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
2013
Journal Article
Use of low-density lipoprotein cholesterol gene score to distinguish patients with polygenic and monogenic familial hypercholesterolaemia: a case-control study
Talmud, Philippa J., Shah, Sonia, Whittall, Ros, Futema, Marta, Howard, Philip, Cooper, Jackie A., Harrison, Seamus C., Li, KaWah, Drenos, Fotios, Karpe, Frederik, Neil, H. Andrew W., Descamps, Olivier S., Langenberg, Claudia, Lench, Nicholas, Kivimaki, Mika, Whittaker, John, Hingorani, Aroon D., Kumari, Meena and Humphries, Steve E. (2013). Use of low-density lipoprotein cholesterol gene score to distinguish patients with polygenic and monogenic familial hypercholesterolaemia: a case-control study. Lancet, 381 (9874), 1293-1301. doi: 10.1016/S0140-6736(12)62127-8
2013
Journal Article
Loci influencing blood pressure identified using a cardiovascular gene-centric array
Ganesh, S.K., Tragante, V., Guo, W., Guo, Y., Lanktree, M.B., Smith, E.N., Johnson, T., Castillo, B.A., Barnard, J., Baumert, J., Chang, Y.-P.C., Elbers, C.C., Farrall, M., Fischer, M.E., Franceschini, N., Gaunt, T.R., Gho, J.M.I.H., Gieger, C., Gong, Y., Isaacs, A., Kleber, M.E., Leach, I.M., McDonough, C.W., Meijs, M.F., Mellander, O., Molony, C.M., Nolte, I.M., Padmanabhan, S., Price, T.S. ... Asselbergs, F.W. (2013). Loci influencing blood pressure identified using a cardiovascular gene-centric array. Human Molecular Genetics, 22 (8), 1663-1678. doi: 10.1093/hmg/dds555
2013
Journal Article
Causal relevance of blood lipid fractions in the development of carotid atherosclerosis mendelian randomization analysis
Shah S., Casas J.-P., Drenos F., Whittaker J., Deanfield J., Swerdlow D.I., Holmes M.V., Kivimaki M., Langenberg C., Wareham N., Gertow K., Sennblad B., Strawbridge R.J., Baldassarre D., Veglia F., Tremoli E., Gigante B., De Faire U., Kumari M., Talmud P.J., Hamsten A., Humphries S.E. and Hingorani A.D. (2013). Causal relevance of blood lipid fractions in the development of carotid atherosclerosis mendelian randomization analysis. Circulation: Cardiovascular Genetics, 6 (1), 63-72. doi: 10.1161/CIRCGENETICS.112.963140
2013
Journal Article
A gene-centric study of common carotid artery remodelling
Harrison S.C., Zabaneh D., Asselbergs F.W., Drenos F., Jones G.T., Shah S., Gertow K., Sennblad B., Strawbridge R.J., Gigante B., Holewijn S., De Graaf J., Vermeulen S., Folkersen L., van Rij A.M., Baldassarre D., Veglia F., Talmud P.J., Deanfield J.E., Agu O., Kivimaki M., Kumari M., Bown M.J., Nyyssonen K., Rauramaa R., Smit A.J., Franco-Cereceda A., Giral P., Mannarino E. ... Humphries S.E. (2013). A gene-centric study of common carotid artery remodelling. Atherosclerosis, 226 (2), 440-446. doi: 10.1016/j.atherosclerosis.2012.11.002
2012
Journal Article
Integration of genetics into a systems model of electrocardiographic traits using humancvd beadchip
