Professor Sally Dunwoodie, Head of Embryology Laboratory Congenital Heart Disease Research Program

"I find it so amazing that we know so little about the most common type of birth defect in both Australia and around the world. Every child deserves the right to a healthy start to life, but sadly this is not always the case,"

- Professor Sally Dunwoodie

Professor Sally Dunwoodie

Head, Embryology Laboratory
Congenital Heart Disease Research Program

Research Overview

Key Research Areas

Research Overview

“Every child deserves the right to a healthy start to life.”

Congenital malformation occurs in 3-6% of births and in 80% of cases the cause is unknown. The heart is the first organ to form and function during the development of an embryo. When it does not form properly the baby is born with a heart defect, collectively described as congenital heart disease (CHD). CHD is the most common type of birth defect. In Australia, 42 babies are born with a heart defect every week.

The Embryology Laboratory is identifying the genetic and environmental causes of birth defects, including CHD. Gene mutations are being identified in patients. Mouse models are being developed to understand how genetic mutations and environmental factors impact on embryogenesis.

Research Projects

There are 4 key projects underway in the Embryology Laboratory, led by Professor Sally Dunwoodie;

1. Genetic causes of congenital malformation

Families with congenital malformation are being recruited and gene mutations are being identified using whole genome sequencing, and in house bioinformatics. Some mutations occur in genes known to cause congenital malformation. These mutations are tested for pathogenicity using an array of in vitro assays. Many mutations arise in “new” genes and thus their relevance to congenital malformation is being established in preclinical models, such as the mouse.

We have discovered that:

  • mutations in DLL3, MESP2, LFNG, HES7, TBX6, or RIPPLY2 cause vertebral defects
  • mutations in genes KYNU or HAAO result in nicotinamide adenine dinucleotide (NAD) deficiency causing multiple congenital malformations in affected individuals

2. Environmental causes of congenital malformation

We are determining if risk factors associated with congenital malformation in humans, disrupt embryogenesis in mice. Moreover, a number of risk factors lead to hypoxia in the embryo; therefore, we use short-term gestational hypoxia to disrupt embryogenesis and determine the molecular and cellular sequelae.

We have discovered that:

  • hypoxia inhibits fibroblast growth factor (FGF) signalling, which disrupts heart and vertebral formation
  • hypoxia induces the unfolded protein response (UPR) and in doing so inhibits FGF signalling

3. Gene-Environment interaction (GxE) as a cause of congenital malformation

A genetic predisposition to a birth defect might, in combination with an adverse environmental stress, disrupt embryogenesis. In mouse, we are exploring the extent to which GxE disrupts embryogenesis.
We have discovered that:

  • GxE causes vertebral and kidney defects in mice

4. Nicotinamide adenine dinucleotide (NAD) deficiency and congenital malformation

In families, we discovered that NAD deficiency causes multiple congenital malformations in affected individuals. In mice, NAD deficiency was prevented and embryo defects averted by dietary supplementation with niacin/vitamin B3. Read more here.

Laboratory Members & Collaborators

Lab Members

Dr Gavin Chapman, Senior Staff Scientist

Dr Hartmut Cuny, Senior Postdoctoral Scientist

Dr Dimuthu Alankarage, Postdoctoral Scientist

Dr Kayleigh Bozon, Postdoctoral Scientist

Dr Debjani Das, Postdoctoral Scientist

Ella Martin, Senior Research Assistant

Joelene Major, Senior Research Assistant

Delicia Sheng, Senior Research Assistant

Victoria O’Reilly, Senior Research Assistant

Dr Annabelle Enriquez, Clinical Geneticist, PhD Student


Dr Gillian Blue, Children’s Hospital at Westmead, Australia

Professor Emma Duncan, King’s College London, UK

Professor Philip Giampietro, University of Illinois-Chicago, USA.

