Overview
Background
Peter Simpson is a recognised expert in the molecular and pathological characterisation of breast and lung cancers. His research is based at the UQ Centre for Clinical Research (UQCCR), where he is the Head of the Cancer Theme and is a Research Group Leader in Cancer Genomics. He has published >150 articles (>12,000 citations, H-index 52; Scopus, May2025) including in Nature, Nature Medicine, Annals of Oncology and the American Journal of Respiratory and Critical Care Medicine. He co-manages the Brisbane Breast Bank (BBB), a tissue bank created to facilitate clinical breast cancer research, and the Debutant lung cancer Program.
Pete also holds a teaching appointment in UQ, where he is passionate about the science and clinical applications of Pathology. He teaches into the UQ Medical Program (Year 1 and 2), as well as to undergraduates. He has co-authored a chapter ‘Breast Diseases’ in the latest edition (11th) of the internationally acclaimed Medical text book Robbins and Cotran Pathologic Basis of Disease.
Outside UQ, Pete is a Fellow of the Faculty of Science in the Royal College of Pathologists of Australasia (FFSc RCPA), a member of the kConFab Executive (https://www.kconfab.org/), a member of the Lobular Breast Cancer Alliance Scientific Advisory Board (https://lobularbreastcancer.org/), and a member of the International Cancer Genome Consortium (Breast Cancer group).
Pete enjoys supervising students at all levels in their careers and collaborating within multidisciplinary teams spanning clinical (e.g. pathology, oncology) and science teams (e.g. in ‘omics, bioinformatics and machine learning).
Availability
- Associate Professor Peter Simpson is:
- Available for supervision
- Media expert
Fields of research
Qualifications
- Doctor of Philosophy, University of Liverpool
Research interests
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Broad Research Program
Cancer is a very heterogeneous disease, making morphological classification and management of patients a significant challenge. Despite great advances it remains difficult to predict which patients are at risk of their disease returning (recurrence), spreading (metastasis) or which patients will gain most benefit to specific therapies. There has therefore been a concerted effort to supplement the morphological classification of disease with molecular data that can provide a clearer appreciation for this complexity and better predict tumour behaviour. This ideology has driven significant advancements in the field of molecular pathology research. My research program embraces these advances in technology to help better understand mechanisms of disease development and progression and help improve the molecular aspects of diagnosis and patient management. Themes of research involve 1) invasive lobular carcinoma of the breast, 2) breast cancer diagnosed in young individuals, and 3) lung cancer.
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Invasive Lobular Carcinoma
Invasive Lobular Carcinoma (ILC) is the most commonly diagnosed ‘special’ morphological type of breast cancer, comprising up to 15% of all cases. The most important biological feature of lobular breast cancer is the functional loss of cell adhesion molecule E-cadherin. This is the glue that holds epithelial cells together. Loss of E-cadherin leads to a growth pattern that can be diffuse and highly invasive through the breast tissue. This leads to a number of important clinical challenges with diagnosing and managing this cancer: the cancer can be hard to palpate or detect by mammographic screening and hard to fully excise during surgery; if the cancer spreads it can again be hard to detect. A large component of Peter's research focuses on aspects of this specific cancer subtype, including understanding molecular determinants that predict tumour behaviour and prognosis, and mechanisms of invasion and metastasis.
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Familial Breast Cancer
Family history is a significant risk factor for the development of breast cancer, often leading to early diagnosis of disease. For some families, the genetic component of this risk is well understood and attributed to pathogenic germline variants in moderate-high risk genes (e.g. BRCA1, BRCA2, PALB2, TP53, ATM, CHEK2). For many families the underlying genetic risk is unknown. Further, some individuals develop breast cancer at a young age when they have no family history. We study clinical samples using a variety of molecular profiling techniques, including whole genome sequencing and digital spatial transcriptomics, and we are interested in understanding the germline and somatic molecular mechanism that contribute to the development of disease. This work is a collaboration with several tissue banks: kConFab, the BBB and the Australian Breast Cancer Tissue Bank.
