, Louisa, additional, Dowty, James G, additional, Walter, Fiona M, additional, Clark, Malcolm, additional, Doncovio, Sally, additional, Etemadmoghadam, Dariush, additional, Fishman, George, additional, Macrae, Finlay, additional, Winship, Ingrid, additional, and McIntosh, Jennifer G, additional
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- 2023
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41. Immune and genomic biomarkers of immunotherapy response in cancer of unknown primary
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Posner, Atara, primary, Sivakumaran, Tharani, additional, Pattison, Andrew, additional, Etemadmoghadam, Dariush, additional, Thio, Niko, additional, Wood, Colin, additional, Fisher, Krista, additional, Webb, Samantha, additional, DeFazio, Anna, additional, Wilcken, Nicholas, additional, Gao, Bo, additional, Karapetis, Christos S, additional, Singh, Madhu, additional, Collins, Ian M, additional, Richardson, Gary, additional, Steer, Christopher, additional, Warren, Mark, additional, Karanth, Narayan, additional, Fellowes, Andrew, additional, Fox, Stephen B, additional, Hicks, Rodney J, additional, Schofield, Penelope, additional, Bowtell, David, additional, Prall, Owen W J, additional, Tothill, Richard William, additional, and Mileshkin, Linda, additional
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- 2023
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42. A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns
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Jiao, Wei, Atwal, Gurnit, Polak, Paz, Karlic, Rosa, Cuppen, Edwin, Al-Shahrour, Fatima, Bailey, Peter J, Biankin, Andrew V, Boutros, Paul C, Campbell, Peter J, Chang, David K, Cooke, Susanna L, Deshpande, Vikram, Faltas, Bishoy M, Faquin, William C, Garraway, Levi, Getz, Gad, Grimmond, Sean M, Haider, Syed, Hoadley, Katherine A, Kaiser, Vera B, Kato, Mamoru, Kübler, Kirsten, Lazar, Alexander J, Li, Constance H, Louis, David N, Margolin, Adam, Martin, Sancha, Nahal-Bose, Hardeep K, Nielsen, G Petur, Nik-Zainal, Serena, Omberg, Larsson, P’ng, Christine, Perry, Marc D, Rheinbay, Esther, Rubin, Mark A, Semple, Colin A, Sgroi, Dennis C, Shibata, Tatsuhiro, Siebert, Reiner, Smith, Jaclyn, Stein, Lincoln D, Stobbe, Miranda D, Sun, Ren X, Thai, Kevin, Wright, Derek W, Wu, Chin-Lee, Yuan, Ke, Zhang, Junjun, Danyi, Alexandra, de Ridder, Jeroen, van Herpen, Carla, Lolkema, Martijn P, Steeghs, Neeltje, Morris, Quaid D, Aaltonen, Lauri A, Abascal, Federico, Abeshouse, Adam, Aburatani, Hiroyuki, Adams, David J, Agrawal, Nishant, Ahn, Keun Soo, Ahn, Sung-Min, Aikata, Hiroshi, Akbani, Rehan, Akdemir, Kadir C, Al-Ahmadie, Hikmat, Al-Sedairy, Sultan T, Alawi, Malik, Albert, Monique, Aldape, Kenneth, Alexandrov, Ludmil B, Ally, Adrian, Alsop, Kathryn, Alvarez, Eva G, Amary, Fernanda, Amin, Samirkumar B, Aminou, Brice, Ammerpohl, Ole, Anderson, Matthew J, Ang, Yeng, Antonello, Davide, Anur, Pavana, Aparicio, Samuel, Appelbaum, Elizabeth L, Arai, Yasuhito, Aretz, Axel, Arihiro, Koji, Ariizumi, Shun-ichi, Armenia, Joshua, Arnould, Laurent, Asa, Sylvia, Assenov, Yassen, Aukema, Sietse, Auman, J Todd, Aure, Miriam RR, Awadalla, Philip, Aymerich, Marta, Bader, Gary D, Baez-Ortega, Adrian, Bailey, Matthew H, Balasundaram, Miruna, Balu, Saianand, Bandopadhayay, Pratiti, Banks, Rosamonde E, Barbi, Stefano, Barbour, Andrew P, Barenboim, Jonathan, Barnholtz-Sloan, Jill, Barr, Hugh, Barrera, Elisabet, Bartlett, John, Bartolome, Javier, Bassi, Claudio, Bathe, Oliver F, Baumhoer, Daniel, Bavi, Prashant, Baylin, Stephen B, Bazant, Wojciech, Beardsmore, Duncan, Beck, Timothy A, Behjati, Sam, Behren, Andreas, Niu, Beifang, Bell, Cindy, Beltran, Sergi, Benz, Christopher, Berchuck, Andrew, Bergmann, Anke K, Bergstrom, Erik N, Berman, Benjamin P, Berney, Daniel M, Bernhart, Stephan H, Beroukhim, Rameen, Berrios, Mario, Bersani, Samantha, Bertl, Johanna, Betancourt, Miguel, Bhandari, Vinayak, Bhosle, Shriram G, Bieg, Matthias, Bigner, Darell, Binder, Hans, Birney, Ewan, Birrer, Michael, Biswas, Nidhan K, Bjerkehagen, Bodil, Bodenheimer, Tom, Boice, Lori, Bonizzato, Giada, De Bono, Johann S, Boot, Arnoud, Bootwalla, Moiz S, Borg, Ake, Borkhardt, Arndt, Boroevich, Keith A, Borozan, Ivan, Borst, Christoph, Bosenberg, Marcus, Bosio, Mattia, Boultwood, Jacqueline, Bourque, Guillaume, Bova, G Steven, Bowen, David T, Bowlby, Reanne, Bowtell, David DL, Boyault, Sandrine, Boyce, Rich, Boyd, Jeffrey, Brazma, Alvis, Brennan, Paul, Brewer, Daniel S, Brinkman, Arie B, Bristow, Robert G, Broaddus, Russell R, Brock, Jane E, Brock, Malcolm, Broeks, Annegien, Brooks, Angela N, Brooks, Denise, Brors, Benedikt, Brunak, Søren, Bruxner, Timothy JC, Bruzos, Alicia L, Buchanan, Alex, Buchhalter, Ivo, Buchholz, Christiane, Bullman, Susan, Burke, Hazel, Burkhardt, Birgit, Burns, Kathleen H, Busanovich, John, Bustamante, Carlos D, Butler, Adam P, Butte, Atul J, Byrne, Niall J, Børresen-Dale, Anne-Lise, Caesar-Johnson, Samantha J, Cafferkey, Andy, Cahill, Declan, Calabrese, Claudia, Caldas, Carlos, Calvo, Fabien, Camacho, Niedzica, Campo, Elias, Cantù, Cinzia, Cao, Shaolong, Carey, Thomas E, Carlevaro-Fita, Joana, Carlsen, Rebecca, Cataldo, Ivana, Cazzola, Mario, Cebon, Jonathan, Cerfolio, Robert, Chadwick, Dianne E, Chakravarty, Dimple, Chalmers, Don, Chan, Calvin Wing Yiu, Chan, Kin, Chan-Seng-Yue, Michelle, Chandan, Vishal S, Chanock, Stephen J, Chantrill, Lorraine A, Chateigner, Aurélien, Chatterjee, Nilanjan, Chayama, Kazuaki, Chen, Hsiao-Wei, Chen, Jieming, Chen, Ken, Chen, Yiwen, Chen, Zhaohong, Cherniack, Andrew D, Chien, Jeremy, Chiew, Yoke-Eng, Chin, Suet-Feung, Cho, Juok, Cho, Sunghoon, Choi, Jung Kyoon, Choi, Wan, Chomienne, Christine, Chong, Zechen, Choo, Su Pin, Chou, Angela, Christ, Angelika N, Christie, Elizabeth L, Chuah, Eric, Cibulskis, Carrie, Cibulskis, Kristian, Cingarlini, Sara, Clapham, Peter, Claviez, Alexander, Cleary, Sean, Cloonan, Nicole, Cmero, Marek, Collins, Colin C, Connor, Ashton A, Cooper, Colin S, Cope, Leslie, Corbo, Vincenzo, Cordes, Matthew G, Cordner, Stephen M, Cortés-Ciriano, Isidro, Covington, Kyle, Cowin, Prue A, Craft, Brian, Craft, David, Creighton, Chad J, Cun, Yupeng, Curley, Erin, Cutcutache, Ioana, Czajka, Karolina, Czerniak, Bogdan, Dagg, Rebecca A, Danilova, Ludmila, Davi, Maria Vittoria, Davidson, Natalie R, Davies, Helen, Davis, Ian J, Davis-Dusenbery, Brandi N, Dawson, Kevin J, De La Vega, Francisco M, De Paoli-Iseppi, Ricardo, Defreitas, Timothy, Dei Tos, Angelo P, Delaneau, Olivier, Demchok, John A, Demeulemeester, Jonas, Demidov, German M, Demircioğlu, Deniz, Dennis, Nening M, Denroche, Robert E, Dentro, Stefan C, Desai, Nikita, Deshwar, Amit G, Desmedt, Christine, Deu-Pons, Jordi, Dhalla, Noreen, Dhani, Neesha C, Dhingra, Priyanka, Dhir, Rajiv, DiBiase, Anthony, Diamanti, Klev, Ding, Li, Ding, Shuai, Dinh, Huy Q, Dirix, Luc, Doddapaneni, HarshaVardhan, Donmez, Nilgun, Dow, Michelle T, Drapkin, Ronny, Drechsel, Oliver, Drews, Ruben M, Serge, Serge, Dudderidge, Tim, Dueso-Barroso, Ana, Dunford, Andrew J, Dunn, Michael, Dursi, Lewis Jonathan, Duthie, Fraser