Dr Katia Nones

Senior Research Fellow (Capacity Bu

Princess Alexandra Hospital Southside Clinical Unit
Faculty of Medicine

Honorary Associate Professor

School of Biomedical Sciences
Faculty of Medicine

Overview

Research Interests

  • Research Interests
    - Genomics - Transcriptomics - DNA Methylation - Cancer

Qualifications

  • Doctor of Agronomy, University of São Paulo
  • Master of Science, University of São Paulo

Publications

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Grants

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Publications

Book Chapter

  • Nones, Katia and Villas-Boas, Silas G. (2010). Evaluation of the beneficial effects of phytonutrients by metabolomics. Genomics, proteomics, and metabolomics in nutraceuticals and functional foods. (pp. 287-296) edited by Debasis Bagchi, Francis C. Lau and Manashi Bagchi. Iowa, USA: Blackwell Publishing.

Journal Article

  • Fielding, 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

  • Fielding, 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 ARTN 1259882, 1-10. doi: 10.3389/fonc.2023.1259882

  • 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

  • Fielding, 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

  • M. 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

  • Stark, 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

  • 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

  • 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

  • Kutasovic, 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. doi: 10.1016/j.hpr.2022.300678

  • Fielding, 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

  • Newell, 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

  • Ramarao-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

  • Creaney, 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

  • Holmes, 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

  • Ganesamoorthy, 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

  • 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. (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

  • Bonazzi, 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

  • Nesic, 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

  • McCart 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

  • Yap, 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

  • 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 (2020). Inferring structural variant cancer cell fraction. Nature Communications, 11 (1) 730. doi: 10.1038/s41467-020-14351-8

  • Aoude, 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

  • Newell, 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

  • Nones, Katia and Patch, Ann-Marie (2020). The Impact of Next Generation Sequencing in Cancer Research. Cancers, 12 (10), 2928. doi: 10.3390/cancers12102928

  • de 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

  • Gordon, 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

  • Campbell, Peter J., Getz, Gad, Korbel, Jan O., Stuart, Joshua M., Jennings, Jennifer L., Stein, Lincoln D., Perry, Marc D., Nahal-Bose, Hardeep K., Ouellette, B. F. Francis, Li, Constance H., Rheinbay, Esther, Nielsen, G. Petur, Sgroi, Dennis C., Wu, Chin-Lee, Faquin, William C., Deshpande, Vikram, Boutros, Paul C., Lazar, Alexander J., Hoadley, Katherine A., Louis, David N., Dursi, L. Jonathan, Yung, Christina K., Bailey, Matthew H., Saksena, Gordon, Raine, Keiran M., Buchhalter, Ivo, Kleinheinz, Kortine, Schlesner, Matthias, Zhang, Junjun ... Hamdy, Freddie C. (2020). Pan-cancer analysis of whole genomes. Nature, 578 (7793), 82-93. doi: 10.1038/s41586-020-1969-6

  • Duijf, 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

  • Nones, 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

  • Fennell, 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

  • Kalimutho, 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

  • Wilmott, 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

  • Fielding, 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

  • Newell, 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

  • Akgül, 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

  • McCart 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

  • Kalimutho, 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

  • Edwards, 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

  • McCart 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

  • Johnson, 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

  • Patch, 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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  • Barnett, Matthew P. G., McNabb, Warren C., Cookson, Adrian L., Zhu, Shuotun, Davy, Marcus, Knoch, Bianca, Nones, Katia, Hodgkinson, Alison J. and Roy, Nicole C. (2010). Changes in colon gene expression associated with increased colon inflammation in interleukin-10 gene-deficient mice inoculated with Enterococcus species. BMC Immunology, 11. doi: 10.1186/1471-2172-11-39

  • Campos, R. L. R., Nones, K., Ledur, M. C., Moura ASAMT, Pinto, L. F. B., Ambo, M., Boschiero, C., Ruy, D. C., Baron, E. E., Ninov, K., Altenhofen, C. A. B., Burt, D. W. and Coutinho, L. L. (2009). Quantitative trait loci associated with fatness in a broiler-layer cross. Animal Genetics, 40 (5), 729-736. doi: 10.1111/j.1365-2052.2009.01910.x