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Lung Cancer Diagnostics
Lung Cancer has the highest mortality of all cancers. Most cases are diagnosed at an advance, inoperable stage and so are associated with a poor prognosis. Endobronchial ultrasound transbronchial needle aspiration (EBUS-TBNA) sampling is an important procedure to make a tissue diagnosis of disease and to provide specimens for molecular testing. Next generation sequencing is an important component of diagnostic practice and therapeutic decision making for lung cancer patients. Our program of work is focused on optimising molecular testing strategies from different types of cancer samples (tissue, supernatant, cfDNA) to improve the success of testing for patients. This is a collaboration with A/Prof David Fielding (https://about.uq.edu.au/experts/9060) from the Department of Thoracic Medicine (RBWH), plus colleagues from Pathology Queensland, QIMR Berghofer and a network of hospitals around Australia.
Research impacts
Breast cancer is the most diagnosed cancer in women worldwide and consequently is the biggest contributor to morbidity and mortality from cancer.
My work in the field of breast cancer genomics has sought to unravel molecular mechanisms driving the evolution of disease, from early lesions through to treatment resistance and metastatic progression. Our work uses various types of ‘omics applications, including whole genome sequencing and spatial transcriptomics, married with detailed cancer morphology assessment. Gene mutations and mutational signature analysis in the context of sporadic and familial breast cancer has revealed pathogenic germline mutations, different mechanisms of genomic evolution and clonal heterogeneity. The work through the International Cancer Genome Consortium contributed to the development of HRDetect (Nature Medicine) for therapeutic decision making.
My work in lobular breast cancer has an international standing. As a research community, we aim to raise the profile of lobular breast cancer as an important, common and yet understudied type of breast cancer. We have demonstrated this disease is in fact a heterogenous subtype, exhibiting morphological variants and diverse genomic features. We developed LobSig as a potential prognostic tool for lobular breast cancer, which is undergoing further validation. We have a program of work to better understand the biology of disease and identify tissue- and blood-based biomarkers of disease progression.
Lung cancer is the highest mortality rate of all cancers worldwide. The Debutant lung cancer clinical research program was established in 2018 and has sought to optimise and expand lung cancer molecular testing applications. The work has been funded by various sources, including Pathology Queensland, Royal Brisbane & Women’s Hospital Foundation, Cancer Council Qld, Cancer Australia, Australian Genomics and the Medical Research Future Fund (MRFF). The work has demonstrated the clinical utility of very small cytology samples and blood (cfDNA) samples using comprehensive genomic assays. The translation of results from this Program could significantly enhance the number of patients eligible for targeted therapies.
Works
Search Professor Peter Simpson’s works on UQ eSpace
2017
Journal Article
Flipping pathology: our experience at an Australian medical school
Koteeswaran, Rajasekaran, Simpson, Peter, Bartle, Emma, Smith, Deborah, Bhutada, Ekta, Ayre, Julie and Lakhani, Sunil R. (2017). Flipping pathology: our experience at an Australian medical school. Medical Science Educator, 27 (2), 409-415. doi: 10.1007/s40670-017-0406-4