A/Professor Eleni Giannoulatou, Victor Chang Cardiac Research Institute

Professor Bob Graham, Victor Chang Cardiac Research Institute

Professor Richard Harvey, Victor Chang Cardiac Research Institute

Dr Haifa Hong, Shanghai Children's Medical Center, China

Professor Edwin Kirk, Sydney Children's Hospital, Australia

Professor Jason Kovacic, Victor Chang Cardiac Research Institute

Professor Kenro Kusumi, Arizona State University, USA

Dr Paul Mark, Spectrum Health, Grand Rapids, USA

Professor Natasha Nassar, University of Sydney

Professor Nicholas Pachter, Genetic Services of Western Australia, Australia

Dr Antonia Shand, Royal Hospital for Children

Dr Hongjun Shi, Westlake Institute for Advanced Study, Hangzhou, China

Professor Gary Sholler, Children’s Hospital at Westmead, Australia

Professor David Sillence, Children’s Hospital at Westmead, Australia

Dr Janine Smith, Children’s Hospital at Westmead, Australia

Professor Roger Stevenson, Greenwood Genetic Center, South Carolina, USA

Professor Paul Thomas, South Australian Health and Medical Research Institute, Adelaide

Professor Peter Turnpenny, Royal Devon & Exeter Hospital, UK

Professor David Winlaw, Children’s Hospital at Westmead, Australia

Dr Nan Wu, Peking Union Medical College Hospital, China

Publication Highlights

Total Publications available by clicking here

ORCID iD available by clicking here

  1. Cuny H, Kristianto E, Hodson MP, Dunwoodie SL. Simultaneous quantification of 26 NAD-related metabolites in plasma, blood, and liver tissue using UHPLC-MS/MS. Analytical Biochemistry. 2021; doi: 10.1016/j.ab.2021.114409
  2. Cuny H, Rapadas R, Gereis J, Martin EMMA, Kirk RB, Shi H, and Dunwoodie SL. NAD deficiency due to environmental factors or gene-environment interactions causes congenital malformations and miscarriage in mice. Proceedings of the National Academy of Sciences. 2020; 117 (7):3738-3747.
  3. Szot JO, Campagnolo C, Cao Y, Iyer KR, Cuny H, Drysdale T, Flores-Daboub JA, Bi W, Westerfield L, Liu P, Leung TN, Choy KW, Chapman G, Xiao R, Siu VM, Dunwoodie SL. Bi-allelic Mutations in NADSYN1 Cause Multiple Organ Defects and Expand the Genotypic Spectrum of Congenital NAD Deficiency Disorders. American Journal of Human Genetics. 2020;106(1):129-136.
  4. Chapman G, Moreau JLM, Ip E, Szot JO, Iyer KR, Shi H, Yam MX, O'Reilly VC, Enriquez A, Greasby JA, Alankarage D, Martin EMMA, Hanna BC, Edwards M, Monger S, Blue GM, Winlaw D, Ritchie HE, Grieve SM, Giannoulatou E, Sparrow DB, Dunwoodie SL. Functional genomics and gene-environment interaction highlight the complexity of Congenital Heart Disease caused by Notch pathway variants. Human Molecular Genetics. 2019: 29(4):566-579.
  5. Alankarage D, Ip E, Szot JO, Munro J, Blue GM, Harrison K, Cuny H, Enriquez E, Troup M, Humphreys DT, Wilson M, Harvey RP, Sholler GF, Graham RM, Ho JWK, Kirk EP, Pachter N, Chapman G, Winlaw DS, Giannoulatou E, Dunwoodie SL. Identification of clinically actionable variants from genome sequencing of families with Congenital Heart Disease. Genetics in Medicine. 2019; 21:1111-1120.
