Genetic Epilepsy Collaboration

image - Genetic Epilepsy Collaboration

Ensuring children born with brain disorders get the best treatments and supports
to enable them and their families to live happy and fulfilled lives. 


Centre for Clinical Genetics

  • Clinical Geneticists: Dr Elizabeth Emma Palmer, Dr Rani Sachdev. 
  • Genetic Counsellors: Rebecca Macintosh. 

Department of Neurology

  • Neurologists: A/Professor Annie Bye (Head of Department).
  • Epilepsy Intervention & Evaluation Coordinator: Fleur Le Marne.
  • Epilepsy Clinical Nurse Consultant: Erin Beavis 

School of Women’s and Children’s Health, UNSW Medicine, UNSW Sydney

  • Lecturer: Dr Elizabeth Emma Palmer 
  • Project Officer / PhD Student: Suzanne Nevin


Clinical Services

Over 250 children with a likely genetic epilepsy are currently seen by the Departments of Neurology and Clinical Genetics at Sydney Children’s Hospital Randwick.  Children present with diverse epilepsy presentations from severe epileptic encephalopathy, to suspected autosomal dominant genetic generalised epilepsy.

Over 200 families have opted to have diagnostic clinical and/ or  research testing to try and understand the cause of their child’s epilepsy, typically including chromosomal microarray, neurometabolic screening and massively parallel sequencing via panel, exome or genome sequencing.

Over 100 children have an established genetic diagnosis: with the diagnostic yield varying significantly between patient groups.  The highest diagnostic yield has been for children with neonatal and early infantile epileptic encephalopathy.  

Identified genetic causes include variants in:

  • ion channel genes (SCN1A, SCN2A, SCN8A, KCNQ2, KCNT2, KCNT1, HCN1)

  • transporter/synaptic genes (GLUT1, DNM1, SZT2, CNTNAP2, DYNC1H1, WWOX, STXBP1, KIAA2022, UBA5, DEAF1, SLC9A6, SLC6A1, ATP1A3, ATP6V0C, CDKL5, ARX, PRRT2, WDR73, SYNGAP1, ST3GAL5, PRRT2, GABRB2)

  • metabolic genes / basic cellular function genes (ARV1, ACAD9, ALG1, AP4S1, ARV1,ASNS, ADSL, ALG13, POLG, NARS2,PARS2,CARS2, ATN1, CLCN4, FGF12, DEPDC5, SETBP1, UBA5)

Genetic diagnoses are being used by families to guide reproductive decision making and have clinical utility with respect to anti-epileptic medication choice, prognostication, surveillance, and management. A team of Clinical Geneticists and Genetic Counsellors navigate families through the testing process and information on diagnoses. Regular clinical/research multidisciplinary meetings are held to guide best clinical practice and foster ongoing collaborative research.


Education Resources

Members of the COGENES group in consultation with families of patients, external geneticists and paediatricians, have created online genetic resources for families and for clinicians who treat patients with genetic epilepsies.  These resources are available on the Paediatric Epilepsy Network NSW (PENNSW).

The genetic resources for families cover:

  • Genetic Epilepsy
  • Genetic Inheritance
  • Genetic testing 
  • What to expect at a genetic appointment? 
  • Other links and resources

The genetic resources for clinicians cover:

  • Genetic testing
  • Diagnostic Yield
  • Chromosomal Microarray
  • Fragile X PCR
  • First-line metabolic testing
  • Exome Panel
  • When to refer to Genetics? 




Associate Professor Ann Bye
Conjoint Associate Professor
I am a Senior Paediatric Neurologist at Sydney Children’s Hospital and until recently Departmental Head of Neurology. I am also Conjoint Associate Professor in the Discipline of Paediatrics in the School of Women's and Children's Health. I served as Vice-President of the Epilepsy Society Australia from 2010-2012 and was a member of the Education Committee from 2006-2010. I have an extensive portfolio of research into paediatric epilepsy and neurology, with over 80 original research articles together with 70 abstracts published in international and national peer reviewed journals. Research topics include genetic epilepsies, neonatal seizures, neuropsychological and language profiles in paediatric epilepsy, MRI correlates of childhood epilepsy syndromes, quality of life in paediatric epilepsy, and education of epilepsy to patients and medical staff.
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Ms Erin Beavis
Clinical Nurse Consultant
I have worked as a Clinical Nurse Consultant at Sydney Children’s Hospital (SCH), Randwick since 2008. Previous to this I was employed at SCH in the Children's Intensive Care Unit, Paediatric Emergency, and in the Neonatal Emergency Transport Service. I hold certificates in both Paediatric Intensive Care and in Midwifery. I am currently a member of the Complex Epilepsy team at SCHN (Randwick), dedicated to the delivery of the highest standard of care to children with epilepsy and their families.

