Overview
Background
My group's research uses large-scale genomic data to address knowledge gaps in disease, with a particular focus on cardiovascular disease.
Research programme
1. Cardiovascular disease research using big-data and genomics: with the goal of improving prevention and treatment of cardiovascular disease. By focusing on underrepresented groups, including women, my research aims to also address inequity in cardiovascular outcomes. I am the lead of the South Asian Genes and Health in Australia (SAGHA) study, which aims to increase representation of Australian South Asians in cardiovascular and genomics research. See saghaus.org for further details.
2. Drug genomics: I'm interested in using genomic approaches to predict drug effects, including identification of drug repurposing opportunities as well as identifying unknown adverse effects of medication.
3. Liver transplant research: In this collaboration with the QLD Liver Transplant Unit, we are using genomics to understand the effect of normo-thermic perfusion (a new organ storage method) on liver function, with the long-term goal of improving our ability to predict transplant outcomes.
Career summary: I was awarded my PhD from University College London (UK) in cardiovascular genetics. I began my post-doctoral fellowship under the mentorship of Prof Peter Visscher at the Queensland Brain Institute in 2013. Between 2016-2018, I was the lead analyst for the International Heart Failure Genetics Consortium (HERMES). In 2018, I was awarded an NHMRC Early Career Researcher Fellowship to investigate the relationship between cardiovascular and brain-related disorders using large-scale genetic and genomic data, under the mentorship of Prof Naomi Wray. I currently hold a National Heart Foundation Future Leader Fellowship.
Recognition:
2024 Australian Academy of Science Ruth Stephens Gani Medal for outstanding contribution to genetics research
2023 1 of 5 global finalists for the Nature Inspiring Women in Science (Scientific Achievement Award)
2023 Lifesciences QLD Rose-Anne Kelso Award
2023: Named in Australia's Top 25 Women in Science by Newscorp
2022 Queensland Young Tall Poppy Award
2022 UQ Foundation Research Excellence Award
2021/2022 Australian Superstar of STEM,
2020 Genetic Society of Australasia Early Career Award
2020 Women in Technology Rising Star Science Award
Availability
- Associate Professor Sonia Shah is:
- Available for supervision
- Media expert
Fields of research
Qualifications
- Masters (Coursework) of Science, The University of Manchester
- Doctor of Philosophy, University College London
Research impacts
Advancing knowledge in cardiovascular disease
Familial Hypercholesterolemia (FH) is a preventable cause of premature disease and death and is relatively common in the general population (~ 1 in 250). FH is considered a monogenic disease, though a monogenic mutation is only identified in ~30% of FH patients. This paradigm-shifting research on FH demonstrated a polygenic contribution to FH (Talmud P et al Lancet 2013;381:1293-301; FWCI 34.8), as a result of which the UK NICE guidelines on FH management were updated, and several UK Diagnostic Laboratories have implemented an additional polygenic test in FH patients, with reports of positive psychosocial impact on patients (Futema et al 2021, Journal of Lipid Research 62:100139). This research is cited in a patent (WO2014181107A1 - Genetic Method of Aiding The Diagnosis and Treatment of Familial Hypercholesterolemia). It has been used to develop a new disease category, termed ‘Polygenic Hypercholesterolemia’, https://www.heartuk.org.uk/genetic-conditions/polygenic-hypercholesterolaemia), cited in the NHS Chief Medical Officer 2016 annual report focused on how genomics can improve health.
I was part of the executive committee for the largest international heart failure consortium (HERMES https://www.hermesconsortium.org/) and co-led the largest (published) genome-wide association study on heart failure (Shah S et al Nat Commun 2020;11:296; FWCI 15.3) at the time, identifying novel disease biology. Our heart failure study has been cited >280 times in 3 years since publication, and has led to new avenues for drug development (e.g. Schmidt AF et al Nat Commun 2020:11:3255).
