Overview
Background
Dr Nones research program is focused in using genomics to better understand the molecular aspects of cancer development and response to treatment. Her work encompassed a series of cancer types including oesophageal, pancreatic, breast and lung cancers. Cancer genomics is impacting patient care through precision medicine. Her work is contributing to two areas: i) our understanding of tumour development and progression by identifying new genes and/or mechanisms that drive cancer progression or response to treatment; and ii) investigating steps to improve the translation of genomics into patient care to improve outcomes for cancer patients.
Availability
- Dr Katia Nones is:
- Available for supervision
Qualifications
- Master of Science, University of São Paulo
- Doctor of Agronomy, University of São Paulo
Research interests
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Research Interests
- Genomics - Transcriptomics - DNA Methylation - Cancer
Works
Search Professor Katia Nones’s works on UQ eSpace
2020
Journal Article
Using whole-genome sequencing data to derive the homologous recombination deficiency scores
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
2020
Journal Article
Estimating the costs of genomic sequencing in cancer control
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
2020
Journal Article
Genomic basis for RNA alterations in cancer
Calabrese, 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
2020
Journal Article
Pan-cancer analysis of whole genomes
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
2020
Journal Article
Comprehensive molecular characterization of mitochondrial genomes in human cancers
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 (2020). Comprehensive molecular characterization of mitochondrial genomes in human cancers. Nature Genetics, 52 (3), 342-352. doi: 10.1038/s41588-019-0557-x
2019
Journal Article
Whole-genome landscape of mucosal melanoma reveals diverse drivers and therapeutic targets
Newell, 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
2019
Journal Article
Mechanisms of genomic instability in breast cancer
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
2019
Journal Article
Whole-genome sequencing reveals clinically relevant insights into the aetiology of familial breast cancers
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
2019
Journal Article
Integrative genome-scale DNA methylation analysis of a large and unselected cohort reveals five distinct subtypes of colorectal adenocarcinomas
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
2019
Journal Article
Patterns of genomic instability in breast cancer
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
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 susceptibility
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
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 blocks
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
2019
Journal Article
Complex structural rearrangements are present in high-grade dysplastic Barrett's oesophagus samples
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
2019
Journal Article
Intratumoural heterogeneity underlies distinct therapy responses and treatment resistance in glioblastoma
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
2019
Conference Publication
Dissecting the heterogeneity of metaplastic breast cancer: a morphological, immunohistochemical and genomic analysis of a large cohort
Reed, A. E. McCart, Kalaw, E., Nones, K., Bettington, M., Lim, M., Bennett, J., Johnstone, K., Kutasovic, J. R., Kazakoff, S., Xu, Q. C., Saunus, J. M., Reid, L. E., Black, D., Niland, C., Ferguson, K., Gresshoff, I., Raghavendra, A., Liu, J. C., Kalinowski, L., Reid, A. S., Davidson, M., Pearson, J. V., Yamaguchi, R., Harris, G., Tse, G., Papadimos, D., Pathmanathan, R., Pathmanathan, N., Tan, P. H. ... Lakhani, S. R. (2019). Dissecting the heterogeneity of metaplastic breast cancer: a morphological, immunohistochemical and genomic analysis of a large cohort. 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-P3-08-03
2019
Journal Article
Phenotypic and molecular dissection of Metaplastic Breast Cancer and the prognostic implications
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
2019
Conference Publication
Using whole genome sequencing and somatic mutation signatures to unravel insight into familial breast cancer aetiology
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
2018
Journal Article
CEP55 is a determinant of cell fate during perturbed mitosis in breast cancer
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
2018
Other Outputs
Genome Scale Epigenetic Profiling Reveals Five Distinct Subtypes of Colorectal Cancer
Fennell, Lochlan, Dumenil, Troy, Hartel, Gunter, Nones, Katia, Bond, Catherine, McKeone, Diane, Bowdler, Lisa, Montgomery, Grant, Wockner, Leesa, 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 (2018). Genome Scale Epigenetic Profiling Reveals Five Distinct Subtypes of Colorectal Cancer. doi: 10.1101/397620
2018
Journal Article
Telomere sequence content can be used to determine ALT activity in tumours
Lee, 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
Funding
Current funding
Supervision
Availability
- Dr Katia Nones is:
- Available for supervision
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Supervision history
Completed supervision
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2021
Doctor Philosophy
Multi-omics: Leveraging omics data integration to identify dysregulated biology in breast cancer
Associate Advisor
Other advisors: Associate Professor Amy McCart Reed, Associate Professor Peter Simpson
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2015
Doctor Philosophy
Structural Variation in Cancer Genomes & the Identification of Personalized DNA-based Cancer Biomarkers
Associate Advisor
Media
Enquiries
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