Ms Fleur Le Marne
Conjoint Lecturer, and Epilepsy Intervention and Evaluation Coordinator
I have worked as the Epilepsy Intervention and Evaluation Coordinator in the Department of Neurology (Sydney Children’s Hospital, Randwick) since 2015. I am a registered psychologist with the Psychology Board of Australia and Conjoint Lecturer with the School of Women’s and Children’s Health (Faculty of Medicine) at the University of New South Wales. I have experience working across a range of Health Improvement projects and am committed to the provision of accessible, high quality educational resources for patients with epilepsy and their parents/carers, and clinicians involved in their care.
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Rebecca Macintosh
Genetic Counsellor
I am a certified genetic counsellor with 10 years clinical experience. I am a full time clinical practitioner and am involved in the research to provide access and support to my patients which I hope provides the best possible outcomes for their care. I am particularly passionate about working with families with children with severe neurodevelopmental disorders. My goal is work with the families to determine what their needs are and ensure we can meet their expectations in order to inform future clinical practice.

Suzanne Nevin
Project Officer and PhD student
I am a project officer for the CoGENes team. I am passionate about understanding the psychosocial impacts of paediatric genetic conditions and working with families to develop resources that meet their needs. I am currently completing my PhD at the School of Women's and Children's Health, UNSW. My PhD is focused on identifying the key features of the psychosocial support needs of families affected with severe neurodevelopmental epilepsies, as well as developing evidence-based resources to improve psychological outcomes.
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Dr Emma Palmer
Clinical Geneticist and Lecturer
I am a paediatrician and Clinical Geneticist (Sydney Children's Hospital), Lecturer, School of Women's and Children's Health, University of New South Wales, and mother. My research passions are how to improve the health outcomes and quality of life for children and adults affected by severe neurodevelopmental genetic disorders and understand and meet the information and support needs of their families.
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Dr Rani Sachdev
Clinical Geneticist and Conjoint Lecturer
I am a paediatric clinical geneticist and have a clinician’s passion for genomics with a specific interest in genetics of severe epilepsy, intellectual disability and neurogenetic syndromes and its practical application at the bedside. Translating the impact of genetic conditions for these inspiring patients and their families to address their specific needs is my passion. My hope is that identification and exploration of a genetic causation for these patients will enable a tailored, holistic approach for each patient and their family.
Read More.


Staff/Team members 
image - Anniebye
Conjoint Associate Professor
Ph (02) 9382 1549
Conjoint Lecturer
image - 118329227 759599204837667 1545994035452809647 N
Research Project Officer
Conjoint Lecturer
Other team members 

Ms Erin Beavis
Clinical Nurse Consultant

Ms Rebecca Macintosh
Genetic Counsellor

Our Research

Current Research

  • The information needs of parents of children with a genetic, or suspected genetic, form of epilepsy:
    This study aims to investigate and understand the information and psychological support needs of parents of children affected with genetic epileptic encephalopathies. Using in-depth qualitative interviews, this research will provide rich and detailed insight into parent experiences, to develop our knowledge of the psychosocial impact of genetic epilepsies. This research will inform the development of resources that will offer psychosocial support tailored to the needs of parents and families. This research is being conducted across the Sydney Children’s Hospital Network, in collaboration with Professor Claire Wakefield, UNSW and Professor Kristine Barlow-Stewart, University of Sydney.
  • Co-development and Evaluation of Mental Health Intervention to provide Psychological Support for Parents of Children with Genetic Epilepsy
    Using co-design methodology this study aims to develop a novel intervention aimed to support parents’ psychological wellbeing throughout their child’s development and illness trajectory. If proven effective and acceptable, this intervention could be translated to promote and enhance the psychological wellbeing of parents health in other healthcare disciplines. This research is being conducted across the Sydney Children’s Hospital Network, in collaboration with Professor Kenneth Nunn.
  • Identification and characterisation of novel genetic causes of developmental and epileptic encephalopathy (EE) by whole Genome Sequencing (WGS)
    30 families are being investigated by whole genome sequencing in collaboration with the Translational Genomics Group at the Garvan Institute. Mechanisms including somatic mosaicism, mitochondrial and complex structural rearrangements are being evaluated. This research has led to the identification of novel genetic causes of DEE, and shown the value of WGS in finding diagnoses for families previously on a long diagnostic odyssey.
    Severe genetic epilepsies of infancy (SGEI) are chronic, complex and often life-limiting diseases with profound impacts on families. Due to advances in genomic diagnoses, natural history data and advanced therapeutics there has never been a better time to translate a genetic diagnosis into improved health care for children with SGEI: aka as ‘Precision and personalised medicine’ (PPM). Our formative research has identified that a major barrier to the implementation of PPM for SGEI is a lack of understandable and accessible information for families and clinicians.