Demonstrating potential clinical application of genomic data
We demonstrated for the first time that genome-wide DNA methylation data may be useful for predicting human phenotypes over and above genetic data (Shah S et al Am J Hum Genet 2015;97:1; FWCI 2.8), as well as future health outcomes including mortality and (Marioni R et al Genome Biology 2015;16:25; FWCI 27.4). This research has been cited in 3 patents (e.g. WO-2018150042- A1 - DNA methylation signatures for determining a survival probability, which is using the findings to develop tests for clinical use), in two books (Handbook of Epigenetics (3rd Edition) and Aging: From Fundamental Biology to Societal Impact), highlighted in the online media site “The Conversation” and cited in the Wikipedia page on ‘Epigenetic Clock’.
Works
Search Professor Sonia Shah’s works on UQ eSpace
2011
Journal Article
Four genetic loci influencing electrocardiographic indices of left ventricular hypertrophy
Shah, Sonia, Nelson, Christopher P., Gaunt, Tom R., van der Harst, Pim, Barnes, Timothy, Braund, Peter S., Lawlor, Debbie A., Casas, Juan-Pablo, Padmanabhan, Sandosh, Drenos, Fotios, Kivimaki, Mika, Talmud, Philippa J., Humphries, Steve E., Whittaker, John, Morris, Richard W., Whincup, Peter H., Dominiczak, Anna, Munroe, Patricia B., Johnson, Toby, Goodall, Alison H., Cambien, Francois, Diemert, Patrick, Hengstenberg, Christian, Ouwehand, Willem H., Felix, Janine F., Glazer, Nicole L., Tomaszewski, Maciej, Burton, Paul R., Tobin, Martin D. ... Samani, Nilesh J. (2011). Four genetic loci influencing electrocardiographic indices of left ventricular hypertrophy. Circulation: Cardiovascular Genetics, 4 (6), 626-635. doi: 10.1161/CIRCGENETICS.111.960203
2011
Journal Article
Meta analysis of candidate gene variants outside the LPA locus with Lp(a) plasma levels in 14,500 participants of six White European cohorts
Zabaneh, Delilah, Kumari, , Meena, Sandhu, Manj, Wareham, Nick, Wainwright, Nick, Papamarkou, Theodore, Hopewell, Jemma, Clarke, Robert, Li, KaWah, Palmen, Jutta, Talmud, Philippa J., Kronenberg, Florian, Lamina, Claudia, Summerer, Monika, Paulweber, Bernhard, Price, Jackie, Fowkes, Gerry, Stewart, Marlene, Drenos, Fotios, Shah, Sonia, Shah, Tina, Casas, Juan-Pablo, Kivimaki, Mika, Whittaker, John, Hingorani, Aroon D. and Humphries, Steve E. (2011). Meta analysis of candidate gene variants outside the LPA locus with Lp(a) plasma levels in 14,500 participants of six White European cohorts. Atherosclerosis, 217 (2), 447-451. doi: 10.1016/j.atherosclerosis.2011.04.015
2010
Conference Publication
A report on the Genetics of Complex Diseases meeting of the British Atherosclerosis Society, Cambridge, UK, 17-18 September 2009
Holmes, Michael V., Shah, Sonia H., Angelakopoulou, Aspasia, Khan, Tauseef, Swerdlow, Daniel, Kuchenbaecker, Karoline, Sofat, Reecha and Shah, Tina (2010). A report on the Genetics of Complex Diseases meeting of the British Atherosclerosis Society, Cambridge, UK, 17-18 September 2009. E. Park, Shannon, Co. Clare, Ireland: Elsevier Ireland. doi: 10.1016/j.atherosclerosis.2009.11.034
2010
Conference Publication
Identification of Genes Associated with Qt Interval Using the 50K Cardio-Metabolic Snp Chip: Results From the Whitehall II Study
Shah, S., Drenos, F., Shah, T., Palmen, J., Sofat, R., Kumari, M., Pallas, J., MacFarlane, P., Whittaker, J., Talmud, P., Humphries, S. and Hingorani, A. (2010). Identification of Genes Associated with Qt Interval Using the 50K Cardio-Metabolic Snp Chip: Results From the Whitehall II Study. 78th Congress of the European-Atherosclerosis-Society, Hamburg Germany, Jun 20-23, 2010.
