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2020 Journal Article Comprehensive molecular characterization of mitochondrial genomes in human cancersYuan, Yuan, Ju, Young Seok, Kim, Youngwook, Li, Jun, Wang, Yumeng, Yoon, Christopher J., Yang, Yang, Martincorena, Inigo, Creighton, Chad J., Weinstein, John N., Xu, Yanxun, Han, Leng, Kim, Hyung-Lae, Nakagawa, Hidewaki, Park, Keunchil, Campbell, Peter J., Liang, Han, 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 ... von Mering, Christian (2020). Comprehensive molecular characterization of mitochondrial genomes in human cancers. Nature Genetics, 52 (3), 342-352. doi: 10.1038/s41588-019-0557-x |
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2019 Journal Article Whole-genome landscape of mucosal melanoma reveals diverse drivers and therapeutic targetsNewell, Felicity, Kong, Yan, Wilmott, James S., Johansson, Peter A., Ferguson, Peter M., Cui, Chuanliang, Li, Zhongwu, Kazakoff, Stephen H., Burke, Hazel, Dodds, Tristan J., Patch, Ann-Marie, Nones, Katia, Tembe, Varsha, Shang, Ping, van der Weyden, Louise, Wong, Kim, Holmes, Oliver, Lo, Serigne, Leonard, Conrad, Wood, Scott, Xu, Qinying, Rawson, Robert V., Mukhopadhyay, Pamela, Dummer, Reinhard, Levesque, Mitchell P., Jönsson, Göran, Wang, Xuan, Yeh, Iwei, Wu, Hong ... Scolyer, Richard A. (2019). Whole-genome landscape of mucosal melanoma reveals diverse drivers and therapeutic targets. Nature Communications, 10 (1) 3163. doi: 10.1038/s41467-019-11107-x |
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2019 Journal Article Mechanisms of genomic instability in breast cancerDuijf, Pascal H.G., Nanayakkara, Devathri, Nones, K., Srihari, Sriganesh, Kalimutho, Murugan and Khanna, Kum Kum (2019). Mechanisms of genomic instability in breast cancer. Trends in Molecular Medicine, 25 (7), 595-611. doi: 10.1016/j.molmed.2019.04.004 |
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2019 Journal Article Whole-genome sequencing reveals clinically relevant insights into the aetiology of familial breast cancersNones, K., Johnson, J., Newell, F., Patch, A. M., Thorne, H., Kazakoff, S. H., de Luca, X. M., Parsons, M. T., Ferguson, K., Reid, L. E., McCart Reed, A. E., Srihari, S., Lakis, V., Davidson, A. L., Mukhopadhyay, P., Holmes, O., Xu, Q., Wood, S., Leonard, C., The Kathleen Cuningham Foundation Consortium for Research into Familial Aspects of Breast Cancer (kConFab), The Australian Breast Cancer Tissue Bank (ABCTB), The Brisbane Breast Bank (BBB), Beesley, J., Harris, J. M., Barnes, D., Degasperi, A., Ragan, M. A., Spurdle, A. B., Khanna, K. K. ... Simpson, P. T. (2019). Whole-genome sequencing reveals clinically relevant insights into the aetiology of familial breast cancers. Annals of Oncology, 30 (7) mdz132, 1071-1079. doi: 10.1093/annonc/mdz132 |
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2019 Journal Article Integrative genome-scale DNA methylation analysis of a large and unselected cohort reveals five distinct subtypes of colorectal adenocarcinomasFennell, Lochlan, Dumenil, Troy, Wockner, Leesa, Hartel, Gunter, Nones, Katia, Bond, Catherine, Borowsky, Jennifer, Liu, Cheng, McKeone, Diane, Bowdler, Lisa, Montgomery, Grant, Klein, Kerenaftali, Hoffmann, Isabell, Patch, Ann-Marie, Kazakoff, Stephen, Pearson, John, Waddell, Nicola, Wirapati, Pratyaksha, Lochhead, Paul, Imamura, Yu, Ogino, Shuji, Shao, Renfu, Tejpar, Sabine, Leggett, Barbara and Whitehall, Vicki (2019). Integrative genome-scale DNA methylation analysis of a large and unselected cohort reveals five distinct subtypes of colorectal adenocarcinomas. Cellular and Molecular Gastroenterology and Hepatology, 8 (2), 269-290. doi: 10.1016/j.jcmgh.2019.04.002 |