2017
Journal Article
A somatic-mutational process recurrently duplicates germline susceptibility loci and tissue-specific super-enhancers in breast cancers
Glodzik, Dominik, Morganella, Sandro, Davies, Helen, Simpson, Peter T., Li, Yilong, Zou, Xueqing, Diez-Perez, Javier, Staaf, Johan, Alexandrov, Ludmil B., Smid, Marcel, Brinkman, Arie B., Rye, Inga Hansine, Russnes, Hege, Raine, Keiran, Purdie, Colin A., Lakhani, Sunil R., Thompson, Alastair M., Birney, Ewan, Stunnenberg, Hendrik G., Van De Vijver, Marc J., Martens, John W. M., Borresen-Dale, Anne-Lise, Richardson, Andrea L., Kong, Gu, Viari, Alain, Easton, Douglas, Evan, Gerard, Campbell, Peter J., Stratton, Michael R. and Nik-Zainal, Serena (2017). A somatic-mutational process recurrently duplicates germline susceptibility loci and tissue-specific super-enhancers in breast cancers. Nature Genetics, 49 (3), 341-348. doi: 10.1038/ng.3771
2017
Conference Publication
Mixed ductal-lobular carcinomas of the breast: Abrogated cell adhesion in the clonal evolution from ductal to lobular morphology
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
2017
Conference Publication
An integrated molecular analysis of invasive lobular carcinoma
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
2017
Conference Publication
Immunohistochemical evaluation of FOXA1 expression and its correlation with breast cancer-specific survival: queensland follow up cohort
Dedina, Liana, Kutasovic, Jamie R., McCart Reed, Amy E., Simpson, Peter T. and Lakhani, Sunil R. (2017). Immunohistochemical evaluation of FOXA1 expression and its correlation with breast cancer-specific survival: queensland follow up cohort. Pathology Update 2017, Sydney Australia, 24 - 26 February 2017. London, United Kingdom: Lippincott Williams & Wilkins. doi: 10.1016/j.pathol.2016.12.174
2017
Conference Publication
Diffquik Stained Cytology Smears Provide Improved Malignant Cell Dna Yields From Lymph Nodes At Endobronchial Ultrasound Transbronchial Needle Aspiration (Ebus-Tbna)
Fielding, D., Dalley, A., Bashirzadeh, F., Singh, M., Nandakumar, L., Reed, McCart A., Black, D., Waddell, N., Kazakoff, Stephen, Nones, Katia, Pearson, John, Lakhani, S. and Simpson, P. (2017). Diffquik Stained Cytology Smears Provide Improved Malignant Cell Dna Yields From Lymph Nodes At Endobronchial Ultrasound Transbronchial Needle Aspiration (Ebus-Tbna). ANZSRS/TSANZ Annual Scientific Meeting, Canberra, Australia, 24-28 March 2017. Richmond, VIC, Australia: Wiley-Blackwell.
2016
Journal Article
Breast cancer genome and transcriptome integration implicates specific mutational signatures with immune cell infiltration
Smid, Marcel, Rodriguez-Gonzalez, F. German, Sieuwerts, Anieta M., Salgado, Roberto, Prager-Van Der Smissen, Wendy J. C., van der Vlugt-Daane, Michelle, Van Galen, Anne, Nik-Zainal, Serena, Staaf, Johan, Brinkman, Arie B., Van De Vijver, Marc J., Richardson, Andrea L., Fatima, Aquila, Berentsen, Kim, Butler, Adam, Martin, Sancha, Davies, Helen R., Debets, Reno, Meijer-Van Gelder, Marion E., Van Deurzen, Carolien H. M., Macgrogan, Gaeetan, Van Den Eynden, Gert G. G. M., Purdie, Colin, Thompson, Alastair M., Caldas, Carlos, Span, Paul N., Simpson, Peter T., Lakhani, Sunil R., Van Laere, Steven ... Martens, John W. M. (2016). Breast cancer genome and transcriptome integration implicates specific mutational signatures with immune cell infiltration. Nature Communications, 7 (1) 12910, 12910.1-12910.9. doi: 10.1038/ncomms12910
2016
Journal Article
Integrating multi-omics data to dissect mechanisms of DNA repair dysregulation in breast cancer