2009
Journal Article
Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip
Talmud, Philippa J., Drenos, Fotios, Shah, Sonia, Shah, Tina, Palmen, Jutta, Verzilli, Claudio, Gaunt, Tom R., Pallas, Jacky, Lovering, Ruth, Li, Kawah, Casas, Juan Pablo, Sofat, Reecha, Kumari, Meena, Rodriguez, Santiago, Johnson, Toby, Newhouse, Stephen J., Dominiczak, Anna, Samani, Nilesh J., Caulfield, Mark, Sever, Peter, Stanton, Alice, Shields, Denis C., Padmanabhan, Sandosh, Melander, Olle, Hastie, Claire, Delles, Christian, Ebrahim, Shah, Marmot, Michael G., Smith, George Davey ... Hingorani, Aroon D. (2009). Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip. American Journal of Human Genetics, 85 (5), 628-642. doi: 10.1016/j.ajhg.2009.10.014
2009
Conference Publication
Complex disease genetics: present and future translational applications
Holmes, Michael V., Shah, Sonia H., Angelakopoulou, Aspasia, Khan, Tauseef, Swerdlow, Daniel, Kuchenbaecker, Karoline, Sofat, Reecha and Tina, Tina (2009). Complex disease genetics: present and future translational applications. London, United Kingdom: BioMed Central. doi: 10.1186/gm104
2009
Conference Publication
IDENTIFICATION OF GENES ASSOCIATED WITH QT INTERVAL USING THE 50K CARDIO-METABOLIC SNP CHIP: RESULTS FROM THE WHITEHALL II STUDY
Shah, S., Drenos, F., Shah, T., Palmen, J., Vezzili, C., Sofat, R., Kumari, M., Kivamaki, M., Pallas, J., MacFarlane, P., Whittaker, J., Talmud, P. J., Humphries, S. E. and Hingorani, A. D. (2009). IDENTIFICATION OF GENES ASSOCIATED WITH QT INTERVAL USING THE 50K CARDIO-METABOLIC SNP CHIP: RESULTS FROM THE WHITEHALL II STUDY. Autumn Meeting of the British-Atherosclerosis-Society, Cambridge England, Sep 17-18, 2009. CLARE: ELSEVIER IRELAND LTD. doi: 10.1016/j.atherosclerosis.2009.09.058
2009
Journal Article
Prox1 maintains muscle structure and growth in the developing heart
Risebro, Catherine A., Searles, Richelle G., Melville, Athalie A. D., Ehler, Elisabeth, Jina, Nipurna, Shah, Sonia, Pallas, Jacky, Hubank, Mike, Dillard, Miriam, Harvey, Natasha L., Schwartz, Robert J., Chien, Kenneth R., Oliver, Guillermo and Riley, Paul R. (2009). Prox1 maintains muscle structure and growth in the developing heart. Development, 136 (3), 495-505. doi: 10.1242/dev.030007
2009
Conference Publication
Genetic Determinants of Ldl-C Levels: Using the 50K Cardio-Metabolic Chip to Explore the Genetic Architecture of Lipid Traits in Whitehall II
Humphries, S., Talmud, P., Drenos, F., Shah, S., Palmen, J., Shah, T., Kumari, M., Pallas, J., Casas, J., Whittaker, J. and Hingorani, A. (2009). Genetic Determinants of Ldl-C Levels: Using the 50K Cardio-Metabolic Chip to Explore the Genetic Architecture of Lipid Traits in Whitehall II. ELSEVIER IRELAND LTD.