R, Dutton-Regester, Ken, Eagles, Jenna, Easton, Douglas F, Edmonds, Stuart, Edwards, Paul A, Edwards, Sandra E, Eeles, Rosalind A, Ehinger, Anna, Eils, Juergen, Eils, Roland, El-Naggar, Adel, Eldridge, Matthew, Ellrott, Kyle, Erkek, Serap, Escaramis, Georgia, Espiritu, Shadrielle MG, Estivill, Xavier, Etemadmoghadam, Dariush, Eyfjord, Jorunn E, Fan, Daiming, Fan, Yu, Farcas, Claudiu, Fassan, Matteo, Fatima, Aquila, Favero, Francesco, Fayzullaev, Nodirjon, Felau, Ina, Fereday, Sian, Ferguson, Martin L, Ferretti, Vincent, Feuerbach, Lars, Field, Matthew A, Fink, J Lynn, Finocchiaro, Gaetano, Fisher, Cyril, Fittall, Matthew W, Fitzgerald, Anna, Fitzgerald, Rebecca C, Flanagan, Adrienne M, Fleshner, Neil E, Flicek, Paul, Foekens, John A, Fong, Kwun M, Fonseca, Nuno A, Foster, Christopher S, Fox, Natalie S, Fraser, Michael, Frazer, Scott, Frenkel-Morgenstern, Milana, Friedman, William, Frigola, Joan, Fronick, Catrina C, Fujimoto, Akihiro, Fujita, Masashi, Fukayama, Masashi, Fulton, Lucinda A, Fulton, Robert S, Furuta, Mayuko, Futreal, P Andrew, Füllgrabe, Anja, Gabriel, Stacey B, Gallinger, Steven, Gambacorti-Passerini, Carlo, Gao, Jianjiong, Gao, Shengjie, Garred, Øystein, Garrison, Erik, Garsed, Dale W, Gehlenborg, Nils, Gelpi, Josep LL, George, Joshy, Gerhard, Daniela S, Gerhauser, Clarissa, Gershenwald, Jeffrey E, Gerstein, Mark, Gerstung, Moritz, Ghori, Mohammed, Ghossein, Ronald, Giama, Nasra H, Gibbs, 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Deurzen, Carolien HM, van de Vijver, Marc J, Veer, L van’t, and von Mering, Christian
- Subjects
Human Biology & Physiology ,Ecology,Evolution & Ethology ,Tumour Biology ,Genetics & Genomics ,Structural Biology & Biophysics ,Computational & Systems Biology - Abstract
In cancer, the primary tumour’s organ of origin and histopathology are the strongest determinants of its clinical behaviour, but in 3% of cases a patient presents with a metastatic tumour and no obvious primary. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, we train a deep learning classifier to predict cancer type based on patterns of somatic passenger mutations detected in whole genome sequencing (WGS) of 2606 tumours representing 24 common cancer types produced by the PCAWG Consortium. Our classifier achieves an accuracy of 91% on held-out tumor samples and 88% and 83% respectively on independent primary and metastatic samples, roughly double the accuracy of trained pathologists when presented with a metastatic tumour without knowledge of the primary. Surprisingly, adding information on driver mutations reduced accuracy. Our results have clinical applicability, underscore how patterns of somatic passenger mutations encode the state of the cell of origin, and can inform future strategies to detect the source of circulating tumour DNA.
- Published
- 2023
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43. Combined burden and functional impact tests for cancer driver discovery using DriverPower
- Author
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- Subjects
Human Biology & Physiology ,Ecology,Evolution & Ethology ,Tumour Biology ,Genetics & Genomics ,Structural Biology & Biophysics ,Computational & Systems Biology - Abstract
The discovery of driver mutations is one of the key motivations for cancer genome sequencing. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancers across 38 tumour types, we describe DriverPower, a software package that uses mutational burden and functional impact evidence to identify driver mutations in coding and non-coding sites within cancer whole genomes. Using a total of 1373 genomic features derived from public sources, DriverPower’s background mutation model explains up to 93% of the regional variance in the mutation rate across multiple tumour types. By incorporating functional impact scores, we are able to further increase the accuracy of driver discovery. Testing across a collection of 2583 cancer genomes from the PCAWG project, DriverPower identifies 217 coding and 95 non-coding driver candidates. Comparing to six published methods used by the PCAWG Drivers and Functional Interpretation Working Group, DriverPower has the highest F1 score for both coding and non-coding driver discovery. This demonstrates that DriverPower is an effective framework for computational driver discovery.
- Published
- 2023
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44. Integrative pathway enrichment analysis of multivariate omics data
- Author
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Paczkowska, Marta, Barenboim, Jonathan, Sintupisut, Nardnisa, Fox, Natalie S, Zhu, Helen, Abd-Rabbo, Diala, Mee, Miles W, Boutros, Paul C, Abascal, Federico, Amin, Samirkumar B, Bader, Gary D, Beroukhim, Rameen, Bertl, Johanna, Boroevich, Keith A, Brunak, Søren, Campbell, Peter J, Carlevaro-Fita, Joana, Chakravarty, Dimple, Chan, Calvin Wing Yiu, Chen, Ken, Choi, Jung Kyoon, Deu-Pons, Jordi, Dhingra, Priyanka, Diamanti, Klev, Feuerbach, Lars, Fink, J Lynn, Fonseca, Nuno A, Frigola, Joan, Gambacorti-Passerini, Carlo, Garsed, Dale W, Gerstein, Mark, Getz, Gad, Gonzalez-Perez, Abel, Guo, Qianyun, Gut, Ivo G, Haan, David, Hamilton, Mark P, Haradhvala, Nicholas J, Harmanci, Arif O, Helmy, Mohamed, Herrmann, Carl, Hess, Julian M, Hobolth, Asger, Hodzic, Ermin, Hong, Chen, Hornshøj, Henrik, Isaev, Keren, Izarzugaza, Jose MG, Johnson, Rory, Johnson, Todd A, Juul, Malene, Juul, Randi Istrup, Kahles, Andre, Kahraman, Abdullah, Kellis, Manolis, Khurana, Ekta, Kim, Jaegil, Kim, Jong K, Kim, 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Vijver, Marc J, and Veer, L van’t
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Human Biology & Physiology ,Ecology,Evolution & Ethology ,Tumour Biology ,Genetics & Genomics ,Structural Biology & Biophysics ,Computational & Systems Biology - Abstract
Multi-omics datasets represent distinct aspects of the central dogma of molecular biology. Such high-dimensional molecular profiles pose challenges to data interpretation and hypothesis generation. ActivePathways is an integrative method that discovers significantly enriched pathways across multiple datasets using statistical data fusion, rationalizes contributing evidence and highlights associated genes. As part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancers across 38 tumor types, we integrated genes with coding and non-coding mutations and revealed frequently mutated pathways and additional cancer genes with infrequent mutations. We also analyzed prognostic molecular pathways by integrating genomic and transcriptomic features of 1780 breast cancers and highlighted associations with immune response and anti-apoptotic signaling. Integration of ChIP-seq and RNA-seq data for master regulators of the Hippo pathway across normal human tissues identified processes of tissue regeneration and stem cell regulation. ActivePathways is a versatile method that improves systems-level understanding of cellular organization in health and disease through integration of multiple molecular datasets and pathway annotations.
