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2022 Journal Article qmotif: determination of telomere content from whole-genome sequence dataHolmes, Oliver, Nones, Katia, Tang, Yue Hang, Loffler, Kelly A., Lee, Michael, Patch, Ann-Marie, Dagg, Rebecca A., Lau, Loretta M. S., Leonard, Conrad, Wood, Scott, Xu, Qinying, Pickett, Hilda A., Reddel, Roger R., Barbour, Andrew P., Grimmond, Sean M., Waddell, Nicola and Pearson, John V. (2022). qmotif: determination of telomere content from whole-genome sequence data. Bioinformatics Advances, 2 (1) vbac005, 1-3. doi: 10.1093/bioadv/vbac005 |
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2022 Journal Article Whole genome deep sequencing analysis of cell-free DNA in samples with low tumour contentGanesamoorthy, Devika, Robertson, Alan James, Chen, Wenhan, Hall, Michael B., Cao, Minh Duc, Ferguson, Kaltin, Lakhani, Sunil R., Nones, Katia, Simpson, Peter T. and Coin, Lachlan J. M. (2022). Whole genome deep sequencing analysis of cell-free DNA in samples with low tumour content. BMC Cancer, 22 (1) 85, 85. doi: 10.1186/s12885-021-09160-1 |
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2022 Journal Article Multiomic profiling of checkpoint inhibitor-treated melanoma: Identifying predictors of response and resistance, and markers of biological discordanceNewell, Felicity, Pires da Silva, Ines, Johansson, Peter A., Menzies, Alexander M., Wilmott, James S., Addala, Venkateswar, Carlino, Matteo S., Rizos, Helen, Nones, Katia, Edwards, Jarem J., Lakis, Vanessa, Kazakoff, Stephen H., Mukhopadhyay, Pamela, Ferguson, Peter M., Leonard, Conrad, Koufariotis, Lambros T., Wood, Scott, Blank, Christian U., Thompson, John F., Spillane, Andrew J., Saw, Robyn P.M., Shannon, Kerwin F., Pearson, John V., Mann, Graham J., Hayward, Nicholas K., Scolyer, Richard A., Waddell, Nicola and Long, Georgina V. (2022). Multiomic profiling of checkpoint inhibitor-treated melanoma: Identifying predictors of response and resistance, and markers of biological discordance. Cancer Cell, 40 (1), 88-102.e7. doi: 10.1016/j.ccell.2021.11.012 |
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2022 Journal Article Patient-derived xenograft models capture genomic heterogeneity in endometrial cancerBonazzi, Vanessa F., Kondrashova, Olga, Smith, Deborah, Nones, Katia, Sengal, Asmerom T., Ju, Robert, Packer, Leisl M., Koufariotis, Lambros T., Kazakoff, Stephen H., Davidson, Aimee L., Ramarao-Milne, Priya, Lakis, Vanessa, Newell, Felicity, Rogers, Rebecca, Davies, Claire, Nicklin, James, Garrett, Andrea, Chetty, Naven, Perrin, Lewis, Pearson, John V., Patch, Ann-Marie, Waddell, Nicola and Pollock, Pamela M. (2022). Patient-derived xenograft models capture genomic heterogeneity in endometrial cancer. Genome Medicine, 14 (1) 3, 1-19. doi: 10.1186/s13073-021-00990-z |
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2022 Journal Article Genomic and molecular analyses identify molecular subtypes of pancreatic cancer recurrenceDreyer, Stephan B., Upstill-Goddard, Rosie, Legrini, Assya, Biankin, Andrew V., Allison, Sarah, Beraldi, Dario, Cameron, Euan, Chang, David K., Cooke, Susanna L., Cunningham, Richard, Dreyer, Stephan, Grimwood, Paul, Kelly, Shane, Marshall, John, McDade, Brian, Musgrove, Elizabeth A., Ramsay, Donna, Evers, Lisa, Rebus, Selma, Rahib, Lola, Serrels, Bryan, Jamieson, Nigel B., McKay, Colin J., Westwood, Paul, Williams, Nicola, Duthie, Fraser, Shen, William, Pea, Antonio, Johns, Amber L. ... Bassi, Claudio (2022). Genomic and molecular analyses identify molecular subtypes of pancreatic cancer recurrence. Gastroenterology, 162 (1), 320-324. doi: 10.1053/j.gastro.2021.09.022 |