2009
Journal Article
Overexpression of MHC class I heavy chain protein in young skeletal muscle leads to severe myositis: implications for juvenile myositis
Li, Charles Kwok-chong, Knopp, Paul, Moncrieffe, Halima, Singh, Bhanu, Shah, Sonia, Nagaraju, Kanneboyina, Varsani, Hemlata, Gao, Bin and Wedderburn, Lucy R. (2009). Overexpression of MHC class I heavy chain protein in young skeletal muscle leads to severe myositis: implications for juvenile myositis. American Journal of Pathology, 175 (3), 1030-1040. doi: 10.2353/ajpath.2009.090196
2009
Conference Publication
Exploring the Genetic Architecture of Lipid Traits in Whitehall II Healthy Men and Women Using the 50K-Snp Cardio-Metabolic Chip
Humphries, S. E., Talmud, P. J., Drenos, F., Shah, S., Palmen, S., Shah, T., Kumari, M., Kivimaki, M., Pallas, J., Casas, J. P., Whittaker, J. and Hingorani, A. (2009). Exploring the Genetic Architecture of Lipid Traits in Whitehall II Healthy Men and Women Using the 50K-Snp Cardio-Metabolic Chip. 23rd Annual Medical and Scientific Meeting of HEART-UK, Liverpool England, Jun 24-26, 2009. ELSEVIER IRELAND LTD. doi: 10.1016/j.atherosclerosis.2009.07.002
2009
Journal Article
Identifying differential exon splicing using linear models and correlation coefficients.
Shah, Sonia H. and Pallas, Jacqueline A. (2009). Identifying differential exon splicing using linear models and correlation coefficients.. BMC bioinformatics, 10 (1) 26, 26.1-26.16. doi: 10.1186/1471-2105-10-26
2009
Journal Article
rHVDM: An R package to predict the activity and targets of a transcription factor
Barenco, M., Papouli, E., Shah, S., Brewer, D., Miller, C. J. and Hubank, M. (2009). rHVDM: An R package to predict the activity and targets of a transcription factor. Bioinformatics, 25 (3), 419-420. doi: 10.1093/bioinformatics/btn639
2006
Journal Article
Annotation of environmental OMICS data: Application to the transcriptomics domain
Morrison N., Wood A.J., Hancock D., Shah S., Hakes L., Gray T., Tiwari B., Kille P., Cossins A., Hegarty M., Allen M.J., Wilson W.H., Olive P., Last K., Kramer C., Bailhache T., Reeves J., Pallett D., Warne J., Nashar K., Parkinson H., Sansone S.-A., Rocca-Serra P., Stevens R., Snape J., Brass A. and Field D. (2006). Annotation of environmental OMICS data: Application to the transcriptomics domain. OMICS A Journal of Integrative Biology, 10 (2), 172-178. doi: 10.1089/omi.2006.10.172
Funding
Current funding
Past funding
Supervision
Availability
- Associate Professor Sonia Shah is:
- Available for supervision
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Supervision history
Current supervision
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Doctor Philosophy
Investigating sex differences in cardiovascular risk factors using genomic data
Principal Advisor
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Doctor Philosophy
Using Genetics and Artificial Intelligence to Support Disease Prediction and Diagnosis
Principal Advisor
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Doctor Philosophy
Using genomics to predict the mechanism-of-action of a chemical entity
Principal Advisor
Other advisors: Professor Irina Vetter
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Doctor Philosophy
Understanding genetic adaptation of the heart to extreme environments
Associate Advisor
Other advisors: Professor Nathan Palpant
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Doctor Philosophy
Using genetics to predict drug efficacy and on-target side effects of pharmacological agents
Associate Advisor
Other advisors: Professor Glenn King, Professor David Evans
Completed supervision
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2024
Doctor Philosophy
Using Transcriptomics technologies in health-related research: Applications and Challenges
Principal Advisor
Other advisors: Dr Quan Nguyen
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2024
Doctor Philosophy
Using genomic data to advance understanding of heart failure aetiology
Principal Advisor
Other advisors: Professor Naomi Wray
Media
Enquiries
Contact Associate Professor Sonia Shah directly for media enquiries about:
- cardiovascular disease
- genetics
- genomics
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