- Published
- 2023
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45. Pathway and network analysis of more than 2500 whole cancer genomes
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Reyna, Matthew A, Haan, David, Paczkowska, Marta, Verbeke, Lieven PC, Vazquez, Miguel, Kahraman, Abdullah, Pulido-Tamayo, Sergio, Barenboim, Jonathan, Wadi, Lina, Dhingra, Priyanka, Shrestha, Raunak, Getz, Gad, Lawrence, Michael S, Pedersen, Jakob Skou, Rubin, Mark A, Wheeler, David A, Brunak, Søren, Izarzugaza, Jose MG, Khurana, Ekta, Marchal, Kathleen, von Mering, Christian, Sahinalp, S Cenk, Valencia, Alfonso, Abascal, Federico, Amin, Samirkumar B, Bader, Gary D, Bandopadhayay, Pratiti, Beroukhim, Rameen, Bertl, Johanna, Boroevich, Keith A, Busanovich, John, Campbell, Peter J, Carlevaro-Fita, Joana, Chakravarty, Dimple, Chan, Calvin Wing Yiu, Chen, Ken, Choi, Jung Kyoon, Deu-Pons, Jordi, Diamanti, Klev, Feuerbach, Lars, Fink, J Lynn, Fonseca, Nuno A, Frigola, Joan, Gambacorti-Passerini, Carlo, Garsed, Dale W, Gerstein, Mark, Guo, Qianyun, Gut, Ivo G, Hamilton, Mark P, Haradhvala, Nicholas J, Harmanci, Arif O, Helmy, Mohamed, Herrmann, Carl, Hess, Julian M, Hobolth, Asger, Hodzic, Ermin, Hong, Chen, Hornshøj, Henrik, Isaev, Keren, Johnson, Rory, Johnson, Todd A, Juul, Malene, Juul, Randi Istrup, Kahles, Andre, Kellis, Manolis, Kim, Jaegil, Kim, Jong K, Kim, Youngwook, Komorowski, Jan, Korbel, Jan O, Kumar, Sushant, Lanzós, Andrés, Larsson, Erik, Lee, Donghoon, Lehmann, Kjong-Van, Li, Shantao, Li, Xiaotong, Lin, Ziao, Liu, Eric Minwei, Lochovsky, Lucas, Lou, Shaoke, Madsen, Tobias, Martincorena, Iñigo, Martinez-Fundichely, Alexander, Maruvka, Yosef E, McGillivray, Patrick D, Meyerson, William, Muiños, Ferran, Mularoni, Loris, Nakagawa, Hidewaki, Nielsen, Morten Muhlig, Park, Keunchil, Park, Kiejung, Pons, Tirso, Reyes-Salazar, Iker, Rheinbay, Esther, Rubio-Perez, Carlota, Saksena, Gordon, Salichos, Leonidas, Sander, Chris, Schumacher, Steven E, Shackleton, Mark, Shapira, Ofer, Shen, Ciyue, Shuai, Shimin, Sidiropoulos, Nikos, Sieverling, Lina, Sinnott-Armstrong, Nasa, Stein, Lincoln D, Tamborero, David, Tiao, Grace, Tsunoda, Tatsuhiko, Umer, Husen M, Uusküla-Reimand, Liis, Wadelius, Claes, Wang, Jiayin, Warrell, Jonathan, Waszak, Sebastian M, Weischenfeldt, Joachim, Wu, Guanming, Yu, Jun, Zhang, Jing, Zhang, Xuanping, Zhang, Yan, Zhao, Zhongming, Zou, Lihua, Reimand, Jüri, Stuart, Joshua M, Raphael, Benjamin J, Aaltonen, Lauri A, Abeshouse, Adam, Aburatani, Hiroyuki, Adams, David J, Agrawal, Nishant, Ahn, Keun Soo, Ahn, Sung-Min, Aikata, Hiroshi, Akbani, Rehan, Akdemir, Kadir C, Al-Ahmadie, Hikmat, Al-Sedairy, Sultan T, Al-Shahrour, Fatima, Alawi, Malik, Albert, Monique, Aldape, Kenneth, Alexandrov, Ludmil B, Ally, Adrian, Alsop, Kathryn, Alvarez, Eva G, Amary, Fernanda, Aminou, Brice, Ammerpohl, Ole, Anderson, Matthew J, Ang, Yeng, Antonello, Davide, Anur, Pavana, Aparicio, Samuel, Appelbaum, Elizabeth L, Arai, Yasuhito, Aretz, Axel, Arihiro, Koji, Ariizumi, Shun-ichi, Armenia, Joshua, Arnould, Laurent, Asa, Sylvia, Assenov, Yassen, Atwal, Gurnit, Aukema, Sietse, Auman, J Todd, Aure, Miriam RR, Awadalla, Philip, Aymerich, Marta, Baez-Ortega, Adrian, Bailey, Matthew H, Bailey, Peter J, Balasundaram, Miruna, Balu, Saianand, Banks, Rosamonde E, Barbi, Stefano, Barbour, Andrew P, Barnholtz-Sloan, Jill, Barr, Hugh, Barrera, Elisabet, Bartlett, John, Bartolome, Javier, Bassi, Claudio, Bathe, Oliver F, Baumhoer, Daniel, Bavi, Prashant, Baylin, Stephen B, Bazant, Wojciech, Beardsmore, Duncan, Beck, Timothy A, Behjati, Sam, Behren, Andreas, Niu, Beifang, Bell, Cindy, Beltran, Sergi, Benz, Christopher, Berchuck, Andrew, Bergmann, Anke K, Bergstrom, Erik N, Berman, Benjamin P, Berney, Daniel M, Bernhart, Stephan H, Berrios, Mario, Bersani, Samantha, Betancourt, Miguel, Bhandari, Vinayak, Bhosle, Shriram G, Biankin, Andrew V, Bieg, Matthias, Bigner, Darell, Binder, Hans, Birney, Ewan, Birrer, Michael, Biswas, Nidhan K, Bjerkehagen, Bodil, Bodenheimer, Tom, Boice, Lori, Bonizzato, Giada, De Bono, Johann S, Boot, Arnoud, Bootwalla, Moiz S, Borg, Ake, Borkhardt, Arndt, Borozan, Ivan, Borst, Christoph, Bosenberg, Marcus, Bosio, Mattia, Boultwood, Jacqueline, Bourque, Guillaume, Boutros, Paul C, Bova, G Steven, Bowen, David T, Bowlby, Reanne, Bowtell, David DL, Boyault, Sandrine, Boyce, Rich, Boyd, Jeffrey, Brazma, Alvis, Brennan, Paul, Brewer, Daniel S, Brinkman, Arie B, Bristow, Robert G, Broaddus, Russell R, Brock, Jane E, Brock, Malcolm, Broeks, Annegien, Brooks, Angela N, Brooks, Denise, Brors, Benedikt, Bruxner, Timothy JC, Bruzos, Alicia L, Buchanan, Alex, Buchhalter, Ivo, Buchholz, Christiane, Bullman, Susan, Burke, Hazel, Burkhardt, Birgit, Burns, Kathleen H, Bustamante, Carlos D, Butler, Adam P, Butte, Atul J, Byrne, Niall J, Børresen-Dale, Anne-Lise, Caesar-Johnson, Samantha J, Cafferkey, Andy, Cahill, Declan, Calabrese, Claudia, Caldas, Carlos, Calvo, Fabien, Camacho, Niedzica, Campo, Elias, Cantù, Cinzia, Cao, Shaolong, Carey, Thomas E, Carlsen, Rebecca, Cataldo, Ivana, Cazzola, Mario, Cebon, Jonathan, Cerfolio, Robert, Chadwick, Dianne E, Chalmers, Don, Chan, Kin, Chan-Seng-Yue, Michelle, Chandan, Vishal S, Chang, David K, Chanock, Stephen J, Chantrill, Lorraine A, Chateigner, Aurélien, Chatterjee, Nilanjan, Chayama, Kazuaki, Chen, Hsiao-Wei, Chen, Jieming, Chen, Yiwen, Chen, Zhaohong, Cherniack, Andrew D, Chien, Jeremy, Chiew, Yoke-Eng, Chin, Suet-Feung, Cho, Juok, Cho, Sunghoon, Choi, Wan, Chomienne, Christine, Chong, Zechen, Choo, Su Pin, Chou, Angela, Christ, Angelika N, Christie, Elizabeth L, Chuah, Eric, Cibulskis, Carrie, Cibulskis, Kristian, Cingarlini, Sara, Clapham, Peter, Claviez, Alexander, Cleary, Sean, Cloonan, Nicole, Cmero, Marek, Collins, Colin C, Connor, Ashton