Our research primarily revolves around the field of genetic epidemiology and genomics, with a particular focus on cardiovascular diseases.

Our Team

• Associate Professor Heng Chew Kiat
• Dr Delicia Ooi Shu Qin

Research Areas

The Singapore Coronary Artery Disease Genetics Studies (SCADGENS) 

Our team of clinical researchers focus on clinically relevant research with the aim of improving outcomes for children with various developmental disorders. The field of research in developmental and behavioural paediatrics is an emerging one in Singapore with vast potential implications for policy and practices. Our clinical-scientists participate in translational neuroscience research, which further informs on early childhood development and clinical care. 

Beyond descriptive research, we emphasise the need for meaningful interventions that can be employed so as to actively change the paths and outcomes for children with developmental disorders. Our scientific work has been published in international peer reviewed journals and presented regularly at numerous local and international conferences with awards won. It has also led to improvements in clinical workflows for children with developmental concerns. Our team also collaborates with national and community organisations (e.g. NCSS, MOE, MCYS) for various projects such as those that evaluate current practices in the early intervention sector and explore new models of care. We also collaborate with other international centers for multi-site studies. 

We welcome other potential collaborations from hospitals and agencies to participate in research.

Our Team

• Adj A/Prof Chong Shang Chee
  
• Dr Kang Ying Qi
  
• Dr Jennifer Kiing
  
• Dr Aishworiya Ramkumar
  
• Dr Evelyn Law
  
• Dr Mulay Kalyani Vijaykumar
• Dr Tammy Lim
• Dr Tan Mae Yue
  

Research Areas

Some of the broad areas of research that we are involved in include:

Child Development in Singapore

Major research partnerships

Our doctors are key members of various collaborative research programmes, and have received competitive research funding from NMRC, Ministry of Health and philantropic organisations (e.g. Lien Foundation, Octava Foundation). 

Center for Holistic Initiatives for Learning and Development (CHILD) 

The Child Development Unit (CDU) is a key partner of the Center for Holistic Initiatives for Learning and Development (CHILD) under the NUS Yong Loo Lin School of Medicine. At CHILD, the CDU is involved in designing and implementing programmes focusing on developmental screening, promoting the developmental and behavioural health of children. CDU is also engaged in studies that focus on community paediatrics, to optimise child development, particularly in children from vulnerable backgrounds. CDU partners with CHILD in research activities with local agencies, community organisations, and also international sites. An example of such a study is the HEAlth and Development Support in Preschool Partnerships (HEADS-UPP) study. 

Growing Up in Singapore Towards healthy Outcomes (GUSTO) 

Our researchers are involved in the GUSTO birth cohort (Growing Up in Singapore Towards healthy Outcomes), studying factors affecting child development including socio-economic status and maternal mood. This includes examining predictors of developmental outcomes of typically developing children including cognition, executive function and school-readiness. We partner with the GUSTO team in innovative research including the neuroimaging and studying of brain connectivity and profiling of children with neurodevelopmental conditions (BRACO-LD) as co-team members. 

Autism Spectrum Disorder

We have multiple ongoing studies, including those exploring new models of care for children on the autism spectrum such as:

• Adaptation and implementation of evidence-based parent training programmes in Singapore
  
• Telemedicine/telehealth based provision of therapy services
  
• Identifying factors associated with better outcomes in children on the autism spectrum
• Feeding difficulties in autism
  
• Design and implementation of school transition programmes
  

Screen Time Exposure in Children

Studies in this area include the effects of screen time exposure on children's cognition, behaviour and social emotional development as well as implementation and evaluation of effective interventions to tackle screen time exposure. Research in this area also encompasses looking at family and environmental factors that can have a positive or negative impact on screen time exposure and its consequences.

Children with Chronic Medical Illnesses

We have a comprehensive ongoing programme studying the unmet needs of children and their families of chronic medical illnesses and the cognitive and behavioural profiles of these children. This involves examining the effects of chronic disease and its treatment on children's development among other aspects.

Through this programme, we will establish the overall burden of care in these children so as to facilitate better resource planning. This includes children who are survivors of haematological cancers and stem cell/bone marrow transplant recipients, children with congenital cardiac disease who are post cardiac surgery, children born premature, children with epilepsy or brain tumours and children with chronic liver disease including liver transplant patients. 

