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2024 Journal Article Spatial intra-tumour heterogeneity and treatment-induced genomic evolution in oesophageal adenocarcinoma: implications for prognosis and therapyBrosda, Sandra, Aoude, Lauren G., Bonazzi, Vanessa F., Patel, Kalpana, Lonie, James M., Belle, Clemence J., Newell, Felicity, Koufariotis, Lambros T., Addala, Venkateswar, Naeini, Marjan M., Simes, John, Walpole, Euan T., Mai, Gang T., Watson, David I., Karapetis, Chris S., Gebski, Val, Barnes, Elizabeth H., Oostendorp, Martijn, Wilson, Kate, Ackland, Stephen P., Shannon, Jenny, Marx, Gavin, Burge, Matthew, Finch, Robert, Thomas, Janine, Varma, Suresh, Nott, Louise, Pearson, John V., Krause, Lutz ... AGITG DOCTOR Investigators (2024). Spatial intra-tumour heterogeneity and treatment-induced genomic evolution in oesophageal adenocarcinoma: implications for prognosis and therapy. Genome Medicine, 16 (1) 90, 90. doi: 10.1186/s13073-024-01362-z |
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2024 Journal Article Germline variants alter immune surveillanceWaddell, Nicola and Addala, Venkateswar (2024). Germline variants alter immune surveillance. Science, 384 (6699), 961-962. doi: 10.1126/science.adp7370 |
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2023 Journal Article Computational immunogenomic approaches to predict response to cancer immunotherapiesAddala, Venkateswar, Newell, Felicity, Pearson, John V., Redwood, Alec, Robinson, Bruce W., Creaney, Jenette and Waddell, Nicola (2023). Computational immunogenomic approaches to predict response to cancer immunotherapies. Nature Reviews Clinical Oncology, 21 (1), 28-46. doi: 10.1038/s41571-023-00830-6 |
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2023 Journal Article The oesophageal adenocarcinoma tumour immune microenvironment dictates outcomes with different modalities of neoadjuvant therapy – results from the AGITG DOCTOR trial and the cancer evolution biobankLonie, James M., Brosda, Sandra, Bonazzi, Vanessa F., Aoude, Lauren G., Patel, Kalpana, Brown, Ian, Sharma, Sowmya, Lampe, Guy, Addala, Venkateswar, Koufariotis, Lambros T., Wood, Scott, Waddell, Nicola, Dolcetti, Riccardo and Barbour, Andrew P. (2023). The oesophageal adenocarcinoma tumour immune microenvironment dictates outcomes with different modalities of neoadjuvant therapy – results from the AGITG DOCTOR trial and the cancer evolution biobank. Frontiers in Immunology, 14 1220129, 1-15. doi: 10.3389/fimmu.2023.1220129 |
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2023 Journal Article Performance of tumour microenvironment deconvolution methods in breast cancer using single-cell simulated bulk mixturesTran, Khoa A., Addala, Venkateswar, Johnston, Rebecca L., Lovell, David, Bradley, Andrew, Koufariotis, Lambros T., Wood, Scott, Wu, Sunny Z., Roden, Daniel, Al-Eryani, Ghamdan, Swarbrick, Alexander, Williams, Elizabeth D., Pearson, John V., Kondrashova, Olga and Waddell, Nicola (2023). Performance of tumour microenvironment deconvolution methods in breast cancer using single-cell simulated bulk mixtures. Nature Communications, 14 (1) 5758, 1-17. doi: 10.1038/s41467-023-41385-5 |
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2023 Journal Article A first-in-class pan-lysyl oxidase inhibitor impairs stromal remodeling and enhances gemcitabine response and survival in pancreatic cancerChitty, Jessica L., Yam, Michelle, Perryman, Lara, Parker, Amelia L., Skhinas, Joanna N., Setargew, Yordanos F. I., Mok, Ellie T. Y., Tran, Emmi, Grant, Rhiannon D., Latham, Sharissa L., Pereira, Brooke A., Ritchie, Shona C., Murphy, Kendelle J., Trpceski, Michael, Findlay, Alison D., Melenec, Pauline, Filipe, Elysse C., Nadalini, Audrey, Velayuthar, Sipiththa, Major, Gretel, Wyllie, Kaitlin, Papanicolaou, Michael, Ratnaseelan, Shivanjali, Phillips, Phoebe A., Sharbeen, George, Youkhana, Janet, Russo, Alice, Blackwell, Antonia, Hastings, Jordan F. ... Cox, Thomas R. (2023). A first-in-class pan-lysyl oxidase inhibitor impairs stromal remodeling and enhances gemcitabine response and survival in pancreatic cancer. Nature Cancer, 4 (9), 1326-1344. doi: 10.1038/s43018-023-00614-y |
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2023 Journal Article Efficient detection and monitoring of pediatric brain malignancies with liquid biopsy based on patient-specific somatic mutation screeningKojic, Marija, Maybury, Mellissa K., Waddell, Nicola, Koufariotis, Lambros T., Addala, Venkateswar, Millar, Amanda, Wood, Scott, Pearson, John V., Hansford, Jordan R., Hassall, Tim and Wainwright, Brandon J. (2023). Efficient detection and monitoring of pediatric brain malignancies with liquid biopsy based on patient-specific somatic mutation screening. Neuro-Oncology, 25 (8), 1507-1517. doi: 10.1093/neuonc/noad032 |