A, Cooke, Susanna L, Cooper, Colin S, Cope, Leslie, Corbo, Vincenzo, Cordes, Matthew G, Cordner, Stephen M, Cortés-Ciriano, Isidro, Covington, Kyle, Cowin, Prue A, Craft, Brian, Craft, David, Creighton, Chad J, Cun, Yupeng, Curley, Erin, Cutcutache, Ioana, Czajka, Karolina, Czerniak, Bogdan, Dagg, Rebecca A, Danilova, Ludmila, Davi, Maria Vittoria, Davidson, Natalie R, Davies, Helen, Davis, Ian J, Davis-Dusenbery, Brandi N, Dawson, Kevin J, De La Vega, Francisco M, De Paoli-Iseppi, Ricardo, Defreitas, Timothy, Dei Tos, Angelo P, Delaneau, Olivier, Demchok, John A, Demeulemeester, Jonas, Demidov, German M, Demircioğlu, Deniz, Dennis, Nening M, Denroche, Robert E, Dentro, Stefan C, Desai, Nikita, Deshpande, Vikram, Deshwar, Amit G, Desmedt, Christine, Dhalla, Noreen, Dhani, Neesha C, Dhir, Rajiv, DiBiase, Anthony, Ding, Li, Ding, Shuai, Dinh, Huy Q, Dirix, Luc, Doddapaneni, HarshaVardhan, Donmez, Nilgun, Dow, Michelle T, Drapkin, Ronny, Drechsel, Oliver, Drews, Ruben M, Serge, Serge, Dudderidge, Tim, Dueso-Barroso, Ana, Dunford, Andrew J, Dunn, Michael, Dursi, Lewis Jonathan, Duthie, Fraser R, Dutton-Regester, Ken, Eagles, Jenna, Easton, Douglas F, Edmonds, Stuart, Edwards, Paul A, Edwards, Sandra E, Eeles, Rosalind A, Ehinger, Anna, Eils, Juergen, Eils, Roland, El-Naggar, Adel, Eldridge, Matthew, Ellrott, Kyle, Erkek, Serap, Escaramis, Georgia, Espiritu, Shadrielle MG, Estivill, Xavier, Etemadmoghadam, Dariush, Eyfjord, Jorunn E, Faltas, Bishoy M, Fan, Daiming, Fan, Yu, Faquin, William C, Farcas, Claudiu, Fassan, Matteo, Fatima, Aquila, Favero, Francesco, Fayzullaev, Nodirjon, Felau, Ina, Fereday, Sian, Ferguson, Martin L, Ferretti, Vincent, Field, Matthew A, Finocchiaro, Gaetano, Fisher, Cyril, Fittall, Matthew W, Fitzgerald, Anna, Fitzgerald, Rebecca C, Flanagan, Adrienne M, Fleshner, Neil E, Flicek, Paul, Foekens, John A, Fong, Kwun M, Foster, Christopher S, Fox, Natalie S, Fraser, Michael, Frazer, Scott, Frenkel-Morgenstern, Milana, Friedman, William, Fronick, Catrina C, Fujimoto, Akihiro, Fujita, Masashi, Fukayama, Masashi, Fulton, Lucinda A, Fulton, Robert S, Furuta, Mayuko, Futreal, P Andrew, Füllgrabe, Anja, Gabriel, Stacey B, Gallinger, Steven, Gao, Jianjiong, Gao, Shengjie, Garraway, Levi, Garred, Øystein, Garrison, Erik, Gehlenborg, Nils, Gelpi, Josep LL, George, Joshy, Gerhard, Daniela S, Gerhauser, Clarissa, Gershenwald, Jeffrey E, Gerstung, Moritz, Ghori, Mohammed, Ghossein, Ronald, Giama, Nasra H, Gibbs, Richard A, Gibson, Bob, Gill, Anthony J, Gill, Pelvender, Giri, Dilip D, Glodzik, Dominik, Gnanapragasam, Vincent J, Goebler, Maria Elisabeth, Goldman, Mary J, Gomez, Carmen, Gonzalez, Santiago, Gonzalez-Perez, Abel, Gordenin, Dmitry A, Gossage, James, Gotoh, Kunihito, Govindan, Ramaswamy, Grabau, Dorthe, Graham, Janet S, Grant, Robert C, Green, Anthony R, Green, Eric, Greger, Liliana, Grehan, Nicola, Grimaldi, Sonia, Grimmond, Sean M, Grossman, Robert L, Grundhoff, Adam, Gundem, Gunes, Gupta, Manaswi, Gupta, Shailja, Gut, Marta, Göke, Jonathan, Ha, Gavin, Haake, Andrea, Haas, Siegfried, Haase, Kerstin, Haber, James E, Habermann, Nina, Hach, Faraz, Haider, Syed, Hama, Natsuko, Hamdy, Freddie C, Hamilton, Anne, Han, Leng, Hanna, George B, Hansmann, Martin, Harismendy, Olivier, Harliwong, Ivon, Harrington, Eoghan, Hasegawa, Takanori, Haussler, David, Hawkins, Steve, Hayami, Shinya, Hayashi, Shuto, Hayes, D Neil, Hayes, Stephen J, Hayward, Nicholas K, Hazell, Steven, He, Yao, Heath, Allison P, Heath, Simon C, Hedley, David, Hegde, Apurva M, Heiman, David I, Heinold, Michael C, Heins, Zachary, Heisler, Lawrence E, Hellstrom-Lindberg, Eva, Heo, Seong Gu, Hepperla, Austin J, Heredia-Genestar, José María, Hersey, Peter, Hilmarsdottir, Holmfridur, Hinton, Jonathan, Hirano, Satoshi, Hiraoka, Nobuyoshi, Hoadley, Katherine A, Hoell, Jessica I, Hoffmann, Steve, Hofmann, Oliver, Holbrook, Andrea, Holik, Aliaksei Z, Hollingsworth, Michael A, Holmes, Oliver, Holt, Robert A, Hong, Eun Pyo, Hong, Jongwhi H, Hooijer, Gerrit K, Hosoda, Fumie, Hou, Yong, Hovestadt, Volker, Howat, William, Hoyle, Alan P, Hruban, Ralph H, Hu, Jianhong, Hu, Taobo, Hua, Xing, Huang, Kuan-lin, Huang, Mei, Huang, Mi Ni, Huang, Vincent, Huang, Yi, Huber, Wolfgang, Hudson, Thomas J, Hummel, Michael, Hung, Jillian A, Huntsman, David, Hupp, Ted R, Huse, Jason, Huska, Matthew R, Hutter, Barbara, Hutter, Carolyn M, Hübschmann, Daniel, Iacobuzio-Donahue, Christine A, Imbusch, Charles David, Imielinski, Marcin, Imoto, Seiya, Isaacs, William B, Ishikawa, Shumpei, Iskar, Murat, Islam, SM Ashiqul, Ittmann, Michael, Ivkovic, Sinisa, Jacquemier, Jocelyne, Jakrot, Valerie, Jamieson, Nigel B, Jang, Gun Ho, Jang, Se Jin, Jayaseelan, Joy C, Jayasinghe, Reyka, Jefferys, Stuart R, Jegalian, Karine, Jennings, Jennifer L, Jeon, Seung-Hyup, Jerman, Lara, Ji, Yuan, Jiao, Wei, Johansson, Peter A, Johns, Amber L, Johns, Jeremy, Jolly, Clemency, Joly, Yann, Jonasson, Jon G, Jones, Corbin D, Jones, David R, Jones, David TW, Jones, Nic, Jones, Steven JM, Jonkers, Jos, Ju, Young Seok, Juhl, Hartmut, Jung, Jongsun, Juul, Sissel, Jäger, Natalie, Kabbe, Rolf, Kaiser, Vera B, Kakavand, Hojabr, Kalimuthu, Sangeetha, von Kalle, Christof, Kang, Koo Jeong, Karaszi, Katalin, Karlan, Beth, Karlić, Rosa, Karsch, Dennis, Kasaian, Katayoon, Kassahn, Karin S, Katai, Hitoshi, Kato, Mamoru, Katoh, Hiroto, Kawakami, Yoshiiku, Kay, Jonathan D, Kazakoff, Stephen H, Kazanov, Marat D, Keays, Maria, Kebebew, Electron, Kefford, Richard F, Kench, James G, Kennedy, Catherine J, Kerssemakers, Jules NA, Khoo, David, Khoo, Vincent, Khuntikeo, Narong, Kilpinen, Helena, Kim, Hark Kyun, Kim, Hyung-Lae, Kim, Hyung-Yong, Kim, Hyunghwan, Kim, Jihoon, King, Tari A, Klapper, Wolfram, Kleinheinz, Kortine, Klimczak, Leszek