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2019 Journal Article Patterns of genomic instability in breast cancerKalimutho, Murugan, Nones, Katia, Srihari, Sriganesh, Duijf, Pascal H.G., Waddell, Nicola and Khanna, Kum Kum (2019). Patterns of genomic instability in breast cancer. Trends in Pharmacological Sciences, 40 (3), 198-211. doi: 10.1016/j.tips.2019.01.005 |
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2019 Journal Article Whole genome sequencing of melanomas in adolescent and young adults reveals distinct mutation landscapes and the potential role of germline variants in disease susceptibilityWilmott, James S., Johansson, Peter A., Newell, Felicity, Waddell, Nicola, Ferguson, Peter, Quek, Camelia, Patch, Ann-Marie, Nones, Katia, Shang, Ping, Pritchard, Antonia L., Kazakoff, Stephen, Holmes, Oliver, Leonard, Conrad, Wood, Scott, Xu, Qinying, Saw, Robyn P. M., Spillane, Andrew J., Stretch, Jonathan R., Shannon, Kerwin F., Kefford, Richard F., Menzies, Alexander M., Long, Georgina V., Thompson, John F., Pearson, John V., Mann, Graham J., Hayward, Nicholas K. and Scolyer, Richard A. (2019). Whole genome sequencing of melanomas in adolescent and young adults reveals distinct mutation landscapes and the potential role of germline variants in disease susceptibility. International Journal of Cancer, 144 (5), 1049-1060. doi: 10.1002/ijc.31791 |
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2019 Journal Article Diff-Quik cytology smears from endobronchial ultrasound transbronchial needle aspiration lymph node specimens as a source of DNA for next-generation sequencing instead of cell blocksFielding, David, Dalley, Andrew J., Bashirzadeh, Farzad, Singh, Mahendra, Nandakumar, Lakshmy, McCart Reed, Amy E., Black, Debra, Kazakoff, Stephen, Pearson, John V., Nones, Katia, Waddell, Nicola, Lakhani, Sunil R. and Simpson, Peter T. (2019). Diff-Quik cytology smears from endobronchial ultrasound transbronchial needle aspiration lymph node specimens as a source of DNA for next-generation sequencing instead of cell blocks. Respiration, 97 (6), 1-14. doi: 10.1159/000495661 |
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2019 Journal Article Complex structural rearrangements are present in high-grade dysplastic Barrett's oesophagus samplesNewell, Felicity, Patel, Kalpana, Gartside, Michael, Krause, Lutz, Brosda, Sandra, Aoude, Lauren G., Loffler, Kelly A., Bonazzi, Vanessa F., Patch, Ann-Marie, Kazakoff, Stephen H., Holmes, Oliver, Xu, Qinying, Wood, Scott, Leonard, Conrad, Lampe, Guy, Lord, Reginald V., Whiteman, David C., Pearson, John V., Nones, Katia, Waddell, Nicola and Barbour, Andrew P. (2019). Complex structural rearrangements are present in high-grade dysplastic Barrett's oesophagus samples. BMC Medical Genomics, 12 (1) 31, 31. doi: 10.1186/s12920-019-0476-9 |
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2019 Journal Article Intratumoural heterogeneity underlies distinct therapy responses and treatment resistance in glioblastomaAkgül, Seçkin, Patch, Ann-Marie, D’souza, Rochelle C. J., Mukhopadhyay, Pamela, Nones, Katia, Kempe, Sarah, Kazakoff, Stephen H., Jeffree, Rosalind L., Stringer, Brett W., Pearson, John V., Waddell, Nicola and Day, Bryan W. (2019). Intratumoural heterogeneity underlies distinct therapy responses and treatment resistance in glioblastoma. Cancers, 11 (2) 190, 190. doi: 10.3390/cancers11020190 |