Gaunt, Tom R, Shah, Sonia, Nelson, Christopher P, Drenos, Fotios, Braund, Peter S., Adeniran, Ismail, Folkersen, Lasse, Lawlor, Debbie A., Casas, Juan-Pablo, Amuzu, Antoinette, Kivimaki, Mika, Whittaker, John, Eriksson, Per, Zhang, Henggui, Hancox, Jules C., Tomaszewski, Maciej, Burton, Paul R., Tobin, Martin D., Humphries, Steve E., Talmud, Philippa J., Macfarlane, Peter W., Hingorani, Aroon D., Samani, Nilesh J., Kumari, Meena and Day, Ian N.M. (2012). Integration of genetics into a systems model of electrocardiographic traits using humancvd beadchip. Circulation: Cardiovascular Genetics, 5 (6), 630-638. doi: 10.1161/CIRCGENETICS.112.962852
2012
Journal Article
Large-scale association analysis provides insights into the genetic architecture and pathophysiology of type 2 diabetes
Morris, Andrew P., Voight, Benjamin F., Teslovich, Tanya M., Ferreira, Teresa, Segre, Ayellet V., Steinthorsdottir, Valgerdur, Strawbridge, Rona J., Khan, Hassan, Grallert, Harald, Mahajan, Anubha, Prokopenko, Inga, Kang, Hyun Min, Dina, Christian, Esko, Tonu, Fraser, Ross M., Kanoni, Stavroula, Kumar, Ashish, Lagou, Vasiliki, Langenberg, Claudia, Luan, Jian'an, Lindgren, Cecilia M., Mueller-Nurasyid, Martina, Pechlivanis, Sonali, Rayner, N. William, Scott, Laura J., Wiltshire, Steven, Yengo, Loic, Kinnunen, Leena, Rossin, Elizabeth J. ... Shah, Sonia (2012). Large-scale association analysis provides insights into the genetic architecture and pathophysiology of type 2 diabetes. Nature Genetics, 44 (9), 981-990. doi: 10.1038/ng.2383
2012
Journal Article
Erratum: Meta-analysis of dense genecentric association studies reveals common and uncommon variants associated with height ((The American Journal of Human Genetics (2010) 88 (6-18))
Lanktree, Matthew B., Guo, Yiran, Murtaza, Muhammed, Glessner, Joseph T., Bailey, Swneke D., Onland-Moret, N. Charlotte, Lettre, Guillaume, Ongen, Halit, Rajagopalan, Ramakrishnan, Johnson, Toby, Shen, Haiqing, Nelson, Christopher P., Klopp, Norman, Baumert, Jens, Padmanabhan, Sandosh, Pankratz, Nathan, Pankow, James S., Shah, Sonia, Taylor, Kira, Barnard, John, Peters, Bas J., Maloney, Cliona M., Lobmeyer, Maximilian T., Stanton, Alice, Zafarmand, M. Hadi, Romaine, Simon P.R., Mehta, Amar, Van Iperen, Erik P.A., Gong, Yan ... Keating, Brendan J. (2012). Erratum: Meta-analysis of dense genecentric association studies reveals common and uncommon variants associated with height ((The American Journal of Human Genetics (2010) 88 (6-18)). American Journal of Human Genetics, 90 (6), 1116-1117. doi: 10.1016/j.ajhg.2012.05.017
2012
Journal Article
Erratum: Large-scale gene-centric meta-analysis across 39 studies identifies type 2 diabetes loci (American Journal of Human Genetics (2012) 90 (410-425))
Saxena, Richa, Elbers, Clara C., Guo, Yiran, Peter, Inga, Gaunt, Tom R., Mega, Jessica L., Lanktree, Matthew B., Tare, Archana, Castillo, Berta Almoguera, Li, Yun R., Johnson, Toby, Bruinenberg, Marcel, Gilbert-Diamond, Diane, Rajagopalan, Ramakrishnan, Voight, Benjamin F., Balasubramanyam, Ashok, Barnard, John, Bauer, Florianne, Baumert, Jens, Bhangale, Tushar, Boehm, Bernhard O., Braund, Peter S., Burton, Paul R., Chandrupatla, Hareesh R., Clarke, Robert, Cooper-DeHoff, Rhonda M., Crook, Errol D., Davey-Smith, George, Day, Ian N. ... Keating, Brendan J. (2012). Erratum: Large-scale gene-centric meta-analysis across 39 studies identifies type 2 diabetes loci (American Journal of Human Genetics (2012) 90 (410-425)). American Journal of Human Genetics, 90 (4), 753-753. doi: 10.1016/j.ajhg.2012.03.001