  6. Shi H, Enriquez A, Rapadas M, Martin EMMA. Wang R, Moreau J, Lim CK, Szot JO, Ip E, Hughes J, Sugimoto K, Humphreys D, McInerney-Leo AM, Leo PJ, Maghzal GJ, Halliday J, Smith J, Colley A, Mark PR, Collins F, Sillence DO, Winlaw DS, Ho J, Guillemin GJ, Brown MA, Kikuchi K, Thomas PQ, Stocker R, Giannoulatou E, Chapman G, Duncan EL, Sparrow DB, Dunwoodie SL. NAD Deficiency, Congenital Malformations and Niacin Supplementation. The New England Journal of Medicine. 2017; 377(6):544-552.
  7. Blue GM, Kirk EP, Giannoulatou E, Sholler GF, Dunwoodie SL, Harvey RP, Winlaw DS. Advances in the genetics of congenital heart disease: A Clinician’s guide. Journal of the American College of Cardiology. 2017; 69(7):859-870.
  8. Shi H, O’Reilly VC, Moreau JLM, Bewes TR, Yam MX, Chapman BE, Grieve SM, Stocker R, Graham RM, Chapman G, Sparrow DB and Dunwoodie SL. Gestational Stress Induces the Unfolded Protein Response Resulting in Heart Defects. Development. 2016; 143(14):2561-2572.
  9. Wu N, Ming X, Xiao J, Wu Z, Chen X, Shinawi M, Shen Y, Yu G, Liu J, Xie H, Gucev ZS, Liu S, Yang N, Al-Kateb H, Chen J, Zhang J, Hauser N, Zhang T, Tasic V, Liu P, Su X, Pan X, Liu C, Wang L, Shen J, Shen J, Chen Y, Zhang T, Zhang J, Choy KW, Wang J, Wang Q, Li S, Zhou W, Guo J, Wang Y, Zhang C, Zhao H, An Y, Zhao Y, Wang J, Liu Z, Zuo Y, Tian Y, Weng X, Sutton VR, Wang H, Ming Y, Kulkarni S, Zhong TP, Giampietro PF, Dunwoodie SL, Cheung SW, Zhang X, Jin L, Lupski JR, Qiu G, Zhang F. TBX6 Null Variants and a Common Hypomorphic Allele in Congenital Scoliosis. New England Journal of Medicine. 2015; 372(4):341-50
  10. McInerney-Leo AM, Sparrow DB, Harris JE, Gardiner BB, Marshall MS, O'Reilly VC, Shi H, Brown MA, Leo PJ, Zankl A*, Dunwoodie SL*, Duncan EL*. Compound heterozygous mutations in RIPPLY2 associated with vertebral segmentation defects. Human Molecular Genetics. 2015; 24(5):1234-42 *equal contribution.
  11. Blue GM, Kirk EP, Giannoulatou E, Dunwoodie SL, Ho JWK, Hilton DCK, White SM, Sholler GF, Harvey RP, Winlaw DS. Targeted next generation sequencing identifies pathogenic variants in familial CHD. Journal of the American College of Cardiology. 2014; 64(23):2498-506.
  12. O'Reilly VC, Lopes Floro K, Shi H, Chapman BE, Preis JI, James AC, Chapman G, Harvey RP, Johnson RS, Grieve SM, Sparrow DB and Dunwoodie SL. Gene-environment interaction demonstrates the vulnerability of the embryonic heart. Developmental Biology. 2014; 391(1):99-110.
  13. Sparrow DB, McInerney-Leo A, Gucev ZS, Gardiner B, Marshall M, Leo PJ, Chapman DL, Tasic V, Shishko A, Brown MA, Duncan EL, Dunwoodie SL. Autosomal Dominant Spondylocostal Dysostosis is Caused by Mutation in TBX6. Human Molecular Genetics. 2013; 15;22(8):1625-31.
  14. Sparrow DB, Chapman G, Smith AJ, Mattar MZ, Major JA, O’Reilly VC, Saga Y, Zackai EH, Dormans DP, Alman BA, McGregorL, Kageyama R, Kusumi K, Dunwoodie SL. A mechanism for gene-environment interaction in the etiology of congenital scoliosis. Cell. 2012; 149(2):295-306.
  15. Chapman G, Sparrow DB, Kremmer E and Dunwoodie SL. Notch inhibition by the ligand Delta-Like 3 defines the mechanism of abnormal vertebral segmentation in spondylocostal dysostosis. Human Molecular Genetics. 2011; 20(5):905-16.
  16. Dunwoodie SL. The role of hypoxia in development of the mammalian embryo. Developmental Cell. 2009; 17(6):755-773.
  17. Sparrow DB, Boyle SC, Sams RS, Mazuruk B, Zhang L, Moeckel GW, Dunwoodie SL, de Caestecker MP. Placental insufficiency causes renal medullary dysplasia in Cited1 mutant mice. Journal of The American Society of Nephrology. 2009; 20(4): 777-86
