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
2015
Journal Article
C9orf72 hexanucleotide repeat expansions in Chinese sporadic amyotrophic lateral sclerosis
He, Ji, Tang, Lu, Benyamin, Beben, Shah, Sonia, Hemani, Gib, Liu, Rong, Ye, Shan, Liu, Xiaolu, Ma, Yan, Zhang, Huagang, Cremin, Katie, Leo, Paul, Wray, Naomi R., Visscher, Peter M., Xu, Huji, Brown, Matthew A., Bartlett, Perry F., Mangelsdorf, Marie and Fan, Dongsheng (2015). C9orf72 hexanucleotide repeat expansions in Chinese sporadic amyotrophic lateral sclerosis. Neurobiology of Aging, 36 (9) 2660.e1, 2660.e1-2660.e8. doi: 10.1016/j.neurobiolaging.2015.06.002
2015
Journal Article
Mendelian randomization of blood lipids for coronary heart disease
Holmes, Michael V., Asselbergs, Folkert W., Palmer, Tom M., Drenos, Fotios, Lanktree, Matthew B., Nelson, Christopher P., Dale, Caroline E., Padmanabhan, Sandosh, Finan, Chris, Swerdlow, Daniel I., Tragante, Vinicius, van Iperen, Erik P. A., Sivapalaratnam, Suthesh, Shah, Sonia, Elbers, Clara C., Shah, Tina, Engmann, Jorgen, Giambartolomei, Claudia, White, Jon, Zabaneh, Delilah, Sofat, Reecha, McLachlan, Stela, Doevendans, Pieter A., Balmforth, Anthony J., Hall, Alistair S., North, Kari E., Almoguera, Berta, Hoogeveen, Ron C., Cushman, Mary ... Casas, Juan P. (2015). Mendelian randomization of blood lipids for coronary heart disease. European Heart Journal, 36 (9), 539-550. doi: 10.1093/eurheartj/eht571
2015
Journal Article
New genetic loci link adipose and insulin biology to body fat distribution
Shungin, Dmitry, Winkler, Thomas W, Croteau-Chonka, Damien C, Ferreira, Teresa, Locke, Adam E, Magi, Reedik, Strawbridge, Rona J, Pers, Tune H, Fischer, Krista, Justice, Anne E, Workalemahu, Tsegaselassie, Wu, Joseph M.W, Buchkovich, Martin L, Heard-Costa, Nancy L, Roman, Tamara S, Drong, Alexander W, Song, Ci, Gustafsson, Stefan, Day, Felix R, Esko, Tonu, Fall, Tove, Kutalik, Zoltan, Luan, Jian'an, Randall, Joshua C, Scherag, Andre, Vedantam, Sailaja, Wood, Andrew R, Chen, Jin, Fehrmann, Rudolf ... Shah, Sonia (2015). New genetic loci link adipose and insulin biology to body fat distribution. Nature, 518 (7538), 187-196. doi: 10.1038/nature14132
2015
Journal Article
Genetic studies of body mass index yield new insights for obesity biology
Locke, Adam E., Kahali, Bratati, Berndt, Sonja I., Justice, Anne E., Pers, Tune H., Day, Felix R., Powell, Corey, Vedantam, Sailaja, Buchkovich, Martin L., Yang, Jian, Croteau-Chonka, Damien C., Esko, Tonu, Fall, Tove, Ferreira, Teresa, Gustafsson, Stefan, Kutalik, Zoltán, Luan, Jian'an, Mägi, Reedik, Randall, Joshua C., Winkler, Thomas W., Wood, Andrew R., Workalemahu, Tsegaselassie, Faul, Jessica D., Smith, Jennifer A., Zhao, Jing Hua, Zhao, Wei, Chen, Jin, Fehrmann, Rudolf, Hedman, Asa K. ... Shah, Sonia (2015). Genetic studies of body mass index yield new insights for obesity biology. Nature, 518 (7538), 197-206. doi: 10.1038/nature14177
2015
Journal Article
DNA methylation age of blood predicts all-cause mortality in later life
Marioni, Riccardo E., Shah, Sonia, McRae, Allan F., Chen, Brian H., Colicino, Elena, Harris, Sarah E., Gibson, Jude, Henders, Anjali K., Redmond, Paul, Cox, Simon R., Pattie, Alison, Corley, Janie, Murphy, Lee, Martin, Nicholas G., Montgomery, Grant W., Feinberg, Andrew P., Fallin, M. Daniele, Multhaup, Michael L., Jaffe, Andrew E., Joehanes, Roby, Schwartz, Joel, Just, Allan C., Lunetta, Kathryn L., Murabito, Joanne M., Starr, John M., Horvath, Steve, Baccarelli, Andrea A., Levy, Daniel, Visscher, Peter M. ... Deary, Ian J. (2015). DNA methylation age of blood predicts all-cause mortality in later life. Genome Biology, 16 (1) 25, 25.1-25.12. doi: 10.1186/s13059-015-0584-6
2014
Journal Article