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2021 Journal Article ROR1 and ROR2 expression in pancreatic cancerLiu, Dongli, Sharbeen, George, Phillips, Phoebe, Johns, Amber L., Gill, Anthony J., Chantrill, Lorraine A., Timpson, Paul, Chou, Angela, Pajic, Marina, Dwarte, Tanya, Herrmann, David, Vennin, Claire, Cox, Thomas R., Pereira, Brooke, Ritchie, Shona, Reed, Daniel A., Chambers, Cecilia R., Metcalf, Xanthe, Nobis, Max, Waddell, Nicola, Pearson, John V., Patch, Ann-Marie, Nones, Katia, Newell, Felicity, Mukhopadhyay, Pamela, Addala, Venkateswar, Kazakoff, Stephen, Holmes, Oliver, Leonard, Conrad ... Ford, Caroline E. (2021). ROR1 and ROR2 expression in pancreatic cancer. BMC Cancer, 21 (1) 1199. doi: 10.1186/s12885-021-08952-9 |
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2021 Journal Article DNA methylation patterns identify subgroups of pancreatic neuroendocrine tumors with clinical associationLakis, Vanessa, Lawlor, Rita T., Newell, Felicity, Patch, Ann-Marie, Mafficini, Andrea, Sadanandam, Anguraj, Koufariotis, Lambros T., Johnston, Rebecca L., Leonard, Conrad, Wood, Scott, Rusev, Borislav, Corbo, Vincenzo, Luchini, Claudio, Cingarlini, Sara, Landoni, Luca, Salvia, Roberto, Milella, Michele, Chang, David, Bailey, Peter, Jamieson, Nigel B., Duthie, Fraser, Gingras, Marie-Claude, Muzny, Donna M., Wheeler, David A., Gibbs, Richard A., Milione, Massimo, Chantrill, Lorraine A., Timpson, Paul, Chou, Angela ... Scarpa, Aldo (2021). DNA methylation patterns identify subgroups of pancreatic neuroendocrine tumors with clinical association. Communications Biology, 4 (1) 155, 1-11. doi: 10.1038/s42003-020-01469-0 |
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2021 Journal Article Acquired RAD51C promoter methylation loss causes parp inhibitor resistance in high-grade serous ovarian carcinomaNesic, Ksenija, Kondrashova, Olga, Hurley, Rachel M., McGehee, Cordelia D., Vandenberg, Cassandra J., Ho, Gwo-Yaw, Lieschke, Elizabeth, Dall, Genevieve, Bound, Nirashaa, Shield-Artin, Kristy, Radke, Marc, Musafer, Ashan, Chai, Zi Qing, Ghamsari, Mohammad Reza Eftekhariyan, Harrell, Maria I., Kee, Damien, Olesen, Inger, McNally, Orla, Traficante, Nadia, Study, Australian Ovarian Cancer, DeFazio, Anna, Bowtell, David D.L., Swisher, Elizabeth M., Weroha, S. John, Nones, Katia, Waddell, Nicola, Kaufmann, Scott H., Dobrovic, Alexander, Wakefield, Matthew J. and Scott, Clare L. (2021). Acquired RAD51C promoter methylation loss causes parp inhibitor resistance in high-grade serous ovarian carcinoma. Cancer Research, 81 (18), 4709-4722. doi: 10.1158/0008-5472.can-21-0774 |
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2021 Journal Article Correction: McCart Reed et al. The Genomic Landscape of Lobular Breast Cancer. Cancers 2021, 13, 1950McCart Reed, Amy E., Foong, Samuel, Kutasovic, Jamie R., Nones, Katia, Waddell, Nicola, Lakhani, Sunil R. and Simpson, Peter T. (2021). Correction: McCart Reed et al. The Genomic Landscape of Lobular Breast Cancer. Cancers 2021, 13, 1950. Cancers, 13 (16) 4010, 4010. doi: 10.3390/cancers13164010 |