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2023 Journal Article Multi-omic features of oesophageal adenocarcinoma in patients treated with preoperative neoadjuvant therapyM. Naeini, Marjan, Newell, Felicity, Aoude, Lauren G., Bonazzi, Vanessa F., Patel, Kalpana, Lampe, Guy, Koufariotis, Lambros T., Lakis, Vanessa, Addala, Venkateswar, Kondrashova, Olga, Johnston, Rebecca L., Sharma, Sowmya, Brosda, Sandra, Holmes, Oliver, Leonard, Conrad, Wood, Scott, Xu, Qinying, Thomas, Janine, Walpole, Euan, Tao Mai, G., Ackland, Stephen P., Martin, Jarad, Burge, Matthew, Finch, Robert, Karapetis, Christos S., Shannon, Jenny, Nott, Louise, Bohmer, Robert, Wilson, Kate ... Waddell, Nicola (2023). Multi-omic features of oesophageal adenocarcinoma in patients treated with preoperative neoadjuvant therapy. Nature Communications, 14 (1) 3155, 3155. doi: 10.1038/s41467-023-38891-x |
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2023 Journal Article Generalising uncertainty improves accuracy and safety of deep learning analytics applied to oncologyMacDonald, Samual, Foley, Helena, Yap, Melvyn, Johnston, Rebecca L., Steven, Kaiah, Koufariotis, Lambros T., Sharma, Sowmya, Wood, Scott, Addala, Venkateswar, Pearson, John V., Roosta, Fred, Waddell, Nicola, Kondrashova, Olga and Trzaskowski, Maciej (2023). Generalising uncertainty improves accuracy and safety of deep learning analytics applied to oncology. Scientific Reports, 13 (1) 7395, 1-14. doi: 10.1038/s41598-023-31126-5 |
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2022 Journal Article Comparison of actionable events detected in cancer genomes by whole-genome sequencing, in silico whole-exome and mutation panelsRamarao-Milne, P, Kondrashova, O, Patch, A-M, Nones, K, Koufariotis, L T, Newell, F, Addala, V, Lakis, V, Holmes, O, Leonard, C, Wood, S, Xu, Q, Mukhopadhyay, P, Naeini, M M, Steinfort, D, Williamson, J P, Bint, M, Pahoff, C, Nguyen, P T, Twaddell, S, Arnold, D, Grainge, C, Basirzadeh, F, Fielding, D, Dalley, A J, Chittoory, H, Simpson, P T, Aoude, L G, Bonazzi, V F ... Waddell, N (2022). Comparison of actionable events detected in cancer genomes by whole-genome sequencing, in silico whole-exome and mutation panels. ESMO Open, 7 (4) 100540, 1-11. doi: 10.1016/j.esmoop.2022.100540 |
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2022 Journal Article Comprehensive genomic and tumour immune profiling reveals potential therapeutic targets in malignant pleural mesotheliomaCreaney, Jenette, Patch, Ann-Marie, Addala, Venkateswar, Sneddon, Sophie A., Nones, Katia, Dick, Ian M., Lee, Y. C. Gary, Newell, Felicity, Rouse, Ebony J., Naeini, Marjan M., Kondrashova, Olga, Lakis, Vanessa, Nakas, Apostolos, Waller, David, Sharkey, Annabel, Mukhopadhyay, Pamela, Kazakoff, Stephen H., Koufariotis, Lambros T., Davidson, Aimee L., Ramarao-Milne, Priya, Holmes, Oliver, Xu, Qinying, Leonard, Conrad, Wood, Scott, Grimmond, Sean M., Bueno, Raphael, Fennell, Dean A., Pearson, John V., Robinson, Bruce W. and Waddell, Nicola (2022). Comprehensive genomic and tumour immune profiling reveals potential therapeutic targets in malignant pleural mesothelioma. Genome Medicine, 14 (1) 58, 1-18. doi: 10.1186/s13073-022-01060-8 |
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2022 Journal Article Erratum: CD155 loss enhances tumor suppression via combined host and tumor-intrinsic mechanisms (The Journal of clinical investigation PII: e159825)Li, Xian-Yang, Das, Indrajit, Lepletier, Ailin, Addala, Venkateswar, Bald, Tobias, Stannard, Kimberley, Barkauskas, Deborah, Liu, Jing, Aguilera, Amelia Roman, Takeda, Kazuyoshi, Braun, Matthias, Nakamura, Kyohei, Jacquelin, Sebastien, Lane, Steven W., Teng, Michele Wl, Dougall, William C. and Smyth, Mark J. (2022). Erratum: CD155 loss enhances tumor suppression via combined host and tumor-intrinsic mechanisms (The Journal of clinical investigation PII: e159825). Journal of Clinical Investigation, 132 (6) e159825. doi: 10.1172/JCI159825 |
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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 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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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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2018 Journal Article Apert's syndrome: study by whole exome sequencingMunshi, Anjana, Khetarpal, Preeti, Das, Satrupa, Rao, Venkateshwar, Valecha, Monica, Bansal, Manita and Kumar, Roshan (2018). Apert's syndrome: study by whole exome sequencing. Genes and Diseases, 5 (2), 119-122. doi: 10.1016/j.gendis.2017.07.008 |
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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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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 |