  • Nones, K., Knoch, B., Dommels, Y. E., Paturi, G., Butts, C., McNabb, W. C. and Roy, N. C. (2009). Multidrug resistance gene deficient (mdr1a(-/-)) mice have an altered caecal microbiota that precedes the onset of intestinal inflammation. Journal of Applied Microbiology, 107 (2), 557-566. doi: 10.1111/j.1365-2672.2009.04225.x

  • Hayashi, A. A., Nones, K., Roy, N. C., McNabb, W. C., Mackenzie, D. S., Pacheco, D. and McCoard, S. (2009). Initiation and elongation steps of mRNA translation are involved in the increase in milk protein yield caused by growth hormone administration during lactation. Journal of Dairy Science, 92 (5), 1889-1899. doi: 10.3168/jds.2008-1334

  • Ambo, M., Moura, A. S., Ledur, M. C., Pinto, L. F., Baron, E. E., Ruy, D. C., Nones, K., Campos, R. L., Boschiero, C., Burt, D. W. and Coutinho, L. L. (2009). Quantitative trait loci for performance traits in a broiler x layer cross. Animal Genetics, 40 (2), 200-208. doi: 10.1111/j.1365-2052.2008.01824.x

  • Knoch, Bianca, Barnett, Matthew P. G., Zhu, Shuotun, Park, Zaneta A., Nones, Katia, Dommels, Yvonne E. M., Knowles, Scott O., McNabb, Warren C. and Roy, Nicole C. (2009). Genome-wide analysis of genes involved in dietary eicosapentaenoic acid- and oleic acid-induced modulation in colon inflammation of interleukin 10 gene deficient mice. Journal of Nutrigenetics and Nutrigenomics, 2 (1), 9-28. doi: 10.1159/000134292

  • Nones, Katia, Dommels, Yvonne E. M., Martell, Sheridan, Butts, Christine, McNabb, Warren C., Park, Zaneta A., Zhu, Shuotun, Hedderley, Duncan, Barnett, Matthew P. G. and Roy, Nicole C. (2009). The effects of dietary curcumin and rutin on colonic inflammation and gene expression in multidrug resistance gene-deficient (mdr1a-/-) mice, a model of inflammatory bowel diseases. British Journal of Nutrition, 101 (2), 169-181. doi: 10.1017/S0007114508009847

  • Ninov, Kerli, Ledur, Mônica Corrêa, Alves, Helena Javiel, Do Rosário, Millor Fernandes, Nones, Kátia and Coutinho, Luiz Lehmann (2008). Investigation of Leptin gene in broiler and layer chicken lines. Scientia agricola, 65 (2), 214-219. doi: 10.1590/S0103-90162008000200016

  • Ye, Xianghai, Brown, Stewart R., Nones, Kátia, Coutinho, Luiz L ., Dekkers, Jack C. M. and Lamont, Susan J. (2007). Associations of myostatin gene polymorphisms with performance and mortality traits in broiler chickens. Genetics Selection Evolution, 39 (1) 73, 73-89. doi: 10.1051/gse:2006029

  • Nones, K., Ledur, M. C., Ruy, D. C., Baron, E. E., Melo, C. M. R., Moura, A. S. A. M. T., Zanella, E. L., Burt, D. W. and Coutinho, L. L. (2006). Mapping QTLs on chicken chromosome 1 for performance and carcass traits in a broiler x layer cross. Animal Genetics, 37 (2), 95-100. doi: 10.1111/j.1365-2052.2005.01387.x

  • Nones, Kátia, Ledur, Mônica Corrêa, Ruy, Deborah Clea, Baron, Erica Elias, Moura, Ana Silvia Alves Meira Tavares and Coutinho, Luiz Lehmann (2005). Genetic linkage map of chicken chromosome 1 from a Brazilian resource population. Scientia Agricola, 62 (1), 12-17. doi: 10.1590/S0103-90162005000100003