Genetic determinants of circulating interleukin-1 receptor antagonist levels and their association with glycemic traits
Herder, Christian, Nuotio, Marja-Liisa, Shah, Sonia, Blankenberg, Stefan, Brunner, Eric J., Carstensen, Maren, Gieger, Christian, Grallert, Harald, Jula, Antti, Kahonen, Mika, Kettunen, Johannes, Kivimaki, Mika, Koenig, Wolfgang, Kristiansson, Kati, Langenberg, Claudia, Lehtimaki, Terho, Luotola, Kari, Marzi, Carola, Mueller, Christian, Peters, Annette, Prokisch, Holger, Raitakari, Olli, Rathmann, Wolfgang, Roden, Michael, Salmi, Marko, Schramm, Katharina, Swerdlow, Daniel, Tabak, Adam G., Thorand, Barbara ... Salomaa, Veikko (2014). Genetic determinants of circulating interleukin-1 receptor antagonist levels and their association with glycemic traits. Diabetes, 63 (12), 4343-4359. doi: 10.2337/db14-0731
2014
Journal Article
Refinement of Variant Selection for the LDL Cholesterol Genetic Risk Score in the Diagnosis of the Polygenic Form of Clinical Familial Hypercholesterolemia and Replication in Samples from 6 Countries
Futema, Marta, Shah, Sonia, Cooper, Jackie A., Li, KahWa, Whittall, Ros A., Sharifi, Mahtab, Goldberg, Olivia, Drogari, Euridiki, Mollaki, Vasilik, Wiegman, Albert, Defesche, Joep, D'Agostino, Maria N., D'Angelo, Antonietta, Rubba, Paolo, Fortunato, Giuliana, Walus-Miarka, Malgorzata, Hegele, Robert A., Aderayo Bamimore, Mary, Durst, Ronen, Leitersdorf, Eran, Mulder, Monique T., Roeters van Lennep, Jeanine E., Sijbrands, Eric J., Whittaker, John C., Talmud, Philippa J. and Humphries, Steve E. (2014). Refinement of Variant Selection for the LDL Cholesterol Genetic Risk Score in the Diagnosis of the Polygenic Form of Clinical Familial Hypercholesterolemia and Replication in Samples from 6 Countries. Clinical Chemistry, 61 (1), 231-238. doi: 10.1373/clinchem.2014.231365
2014
Journal Article
Genetic and environmental exposures constrain epigenetic drift over the human life course
Shah, Sonia, McRae, Allan F., Marioni, Riccardo E., Harris, Sarah E., Gibson, Jude, Henders, Anjali K., Redmond, Paul, Cox, Simon R., Pattie, Alison, Corley, Janie, Murphy, Lee, Martin, Nicholas G., Montgomery, Grant W., Starr, John M., Wray, Naomi R., Deary, Ian J. and Visscher, Peter M. (2014). Genetic and environmental exposures constrain epigenetic drift over the human life course. Genome Research, 24 (11), 1725-1733. doi: 10.1101/gr.176933.114
2014
Journal Article
Low levels of IgM antibodies against phosphorylcholine are associated with fast carotid intima media thickness progression and cardiovascular risk in men
Gigante, Bruna, Leander, Karin, Vikström, Max, Baldassarre, Damiano, Veglia, Fabrizio, Strawbridge, Rona J., McLeod, Olga, Gertow, Karl, Sennblad, Bengt, Shah, Sonia, Zabaneh, Delilah, Humphries, Steve E., Kauhanen, Jussi, Rauramaa, Rainer, Smit, Andries J., Mannarino, Elmo, Giral, Philippe, Tremoli, Elena, Hamsten, Anders, Frostegård, Johan and de Faire, Ulf (2014). Low levels of IgM antibodies against phosphorylcholine are associated with fast carotid intima media thickness progression and cardiovascular risk in men. Atherosclerosis, 236 (2), 394-399. doi: 10.1016/j.atherosclerosis.2014.07.030
2014
Journal Article
Association between alcohol and cardiovascular disease: Mendelian randomisation analysis based on individual participant data
Holmes, Michael V., Dale, Caroline E., Zuccolo, Luisa, Silverwood, Richard J., Guo, Yiran, Ye, Zheng, Prieto-Merino, David, Dehghan, Abbas, Trompet, Stella, Wong, Andrew, Cavadino, Alana, Drogan, Dagmar, Padmanabhan, Sandosh, Li, Shanshan, Yesupriya, Ajay, Leusink, Maarten, Sundstrom, Johan, Hubacek, Jaroslav A., Pikhart, Hynek, Swerdlow, Daniel I., Panayiotou, Andrie G., Borinskaya, Svetlana A., Finan, Chris, Shah, Sonia, Kuchenbaecker, Karoline B., Shah, Tina, Engmann, Jorgen, Folkersen, Lasse, Eriksson, Per ... Casas, Juan P. (2014). Association between alcohol and cardiovascular disease: Mendelian randomisation analysis based on individual participant data. BMJ - British Medical Journal, 349 (jul10 6) g4164, g4164-g4164. doi: 10.1136/bmj.g4164