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2019 Journal Article Phenotypic and molecular dissection of Metaplastic Breast Cancer and the prognostic implicationsMcCart Reed, Amy Ellen, Kalaw, Emarene, Nones, Katia, Bettington, Mark, Lim, Malcolm, Bennett, James, Johnstone, Kate, Kutasovic, Jamie Rose, Saunus, Jodi Marie, Kazakoff, Stephen, Xu, Qinying, Wood, Scott, Holmes, Oliver, Leonard, Conrad, Reid, Lynne Estelle, Black, Debra, Niland, Colleen, Ferguson, Kaltin, Gresshoff, Irma, Raghavendra, Ashwini, Harvey, Kate, Cooper, Caroline, Liu, Cheng, Kalinowski, Lauren, Reid, Andrew Scott, Davidson, Morgan, Pearson, John V, Pathmanathan, Nirmala, Tse, Gary ... Lakhani, Sunil R. (2019). Phenotypic and molecular dissection of Metaplastic Breast Cancer and the prognostic implications. Journal of Pathology, 247 (2), 214-227. doi: 10.1002/path.5184 |
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2018 Journal Article CEP55 is a determinant of cell fate during perturbed mitosis in breast cancerKalimutho, Murugan, Sinha, Debottam, Jeffery, Jessie, Nones, Katia, Srihari, Sriganesh, Fernando, Winnie C., Duijf, Pascal H. G., Vennin, Claire, Raninga, Prahlad, Nanayakkara, Devathri, Mittal, Deepak, Saunus, Jodi M., Lakhani, Sunil R., López, J Alejandro, Spring, Kevin J., Timpson, Paul, Gabrielli, Brian, Waddell, Nicola and Khanna, Kum Kum (2018). CEP55 is a determinant of cell fate during perturbed mitosis in breast cancer. EMBO Molecular Medicine, 10 (9) e8566. doi: 10.15252/emmm.201708566 |
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2018 Journal Article Telomere sequence content can be used to determine ALT activity in tumoursLee, Michael, Teber, Erdahl T, Holmes, Oliver, Nones, Katia, Patch, Ann-Marie, Dagg, Rebecca A, Lau, Loretta M S, Lee, Joyce H, Napier, Christine E, Arthur, Jonathan W, Grimmond, Sean M, Hayward, Nicholas K, Johansson, Peter A, Mann, Graham J, Scolyer, Richard A, Wilmott, James S, Reddel, Roger R, Pearson, John V, Waddell, Nicola and Pickett, Hilda A (2018). Telomere sequence content can be used to determine ALT activity in tumours. Nucleic Acids Research, 46 (10), 4903-4918. doi: 10.1093/nar/gky297 |
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2018 Journal Article Early changes in CD4+ T-cell activation following blood-stage Plasmodium falciparum infectionEdwards, Chelsea L., Ng, Susanna S., Corvino, Dillon, Montes de Oca, Marcela, Rivera, Fabian de Labastida, Nones, Katia, Lakis, Vanessa, Waddell, Nicola, Amante, Fiona H., McCarthy, James S. and Engwerda, Christian R. (2018). Early changes in CD4+ T-cell activation following blood-stage Plasmodium falciparum infection. The Journal of Infectious Diseases, 218 (7), 1119-1129. doi: 10.1093/infdis/jiy281 |
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2018 Journal Article Mixed ductal-lobular carcinomas: evidence for progression from ductal to lobular morphologyMcCart Reed, Amy E., Kutasovic, Jamie R., Nones, Katia, Saunus, Jodi M., Da Silva, Leonard, Newell, Felicity, Kazakoff, Stephen, Melville, Lewis, Jayanthan, Janani, Vargas, Ana Cristina, Reid, Lynne E., Beesley, Jonathan, Chen, Xiao Qing, Patch, Anne Marie, David Clouston, D., Porter, Alan, Evans, Elizabeth, Pearson, John V., Chenevix-Trench, Georgia, Cummings, Margaret C., Waddell, Nic, Lakhani, Sunil R. and Simpson, Peter T. (2018). Mixed ductal-lobular carcinomas: evidence for progression from ductal to lobular morphology. The Journal of Pathology, 244 (4), 460-468. doi: 10.1002/path.5040 |