Liu, Chao, Rohart, Florian, Simpson, Peter T., Khanna, Kum Kum, Ragan, Mark A. and Le Cao, Kim-Anh (2016). Integrating multi-omics data to dissect mechanisms of DNA repair dysregulation in breast cancer. Scientific Reports, 6 (1) 34000, 34000.1-34000.11. doi: 10.1038/srep34000
2016
Journal Article
Landscape of somatic mutations in 560 breast cancer whole-genome sequences
Nik-Zainal, Serena, Davies, Helen, Staaf, Johan, Ramakrishna, Manasa, Glodzik, Dominik, Zou, Xueqing, Martincorena, Inigo, Alexandrov, Ludmil B., Martin, Sancha, Wedge, David C., Van Loo, Peter, Ju, Young Seok, Smid, Marcel, Brinkman, Arie B., Morganella, Sandro, Aure, Miriam R., Lingjaerde, Ole Christian, Langerod, Anita, Ringner, Markus, Ahn, Sung-Min, Boyault, Sandrine, Brock, Jane E., Broeks, Annegien, Butler, Adam, Desmedt, Christine, Dirix, Luc, Dronov, Serge, Fatima, Aquila, Foekens, John A. ... Stratton, Michael R. (2016). Landscape of somatic mutations in 560 breast cancer whole-genome sequences. Nature, 534 (7605), 47-+. doi: 10.1038/nature17676
2016
Journal Article
Point mutations in Exon 1B of APC Reveal Gastric Adenocarcinoma and Proximal Polyposis of the Stomach as a Familial Adenomatous Polyposis Variant
Li, Jun, Woods, Susan L., Healey, Sue, Beesley, Jonathan, Chen, Xiaoqing, Lee, Jason S., Sivakumaran, Haran, Wayte, Nicci, Nones, Katia, Waterfall, Joshua J., Pearson, John, Patch, Anne-Marie, Senz, Janine, Ferreira, Manuel A., Kaurah, Pardeep, Mackenzie, Robertson, Heravi-Moussavi, Alireza, Hansford, Samantha, Lannagan, Tamsin R. M., Spurdle, Amanda B., Simpson, Peter T., da Silva, Leonard, Lakhani, Sunil R., Clouston, Andrew D., Bettington, Mark, Grimpen, Florian, Busuttil, Rita A., Di Costanzo, Natasha, Boussioutas, Alex ... Chenevix-Trench, Georgia (2016). Point mutations in Exon 1B of APC Reveal Gastric Adenocarcinoma and Proximal Polyposis of the Stomach as a Familial Adenomatous Polyposis Variant. American Journal of Human Genetics, 98 (5), 830-842. doi: 10.1016/j.ajhg.2016.03.001
2016
Journal Article
Novel highly specific anti-periostin antibodies uncover the functional importance of the fascilin 1-1 domain and highlight preferential expression of periostin in aggressive breast cancer
Field, Sarah, Uyttenhove, Catherine, Stroobant, Vincent, Cheou, Paméla, Coutelier, Jean-Paul, Simpson, Peter T., Cummings, Margaret C., Saunus, Jodi M., Reid, Lynne E., Kutasovic, Jamie R., McNicol, Anne Marie, Kim, Ba Reun, Kim, Jae Ho, Lakhani, Sunil R., Neville, A. Munro, Van Snick, Jacques and Jat, Parmjit S. (2016). Novel highly specific anti-periostin antibodies uncover the functional importance of the fascilin 1-1 domain and highlight preferential expression of periostin in aggressive breast cancer. International Journal of Cancer, 138 (8), 1959-1970. doi: 10.1002/ijc.29946
2016
Journal Article
Understanding the functional impact of copy number alterations in breast cancer using a network modeling approach
Srihari, Sriganesh, Kalimutho, Murugan, Lal, Samir, Singla, Jitin, Patel, Dhaval, Simpson, Peter T., Khanna, Kum Kum and Ragan, Mark A. (2016). Understanding the functional impact of copy number alterations in breast cancer using a network modeling approach. Molecular Biosystems, 12 (3), 963-972. doi: 10.1039/C5MB00655D
2016
Conference Publication
An integrative analysis of invasive lobular breast cancer
Lal, Samir, McCart Reed, Amy E, Nones, Katia, Wockner Leesa, Song, Sarah, Waddell, Nic, Lakhani, Sunil and Simpson, Peter t (2016). An integrative analysis of invasive lobular breast cancer. Lorne Cancer Conference, Lorne VIC, Australia, February 11-13th 2016.