Executive Function (EF) and Attention Deficit Hyperactivity Disorder (ADHD)

EF refers to a set of skills (e.g. Focus, Planning, Memory) that is important to school success. These are better predictors of academic success than IQ alone. Studies in this area include factors that influence and predict EF such as why some children have better EF skills than others and what affects this. We also look at the best intervention methods to improve these skills in children including the use of computer based intervention programs to improve EF. For instance, our team members have identified among children with preschool ADHD, the factors that determine who will go on to have persistent childhood ADHD and who will instead improve as they grow older.

Our team conducts research on many different aspects of paediatric endocrinology and diabetes. Specifically, our research focus has centred around various aspects of paediatric obesity and its associated metabolic complications, including genetics, developmental origins, environmental risk factors and the neurobiology of obesity. This is especially important in light of the escalating prevalence of childhood obesity, which poses significant impact on population health and is associated with a high economic burden. 

Our Team

• Associate Professor Loke Kah Yin
• Professor Lee Yung Seng
  
• Dr Cindy Ho
• Dr Yvonne Lim
  
• Dr Andrew Sng
  
• Dr Nicholas Ng
  
• Dr Delicia Ooi Shu Qin
  
  

Research Areas

Obesity, Appetite, and Diabetes

1. OBesity in Singapore Children (OBSiC) study: To identify and functionally characterise genetic variants/genes associated with severe childhood obesity
   
2. Metabolically healthy/unhealthy obesity: To examine factors and underlying mechanisms involved in the pathogenesis of metabolic complications in the obese phenotype 
3. Neural and cognitive mechanisms that predict risk for the development of obesity
4. Bioengineering microbes that can be used for weight management and the treatment of obesity
   
5. The Appetite Toolbox Study: Improving eating self-regulation skills in paediatric overweight or obesity 
   
6. Lifestyle interventions for the management of paediatric obesity and diabetes
   
7. Quality of life and reasons for poor compliance in paediatric diabetes 
   
   

Developmental Origins of Health and Disease (DoHAD)

Several of our researchers are investigators of the Growing Up in Singapore Towards healthy Outcomes (GUSTO) and Singapore PREconception Study of long-term maternal and child Outcomes (S-PRESTO), which are major collaborative birth cohort studies in Singapore aiming to study various developmental aspects of health and disease. Specifically, our team has an interest in examining the early life risk factors (developmental origins) involved in the development of obesity and metabolic health in later life. 

Fertility 

Advances in cancer treatment have led to improved long term survival after childhood cancer, but often at a price of impaired future fertility. The use of gonadotoxic chemotherapeutic agents can cause gonadal dysfunction in prepubertal children. Hence, fertility preservation in young cancer patients may aid in assisting with their fertility in the future. Our team aims to optimize the method of fertility preservation and study how these can be used for assisted reproduction and fertility. 

Congenital Adrenal Disorders 

Congenital adrenal disorders (CAD) are a mixed group of conditions that encompasses in-born disorders of the adrenal gland, which is a gland that produces important hormones for normal body function. Our team has been conducting research on the genetics of congenital adrenal hyperplasia, which is a form of CAD. We are particularly interested to evaluate the genetic frequency of various genetic errors (mutation) causing CAD, and the clinical manifestations of these genetic errors in the South East Asian population. 

The mission of the Division of Paediatric Haematology-Oncology is to provide quality clinical care for children with cancer and haematological disorders. Ultimately, we aim to develop effective therapies through clinical trials, improvements in haematological progenitor cell transplantation, translational research and international outreach.

We seek to improve the outcome of children with cancer in Southeast Asia through the integration of education, research and clinical care. The annual St Jude-Viva Forum in Paediatrics Oncology is the combined effort of the St Jude International Outreach Program and Viva Foundation for Children with Cancer, with the aim of providing paediatric oncologist in Asia the opportunity to learn and network with each other to foster collaborations. The Viva-Asia Acute Leukaemia and the Viva-Asia BMT Working Groups meet at the Forum each year to enhance regional collaboration and provide the opportunity to learn from each other's experience.