J, Knappskog, Stian, Kneba, Michael, Knoppers, Bartha M, Koh, Youngil, Komura, Daisuke, Komura, Mitsuhiro, Kong, Gu, Kool, Marcel, Korchina, Viktoriya, Korshunov, Andrey, Koscher, Michael, Koster, Roelof, Kote-Jarai, Zsofia, Koures, Antonios, Kovacevic, Milena, Kremeyer, Barbara, Kretzmer, Helene, Kreuz, Markus, Krishnamurthy, Savitri, Kube, Dieter, Kumar, Kiran, Kumar, Pardeep, Kumar, Yogesh, Kundra, Ritika, Kübler, Kirsten, Küppers, Ralf, Lagergren, Jesper, Lai, Phillip H, Laird, Peter W, Lakhani, Sunil R, Lalansingh, Christopher M, Lalonde, Emilie, Lamaze, Fabien C, Lambert, Adam, Lander, Eric, Landgraf, Pablo, Landoni, Luca, Langerød, Anita, Larsimont, Denis, Lathrop, Mark, Lau, Loretta MS, Lawerenz, Chris, Lawlor, Rita T, Lazar, Alexander J, Lazic, Ana Mijalkovic, Le, Xuan, Lee, Darlene, Lee, Eunjung Alice, Lee, Hee Jin, Lee, Jake June-Koo, Lee, Jeong-Yeon, Lee, Juhee, Lee, Ming Ta Michael, Lee-Six, Henry, Lehrach, Hans, Lenze, Dido, Leonard, Conrad R, Leongamornlert, Daniel A, Leshchiner, Ignaty, Letourneau, Louis, Letunic, Ivica, Levine, Douglas A, Lewis, Lora, Ley, Tim, Li, Chang, Li, Constance H, Li, Haiyan Irene, Li, Jun, Li, Lin, Li, Siliang, Li, Xiaobo, Li, Xinyue, Li, Yilong, Liang, Han, Liang, Sheng-Ben, Lichter, Peter, Lin, Pei, Linehan, WM, Lingjærde, Ole Christian, Liu, Dongbing, Liu, Fei-Fei Fei, Liu, Fenglin, Liu, Jia, Liu, Xingmin, Livingstone, Julie, Livitz, Dimitri, Livni, Naomi, Loeffler, Markus, Long, Georgina V, Lopez-Guillermo, Armando, Louis, David N, Lovat, Laurence B, Lu, Yiling, Lu, Yong-Jie, Lu, Youyong, Luchini, Claudio, Lungu, Ilinca, Luo, Xuemei, Luxton, Hayley J, Lynch, Andy G, Lype, Lisa, López, Cristina, López-Otín, Carlos, Z, Eric, Ma, Yussanne, MacGrogan, Gaetan, MacRae, Shona, Macintyre, Geoff, Maejima, Kazuhiro, Mafficini, Andrea, Maglinte, Dennis T, Maitra, Arindam, Majumder, Partha P, Malcovati, Luca, Malikic, Salem, Malleo, Giuseppe, Mann, Graham J, Mantovani-Löffler, Luisa, Marchegiani, Giovanni, Mardis, Elaine R, Margolin, Adam A, Marin, Maximillian G, Markowetz, Florian, Markowski, Julia, Marks, Jeffrey, Marques-Bonet, Tomas, Marra, Marco A, Marsden, Luke, Martens, John WM, Martin, Sancha, Martin-Subero, Jose I, Mashl, R Jay, Massie, Charlie E, Matthew, Thomas J, Matthews, Lucy, Mayer, Erik, Mayes, Simon, Mayo, Michael, Mbabaali, Faridah, McCune, Karen, McDermott, Ultan, McLellan, Michael D, McPherson, John D, McPherson, John R, McPherson, Treasa A, Meier, Samuel R, Meng, Alice, Meng, Shaowu, Menzies, Andrew, Merrett, Neil D, Merson, Sue, Meyerson, Matthew, Mieczkowski, Piotr A, Mihaiescu, George L, Mijalkovic, Sanja, Mikkelsen, Tom, Milella, Michele, Mileshkin, Linda, Miller, Christopher A, Miller, David K, Miller, Jessica K, Mills, Gordon B, Milovanovic, Ana, Minner, Sarah, Miotto, Marco, Arnau, Gisela Mir, Mirabello, Lisa, Mitchell, Chris, Mitchell, Thomas J, Miyano, Satoru, Miyoshi, Naoki, Mizuno, Shinichi, Molnár-Gábor, Fruzsina, Moore, Malcolm J, Moore, Richard A, Morganella, Sandro, Morris, Quaid D, Morrison, Carl, Mose, Lisle E, Moser, Catherine D, Mungall, Andrew J, Mungall, Karen, Musgrove, Elizabeth A, Mustonen, Ville, Mutch, David, Muyas, Francesc, Muzny, Donna M, Muñoz, Alfonso, Myers, Jerome, Myklebost, Ola, Möller, Peter, Nagae, Genta, Nagrial, Adnan M, Nahal-Bose, Hardeep K, Nakagama, Hitoshi, Nakamura, Hiromi, Nakamura, Toru, Nakano, Kaoru, Nandi, Tannistha, Nangalia, Jyoti, Nastic, Mia, Navarro, Arcadi, Navarro, Fabio CP, Neal, David E, Nettekoven, Gerd, Newell, Felicity, Newhouse, Steven J, Newton, Yulia, Ng, Alvin Wei Tian, Ng, Anthony, Nicholson, Jonathan, Nicol, David, Nie, Yongzhan, Nielsen, G Petur, Nik-Zainal, Serena, Noble, Michael S, Nones, Katia, Northcott, Paul A, Notta, Faiyaz, O’Connor, Brian D, O’Donnell, Peter, O’Donovan, Maria, O’Meara, Sarah, O’Neill, Brian Patrick, O’Neill, J Robert, Ocana, David, Ochoa, Angelica, Oesper, Layla, Ogden, Christopher, Ohdan, Hideki, Ohi, Kazuhiro, Ohno-Machado, Lucila, Oien, Karin A, Ojesina, Akinyemi I, Ojima, Hidenori, Okusaka, Takuji, Omberg, Larsson, Ong, Choon Kiat, Ossowski, Stephan, Ott, German, Ouellette, BF Francis, P’ng, Christine, Paiella, Salvatore, Pairojkul, Chawalit, Pajic, Marina, Pan-Hammarström, Qiang, Papaemmanuil, Elli, Papatheodorou, Irene, Paramasivam, Nagarajan, Park, Ji Wan, Park, Joong-Won, Park, Peter J, Parker, Joel S, Parsons, Simon L, Pass, Harvey, Pasternack, Danielle, Pastore, Alessandro, Patch, Ann-Marie, Pauporté, Iris, Pea, Antonio, Pearson, John V, Pedamallu, Chandra Sekhar, Pederzoli, Paolo, Peifer, Martin, Pennell, Nathan A, Perou, Charles M, Perry, Marc D, Petersen, Gloria M, Peto, Myron, Petrelli, Nicholas, Petryszak, Robert, Pfister, Stefan M, Phillips, Mark, Pich, Oriol, Pickett, Hilda A, Pihl, Todd D, Pillay, Nischalan, Pinder, Sarah, Pinese, Mark, Pinho, Andreia V, Pitkänen, Esa, Pivot, Xavier, Piñeiro-Yáñez, Elena, Planko, Laura, Plass, Christoph, Polak, Paz, Popescu, Irinel, Potapova, Olga, Prasad, Aparna, Preston, Shaun R, Prinz, Manuel, Pritchard, Antonia L, Prokopec, Stephenie D, Provenzano, Elena, Puente, Xose S, Puig, Sonia, Puiggròs, Montserrat, Pupo, Gulietta M, Purdie, Colin A, Quinn, Michael C, Rabionet, Raquel, Rader, Janet S, Radlwimmer, Bernhard, Radovic, Petar, Raeder, Benjamin, Raine, Keiran M, Ramakrishna, Manasa, Ramakrishnan, Kamna, Ramalingam, Suresh, Rathmell, W Kimryn, Rausch, Tobias, Reifenberger, Guido, Reis-Filho, Jorge, Reuter, Victor, Reynolds, Sheila M, Riazalhosseini, Yasser, Richardson, Andrea L, Richter, Julia, Ringel, Matthew, Ringnér, Markus, Rino, Yasushi, Rippe, Karsten, Roach, Jeffrey, Roberts, Lewis R, Roberts, Nicola D, Roberts, Steven A, Robertson, A Gordon, Robertson, Alan J, Rodriguez, Javier Bartolomé, Rodriguez-Martin, Bernardo, Rodríguez-González, F Germán, Roehrl, Michael