2014
Journal Article
Contribution of genetic variation to transgenerational inheritance of DNA methylation
McRae, Allan F., Powell, Joseph E., Henders, Anjali K., Bowdler, Lisa, Hemani, Gibran, Shah, Sonia, Painter, Jodie N., Martin, Nicholas G., Visscher, Peter M. and Montgomery, Grant W. (2014). Contribution of genetic variation to transgenerational inheritance of DNA methylation. Genome Biology, 15 (5) R73, 1-10. doi: 10.1186/gb-2014-15-5-r73
2014
Journal Article
Genome-wide trans-ancestry meta-analysis provides insight into the genetic architecture of type 2 diabetes susceptibility
DIAbetes Genetics Replication And Meta-analysis (DIAGRAM) Consortium, Asian Genetic Epidemiology Network Type 2 Diabetes (AGEN-T2D) Consortium, South Asian Type 2 Diabetes (SAT2D) Consortium, Mexican American Type 2 Diabetes (MAT2D) Consortium, Type 2 Diabetes Genetic Exploration by Next-generation sequencing in multi-Ethnic Samples (T2D-GENES) Consortium, Shah, Sonia and Yengo, Loic (2014). Genome-wide trans-ancestry meta-analysis provides insight into the genetic architecture of type 2 diabetes susceptibility. Nature Genetics, 46 (3), 234-246. doi: 10.1038/ng.2897
2014
Journal Article
Gene-centric meta-analysis in 87,736 individuals of European ancestry identifies multiple blood-pressure-related loci
Tragante, Vinicius, Barnes, Michael R., Ganesh, Santhi K., Lanktree, Matthew B., Guo, Wei, Franceschini, Nora, Smith, Erin N., Johnson, Toby, Holmes, Michael V., Padmanabhan, Sandosh, Karczewski, Konrad J., Almoguera, Berta, Barnard, John, Baumert, Jens, Chang, Yen-Pei Christy, Elbers, Clara C., Farrall, Martin, Fischer, Mary E., Gaunt, Tom R., Gho, Johannes M. I. H., Gieger, Christian, Goel, Anuj, Gong, Yan, Isaacs, Aaron, Kleber, Marcus E., Leach, Irene Mateo, McDonough, Caitrin W., Meijs, Matthijs F. L., Melander, Olle ... Keating, Brendan J. (2014). Gene-centric meta-analysis in 87,736 individuals of European ancestry identifies multiple blood-pressure-related loci. American Journal of Human Genetics, 94 (3), 349-360. doi: 10.1016/j.ajhg.2013.12.016
2013
Journal Article
Discovery and refinement of loci associated with lipid levels
Willer C.J., Schmidt E.M., Sengupta S., Peloso G.M., Gustafsson S., Kanoni S., Ganna A., Chen J., Buchkovich M.L., Mora S., Beckmann J.S., Bragg-Gresham J.L., Chang H.-Y., Demirkan A., Den Hertog H.M., Do R., Donnelly L.A., Ehret G.B., Esko T., Feitosa M.F., Ferreira T., Fischer K., Fontanillas P., Fraser R.M., Freitag D.F., Gurdasani D., Heikkila K., Hypponen E., Isaacs A. ... Abecasis G.R. (2013). Discovery and refinement of loci associated with lipid levels. Nature Genetics, 45 (11), 1274-1285. doi: 10.1038/ng.2797
2013
Journal Article
Gene-centric association signals for haemostasis and thrombosis traits identified with the HumanCVD BeadChip
Gaunt T.R., Zabaneh D., Shah S., Guyatt A., Ladroue C., Kumari M., Drenos F., Shah T., Talmud P.J., Casas J.P., Lowe G., Rumley A., Lawlor D.A., Kivimaki M., Whittaker J., Hingorani A.D., Humphries S.E. and Day I.N. (2013). Gene-centric association signals for haemostasis and thrombosis traits identified with the HumanCVD BeadChip. Thrombosis and Haemostasis, 110 (5), 995-1003. doi: 10.1160/TH13-02-0087
2013
Journal Article
Common variants associated with plasma triglycerides and risk for coronary artery disease
