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2025 Journal Article Erratum: Multiomic profiling of checkpoint inhibitor-treated melanoma: Identifying predictors of response and resistance, and markers of biological discordance (Cancer Cell (2022) 40(1) (88–102.e7), (S1535610821006127), (10.1016/j.ccell.2021.11.012))Newell, 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. (2025). Erratum: Multiomic profiling of checkpoint inhibitor-treated melanoma: Identifying predictors of response and resistance, and markers of biological discordance (Cancer Cell (2022) 40(1) (88–102.e7), (S1535610821006127), (10.1016/j.ccell.2021.11.012)). Cancer Cell, 43 (3), 563. doi: 10.1016/j.ccell.2025.01.011 |
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2025 Journal Article Spatial Transcriptomics Reveals Novel Mechanisms Involved in Perineural Invasion in Pancreatic Ductal AdenocarcinomasLakis, Vanessa, Chan, Noni L, Lyons, Ruth, Blackburn, Nicola, Nguyen, Tam Hong, Chang, Crystal, Masel, Andrew, West, Nicholas P., Boyle, Glen M., Patch, Ann-Marie, Gill, Anthony J. and Nones, Katia (2025). Spatial Transcriptomics Reveals Novel Mechanisms Involved in Perineural Invasion in Pancreatic Ductal Adenocarcinomas. Cancers, 17 (5) 852, 852-5. doi: 10.3390/cancers17050852 |
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2024 Journal Article Performance of somatic structural variant calling in lung cancer using Oxford Nanopore sequencing technologyLiu, Lingchen, Zhang, Jia, Wood, Scott, Newell, Felicity, Leonard, Conrad, Koufariotis, Lambros T., Nones, Katia, Dalley, Andrew J., Chittoory, Haarika, Bashirzadeh, Farzad, Son, Jung Hwa, Steinfort, Daniel, Williamson, Jonathan P., Bint, Michael, Pahoff, Carl, Nguyen, Phan T., Twaddell, Scott, Arnold, David, Grainge, Christopher, Simpson, Peter T., Fielding, David, Waddell, Nicola and Pearson, John V. (2024). Performance of somatic structural variant calling in lung cancer using Oxford Nanopore sequencing technology. BMC genomics, 25 (1) 898. doi: 10.1186/s12864-024-10792-3 |
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2024 Journal Article Evaluation of Endobronchial Ultrasound-Guided Transbronchial Needle Aspiration (EBUS-TBNA) samples from advanced non-small cell lung cancer for whole genome, whole exome and comprehensive panel sequencingFielding, David, Lakis, Vanessa, Dalley, Andrew J., Chittoory, Haarika, Newell, Felicity, Koufariotis, Lambros T., Patch, Ann-Marie, Kazakoff, Stephen, Bashirzadeh, Farzad, Son, Jung Hwa, Ryan, Kimberley, Steinfort, Daniel, Williamson, Jonathan P., Bint, Michael, Pahoff, Carl, Nguyen, Phan Tien, Twaddell, Scott, Arnold, David, Grainge, Christopher, Pattison, Andrew, Fairbairn, David, Gune, Shailendra, Christie, Jemma, Holmes, Oliver, Leonard, Conrad, Wood, Scott, Pearson, John V., Lakhani, Sunil R., Waddell, Nicola ... Nones, Katia (2024). Evaluation of Endobronchial Ultrasound-Guided Transbronchial Needle Aspiration (EBUS-TBNA) samples from advanced non-small cell lung cancer for whole genome, whole exome and comprehensive panel sequencing. Cancers, 16 (4) 785. doi: 10.3390/cancers16040785 |