HA, Rohde, Marius, Rokutan, Hirofumi, Romieu, Gilles, Rooman, Ilse, Roques, Tom, Rosebrock, Daniel, Rosenberg, Mara, Rosenstiel, Philip C, Rosenwald, Andreas, Rowe, Edward W, Royo, Romina, Rozen, Steven G, Rubanova, Yulia, Rudneva, Vasilisa A, Rusev, Borislav C, Ruzzenente, Andrea, Rätsch, Gunnar, Sabarinathan, Radhakrishnan, Sabelnykova, Veronica Y, Sadeghi, Sara, Saini, Natalie, Saito-Adachi, Mihoko, Salcedo, Adriana, Salgado, Roberto, Sallari, Richard, Saller, Charles, Salvia, Roberto, Sam, Michelle, Samra, Jaswinder S, Sanchez-Vega, Francisco, Sanders, Grant, Sarin, Rajiv, Sarrafi, Iman, Sasaki-Oku, Aya, Sauer, Torill, Sauter, Guido, Saw, Robyn PM, Scardoni, Maria, Scarlett, Christopher J, Scarpa, Aldo, Scelo, Ghislaine, Schadendorf, Dirk, Schein, Jacqueline E, Schilhabel, Markus B, Schlesner, Matthias, Schlomm, Thorsten, Schmidt, Heather K, Schramm, Sarah-Jane, Schreiber, Stefan, Schultz, Nikolaus, Schwarz, Roland F, Scolyer, Richard A, Scott, David, Scully, Ralph, Seethala, Raja, Segre, Ayellet V, Selander, Iris, Semple, Colin A, Senbabaoglu, Yasin, Sengupta, Subhajit, Sereni, Elisabetta, Serra, Stefano, Sgroi, Dennis C, Shah, Nimish C, Shahabi, Sagedeh, Shang, Catherine A, Shang, Ping, Shelton, Troy, Shen, Hui, Shepherd, Rebecca, Shi, Ruian, Shi, Yan, Shiah, Yu-Jia, Shibata, Tatsuhiro, Shih, Juliann, Shimizu, Eigo, Shimizu, Kiyo, Shin, Seung Jun, Shiraishi, Yuichi, Shmaya, Tal, Shmulevich, Ilya, Shorser, Solomon I, Short, Charles, Shringarpure, Suyash S, Shriver, Craig, Siebert, Reiner, Sieuwerts, Anieta M, Signoretti, Sabina, Sikora, Katarzyna O, Simbolo, Michele, Simon, Ronald, Simons, Janae V, Simpson, Jared T, Simpson, Peter T, Singer, Samuel, Sipahimalani, Payal, Skelly, Tara J, Smid, Marcel, Smith, Jaclyn, Smith-McCune, Karen, Socci, Nicholas D, Sofia, Heidi J, Soloway, Matthew G, Song, Lei, Sood, Anil K, Sothi, Sharmila, Sotiriou, Christos, Soulette, Cameron M, Span, Paul N, Spellman, Paul T, Sperandio, Nicola, Spillane, Andrew J, Spiro, Oliver, Spring, Jonathan, Staaf, Johan, Stadler, Peter F, Staib, Peter, Stark, Stefan G, Stebbings, Lucy, Stefánsson, Ólafur Andri, Stegle, Oliver, Stenhouse, Alasdair, Stewart, Chip, Stilgenbauer, Stephan, Stobbe, Miranda D, Stratton, Michael R, Stretch, Jonathan R, Struck, Adam J, Stunnenberg, Henk G, Su, Hong, Su, Xiaoping, Sun, Ren X, Sungalee, Stephanie, Susak, Hana, Suzuki, Akihiro, Sweep, Fred, Szczepanowski, Monika, Sültmann, Holger, Yugawa, Takashi, Tam, Angela, Tan, Benita Kiat Tee, Tan, Donghui, Tan, Patrick, Tanaka, Hiroko, Taniguchi, Hirokazu, Tanskanen, Tomas J, Tarabichi, Maxime, Tarnuzzer, Roy, Tarpey, Patrick, Taschuk, Morgan L, Tatsuno, Kenji, Tavaré, Simon, Taylor, Darrin F, Taylor-Weiner, Amaro, Teague, Jon W, Teh, Bin Tean, Tembe, Varsha, Temes, Javier, Thai, Kevin, Thayer, Sarah P, Thiessen, Nina, Thomas, Gilles, Thomas, Sarah, Thompson, Alan, Thompson, Alastair M, Thompson, John FF, Thompson, R Houston, Thorne, Heather, Thorne, Leigh B, Thorogood, Adrian, Tijanic, Nebojsa, Timms, Lee E, Tirabosco, Roberto, Tojo, Marta, Tommasi, Stefania, Toon, Christopher W, Toprak, Umut H, Torrents, David, Tortora, Giampaolo, Tost, Jörg, Totoki, Yasushi, Townend, David, Traficante, Nadia, Treilleux, Isabelle, Trotta, Jean-Rémi, Trümper, Lorenz HP, Tsao, Ming, MC Tubio, Jose, Tucker, Olga, Turkington, Richard, Turner, Daniel J, Tutt, Andrew, Ueno, Masaki, Ueno, Naoto T, Umbricht, Christopher, Underwood, Timothy J, Urban, Lara, Urushidate, Tomoko, Ushiku, Tetsuo, Van Den Berg, David J, Van Laere, Steven, Van Loo, Peter, Van Meir, Erwin G, Van den Eynden, Gert G, Van der Kwast, Theodorus, Vasudev, Naveen, Vedururu, Ravikiran, Veluvolu, Umadevi, Vembu, Shankar, Vermeulen, Peter, Verrill, Clare, Viari, Alain, Vicente, David, Vicentini, Caterina, VijayRaghavan, K, Viksna, Juris, Vilain, Ricardo E, Villasante, Izar, 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Human Biology & Physiology ,Ecology,Evolution & Ethology ,Tumour Biology ,Genetics & Genomics ,Structural Biology & Biophysics ,Computational & Systems Biology - Abstract
The catalog of cancer driver mutations in protein-coding genes has greatly expanded in the past decade. However, non-coding cancer driver mutations are less well-characterized and only a handful of recurrent non-coding mutations, most notably TERT promoter mutations, have been reported. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancer across 38 tumor types, we perform multi-faceted pathway and network analyses of non-coding mutations across 2583 whole cancer genomes from 27 tumor types compiled by the ICGC/TCGA PCAWG project that was motivated by the success of pathway and network analyses in prioritizing rare mutations in protein-coding genes. While few non-coding genomic elements are recurrently mutated in this cohort, we identify 93 genes harboring non-coding mutations that cluster into several modules of interacting proteins. Among these are promoter mutations associated with reduced mRNA expression in TP53, TLE4, and TCF4. We find that biological processes had variable proportions of coding and non-coding mutations, with chromatin remodeling and proliferation pathways altered primarily by coding mutations, while developmental pathways, including Wnt and Notch, altered by both coding and non-coding mutations. RNA splicing is primarily altered by non-coding mutations in this cohort, and samples containing non-coding mutations in well-known RNA splicing factors exhibit similar gene expression signatures as samples with coding mutations in these genes. These analyses contribute a new repertoire of possible cancer genes and mechanisms that are altered by non-coding mutations and offer insights into additional cancer vulnerabilities that can be investigated for potential therapeutic treatments.