    GeneCOMPASS will incorporate the design and evaluation of an innovative research program encompassing a comprehensive knowledge portal and effective knowledge dissemination to caregivers and clinicians related to PPM for SGEI. The “knowledge” required will be based on requests/questions from caregivers and clinicians in a pilot study related to the ten most common genes associated with SGEI.It is anticipated this desired knowledge will relate to the natural history and associated comorbidities of individual SGEI, and optimal management including currently available therapies, advanced therapeutic trials, and mental health resources.

    The significance of the project lies in its anticipated positive impact on caregivers and clinicians, including improved knowledge, communication and self-efficacy in a landscape of fast-moving genomic testing. Successful completion of the pilot will enable expansion of the model for other neurogenetic disorders and integration into the health care system. GeneCOMPASS will be guided by our consumer reference group and a steering committee of paediatricians, neurologists, health service delivery experts, implementation and behavioural scientists.

  • A Facebook delivered physical activity focused group lifestyle intervention for the families of children with genetic epilepsy
    This pilot study aims to determine the feasibility, acceptability and preliminary effectiveness of using an online platform to deliver a group-based physical activity intervention for the families of children with genetic epilepsy. This project is delivered through UNSW School of Psychiatry and the Black Dog Institute, coordinated by Associate Professor Simon Rosenbaum and PhD candidate Grace McKeon.
  • Co-design of a family day for Genetic Epilepsy
    In collaboration with Dr Alison McEwen, and Gemma McErlean, UTS, we are co-supervising Masters student Ella West in the co-design of a family day for Genetic Epilepsy at SCHN with our consumer reference group. 
  • Exploration of the opportunities, challenges and barriers to implementation of advanced therapeutics for genetic epilepsy
    Members of the CoGENES team are collaborating with KidsResearch, SCHN, the Children’s Medical Research Institute and colleagues in the School of Women and Children’s Health, UNSW to consider the best ways of implementing precision medicine for the genetic epilepsies across SCHN.
  • Neurodevelopmental outcomes and clinical utility of genetic testing in a cohort of Australian families with self-limited neonatal-infantile epilepsy
    This project is being led by Dr Emily Innes, Neurology Fellow at CHW. This project aims to assess whether there are long term developmental effects of this group of genetic epilepsy conditions, using child and adult developmental assessments of gene positive families, as well as assessing the clinical utility of genetic testing in this cohort and its potential impact on management

Selected Publications

Book chapters

  • Palmer E, 2020, 'Potassium Channel Mutations in Epilepsy', in Bhattacharjee A (ed.), The Oxford Handbook of Neuronal Ion Channels, Oxford University Press, Oxford, UK
  • Palmer EE; Sachdev R; Kandula T; Macintosh R; Kirk E; Bye A, 2017, 'Genetics of Epileptic Encephalopathies', eLS, pp. 1 - 11