2016
Book Chapter
Future role of molecular profiling in small breast samples and personalised medicine
Sim, Sarah Yen Mi, Simpson, Peter T., Cummings, Margaret C. and Lakhani, Sunil R. (2016). Future role of molecular profiling in small breast samples and personalised medicine. A comprehensive guide to core needle biopsies of the breast. (pp. 803-817) edited by Sandra J. Shin. Cham, Switzerland: Springer International Publishing. doi: 10.1007/978-3-319-26291-8_23
2016
Journal Article
An epithelial to mesenchymal transition programme does not usually drive the phenotype of invasive lobular carcinomas
McCart Reed, Amy E., Kutasovic, Jamie R., Vargas, Ana Cristina, Jayanthan, Janani, Al-Murrani, Amel, Reid, Lynne E., Chambers, Rachael, Da Silva, Leonard, Melville, Lewis, Evans, Elizabeth, Porter, Alan, Papadimos, David, Thompson, Erik W., Lakhani, Sunil R. and Simpson, Peter T. (2016). An epithelial to mesenchymal transition programme does not usually drive the phenotype of invasive lobular carcinomas. Journal of Pathology, 238 (4), 489-494. doi: 10.1002/path.4668
2016
Conference Publication
Next Generation Sequencing On Endobronchial Ultrasound Transbronchial Needle Aspirate Lymph Node Specimens in Lung Cancer Shows a High Incidence of Mutations and Consistency with Single Gene Testing
Fielding, D., Bashirzadeh, F., Singh, M., Nandakumar, L., Reed, Mccart A., Black, D., Dalley, A., Pearson, J., Nones, K., Waddell, N., Simpson, P. and Lakhani, S. (2016). Next Generation Sequencing On Endobronchial Ultrasound Transbronchial Needle Aspirate Lymph Node Specimens in Lung Cancer Shows a High Incidence of Mutations and Consistency with Single Gene Testing. Thoracic Society of Australia & New Zealand and the Australian & New Zealand Society of Respiratory Science, Annual Scientific Meeting, Perth, WA, Australia, 1-6 April 2016. Wiley. doi: 10.1111/resp.12754_12
2016
Conference Publication
Identifying genetic vulnerabilities in cancers driven by defects in DNA-damage response
Srihari, S., Singla, J., Wong, L., Simpson, P. T., Khanna, K. K. and Ragan, M. A. (2016). Identifying genetic vulnerabilities in cancers driven by defects in DNA-damage response. 38th Annual CTRC-AACR San Antonio Breast Cancer Symposium, San Antonio, Texas, 8-12 December 2015. Philadelphia, PA, United States: American Association for Cancer Research. doi: 10.1158/1538-7445.SABCS15-PD6-05
2016
Book Chapter
Future role of molecular profiling in small breast samples and personalized medicine
Sim, Sarah Yen Mi, Simpson, Peter T., Cummings, Margaret C. and Lakhani, Sunil R. (2016). Future role of molecular profiling in small breast samples and personalized medicine. A comprehensive guide to core needle biopsies of the breast. (pp. 803-817) edited by Sandra J. Shin. Cham, Switzerland: Springer. doi: 10.1007/978-3-319-26291-8
2015
Journal Article
TGFβ isoforms and receptors mRNA expression in breast tumours: Prognostic value and clinical implications
Chen, Chenfeng, Zhao, Kong-Nan, Masci, Paul P., Lakhani, Sunil R., Antonsson, Annika, Simpson, Peter T. and Vitetta, Luis (2015). TGFβ isoforms and receptors mRNA expression in breast tumours: Prognostic value and clinical implications. BMC Cancer, 15 (1010) 1010, 1010. doi: 10.1186/s12885-015-1993-3
2015
Journal Article
Integrated genomic and transcriptomic analysis of human brain metastases identifies recurrently altered pathways of potential clinical significance