We have established a web conferencing system used for:

• Guiding MRD studies in childhood Acute Myelogenous Leukaemia (AML) for national protocols in Japan and Taiwan
• Training scientists from Japan, Taiwan, Hong Kong and South Korea
• Overseas paediatric cancer centres from Canada, India, Saudi Arabia and Brazil to have consultations with us
  

Our Team

• Professor Dario Campana
• Elaine Coustan-Smith
• Associate Professor Allen Yeoh
  
• Dr Shawn Lee
  
• Dr Bernice Oh
  

Clinical Trials

Acute Leukaemias and CAR-T Therapy using Multiple CARS and Cell Marker Profiling in High Risk and Relapsed B-lineage ALL (ALACART) Study

This is the first Chimeric Antigen Receptor T-cell (CAR-T) clinical trial in Singapore, where we will treat high risk B-cell Acute Lymphoblastic Leukaemia (B-ALL) across a span of age ranges, from six months to 80 years of age. This is a cellular therapy trial that aims to treat high risk B-ALL using a number of antigen targets including CD19, CD22 and CD123. 

Malaysia-Singapore ALL 2020 Study

This is the successor trial of the recently reported Ma-Spore ALL 2010 (Ariffin et al, JCO 2023; Yeoh et al, JCO 2018) and 2003 studies (Yeoh et al. J Clin Oncol 2012) for children and adolescents with Acute Lymphoblastic Leukaemia (ALL). It is a multi-centre study involving NUH and KK Women's and Children's Hospital in Singapore, and the University Malaya and Sime Darby Medical Centre in Malaysia. The Malaysia Singapore (Ma-Spore) ALL 2010 study uses minimal residual disease (MRD) levels to determine early response to remission induction and tailor the intensity of chemotherapy

Malaysia-Singapore AML 2010 Study

This multi-centre study for children and adolescents with AML involves the same institutions participating to Ma-Spore ALL 2010. It uses a modification of the MRC AML 10 treatment back bone replacing the second anthracycline block with high dose cytarabine in efforts to avert cardiotoxicity. It relies on MRD quantitation by flow cytometry and newly identified markers to assess response and select treatment intensity.

Singapore Paediatric Oncology Group Protocol for Osteosarcoma

This study uses multi-agent chemotherapy, cisplatin, doxorubicin, high dose methotrexate, ifosfamide with etoposide for metastatic patients, and limb salvage surgery with biological materials (host bone) or prosthesis.

Intra-arterial Chemotherapy with Melphalan for Advanced Intraocular Retinoblastoma Study

This study uses super-selective intra-arterial (ophthalmic artery) chemotherapy in the treatment of advanced intra-ocular retinoblastoma, Reese Ellsworth (RE) IV & V or International Intra-ocular Retinoblastoma Classification (ICIR) C, D & E.

Translational Research

Gene Expression Profiling in Acute Leukaemia

Mononuclear cells from bone marrow of patients on the Ma-Spore ALL 2010 and AML 2010 studies are interrogated using whole genome gene expression profiling and newly discovered algorithms to determine its value in disease subgrouping and prognosis.

Immune Profiling in Acute Leukaemias 

We interrogate the immune profile (immunophenotype, RNAseq, TCRsequencing, single-cell RNAseq) of patients undergoing therapy for acute leukaemias and cellular therapies to determine their correlations and influence on outcomes.

New Markers for MRD Studies in ALL and AML

Relying on extensive expertise in MRD monitoring and advanced instrumentation, we are validating recently discovered markers for MRD studies by flow cytometry in ALL and AML in both paediatric and adult patients.

Pharmacogenomics Studies

We are studying the impact of gene mutations and pharmacogenetics on treatment outcome in children with ALL. We have also found that genetic ancestry influences molecular subtypes of ALL and has impact on outcomes. We are therefore aiming to study these racial differences in toxicities and outcomes. We are also determining the pharmacogenomics of thiopurine metabolism, specifically TPMT and NUDT15, in Asian patients. Finally, we are studying Thiopurine Methyltransferase (TPMT) and Catechol-O-methyltransferase (COMT) polymorphisms in children with solid tumours who received cisplatin correlating the findings with those of audiometric testing.