Journal Articles

  • Nevin, S.N., Wakefield, C.E., Schilstra, C., McGill, B.C., Bye, A., & Palmer, E.E. (2020). The information needs of parents of children with early-onset epilepsy: A systematic review. Epilepsy & Behavior Volume 112, November 2020, 107382.
  • Ng, EWM, Le Marne, F, Sinclair, KG, Lorentzos, MS, Waak, M, Deuble, N, Georgeson, T, Rao, A, Rikhi ,S, Mallit, KA, Bye, A. The evaluation of an educational video counselling key messages for doctors and families following a first afebrile seizure. Journal of Paediatrics and Child Health. (in press)
  • Nabais Sá MJ; Jensik PJ; McGee SR; Parker MJ; Lahiri N; McNeil EP; Kroes HY; Hagerman RJ; Harrison RE; Montgomery T; Splitt M; Palmer EE; Sachdev RK; Mefford HC; Scott AA; Martinez-Agosto JA; Lorenz R; Orenstein N; Berg JN; Amiel J; Heron D; Keren B; Cobben JM; Menke LA; Marco EJ; Graham JM; Pierson TM; Karimiani EG; Maroofian R; Manzini MC; Cauley ES; Colombo R; Odent S; Dubourg C; Phornphutkul C; de Brouwer APM; de Vries BBA; Vulto-vanSilfhout AT, 2019, 'De novo and biallelic DEAF1 variants cause a phenotypic spectrum', Genetics in Medicine, vol. 21, pp. 2059 - 2069.
  • Lanoue V; Chai YJ; Brouillet JZ; Weckhuysen S; Palmer EE; Collins BM; Meunier FA, 2019, 'STXBP1 encephalopathy: Connecting neurodevelopmental disorders with α-synucleinopathies?', Neurology, vol. 93, pp. 114 - 123.
  • Le Marne FA; Towns SJ; Gaskin C; Ho J; Baker R; Beavis E; Bye AM, 2019, 'Implementing a new adolescent epilepsy service: Improving patient experience and readiness for transition', Journal of Paediatrics and Child Health, vol. 55, pp. 819 - 825. 
  • Palmer EE; Hong S; Al Zahrani F; Hashem MO; Aleisa FA; Ahmed HMJ; Kandula T; Macintosh R; Minoche AE; Puttick C; Gayevskiy V; Drew AP; Cowley MJ; Dinger M; Rosenfeld JA; Xiao R; Cho MT; Yakubu SF; Henderson LB; Guillen Sacoto MJ; Begtrup A; Hamad M; Shinawi M; Andrews MV; Jones MC; Lindstrom K; Bristol RE; Kayani S; Snyder M; Villanueva MM; Schteinschnaider A; Faivre L; Thauvin C; Vitobello A; Roscioli T; Kirk EP; Bye A; Merzaban J; Jaremko Ł; Jaremko M; Sachdev RK; Alkuraya FS; Arold ST, 2019, 'De Novo Variants Disrupting the HX Repeat Motif of ATN1 Cause a Recognizable Non-Progressive Neurocognitive Syndrome', American Journal of Human Genetics, vol. 104, pp. 542 - 552.
  • Palmer EE; Schofield D; Shrestha R; Kandula T; Macintosh R; Lawson JA; Andrews I; Sampaio H; Johnson AM; Farrar MA; Cardamone M; Mowat D; Elakis G; Lo W; Zhu Y; Ying K; Morris P; Tao J; Dias KR; Buckley M; Dinger ME; Cowley MJ; Roscioli T; Kirk EP; Bye A; Sachdev RK, 2018, 'Integrating exome sequencing into a diagnostic pathway for epileptic encephalopathy: Evidence of clinical utility and cost effectiveness', Molecular Genetics and Genomic Medicine, vol. 6, pp. 186 - 199.
  • Gennarino VA; Palmer EE; McDonell LM; Wang L; Adamski CJ; Koire A; See L; Chen CA; Schaaf CP; Rosenfeld JA; Panzer JA; Moog U; Hao S; Bye A; Kirk EP; Stankiewicz P; Breman AM; McBride A; Kandula T; Dubbs HA; Macintosh R; Cardamone M; Zhu Y; Ying K; Dias KR; Cho MT; Henderson LB; Baskin B; Morris P; Tao J; Cowley MJ; Dinger ME; Roscioli T; Caluseriu O; Suchowersky O; Sachdev RK; Lichtarge O; Tang J; Boycott KM; Holder JL; Zoghbi HY, 2018, 'A Mild PUM1 Mutation Is Associated with Adult-Onset Ataxia, whereas Haploinsufficiency Causes Developmental Delay and Seizures', Cell, vol. 172, pp. 924 - 936.e11.
  • Palmer EE; Stuhlmann T; Weinert S; Haan E; Van Esch H; Holvoet M; Boyle J; Leffler M; Raynaud M; Moraine C; Van Bokhoven H; Kleefstra T; Kahrizi K; Najmabadi H; Ropers HH; Delgado MR; Sirsi D; Golla S; Sommer A; Pietryga MP; Chung WK; Wynn J; Rohena L; Bernardo E; Hamlin D; Faux BM; Grange DK; Manwaring L; Tolmie J; Joss S; Study DDD; Cobben JM; Duijkers FAM; Goehringer JM; Challman TD; Hennig F; Fischer U; Grimme A; Suckow V; Musante L; Nicholl J; Shaw M; Lodh SP; Niu Z; Rosenfeld JA; Stankiewicz P; Jentsch TJ; Gecz J; Field M; Kalscheuer VM, 2018, 'De novo and inherited mutations in the X-linked gene CLCN4 are associated with syndromic intellectual disability and behavior and seizure disorders in males and females', Molecular Psychiatry, vol. 23, pp. 222 - 230.