Saunus, Jodi M., Quinn, MIchael C. J., Patch, Ann-Marie, Pearson, John V., Bailey, Peter J., Nones, Katia, McCart Reed, Amy E., Miller, David, Peter J. Wilson, Al-Ejeh, Fares, Mariasegaram, Mythily, Lau, Queenie, Withers, Teresa, Jeffree, Rosalind L., Reid, Lynne E., Da Silva, Leonard, Matsika, Admire, Niland, Colleen M., Cummings, Margaret C., Bruxner, Timothy J. C., Christ, Angelika N., Harliwong, Ivon, Idrisoglu, Senel, Manning, Suzanne, Nourse, Craig, Nourbakhsh, Ehsan, Wani, Shivangi, Anderson, Matthew J., Fink, J. Lynn ... Lakhani, Sunil R. (2015). Integrated genomic and transcriptomic analysis of human brain metastases identifies recurrently altered pathways of potential clinical significance. Journal of Pathology, 237 (3), 363-378. doi: 10.1002/path.4583
Funding
Current funding
Supervision
Availability
- Associate Professor Peter Simpson is:
- Available for supervision
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Supervision history
Current supervision
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Doctor Philosophy
Developing optimal transport models for spatial and single cell data to understand cancer progression
Associate Advisor
Other advisors: Professor Jessica Mar, Dr Quan Nguyen
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Doctor Philosophy
Investigating therapeutic vulnerabilities in breast cancer.
Associate Advisor
Other advisors: Professor Sunil Lakhani, Associate Professor Amy McCart Reed
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Doctor Philosophy
Breast cancer metastasis prediction via machine learning and spatial cellular pathology
Associate Advisor
Other advisors: Dr Nan Ye, Dr Quan Nguyen
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Doctor Philosophy
Circulating biomarkers in invasive lobular breast carcinoma
Associate Advisor
Other advisors: Professor Sunil Lakhani, Associate Professor Amy McCart Reed
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Master Philosophy
Applications of Molecular Genetics in Translational Breast Cancer Research
Associate Advisor
Other advisors: Associate Professor Amy McCart Reed, Professor Sunil Lakhani
Completed supervision
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2025
Doctor Philosophy
Studies on the utility of Endobronchial Ultrasound Transbronchial Needle Aspiration (EBUS TBNA) samples in novel investigations of lung cancer genomics, and immune responses
Principal Advisor
Other advisors: Professor Sunil Lakhani
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2021
Doctor Philosophy
Multi-omics: Leveraging omics data integration to identify dysregulated biology in breast cancer
Principal Advisor
Other advisors: Associate Professor Amy McCart Reed, Dr Katia Nones
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2018
Doctor Philosophy
Genomic and transcriptomic biomarkers of prognosis in invasive lobular breast cancer.
Principal Advisor
Other advisors: Associate Professor Amy McCart Reed, Professor Sunil Lakhani
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2016
Doctor Philosophy
Intratumour heterogeneity in the development and progression of breast cancer
Principal Advisor
Other advisors: Associate Professor Amy McCart Reed, Professor Sunil Lakhani
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2016
Doctor Philosophy
Computational analysis of DNA repair pathways in breast cancer
Associate Advisor
Other advisors: Honorary Professor Kum Kum Khanna
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2016
Doctor Philosophy
Identification of new prognostic biomarker for triple negative breast cancer
Associate Advisor
Other advisors: Dr Jodi Saunus, Professor Sunil Lakhani
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2013
Doctor Philosophy
A Search For Novel Cancer Susceptibility Genes
Associate Advisor
Other advisors: Professor Sunil Lakhani, Professor Melissa Brown
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2013
Doctor Philosophy
Clinical-Pathological and Molecular Analysis to Understand Breast Cancer Progression
Associate Advisor
Other advisors: Professor Sunil Lakhani
Media
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