- Published
- 2023
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46. Divergent mutational processes distinguish hypoxic and normoxic tumours
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Human Biology & Physiology ,Ecology,Evolution & Ethology ,Tumour Biology ,Genetics & Genomics ,Structural Biology & Biophysics ,Computational & Systems Biology - Abstract
Many primary tumours have low levels of molecular oxygen (hypoxia), and hypoxic tumours respond poorly to therapy. Pan-cancer molecular hallmarks of tumour hypoxia remain poorly understood, with limited comprehension of its associations with specific mutational processes, non-coding driver genes and evolutionary features. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancers across 38 tumour types, we quantify hypoxia in 1188 tumours spanning 27 cancer types. Elevated hypoxia associates with increased mutational load across cancer types, irrespective of underlying mutational class. The proportion of mutations attributed to several mutational signatures of unknown aetiology directly associates with the level of hypoxia, suggesting underlying mutational processes for these signatures. At the gene level, driver mutations in TP53, MYC and PTEN are enriched in hypoxic tumours, and mutations in PTEN interact with hypoxia to direct tumour evolutionary trajectories. Overall, hypoxia plays a critical role in shaping the genomic and evolutionary landscapes of cancer.
- Published
- 2023
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47. Genomic footprints of activated telomere maintenance mechanisms in cancer
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Haiyan Irene, Li, Jun, Li, Lin, Li, Shantao, Li, Siliang, Li, Xiaobo, Li, Xiaotong, Li, Xinyue, Liang, Han, Liang, Sheng-Ben, Lichter, Peter, Lin, Pei, Lin, Ziao, Linehan, WM, Lingjærde, Ole Christian, Liu, Dongbing, Liu, Eric Minwei, Liu, Fei-Fei Fei, Liu, Fenglin, Liu, Jia, Liu, Xingmin, Livingstone, Julie, Livitz, Dimitri, Livni, Naomi, Lochovsky, Lucas, Loeffler, Markus, Long, Georgina V, Lopez-Guillermo, Armando, Lou, Shaoke, Louis, David N, Lovat, Laurence B, Lu, Yiling, Lu, Yong-Jie, Lu, Youyong, Luchini, Claudio, Lungu, Ilinca, Luo, Xuemei, Luxton, Hayley J, Lype, Lisa, López, Cristina, López-Otín, Carlos, Z, Eric, Ma, Yussanne, MacGrogan, Gaetan, MacRae, Shona, Madsen, Tobias, Maejima, Kazuhiro, Mafficini, Andrea, Maglinte, Dennis T, Maitra, Arindam, Majumder, Partha P, Malcovati, Luca, Malikic, Salem, Malleo, Giuseppe, Mann, Graham J, Mantovani-Löffler, Luisa, Marchal, Kathleen, Marchegiani, Giovanni, Mardis, Elaine R, Margolin, Adam A, Marin, Maximillian G, Markowski, Julia, Marks, Jeffrey, Marques-Bonet, Tomas, Marra, Marco A, Marsden, Luke, Martens, John WM, Martin, Sancha, Martin-Subero, Jose I, Maruvka, Yosef E, Mashl, R Jay, Massie, Charlie E, Matthew, Thomas J, Matthews, Lucy, Mayer, Erik, Mayes, Simon, Mayo, Michael, Mbabaali, Faridah, McCune, Karen, McDermott, Ultan, McGillivray, Patrick D, McLellan, Michael D, McPherson, John D, McPherson, John R, McPherson, Treasa A, Meier, Samuel R, Meng, Alice, Meng, Shaowu, Menzies, Andrew, Merrett, Neil D, Merson, Sue, Meyerson, William, Mieczkowski, Piotr A, Mihaiescu, George L, Mijalkovic, Sanja, Mikkelsen, Tom, Milella, Michele, Mileshkin, Linda, Miller, Christopher A, Miller, David K, Miller, Jessica K, Mills, Gordon B, Milovanovic, Ana, Minner, Sarah, Miotto, Marco, Arnau, Gisela Mir, Mirabello, Lisa, Mitchell, Chris, Mitchell, Thomas J, Miyoshi, Naoki, Mizuno, Shinichi, Molnár-Gábor, Fruzsina, Moore, Malcolm J, Moore, Richard A, Morganella, Sandro, Morris, Quaid D, Morrison, Carl, Mose, Lisle E, Moser, 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Okusaka, Takuji, Omberg, Larsson, Ong, Choon Kiat, Ott, German, Ouellette, BF Francis, P’ng, Christine, Paczkowska, Marta, Paiella, Salvatore, Pairojkul, Chawalit, Pajic, Marina, Pan-Hammarström, Qiang, Papaemmanuil, Elli, Papatheodorou, Irene, Paramasivam, Nagarajan, Park, Ji Wan, Park, Joong-Won, Park, Keunchil, Park, Kiejung, Parker, Joel S, Parsons, Simon L, Pass, Harvey, Pasternack, Danielle, Pastore, Alessandro, Patch, Ann-Marie, Pauporté, Iris, Pea, Antonio, Pedamallu, Chandra Sekhar, Pedersen, Jakob Skou, Pederzoli, Paolo, Peifer, Martin, Pennell, Nathan A, Perou, Charles M, Perry, Marc D, Petersen, Gloria M, Peto, Myron, Petrelli, Nicholas, Petryszak, Robert, Pfister, Stefan M, Phillips, Mark, Pich, Oriol, Pickett, Hilda A, Pihl, Todd D, Pillay, Nischalan, Pinder, Sarah, Pinese, Mark, Pinho, Andreia V, Pitkänen, Esa, Pivot, Xavier, Piñeiro-Yáñez, Elena, Planko, Laura, Plass, Christoph, Polak, Paz, Pons, Tirso, Popescu, Irinel, Potapova, Olga, Prasad, Aparna, Preston, Shaun R, 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Paresh, Vázquez-García, Ignacio, Waddell, Nick M, Wadelius, Claes, Wadi, Lina, Wagener, Rabea, Wang, Jian, Wang, Jiayin, Wang, Linghua, Wang, Qi, Wang, Wenyi, Wang, Yumeng, Wang, Zhining, Waring, Paul M, Warnatz, Hans-Jörg, Warrell, Jonathan, Warren, Anne Y, Waszak, Sebastian M, Wedge, David C, Weichenhan, Dieter, Weinberger, Paul, Weinstein, John N, Weisenberger, Daniel J, Welch, Ian, Wendl, Michael C, Werner, Johannes, Whalley, Justin P, Wheeler, David A, Whitaker, Hayley C, Wigle, Dennis, Wilkerson, Matthew D, Williams, Ashley, Wilmott, James S, Wilson, Gavin W, Wilson, Julie M, Wilson, Richard K, Winterhoff, Boris, Wintersinger, Jeffrey A, Wiznerowicz, Maciej, Wolf, Stephan, Wong, Bernice