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2023 Journal Article Discrepancies in tumor mutation burden reporting from sequential endobronchial ultrasound transbronchial needle aspiration samples within single lymph node stations - brief reportFielding, David, Dalley, Andrew J., Singh, Mahendra, Nandakumar, Lakshmy, Lakis, Vanessa, Chittoory, Haarika, Fairbairn, David, Patch, Ann-Marie, Kazakoff, Stephen H., Ferguson, Kaltin, Bashirzadeh, Farzad, Bint, Michael, Pahoff, Carl, Son, Jung Hwa, Ryan, Kimberley, Hodgson, Alan, Sharma, Sowmya, Pearson, John V., Waddell, Nicola, Lakhani, Sunil R., Hartel, Gunter, Simpson, Peter T. and Nones, Katia (2023). Discrepancies in tumor mutation burden reporting from sequential endobronchial ultrasound transbronchial needle aspiration samples within single lymph node stations - brief report. Frontiers in Oncology, 13 1259882, 1-10. doi: 10.3389/fonc.2023.1259882 |
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2023 Journal Article Whole genome sequencing in advanced lung cancer can be performed using diff-quik cytology smears derived from endobronchial ultrasound, transbronchial needle aspiration (EBUS TBNA)Fielding, David, Dalley, Andrew J., Singh, Mahendra, Nandakumar, Lakshmy, Lakis, Vanessa, Chittoory, Haarika, Fairbairn, David, Ferguson, Kaltin, Bashirzadeh, Farzad, Bint, Michael, Pahoff, Carl, Son, Jung Hwa, Hodgson, Alan, Pearson, John V., Waddell, Nicola, Lakhani, Sunil R., Hartel, Gunter, Nones, Katia and Simpson, Peter T. (2023). Whole genome sequencing in advanced lung cancer can be performed using diff-quik cytology smears derived from endobronchial ultrasound, transbronchial needle aspiration (EBUS TBNA). Lung, 201 (4), 407-413. doi: 10.1007/s00408-023-00631-9 |
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2023 Journal Article Evaluating Diff‐Quik cytology smears for large‐panel mutation testing in lung cancer—Predicting DNA content and success with low‐malignant‐cellularity samplesFielding, David I., Dalley, Andrew J., Singh, Mahendra, Nandakumar, Lakshmy, Lakis, Vanessa, Chittoory, Haarika, Fairbairn, David, Patch, Ann‐Marie, Kazakoff, Stephen H., Ferguson, Kaltin, Bashirzadeh, Farzad, Bint, Michael, Pahoff, Carl, Son, Jung Hwa, Hodgson, Alan, Sharma, Sowmya, Waddell, Nicola, Lakhani, Sunil R., Hartel, Gunter, Nones, Katia and Simpson, Peter T. (2023). Evaluating Diff‐Quik cytology smears for large‐panel mutation testing in lung cancer—Predicting DNA content and success with low‐malignant‐cellularity samples. Cancer Cytopathology, 131 (6), 373-382. doi: 10.1002/cncy.22690 |
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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 Publisher Correction: Comprehensive molecular characterization of mitochondrial genomes in human cancers (Nature Genetics, (2020), 52, 3, (342-352), 10.1038/s41588-019-0557-x)Yuan, 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 (2023). Publisher Correction: Comprehensive molecular characterization of mitochondrial genomes in human cancers (Nature Genetics, (2020), 52, 3, (342-352), 10.1038/s41588-019-0557-x). Nature Genetics, 55 (5), 893-893. doi: 10.1038/s41588-020-0587-4 |
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2023 Journal Article Author Correction: Comprehensive molecular characterization of mitochondrial genomes in human cancers (Nature Genetics, (2020), 52, 3, (342-352), 10.1038/s41588-019-0557-x)Yuan, 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 (2023). Author Correction: Comprehensive molecular characterization of mitochondrial genomes in human cancers (Nature Genetics, (2020), 52, 3, (342-352), 10.1038/s41588-019-0557-x). Nature Genetics, 55 (5), 892-892. doi: 10.1038/s41588-020-0629-y |