2012
Journal Article
Large-scale gene-centric meta-analysis across 39 studies identifies type 2 diabetes loci
Saxena, Richa, Elbers, Clara C., Guo, Yiran, Peter, Inga, Gaunt, Tom R., Mega, Jessica L., Lanktree, Matthew B., Tare, Archana, Castillo, Berta A., Li, Yun R., Johnson, Toby, Bruinenberg, Marcel, Gilbert-Diamond, Diane, Rajagopalan, Ramakrishnan, Voight, Benjamin F., Balasubramanyam, Ashok, Barnard, John, Bauer, Florianne, Baumert, Jens, Bhangale, Tushar, Bohm, Bernhard O., Braund, Peter S., Burton, Paul R., Chandrupatla, Hareesh R., Clarke, Robert, Cooper-Dehoff, Rhonda M., Crook, Errol D., Davey-Smith, George, Day, Ian N. ... Keating, Brendan J. (2012). Large-scale gene-centric meta-analysis across 39 studies identifies type 2 diabetes loci. American Journal of Human Genetics, 90 (3), 410-425. doi: 10.1016/j.ajhg.2011.12.022
2012
Journal Article
Cholesteryl ester transfer protein (CETP) polymorphisms affect mRNA splicing, HDL levels, and sex-dependent cardiovascular risk
Papp, Audrey C., Pinsonneault, Julia K., Wang, Danxin, Newman, Leslie C., Gong, Yan, Johnson, Julie A., Pepine, Carl J., Kumari, Meena, Hingorani, Aroon D., Talmud, Philippa J., Shah, Sonia, Humphries, Steve E. and Sadee, Wolfgang (2012). Cholesteryl ester transfer protein (CETP) polymorphisms affect mRNA splicing, HDL levels, and sex-dependent cardiovascular risk. PLoS ONE, 7 (3) e31930, e31930.1-e31930.9. doi: 10.1371/journal.pone.0031930
2012
Journal Article
Identification of the BCAR1-CFDP1-TMEM170A locus as a determinant of carotid intima-media thickness and coronary artery disease risk
Gertow, Karl, Sennblad, Bengt, Strawbridge, Rona J., Ohrvik, John, Zabaneh, Delilah, Shah, Sonia, Veglia, Fabrizio, Fava, Cristiano, Kavousi, Maryam, McLachlan, Stela, Kivimaki, Mika, Bolton, Jennifer L., Folkersen, Lasse, Gigante, Bruna, Leander, Karin, Vikstrom, Max, Larsson, Malin, Silveira, Angela, Deanfield, John, Voight, Benjamin F., Fontanillas, Pierre, Sabater-Lleal, Maria, Colombo, Gualtiero I., Kumari, Meena, Langenberg, Claudia, Wareham, Nick J., Uitterlinden, André G., Gabrielsen, Anders, Hedin, Ulf ... Hamsten, Anders (2012). Identification of the BCAR1-CFDP1-TMEM170A locus as a determinant of carotid intima-media thickness and coronary artery disease risk. Circulation: Cardiovascular Genetics, 5 (6), 656-665. doi: 10.1161/CIRCGENETICS.112.963660
2012
Journal Article
Large-scale association analyses identify new loci influencing glycemic traits and provide insight into the underlying biological pathways
Scott, Robert A., Lagou, Vasiliki, Welch, Ryan P., Wheeler, Eleanor, Montasser, May E., Luan, Jian’an, Mägi, Reedik, Strawbridge, Rona J., Rehnberg, Emil, Gustafsson, Stefan, Kanoni, Stavroula, Rasmussen-Torvik, Laura J., Yengo, Loïc, Lecoeur, Cecile, Shungin, Dmitry, Sanna, Serena, Sidore, Carlo, Johnson, Paul C. D., Jukema, J. Wouter, Johnson, Toby, Mahajan, Anubha, Verweij, Niek, Thorleifsson, Gudmar, Hottenga, Jouke-Jan, Shah, Sonia, Smith, Albert V., Sennblad, Bengt, Gieger, Christian, Salo, Perttu ... Barroso, Inês (2012). Large-scale association analyses identify new loci influencing glycemic traits and provide insight into the underlying biological pathways. Nature Genetics, 44 (9), 991-1005. doi: 10.1038/ng.2385