  • Palmer EE; Kumar R; Gordon CT; Shaw M; Hubert L; Carroll R; Rio M; Murray L; Leffler M; Dudding-Byth T; Oufadem M; Lalani SR; Lewis AM; Xia F; Tam A; Webster R; Brammah S; Filippini F; Pollard J; Spies J; Minoche AE; Cowley MJ; Risen S; Powell-Hamilton NN; Tusi JE; Immken LD; Nagakura H; Bole-Feysot C; Nitschké P; Garrigue A; de Saint Basile G; Kivuva E; Scott RH; Rendon A; Munnich A; Newman W; Kerr B; Besmond C; Rosenfeld JA; Amiel J; Field M; Gecz J, 2017, 'A Recurrent De Novo Nonsense Variant in ZSWIM6 Results in Severe Intellectual Disability without Frontonasal or Limb Malformations', American Journal of Human Genetics, vol. 101, pp. 995 - 1005.
  • Le Marne FA; Butler S; Beavis E; Gill D; Bye AME, 2018, 'EpApp: Development and evaluation of a smartphone/tablet app for adolescents with epilepsy', Journal of Clinical Neuroscience, vol. 50, pp. 214 - 220.
  • Gururaj S; Palmer EE; Sheehan GD; Kandula T; Macintosh R; Ying K; Morris P; Tao J; Dias KR; Zhu Y; Dinger ME; Cowley MJ; Kirk EP; Roscioli T; Sachdev R; Duffey ME; Bye A; Bhattacharjee A, 2017, 'A De Novo Mutation in the Sodium-Activated Potassium Channel KCNT2 Alters Ion Selectivity and Causes Epileptic Encephalopathy', Cell Reports, vol. 21, pp. 926 - 933.
  • Von Spiczak S; Helbig KL; Shinde DN; Huether R; Pendziwiat M; Lourenço C; Nunes ME; Sarco DP; Kaplan RA; Dlugos DJ; Kirsch H; Slavotinek A; Cilio MR; Cervenka MC; Cohen JS; McClellan R; Fatemi A; Yuen A; Sagawa Y; Littlejohn R; McLean SD; Hernandez-Hernandez L; Maher B; Møller RS; Palmer E; Lawson JA; Campbell CA; Joshi CN; Kolbe DL; Hollingsworth G; Neubauer BA; Muhle H; Stephani U; Scheffer IE; Pena SDJ; Sisodiya SM; Helbig I, 2017, 'DNM1 encephalopathy', Neurology, vol. 89, pp. 385 - 394.
  • Le Marne FA; McGinness H; Slade R; Cardamone M; Balbir Singh S; Connolly AM; Bye AME, 2016, 'Evaluation of an E-learning resource on approach to the first unprovoked seizure', Journal of Paediatrics and Child Health, vol. 52, pp. 896 - 900.
  • Smogavec M; Cleall A; Hoyer J; Lederer D; Nassogne MC; Palmer EE; Deprez M; Benoit V; Maystadt I; Noakes C; Leal A; Shaw M; Gecz J; Raymond L; Reis A; Shears D; Brockmann K; Zweier C, 2016, 'Eight further individuals with intellectual disability and epilepsy carrying bi-allelic CNTNAP2 aberrations allow delineation of the mutational and phenotypic spectrum', Journal of Medical Genetics, vol. 53, pp. 820 - 827.
  • Zerem A; Haginoya K; Lev D; Blumkin L; Kivity S; Linder I; Shoubridge C; Palmer EE; Field M; Boyle J; Chitayat D; Gaillard WD; Kossoff EH; Willems M; Geneviève D; Tran-Mau-Them F; Epstein O; Heyman E; Dugan S; Masurel-Paulet A; Piton A; Kleefstra T; Pfundt R; Sato R; Tzschach A; Matsumoto N; Saitsu H; Leshinsky-Silver E; Lerman-Sagie T, 2016, 'The molecular and phenotypic spectrum of IQSEC2-related epilepsy', Epilepsia, vol. 57, pp. 1858 - 1869.
  • Palmer EE, 2016, 'Dissecting the clinical outcome and cause of abnormalities of the corpus callosum', Developmental Medicine and Child Neurology, vol. 58, pp. 430 - 431.
  • Palmer EE; Jarrett KE; Sachdev RK; Zahrani FA; Hashem MO; Ibrahim N; Sampaio H; Kandula T; Macintosh R; Gupta R; Conlon DM; Billheimer JT; Rader DJ; Funato K; Walkey CJ; Lee CS; Loo C; Brammah S; Elakis G; Zhu Y; Buckley M; Kirk EP; Bye A; Alkuraya FS; Roscioli T; Lagor WR, 2016, 'Neuronal deficiency of ARV1 causes an autosomal recessive epileptic encephalopathy', Human Molecular Genetics, vol. 25, pp. 3042 - 3054.
  • Palmer EE; Hayner J; Sachdev R; Cardamone M; Kandula T; Morris P; Dias KR; Tao J; Miller D; Zhu Y; Macintosh R; Dinger ME; Cowley MJ; Buckley MF; Roscioli T; Bye A; Kilberg MS; Kirk EP, 2015, 'Asparagine Synthetase Deficiency causes reduced proliferation of cells under conditions of limited asparagine', Molecular Genetics and Metabolism, vol. 116, pp. 178 - 186.
  • Palmer EE; Mowat D, 2014, 'Agenesis of the corpus callosum: A clinical approach to diagnosis', American Journal of Medical Genetics, Part C: Seminars in Medical Genetics, vol. 166, pp. 184 - 197.