Cell Therapy of Cancer

We have developed unique methods to expand and activate NK cells, as well as to redirect NK cells and T lymphocytes through genetic engineering. These methods, which have been adapted to clinical-grade conditions, are being applied to treat children and adults with different malignancies. Research in the laboratory aims at discovering novel ways to redirect immune cells and at enhancing their anti-cancer potential.

Three cell therapy-based clinical protocols have been approved by NUH and Singapore General Hospital ethical boards and the Health Science Authority of Singapore. These protocols use expanded allogeneic NK cells to treat children and adults with various malignancies including AML, myelodysplastic syndrome, T-cell ALL, sarcoma and neuroblastoma.

Outreach Programmes

We are involved with St Jude Global to develop protocols and guidelines for the developing world and LMIC countries, for example, the Adapted Resource and Implementation Application (ARIA) protocols for specific tumours. 

We also organise a Pre-Forum Workshop specifically for our colleagues in the developing countries of the region. In the past years, we have discussed effective leukaemia and solid tumour protocols for countries with limited resources, palliative care, hospital registries, supportive care and effective fund raising.

In collaboration with St. Jude Children's Research Hospital, we have established a twinning partnership with the Southern Philippines Medical Centre (SPMC), a government referral centre for the whole island of Mindanao. We have also developed a Retinoblastoma Program for Mindanao Island in collaboration with Dana Farber Children's Hospital Cancer Centre and St. Jude Children's Research Hospital, supported by the Khoo Teck Puat Foundation and the Viva Foundation for Children with Cancer. The project aims at facilitating early diagnosis through education and developing SPMC as a referral centre.

Blood / Marrow Transplantation

Novel Preparative / Conditioning Regimens

Development of successive novel preparative regimens with aims to:

• Minimise treatment-related toxicities
• Improve donor engraftment
• Control graft-versus-host disease (GVHD)
• Preserve 'graft-versus-leukaemia (GVL) / 'graft-versus-tumour' (GVT) and 'graft-versus-infections' (GVI) activities
• Sensitise cancer cells to effector cells in stem cell grafts
• Enhance post-transplant immune reconstitution
• Shorten length of stays as inpatient and costs containment

Immune Reconstitution

Development of laboratory approaches to study immune recovery of patients who received any of these:

• Engineered donor grafts, e.g. selective T-cell depletion
• Unmanipulated donor grafts, e.g. post-transplant cyclophosphamide
• Donor lymphocytes, e.g. NK cells, T-cells

MRD-based Intervention

MRD-based intervention in patients eligible for advanced cellular therapy and/or BMT, aimed to improve pre-BMT disease status and/or post-BMT disease control.

Survivorship / Late Effects

Philanthropic supported clinical research programmes in:

• Hormonal and fertility preservation (in collaboration with endocrinology)
• Neuro-cognitive development (in collaboration with neuro-development paediatrics)
• Physical rehabilitation programme led by allied health professional or nurse

Research Database

We have been a research centre with the "National Marrow Donor Program" (NMDP), USA and the "Centre for International Blood and Marrow Transplant Research" (CIBMTR), USA since 2002.

We perform clinical as well as laboratory research so as to improve our understanding of kidney diseases in Asia with the ultimate aim of improving diagnostic and treatment approaches which may be unique to our population. Our group has published more than 100 papers in medical journals, presented more than 300 papers in medical conferences, and won more than 20 regional and international research awards. We have an established Paediatric Renal Immunology and Genetics Laboratory focusing on the genetics and immunology of kidney diseases in Asian children and adolescents.

Our Team

• Professor Yap Hui Kim
• Dr Ng Kar Hui
• Dr Perry Lau Yew Weng
• Dr Isaac Liu
• Dr Zhao Yaochun
• Dr Chan Chang Yien
• Dr Sharon Teo Sher Leen

Research Areas

Genetics Research

Our genetics research arm involves genetic testing for patients with primary glomerular disease using advanced techniques, in collaboration with scientists from Agency for Science, Technology and Research (A*STAR) and NUS. Our preliminary research work have found that the genetics of our Asian population differ significantly from those of Caucasian patients. Genetic testing can potentially help doctors decide on individualised medical treatment.