2012
Journal Article
Comparative analysis of genome-wide association studies signals for lipids, diabetes, and coronary heart disease: Cardiovascular Biomarker Genetics Collaboration
Angelakopoulou, Aspasia, Shah, Tina, Sofat, Reecha, Shah, Sonia, Berry, Diane J., Cooper, Jackie, Palmen, Jutta, Tzoulaki, Ioanna, Wong, Andrew, Jefferis, Barbara J., Maniatis, Nikolas, Drenos, Fotios, Gigante, Bruna, Hardy, Rebecca, Laxton, Ross C., Leander, Karin, Motterle, Anna, Simpson, Iain A., Smeeth, Liam, Thomson, Andy, Verzilli, Claudio, Kuh, Diana, Ireland, Helen, Deanfield, John, Caulfield, Mark, Wallace, Chris, Samani, Nilesh, Munroe, Patricia B., Lathrop, Mark ... Hingorani, Aroon D. (2012). Comparative analysis of genome-wide association studies signals for lipids, diabetes, and coronary heart disease: Cardiovascular Biomarker Genetics Collaboration. European Heart Journal, 33 (3), 393-407. doi: 10.1093/eurheartj/ehr225
2012
Journal Article
IRS1 gene variants, dysglycaemic metabolic changes and type-2 diabetes risk
Yiannakouris, N., Cooper, J. A., Shah, S., Drenos, F., Ireland, H. A., Stephens, J. W., Li, K.-W., Elkeles, R., Godsland, I. F., Kivimaki, M., Hingorani, A. D., Kumari, M., Talmud, P. J. and Humphries, S. E. (2012). IRS1 gene variants, dysglycaemic metabolic changes and type-2 diabetes risk. Nutrition, Metabolism and Cardiovascular Diseases, 22 (12), 1024-1030. doi: 10.1016/j.numecd.2011.05.009
2012
Journal Article
Use of Allele-Specific FAIRE to Determine Functional Regulatory Polymorphism Using Large-Scale Genotyping Arrays
Smith, Andrew J. P., Howard, Philip, Shah, Sonia, Eriksson, Per, Stender, Stefan, Giambartolomei, Claudia, Folkersen, Lasse, Tybjaerg-Hansen, Anne, Kumari, Meena, Palmen, Jutta, Hingorani, Aroon D., Talmud, Philippa J. and Humphries, Steve E. (2012). Use of Allele-Specific FAIRE to Determine Functional Regulatory Polymorphism Using Large-Scale Genotyping Arrays. PLoS Genetics, 8 (8) e1002908, e1002908.1-e1002908.10. doi: 10.1371/journal.pgen.1002908
2011
Journal Article
Transcriptomic analyses of murine resolution-phase macrophages
Stables, Melanie J., Shah, Sonia, Camon, Evelyn B., Lovering, Ruth C., Newson, Justine, Bystrom, Jonas, Farrow, Stuart and Gilroy, Derek W. (2011). Transcriptomic analyses of murine resolution-phase macrophages. Blood, 118 (26), e192-e208. doi: 10.1182/blood-2011-04-345330
2011
Journal Article
Blood pressure loci identified with a gene-centric array
Johnson, Toby, Gaunt, Tom R., Newhouse, Stephen J., Padmanabhan, Sandosh, Tomaszewski, Marciej, Kumari, Meena, Morris, Richard W., Tzoulaki, Ioanna, O'Brien, Eoin T., Poulter, Neil R., Sever, Peter, Shields, Denis C., Thom, Simon, Wannamethee, Sasiwarang G., Whincup, Peter H., Brown, Morris J., Connell, John M., Dobson, Richard J., Howard, Philip J., Mein, Charles A., Onipinla, Abiodun, Shaw-Hawkins, Sue, Zhang, Yun, Smith, George Davey, Day, Ian N. M., Lawlor, Debbie A., Goodall, Alison H.., Fowkes, F. Gerald, Abecasis, Goncalo R. ... Munroe, Patricia B. (2011). Blood pressure loci identified with a gene-centric array. American Journal of Human Genetics, 89 (6), 688-700. doi: 10.1016/j.ajhg.2011.10.013