Do, Ron, Willer, Cristen J., Schmidt, Ellen M., Sengupta, Sebanti, Gao, Chi, Peloso, Gina M., Gustafsson, Stefan, Kanoni, Stavroula, Ganna, Andrea, Chen, Jin, Buchkovich, Martin L., Mora, Samia, Beckmann, Jacques S., Bragg-Gresham, Jennifer L., Chang, Hsing-Yi, Demirkan, Ayse, Den Hertog, Heleen M., Donnelly, Louise A., Ehret, Georg B., Esko, Tonu, Feitosa, Mary F., Ferreira, Teresa, Fischer, Krista, Fontanillas, Pierre, Fraser, Ross M., Freitag, Daniel F., Gurdasani, Deepti, Heikkila, Kauko, Hyppoenen, Elina ... Kathiresan, Sekar (2013). Common variants associated with plasma triglycerides and risk for coronary artery disease. Nature Genetics, 45 (11), 1345-1352. doi: 10.1038/ng.2795
2013
Journal Article
Population Genomics of Cardiometabolic Traits: Design of the University College London-London School of Hygiene and Tropical Medicine-Edinburgh-Bristol (UCLEB) Consortium
Shah, Tina, Engmann, Jorgen, Dale, Caroline, Shah, Sonia, White, Jon, Giambartolomei, Claudia, McLachlan, Stela, Zabaneh, Delilah, Cavadino, Alana, Finan, Chris, Wong, Andrew, Amuzu, Antoinette, Ong, Ken, Gaunt, Tom, Holmes, Michael V., Warren, Helen, Davies, Teri-Louise, Drenos, Fotios, Cooper, Jackie, Sofat, Reecha, Caulfield, Mark, Ebrahim, Shah, Lawlor, Debbie A., Talmud, Philippa J., Humphries, Steve E., Power, Christine, Hypponen, Elina, Richards, Marcus, Hardy, Rebecca ... Hingorani, Aroon D. (2013). Population Genomics of Cardiometabolic Traits: Design of the University College London-London School of Hygiene and Tropical Medicine-Edinburgh-Bristol (UCLEB) Consortium. PLoS ONE, 8 (8) e71345, e71345. doi: 10.1371/journal.pone.0071345
2013
Journal Article
Loci influencing blood pressure identified using a cardiovascular gene-centric array
Ganesh, Santhi K., Tragante, Vinicius, Guo, Wei, Guo, Yiran, Lanktree, Matthew B., Smith, Erin N., Johnson, Toby, Castillo, Berta Almoguera, Barnard, John, Baumert, Jens, Chang, Yen-Pei Christy, Elbers, Clara C., Farrall, Martin, Fischer, Mary E., Gaunt, Nora Franceschini, H. Gho, Johannes M.I., Gieger, Christian, Gong, Yan, Isaacs, Aaron, Kleber, Marcus E., Leach, Irene Mateo, McDonough, Caitrin W., Meijs, Matthijs F.L., Mellander, Olle, Molony, Cliona M., Nolte, Ilja M., Price, Sandosh Padmanabhan, Rajagopalan, Ramakrishnan, Shaffer, Jonathan ... Asselbergs, Folkert W. (2013). Loci influencing blood pressure identified using a cardiovascular gene-centric array. Human Molecular Genetics, 22 (16) ddt177, 3394-3395. doi: 10.1093/hmg/ddt177
2013
Journal Article
Gene-centric analysis identifies variants associated with interleukin-6 levels and shared pathways with other inflammation markers
Shah T., Zabaneh D., Gaunt T., Swerdlow D.I., Shah S., Talmud P.J., Day I.N., Whittaker J., Holmes M.V., Sofat R., Humphries S.E., Kivimaki M., Kumari M., Hingorani A.D. and Casas J.P. (2013). Gene-centric analysis identifies variants associated with interleukin-6 levels and shared pathways with other inflammation markers. Circulation: Cardiovascular Genetics, 6 (2), 163-170. doi: 10.1161/CIRCGENETICS.112.964254
2013
Journal Article
Influence of common genetic variation on blood lipid levels, cardiovascular risk, and coronary events in two British prospective cohort studies
Shah S., Casas J.P., Gaunt T.R., Cooper J., Drenos F., Zabaneh D., Swerdlow D.I., Shah T., Sofat R., Palmen J., Kumari M., Kivimaki M., Ebrahim S., Smith G.D., Lawlor D.A., Talmud P.J., Whittaker J., Day I.N.M., Hingorani A.D. and Humphries S.E. (2013). Influence of common genetic variation on blood lipid levels, cardiovascular risk, and coronary events in two British prospective cohort studies. European Heart Journal, 34 (13), 972-981. doi: 10.1093/eurheartj/ehs243
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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