  18. Sparrow D, Guillen-Navarro E, Fatkin D, Dunwoodie SL. Mutation of HAIRY-AND-ENHANCER-OF-SPLIT-7 in Humans Causes Spondylocostal Dysostosis. Human Molecular Genetics. 2008; 17(23):3761-6.
  19. Sparrow DB, Chapman G, Wouters MA, Whittock NV, Ellard S, Fatkin D, Turnpenny PD, Kusumi K, Sillence D, Dunwoodie SL. Mutation of the LUNATIC FRINGE gene in humans causes spondylocostal dysostosis with a severe vertebral phenotype. American Journal of Human Genetics. 2006; 78(1):28-37.
  20. Whittock NV, Sparrow DB, Wouters MA, Sillence D, Ellard D, Dunwoodie SL, Peter D. Turnpenny. Mutated MESP2 causes spondylocostal dysostosis in humans. American Journal Human Genetics. 2004; 74(6):1249-54.
  21. Turnpenny PD, Whittock N, Duncan J, Dunwoodie SL, Kusumi K, Ellard S. Novel mutations in DLL3, a somitogenesis gene encoding a ligand for the Notch signalling pathway, cause a consistent pattern of abnormal vertebral segmentation in spondylocostal dysostosis. Journal of Medical Genetics. 2003; 40:333-39.
  22. Martinez Barbera JP, Rodriguez TA, Greene N, Weniger WJ, Simeone A, Copp A, Beddington RSP, Dunwoodie SL. Administration of folic acid prevents exencephaly in Cited2 deficient mice. Human Molecular Genetics. 2002; 11(3):283-93.
  23. Dunwoodie SL*, Clements M, Sparrow DB, Sa X, Conlon RA, Beddington RSP. Axial skeletal defects caused by mutation in the spondylocostal dysostosis/pudgy gene Dll3 are associated with disruption of the segmentation clock within the presomitic mesoderm. Development. 2002; 129:1795-806. (*Corresponding author).
  24. Avner P, Bruls T, Poras I, Eley L, Gas S, Ruiz P, Wiles MV, Sousa-Nunes R, Kettleborough R, Rana A, Morrisette J, Bentley L, Goldsworthy M, Haynes A, Herbert E, Southam L, Taghavi V, Sartory E, Lehrach H, Weissenbach J, Manenti G, Rodriguez-Tome P, Beddington RSP, Dunwoodie SL, Cox R. A radiation hybrid transcript map of the mouse genome. Nature Genetics. 2001; 29(2):194-200.
  25. Harrison SM, Dunwoodie SL., Arkell RM, Lehrach H, Beddington RSP. Isolation of novel tissue-specific genes from cDNA libraries representing the individual tissue constituents of the gastrulating mouse embryo. Development. 1995; 121:2479-489.

To read more of Professor Sally Dunwoodie's work, please click here and here.

Sally Dunwoodie Journals

CHD gene website

This is a list of genes, known to reproducibly cause human congenital heart disease (CHD) when mutated (human curated - high confidence CHD list). It has utility for clinicians and geneticists for prioritising variants found in exome or genome sequences. Details about the curation process and inclusion criteria for genes have been published and can be found here.

To visit the website, click here.

This gene list will continue to be updated to account for the growing number of published data about human gene-disease-relationships.

For enquiries regarding the gene list, please email

Acknowledgement of Country

The Victor Chang Cardiac Research Institute acknowledges Traditional Owners of Country throughout Australia and recognises the continuing connection to lands, waters and communities. We pay our respect to Aboriginal and Torres Strait Islander cultures; and to Elders past and present.

Victor Chang Cardiac Research Institute - The Home of Heart Research for 30 Years