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2023 Journal Article Australian genomics: outcomes of a 5-year national program to accelerate the integration of genomics in healthcareStark, Zornitza, Boughtwood, Tiffany, Haas, Matilda, Braithwaite, Jeffrey, Gaff, Clara L., Goranitis, Ilias, Spurdle, Amanda B., Hansen, David P., Hofmann, Oliver, Laing, Nigel, Metcalfe, Sylvia, Newson, Ainsley J., Scott, Hamish S., Thorne, Natalie, Ward, Robyn L., Dinger, Marcel E., Best, Stephanie, Long, Janet C., Grimmond, Sean M., Pearson, John, Waddell, Nicola, Barnett, Christopher P., Cook, Matthew, Field, Michael, Fielding, David, Fox, Stephen B., Gecz, Jozef, Jaffe, Adam, Leventer, Richard J. ... North, Kathryn N. (2023). Australian genomics: outcomes of a 5-year national program to accelerate the integration of genomics in healthcare. American Journal of Human Genetics, 110 (3), 419-426. doi: 10.1016/j.ajhg.2023.01.018 |
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2023 Journal Article Author Correction: Pan-cancer analysis of whole genomes (Nature, (2020), 578, 7793, (82-93), 10.1038/s41586-020-1969-6)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., Al-Shahrour, Fatima, 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 ... von Mering, Christian (2023). Author Correction: Pan-cancer analysis of whole genomes (Nature, (2020), 578, 7793, (82-93), 10.1038/s41586-020-1969-6). Nature, 614 (7948). doi: 10.1038/s41586-022-05598-w |
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2023 Conference Publication Diff-Quik smears from EBUS TBNA procedures: Evaluating measures of tumour cellularity and feasibility of whole genome sequencing (WGS)Fielding, David, Dalley, Andrew, Singh, Mahendra, Nandakumar, Lakshmy, Lakis, Vanessa, Chittoory, Haarika, Bashirzadeh, Farzad, Bint, Michael, Pahoff, Carl, Son, Jung, Hodgson, Alan, Sharma, Sowmya, Godbolt, David, Coleman, Kylie, Whitfield, Lenore, Waddell, Nicola, Lakhani, Sunil, Nones, Katia, Hartel, Gunter and Simpson, Peter (2023). Diff-Quik smears from EBUS TBNA procedures: Evaluating measures of tumour cellularity and feasibility of whole genome sequencing (WGS). 26th Congress of the Asian Pacific Society of Respirology Above and Beyond, Seoul, Korea, 17-20 November 2022. Richmond, VIC, Australia: John Wiley & Sons. doi: 10.1111/resp.14433 |
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2022 Journal Article Author Correction: Inferring structural variant cancer cell fraction (Nature Communications, (2020), 11, 1, (730), 10.1038/s41467-020-14351-8)Cmero, 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 (2022). Author Correction: Inferring structural variant cancer cell fraction (Nature Communications, (2020), 11, 1, (730), 10.1038/s41467-020-14351-8). Nature Communications, 13 (1) 7568. doi: 10.1038/s41467-022-32338-5 |
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2022 Journal Article Author Correction: Divergent mutational processes distinguish hypoxic and normoxic tumours (Nature Communications, (2020), 11, 1, (737), 10.1038/s41467-019-14052-x)Bhandari, Vinayak, Li, Constance H., Bristow, Robert G., Boutros, Paul C., 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., Al-Shahrour, Fatima, 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 ... von Mering, Christian (2022). Author Correction: Divergent mutational processes distinguish hypoxic and normoxic tumours (Nature Communications, (2020), 11, 1, (737), 10.1038/s41467-019-14052-x). Nature Communications, 13 (1) 7569. doi: 10.1038/s41467-022-32339-4 |