Conference Publication

  • Simpson, P., Nones, K., Johnson, J., Newell, F., Patch, A-M, Thorne, H., Kazakoff, S., De Luca, X., Parsons, M., Ferguson, K., Reid, L., Reed, A. McCart, Srihari, S., Lakis, V., Davidson, A., Mukhopadhyay, P., Holmes, O., Xu, Q., Wood, S., Leonard, C., Beasley, J., Degasperi, A., Nik-Zainal, S., Ragan, M., Spurdle, A., Khanna, K. K., Lakhani, S., Pearson, J., Chenevix-Trench, G. and Waddell, N. (2019). Using whole genome sequencing and somatic mutation signatures to unravel insight into familial breast cancer aetiology. San Antonio Breast Cancer Symposium, San Antonio, TX, United States, 4-8 December 2018. Philadelphia, PA, United States: American Association for Cancer Research. doi: 10.1158/1538-7445.SABCS18-P5-10-01

  • Lal, S., Reed, A. McCart, Nones, K., Wockner, L., Song, S., Lakhani, S. and Simpson, P. (2017). An integrated molecular analysis of invasive lobular carcinoma. 39th Annual San Antonio Breast Cancer Symposium, San Antonio, Texas, 6-10 December 2016. Philadelphia, PA, United States: American Association for Cancer Research. doi: 10.1158/1538-7445.SABCS16-P1-05-16

  • Reed, A. E. McCart, Kutasovic, J. R., Nones, K., da Silva, L., Melville, L., Jayanthan, J., Vargas, A. C., Reid, L. E., Saunus, J. M., Cummings, M. M., Porter, A., Evans, E., Waddell, N., Lakhani, S. R. and Simpson, P. T. (2017). Mixed ductal-lobular carcinomas of the breast: Abrogated cell adhesion in the clonal evolution from ductal to lobular morphology. San Antonio Breast Cancer Symposium, San Antonio, TX, United States, 6-10 December 2016. Philadelphia, PA, United States: American Association for Cancer Research. doi: 10.1158/1538-7445.SABCS16-P1-07-08

  • Saunus, J. M., Quinn, M. C. J., Patch, A. M., Pearson, J. V., Bailey, P. J., Cloonan, N., Nones, K., Miller, D., Mariasegaram, M., Lau, Q., Jeffree, L., Khanna, K. K., Chenevix-Trench, G., Grimmond, S. M., Simpson, P. T., Waddell, N. and Lakhani, S. R. (2015). Genomic and transcriptomic landscapes of human brain metastases. 15th International Biennial Congress of the Metastasis Research Society, Heidelberg, Germany, June 28th–July 1st, 2014. Dordrecht, Netherlands: Springer Netherlands. doi: 10.1007/s10585-015-9708-3

  • Packer, L., Byron, S., Mahon, C., Loch, D., Wortmann, A., Nones, K., Grimmond, S., Pearson, J., Waddell, N. and Pollock, P. (2014). Elucidating mechanisms of resistance to FGFR inhibitors in endometrial cancer. 26th EORTC-NCI-AACR Symposium on Molecular Targets and Cancer Therapeutics, Barcelona Spain, 18-21 November 2014. Kidlington, Oxford, United Kingdom: Pergamon Press. doi: 10.1016/S0959-8049(14)70220-5

  • Chin, V. T., Waddell, N., Nones, K., Quek, K., Mawson, A., Johns, A., Grimmond, S. and Biankin, A. (2012). Individualised Measurement of Tumour-Derived Circulating Dna in Patients with Pancreatic Cancer: a Marker of Prognosis and Therapeutic Response. Medical Oncology Group of Australia Incorporated Annual Scientific Meeting, Brisbane, QLD, Australia, 8-10 August 2012. Chichester, West Sussex, United Kingdom: Wiley-Blackwell. doi: 10.1111/j.1743-7563.2012.01578.x

Grants (Administered at UQ)