H, Wong, Tina, Wong, Winghing, Woo, Youngchoon, Wood, Scott, Wouters, Bradly G, Wright, Adam J, Wright, Derek W, Wright, Mark H, Wu, Chin-Lee, Wu, Dai-Ying, Wu, Guanming, Wu, Jianmin, Wu, Kui, Wu, Yang, Wu, Zhenggang, Xi, Liu, Xia, Tian, Xiang, Qian, Xiao, Xiao, Xing, Rui, Xiong, Heng, Xu, Qinying, Xu, Yanxun, Xue, Hong, Yachida, Shinichi, Yakneen, Sergei, Yamaguchi, Rui, Yamaguchi, Takafumi N, Yamamoto, Masakazu, Yamamoto, Shogo, Yamaue, Hiroki, Yang, Fan, Yang, Huanming, Yang, Jean Y, Yang, Liming, Yang, Shanlin, Yang, Tsun-Po, Yang, Yang, Yaspo, Marie-Laure, Yates, Lucy, Yau, Christina, Ye, Chen, Ye, Kai, Yellapantula, Venkata D, Yoon, Christopher J, Yousif, Fouad, Yu, Jun, Yu, Kaixian, Yu, Willie, Yu, Yingyan, Yuan, Ke, Yuan, Yuan, Yuen, Denis, Yung, Christina K, Zaikova, Olga, Zapatka, Marc, Zenklusen, Jean C, Zenz, Thorsten, Zeps, Nikolajs, Zhang, Fan, Zhang, Hailei, Zhang, Hongwei, Zhang, Hongxin, Zhang, Jiashan, Zhang, Jing, Zhang, Junjun, Zhang, Xiuqing, Zhang, Xuanping, Zhang, Yan, Zhang, Zemin, Zhao, Zhongming, Zheng, Liangtao, Zheng, Xiuqing, Zhou, Wanding, Zhou, Yong, Zhu, Bin, Zhu, Hongtu, Zhu, Jingchun, Zhu, Shida, Zou, Lihua, Zou, Xueqing, deFazio, Anna, van As, Nicholas, van Deurzen, Carolien HM, van de Vijver, Marc J, Veer, L van’t, and von Mering, Christian
- Subjects
Human Biology & Physiology ,Ecology,Evolution & Ethology ,Tumour Biology ,Genetics & Genomics ,Structural Biology & Biophysics ,Computational & Systems Biology - Abstract
Cancers require telomere maintenance mechanisms for unlimited replicative potential. They achieve this through TERT activation or alternative telomere lengthening associated with ATRX or DAXX loss. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, we dissect whole-genome sequencing data of over 2500 matched tumor-control samples from 36 different tumor types aggregated within the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium to characterize the genomic footprints of these mechanisms. While the telomere content of tumors with ATRX or DAXX mutations (ATRX/DAXXtrunc) is increased, tumors with TERT modifications show a moderate decrease of telomere content. One quarter of all tumor samples contain somatic integrations of telomeric sequences into non-telomeric DNA. This fraction is increased to 80% prevalence in ATRX/DAXXtrunc tumors, which carry an aberrant telomere variant repeat (TVR) distribution as another genomic marker. The latter feature includes enrichment or depletion of the previously undescribed singleton TVRs TTCGGG and TTTGGG, respectively. Our systematic analysis provides new insight into the recurrent genomic alterations associated with telomere maintenance mechanisms in cancer.
- Published
- 2023
- Full Text
- View/download PDF
48. Synthetic lethality between CCNE1 amplification and loss of BRCA1
- Author
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Australian Ovarian Cancer Study Group, Etemadmoghadam, Dariush, Weir, Barbara A., Au-Yeung, George, Alsop, Kathryn, Mitchell, Gillian, George, Joshy, Davis, Sally, D'Andrea, Alan D., Simpson, Kaylene, Hahn, William C., and Bowtell, David D. L.
- Published
- 2013
49. Whole–genome characterization of chemoresistant ovarian cancer
- Author
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Patch, Ann-Marie, Christie, Elizabeth L., Etemadmoghadam, Dariush, Garsed, Dale W., George, Joshy, Fereday, Sian, Nones, Katia, Cowin, Prue, Alsop, Kathryn, Bailey, Peter J., Kassahn, Karin S., Newell, Felicity, Quinn, Michael C. J., Kazakoff, Stephen, Quek, Kelly, Wilhelm-Benartzi, Charlotte, Curry, Ed, Leong, Huei San, Hamilton, Anne, Mileshkin, Linda, Au-Yeung, George, Kennedy, Catherine, Hung, Jillian, Chiew, Yoke-Eng, Harnett, Paul, Friedlander, Michael, Quinn, Michael, Pyman, Jan, Cordner, Stephen, O’Brien, Patricia, Leditschke, Jodie, Young, Greg, Strachan, Kate, Waring, Paul, Azar, Walid, Mitchell, Chris, Traficante, Nadia, Hendley, Joy, Thorne, Heather, Shackleton, Mark, Miller, David K., Arnau, Gisela Mir, Tothill, Richard W., Holloway, Timothy P., Semple, Timothy, Harliwong, Ivon, Nourse, Craig, Nourbakhsh, Ehsan, Manning, Suzanne, Idrisoglu, Senel, Bruxner, Timothy J. C., Christ, Angelika N., Poudel, Barsha, Holmes, Oliver, Anderson, Matthew, Leonard, Conrad, Lonie, Andrew, Hall, Nathan, Wood, Scott, Taylor, Darrin F., Xu, Qinying, Fink, J. Lynn, Waddell, Nick, Drapkin, Ronny, Stronach, Euan, Gabra, Hani, Brown, Robert, Jewell, Andrea, Nagaraj, Shivashankar H., Markham, Emma, Wilson, Peter J., Ellul, Jason, McNally, Orla, Doyle, Maria A., Vedururu, Ravikiran, Stewart, Collin, Lengyel, Ernst, Pearson, John V., Waddell, Nicola, deFazio, Anna, Grimmond, Sean M., and Bowtell, David D. L.
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- 2015
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50. SIK2 Is a Centrosome Kinase Required for Bipolar Mitotic Spindle Formation that Provides a Potential Target for Therapy in Ovarian Cancer
- Author
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Ahmed, Ahmed Ashour, Lu, Zhen, Jennings, Nicholas B., Etemadmoghadam, Dariush, Capalbo, Luisa, Jacamo, Rodrigo O., Barbosa-Morais, Nuno, Le, Xiao-Feng, Vivas-Mejia, Pablo, Lopez-Berestein, Gabriel, Grandjean, Geoffrey, Bartholomeusz, Geoffrey, Liao, Warren, Andreeff, Michael, Bowtell, David, Glover, David M., Sood, Anil K., and Bast, Robert C., Jr.
- Published
- 2010
- Full Text
- View/download PDF
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