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
-
Research Interests
- Genomics - Transcriptomics - DNA Methylation - Cancer
Works
Search Professor Katia Nones’s works on UQ eSpace
2024
Journal Article
Performance of somatic structural variant calling in lung cancer using Oxford Nanopore sequencing technology
Liu, 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
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 sequencing
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
2023
Journal Article
Discrepancies in tumor mutation burden reporting from sequential endobronchial ultrasound transbronchial needle aspiration samples within single lymph node stations - brief report
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
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
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 samples
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
2023
Journal Article
Multi-omic features of oesophageal adenocarcinoma in patients treated with preoperative neoadjuvant therapy
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
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
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
2023
Journal Article
Australian genomics: outcomes of a 5-year national program to accelerate the integration of genomics in healthcare
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
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
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
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
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
2022
Journal Article
Shariant platform: Enabling evidence sharing across Australian clinical genetic-testing laboratories to support variant interpretation
Tudini, 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
2022
Journal Article
Comprehensive histopathologic and genomic analysis of a novel case of lipoblastoma-like tumour of the vulva demonstrating malignant behaviour
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
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 yield
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
2022
Journal Article
Comparative genomics provides etiological and biological insights into melanoma subtypes
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
2022
Journal Article
Comparison of actionable events detected in cancer genomes by whole-genome sequencing, in silico whole-exome and mutation panels
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
2022
Journal Article
Comprehensive genomic and tumour immune profiling reveals potential therapeutic targets in malignant pleural mesothelioma
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
2022
Journal Article
qmotif: determination of telomere content from whole-genome sequence data
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
Funding
Current funding
Supervision
Availability
- Dr Katia Nones is:
- Available for supervision
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Supervision history
Completed supervision
-
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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