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2022 Journal Article Shariant platform: Enabling evidence sharing across Australian clinical genetic-testing laboratories to support variant interpretationTudini, Emma, Andrews, James, Lawrence, David M., King-Smith, Sarah L., Baker, Naomi, Baxter, Leanne, Beilby, John, Bennetts, Bruce, Beshay, Victoria, Black, Michael, Boughtwood, Tiffany F., Brion, Kristian, Cheong, Pak Leng, Christie, Michael, Christodoulou, John, Chong, Belinda, Cox, Kathy, Davis, Mark R., Dejong, Lucas, Dinger, Marcel E., Doig, Kenneth D., Douglas, Evelyn, Dubowsky, Andrew, Ellul, Melissa, Fellowes, Andrew, Fisk, Katrina, Fortuno, Cristina, Friend, Kathryn, Gallagher, Renee L. ... and on behalf of the Shariant Consortium (2022). Shariant platform: Enabling evidence sharing across Australian clinical genetic-testing laboratories to support variant interpretation. American Journal of Human Genetics, 109 (11), 1960-1973. doi: 10.1016/j.ajhg.2022.10.006 |
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2022 Journal Article Comprehensive histopathologic and genomic analysis of a novel case of lipoblastoma-like tumour of the vulva demonstrating malignant behaviourKutasovic, Jamie R., Nones, Katia, Lakis, Vanessa, Koufariotis, Lambros T., Ferguson, Kaltin, McCart Reed, Amy E., Simpson, Peter T., Lakhani, Sunil R., Mar Fan, Helen, Higgins, Megan, Davies, Janene, Payton, Diane and Taege, Lucinda (2022). Comprehensive histopathologic and genomic analysis of a novel case of lipoblastoma-like tumour of the vulva demonstrating malignant behaviour. Human Pathology Reports, 30 300678, 300678-30. doi: 10.1016/j.hpr.2022.300678 |
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2022 Journal Article Prospective optimization of endobronchial ultrasound-guided transbronchial needle aspiration lymph node assessment for lung cancer: Three needle agitations are noninferior to 10 agitations for adequate tumor cell and DNA yieldFielding, David, Dalley, Andrew J., Singh, Mahendra, Nandakumar, Lakshmy, Nones, Katia, Lakis, Vanessa, Chittoory, Haarika, Ferguson, Kaltin, Bashirzadeh, Farzad, Bint, Michael, Pahoff, Carl, Son, Jung Hwa, Hodgson, Alan, Sharma, Sowmya, Godbolt, David, Coleman, Kylie, Whitfield, Lenore, Waddell, Nicola, Lakhani, Sunil R., Hartel, Gunter and Simpson, Peter T. (2022). Prospective optimization of endobronchial ultrasound-guided transbronchial needle aspiration lymph node assessment for lung cancer: Three needle agitations are noninferior to 10 agitations for adequate tumor cell and DNA yield. JTO Clinical and Research Reports, 3 (10) 100403, 100403. doi: 10.1016/j.jtocrr.2022.100403 |
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2022 Journal Article Comparative genomics provides etiological and biological insights into melanoma subtypesNewell, Felicity, Johansson, Peter A., Wilmott, James S., Nones, Katia, Lakis, Vanessa, Pritchard, Antonia L., Lo, Serigne N., Rawson, Robert V., Kazakoff, Stephen H., Colebatch, Andrew J., Koufariotis, Lambros T., Ferguson, Peter M., Wood, Scott, Leonard, Conrad, Law, Matthew H., Brooks, Kelly M., Broit, Natasa, Palmer, Jane M., Couts, Kasey L., Vergara, Ismael A., Long, Georgina V., Barbour, Andrew P., Nieweg, Omgo E., Shivalingam, Brindha, Robinson, William A., Stretch, Jonathan R., Spillane, Andrew J., Saw, Robyn P.M., Shannon, Kerwin F. ... Hayward, Nicholas K. (2022). Comparative genomics provides etiological and biological insights into melanoma subtypes. Cancer Discovery, 12 (12), OF1-OF24. doi: 10.1158/2159-8290.cd-22-0603 |
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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 |