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2018 Journal Article Characterization of a novel breast cancer cell line derived from a metastatic bone lesion of a breast cancer patientJohnson, Julie, Bessette, Darrell C., Saunus, Jodi M., Smart, Chanel E., Song, Sarah, Johnston, Rebecca L., Cocciardi, Sibylle, Rozali, Esdy N., Johnstone, Cameron N., Vargas, Ana Christina, Kazakoff, Stephen H., BioBank, Victorian Cancer, Khanna, Kum Kum, Lakhani, Sunil R., Chenevix-Trench, Georgia, Simpson, Peter T., Nones, Katia, Waddell, Nicola and Al-Ejeh, Fares (2018). Characterization of a novel breast cancer cell line derived from a metastatic bone lesion of a breast cancer patient. Breast Cancer Research and Treatment, 170 (1), 179-188. doi: 10.1007/s10549-018-4719-9 |
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2018 Journal Article Germline and somatic variant identification using BGISEQ-500 and HiSeq X Ten whole genome sequencingPatch, Ann-Marie, Nones, Katia, Kazakoff, Stephen H., Newell, Felicity, Wood, Scott, Leonard, Conrad, Holmes, Oliver, Xu, Qinying, Addala, Venkateswar, Creaney, Jenette, Robinson, Bruce W., Fu, Shujin, Geng, Chunyu, Li, Tong, Zhang, Wenwei, Liang, Xinming, Rao, Junhua, Wang, Jiahao, Tian, Mingyu, Zhao, Yonggang, Teng, Fei, Gou, Honglan, Yang, Bicheng, Jiang, Hui, Mu, Feng, Pearson, John V. and Waddell, Nicola (2018). Germline and somatic variant identification using BGISEQ-500 and HiSeq X Ten whole genome sequencing. PloS One, 13 (1) e0190264, e0190264. doi: 10.1371/journal.pone.0190264 |
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2018 Journal Article Copy number profiles of paired primary and metastatic colorectal cancersKawamata, Futoshi, Patch, Ann-Marie, Nones, Katia, Bond, Catherine, McKeone, Diane, Pearson, Sally-Ann, Homma, Shigenori, Liu, Cheng, Fennell, Lochlan, Dumenil, Troy, Hartel, Gunter, Kobayasi, Nozomi, Yokoo, Hideki, Fukai, Moto, Nishihara, Hiroshi, Kamiyama, Toshiya, Burge, Matthew E., Karapetis, Christos S., Taketomi, Akinobu, Leggett, Barbara, Waddell, Nicola and Whitehall, Vicki (2018). Copy number profiles of paired primary and metastatic colorectal cancers. Oncotarget, 9 (3), 3394-3405. doi: 10.18632/oncotarget.23277 |
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2017 Journal Article Identification of unique neoantigen qualities in long-term survivors of pancreatic cancerBalachandran, Vinod P., Łuksza, Marta, Zhao, Julia N., Makarov, Vladimir, Moral, John Alec, Remark, Romain, Herbst, Brian, Askan, Gokce, Bhanot, Umesh, Senbabaoglu, Yasin, Wells, Daniel K., Cary, Charles Ian Ormsby, Grbovic-Huezo, Olivera, Attiyeh, Marc, Medina, Benjamin, Zhang, Jennifer, Loo, Jennifer, Saglimbeni, Joseph, Abu-Akeel, Mohsen, Zappasodi, Roberta, Riaz, Nadeem, Smoragiewicz, Martin, Larkin Kelley, Z., Basturk, Olca, Gönen, Mithat, Levine, Arnold J., Allen, Peter J., Fearon, Douglas T., Merad, Miriam ... Bassi, Claudio (2017). Identification of unique neoantigen qualities in long-term survivors of pancreatic cancer. Nature, 551 (7681), 512-516. doi: 10.1038/nature24462 |
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2017 Journal Article Corrigendum: Whole-genome landscape of pancreatic neuroendocrine tumoursScarpa, Aldo, Chang, David K., Nones, Katia, Corbo, Vincenzo, Patch, Ann-Marie, Bailey, Peter, Lawlor, Rita T., Johns, Amber L., Miller, David K., Mafficini, Andrea, Rusev, Borislav, Scardoni, Maria, Antonello, Davide, Barbi, Stefano, Sikora, Katarzyna O., Cingarlini, Sara, Vicentini, Caterina, McKay, Skye, Quinn, Michael C J, Bruxner, Timothy J C, Christ, Angelika N., Harliwong, Ivon, Idrisoglu, Senel, McLean, Suzanne, Nourse, Craig, Nourbakhsh, Ehsan, Wilson, Peter J., Anderson, Matthew J., Fink, J Lynn ... Grimmond, Sean M (2017). Corrigendum: Whole-genome landscape of pancreatic neuroendocrine tumours. Nature, 550 (7677), 548-548. doi: 10.1038/nature24026 |