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2021 Journal Article The genomic landscape of lobular breast cancerMcCart Reed, Amy E., Foong, Samuel, Kutasovic, Jamie R., Nones, Katia, Waddell, Nicola, Lakhani, Sunil R. and Simpson, Peter T. (2021). The genomic landscape of lobular breast cancer. Cancers, 13 (8) 1950, 1950. doi: 10.3390/cancers13081950 |
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2021 Journal Article Abstract PR007: Genomic characterization of endometrial cancer patient-derived xenografts reveals intratumor heterogeneityKondrashova, Olga, Bonazzi, Vanessa F., Smith, Deborah, Nones, Katia, Sengal, Asmerom, Ju, Robert, Packer, Leisl M., Koufariotis, Lambros T, Kazakoff, Stephen H., Davidson, Aimee L., Ramarao-Milne, Priya, Lakis, Vanessa, Newell, Felicity, Rogers, Rebecca, Davies, Claire, Chetty, Naven, Perrin, Lewis, Pearson, John, Patch, Ann-Marie, Garrett, Andrea, Waddell, Nicola, Pollock, Pamela and Nicklin, James (2021). Abstract PR007: Genomic characterization of endometrial cancer patient-derived xenografts reveals intratumor heterogeneity. Clinical Cancer Research, 27 (3_Supplement). doi: 10.1158/1557-3265.endomet20-pr007 |
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2021 Journal Article Verifying explainability of a deep learning tissue classifier trained on RNA-seq dataYap, Melvyn, Johnston, Rebecca L., Foley, Helena, MacDonald, Samual, Kondrashova, Olga, Tran, Khoa A., Nones, Katia, Koufariotis, Lambros T., Bean, Cameron, Pearson, John V., Trzaskowski, Maciej and Waddell, Nicola (2021). Verifying explainability of a deep learning tissue classifier trained on RNA-seq data. Scientific Reports, 11 (1) 2641. doi: 10.1038/s41598-021-81773-9 |
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2021 Journal Article Targeting DNA damage response and replication stress in pancreatic cancerDreyer, Stephan B., Upstill-Goddard, Rosie, Paulus-Hock, Viola, Paris, Clara, Lampraki, Eirini-Maria, Dray, Eloise, Serrels, Bryan, Caligiuri, Giuseppina, Rebus, Selma, Plenker, Dennis, Galluzzo, Zachary, Brunton, Holly, Cunningham, Richard, Tesson, Mathias, Nourse, Craig, Bailey, Ulla-Maja, Jones, Marc D., Moran-Jones, Kim, Wright, Derek W., Duthie, Fraser, Oien, Karin, Evers, Lisa, McKay, Colin J., McGregor, Grant A., Gulati, Aditi, Brough, Rachel, Bajrami, Ilirjana, Pettitt, Stephan, Dziubinski, Michele L. ... Sansom, Owen J. (2021). Targeting DNA damage response and replication stress in pancreatic cancer. Gastroenterology, 160 (1), 362-377.e13. doi: 10.1053/j.gastro.2020.09.043 |
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2020 Journal Article Inferring structural variant cancer cell fractionCmero, Marek, Yuan, Ke, Ong, Cheng Soon, Schröder, Jan, Adams, David J., Anur, Pavana, Beroukhim, Rameen, Boutros, Paul C., Bowtell, David D. L., Campbell, Peter J., Cao, Shaolong, Christie, Elizabeth L., Cun, Yupeng, Dawson, Kevin J., Demeulemeester, Jonas, Dentro, Stefan C., Deshwar, Amit G., Donmez, Nilgun, Drews, Ruben M., Eils, Roland, Fan, Yu, Fittall, Matthew W., Garsed, Dale W., Gerstung, Moritz, Getz, Gad, Gonzalez, Santiago, Ha, Gavin, Haase, Kerstin, Imielinski, Marcin ... von Mering, Christian (2020). Inferring structural variant cancer cell fraction. Nature Communications, 11 (1) 730. doi: 10.1038/s41467-020-14351-8 |