2011
Journal Article
Meta-analysis of Dense Genecentric Association Studies Reveals Common and Uncommon Variants Associated with Height
Lanktree, Matthew B., Guo, Yiran, Murtaza, Muhammed, Glessner, Joseph T., Bailey, Swneke D., Onland-Moret, N. Charlotte, Lettre, Guillaume, Ongen, Halit, Rajagopalan, Ramakrishnan, Johnson, Toby, Shen, Haiqing, Nelson, Christopher P., Klopp, Norman, Baumert, Jens, Padmanabhan, Sandosh, Pankratz, Nathan, Pankow, James S., Shah, Sonia, Taylor, Kira, Barnard, John, Peters, Bas J., Maloney, Cliona M., Lobmeyer, Maximilian T., Stanton, Alice, Zafarmand, M. Hadi, Romaine, Simon P. R., Mehta, Amar, van Iperen, Erik P. A., Gong, Yan ... Keating, Brendan J. (2011). Meta-analysis of Dense Genecentric Association Studies Reveals Common and Uncommon Variants Associated with Height. American Journal of Human Genetics, 88 (1), 6-18. doi: 10.1016/j.ajhg.2010.11.007
2011
Journal Article
ChIP-on-chip analysis reveals angiopoietin 2 (Ang2, ANGPT2) as a novel target of steroidogenic factor-1 (SF-1, NR5A1) in the human adrenal gland
Ferraz-de-Souza, Bruno, Lin, Lin, Shah, Sonia, Jina, Nipurna, Hubank, Mike, Dattani, Mehul T. and Achermann, John C. (2011). ChIP-on-chip analysis reveals angiopoietin 2 (Ang2, ANGPT2) as a novel target of steroidogenic factor-1 (SF-1, NR5A1) in the human adrenal gland. FASEB Journal, 25 (4), 1166-1175. doi: 10.1096/fj.10-170522
2011
Journal Article
Genetic Variants Associated with von Willebrand Factor Levels in Healthy Men and Women Identified Using the HumanCVD BeadChip
Zabaneh, Delilah, Gaunt, Tom R., Kumari, Meena, Drenos, Fotios, Shah, Sonia, Berry, Diane, Power, Chris, Hypponen, Elina, Shah, Tina, Palmen, Jutta, Pallas, Jacky, Talmud, Philippa J., Casas, Juan Pablo, Sofat, Reecha, Lowe, Gordon, Rumley, Ann, Morris, Richard W., Whincup, Peter H., Rodriguez, Santiago, Ebrahim, Shah, Marmot, Michael G., Smith, George Davey, Lawlor, Debbie A., Kivimaki, Mika, Whittaker, John, Hingorani, Aroon D., Day, Ian N. and Humphries, Steve E. (2011). Genetic Variants Associated with von Willebrand Factor Levels in Healthy Men and Women Identified Using the HumanCVD BeadChip. Annals of Human Genetics, 75 (4), 456-467. doi: 10.1111/j.1469-1809.2011.00654.x
Funding
Current funding
Past funding
Supervision
Availability
- Associate Professor Sonia Shah is:
- Available for supervision
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Supervision history
Current supervision
-
Doctor Philosophy
Using Genetics and Artificial Intelligence to Support Disease Prediction and Diagnosis
Principal Advisor
-
Doctor Philosophy
Investigating sex differences in cardiovascular risk factors using genomic data
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
Using genetics to predict drug efficacy and on-target side effects of pharmacological agents
Associate Advisor
Other advisors: Professor Glenn King, Professor David Evans
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Doctor Philosophy
Understanding genetic adaptation of the heart to extreme environments
Associate Advisor
Other advisors: Professor Nathan Palpant
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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