2020: Philanthropic funding for GeneCOMPASS pilot ($130,000)

2020: Australian Epilepsy Research Fund “Preparing Australia for Precision Medicine in the Developmental and Epileptic Encephalopathies” ($686,537)  

2019: Sydney Children’s Hospital Foundation Research Starter Grant “Improving Support And Providing Integrated Care For Children With Chronic Genetic Conditions” ($20,000)

2019: Luminesce Alliance. Funding to support PhD project Suzanne Nevin ($80,000)

2017: SPHERE funding for CoGENES project Officer “Improving Clinical Care and Support for Children with Severe Early-Onset Epilepsies and Their Families.” ($17,000)

2016: NHMRC Postgraduate PhD Scholarship Grant “Application of Next Generation Sequencing for the Diagnosis of Epileptic Encephalopathy – the science, the costings and the impact.” ($127,000) CIA

2016: NSW Genomics Collaborative Grant: “Drug resistant childhood onset epilepsy with intellectual disability: leveraging genomic sequencing to identify novel genes and neurodevelopmental pathways and determine optimal diagnostic protocols” ($180,000)

Support our Research

Visis the CoGenes Website to Donate and Make a Difference

Help us ensure best diagnosis, treatments & support for children born with brain disorders

Every two days, a child is born in Australia with a genetic epilepsy. Genetic epilepsy can cause serious brain damage, and children can experience life-threatening seizures several times a day. Children may lose the ability to talk, walk and even smile. Families can feel confused and alone.

Our clinical research is designed to give children with genetic epilepsy and their families hope. Using the latest genomic technologies, our research is identifying genetic causes for many children. We work in collaboration with international researchers to show how new treatments can be tailored to a child’s genetic diagnoses: opening up the possibility of reducing seizures and even curing these individually rare and chronic conditions. We are developing resources with families to educate, support and empower.

Your donation will enable us to progress ground-breaking research in gene-discovery, precision medicine, and improved models of care, improving these children’s lives.


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