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2020 Journal Article Pathogenic germline variants are associated with poor survival in stage III/IV melanoma patientsAoude, Lauren G., Bonazzi, Vanessa F., Brosda, Sandra, Patel, Kalpana, Koufariotis, Lambros T., Oey, Harald, Nones, Katia, Wood, Scott, Pearson, John V., Lonie, James M., Arneil, Melissa, Atkinson, Victoria, Smithers, B. Mark, Waddell, Nicola and Barbour, Andrew P. (2020). Pathogenic germline variants are associated with poor survival in stage III/IV melanoma patients. Scientific Reports, 10 (1) 17687, 17687. doi: 10.1038/s41598-020-74956-3 |
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2020 Journal Article Whole-genome sequencing of acral melanoma reveals genomic complexity and diversityNewell, Felicity, Wilmott, James S., Johansson, Peter A., Nones, Katia, Addala, Venkateswar, Mukhopadhyay, Pamela, Broit, Natasa, Amato, Carol M., Van Gulick, Robert, Kazakoff, Stephen H., Patch, Ann-Marie, Koufariotis, Lambros T., Lakis, Vanessa, Leonard, Conrad, Wood, Scott, Holmes, Oliver, Xu, Qinying, Lewis, Karl, Medina, Theresa, Gonzalez, Rene, Saw, Robyn P. M., Spillane, Andrew J., Stretch, Jonathan R., Rawson, Robert V., Ferguson, Peter M., Dodds, Tristan J., Thompson, John F., Long, Georgina V., Levesque, Mitchell P. ... Hayward, Nicholas K. (2020). Whole-genome sequencing of acral melanoma reveals genomic complexity and diversity. Nature Communications, 11 (1) 5259, 5259. doi: 10.1038/s41467-020-18988-3 |
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2020 Journal Article The Impact of Next Generation Sequencing in Cancer ResearchNones, Katia and Patch, Ann-Marie (2020). The Impact of Next Generation Sequencing in Cancer Research. Cancers, 12 (10) 2928, 2928-4. doi: 10.3390/cancers12102928 |
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2020 Journal Article Using whole-genome sequencing data to derive the homologous recombination deficiency scoresde Luca, Xavier M., Newell, Felicity, Kazakoff, Stephen H., Hartel, Gunter, McCart Reed, Amy E., Holmes, Oliver, Xu, Qinying, Wood, Scott, Leonard, Conrad, Pearson, John V., Lakhani, Sunil R., Waddell, Nicola, Nones, Katia and Simpson, Peter T. (2020). Using whole-genome sequencing data to derive the homologous recombination deficiency scores. npj Breast Cancer, 6 (1) 33, 33. doi: 10.1038/s41523-020-0172-0 |
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2020 Journal Article Estimating the costs of genomic sequencing in cancer controlGordon, Louisa G., White, Nicole M., Elliott, Thomas M., Nones, Katia, Beckhouse, Anthony G., Rodriguez-Acevedo, Astrid J., Webb, Penelope M., Lee, Xing J., Graves, Nicholas and Schofield, Deborah J. (2020). Estimating the costs of genomic sequencing in cancer control. BMC Health Services Research, 20 (1) 492, 492. doi: 10.1186/s12913-020-05318-y |
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2020 Journal Article Genomic basis for RNA alterations in cancerCalabrese, Claudia, Davidson, Natalie R., Demircioğlu, Deniz, Fonseca, Nuno A., He, Yao, Kahles, André, Lehmann, Kjong-Van, Liu, Fenglin, Shiraishi, Yuichi, Soulette, Cameron M., Urban, Lara, Greger, Liliana, Li, Siliang, Liu, Dongbing, Perry, Marc D., Xiang, Qian, Zhang, Fan, Zhang, Junjun, Bailey, Peter, Erkek, Serap, Hoadley, Katherine A., Hou, Yong, Huska, Matthew R., Kilpinen, Helena, Korbel, Jan O., Marin, Maximillian G., Markowski, Julia, Nandi, Tannistha, Pan-Hammarström, Qiang ... von Mering, Christian (2020). Genomic basis for RNA alterations in cancer. Nature, 578 (7793), 129-136. doi: 10.1038/s41586-020-1970-0 |