Immunology Research

Our immunology research arm is focused on nephrotic syndrome, mainly minimal change nephrotic syndrome and focal segmental glomerulosclerosis. The mechanisms of these diseases are still not fully understood. Our group was the first to describe the role of interleukin-13 (or IL-13) in children with relapses of the nephrotic syndrome. We have also developed an IL-13 overexpression animal model of nephrotic syndrome in order to further study the molecular signalling mechanisms that may be involved in the development of disease. Our latest work has identified the immunological abnormality in children with a serious form of nephrotic syndrome, namely focal segmental glomerulosclerosis, which predicts response to treatment with an anti-B lymphocyte monoclonal antibody, thus enabling children to be better treated to prevent progression to kidney failure. This work may in future lead to new potential targeted therapy in this disease.

Clinical Research

Our clinical research arm focuses on the diagnosis and prevention of early cardiovascular disease in children with chronic kidney disease via means of novel biomarkers, ambulatory blood pressure monitoring, and specialised scans of the heart and blood vessels.

Research Studies

The DRAGoN Study: Deciphering diversities: Renal Asian Genetics Network

​What is DRAGoN? DRAGoN is a research consortium set up by paediatric nephrologists in NUS, in collaboration with scientists from the Genome Institute of Singapore, to investigate glomerular and proteinuric renal diseases in Asians. Why was DRAGoN set up? Primary glomerular disease, including focal segmental glomerulosclerosis (FSGS), is a common cause of renal failure in adults and children worldwide. Current treatment is empirical and involves immunosuppressive drugs which are toxic, expensive and with only moderate response rates. Proteinuric or familial haematuric diseases are traditionally monogenic diseases, involving as many as 40 to 50 known genes. With new sequencing techniques, concomitant variants in different genes are increasingly recognised as important. In addition, extrapolating from studies in African Americans involving MYH9 and APOL1 as significant risk alleles, FSGS can also be a polygenic disorder.

​

Genetics of renal kidney diseases in Asia is largely understudied. There has been evidence that the genetic causes of glomerular diseases in Asia differ from other parts of the world. For example, Asian children with sporadic steroid-resistant nephrotic syndrome have a much lower prevalence of podocin mutations compared to Caucasian and Middle East patients. A dedicated Asian genetic network allows for more comprehensive and systematic research to decipher the unique Asian genetic makeup. Additionally, Malays who have a higher risk of renal failure are largely understudied in the world.

Our Mission

Our mission is to advance our understanding of the demographics, causes and genetics of glomerular diseases in Asians, and eventually to provide an evidence base for clinical management and explore innovative treatment strategies for genetically based diseases. We hope this network can systematically study the genetics of renal diseases in Asia.

Aims and Methods

This study is divided into two parts, namely Genome-wide association studies (GWAS) and Next Generation Sequencing (NGS).

1. Genome-wide Association Studies (GWAS)

   This aims to identify genetic risk alleles that may be important in disease susceptibility in primary sporadic FSGS in Asia.

2. Next Generation Sequencing (NGS)

   This aims to identify potentially disease-causing genetic mutations in patients with primary proteinuric glomerular diseases which are either familial; of congenital or infantile-onset; or resistant to all forms of immunosuppressive therapy.

   We will first screen >100 genes known to cause glomerular diseases using targeted gene sequencing. If no definitely or probably pathogenic variants were found in known genes, then exome sequencing may be performed to identify novel genes.

Our secondary aims include preliminary in-vitro functional work on the identified genetic variants, and establishment of a comprehensive phenotype database in Asia to foster future collaborations.

There is no age limit for recruited subjects. Adult subjects are welcome.

Inclusion Criteria

1. Congenital or infantile nephrotic syndrome with onset in first year of life
   OR
2. Steroid-resistant nephrotic syndrome (include initial and late steroid resistance) with onset before 25 years of age
   OR
3. Persistent subnephrotic proteinuria with likely genetic etiology

Availability of histological evidence is important. Primary evidence should be as one of the following forms:

1. Histological slides (preferred)
2. Biopsy in paraffin block (preferred)
3. Renal biopsy samples in formalin (to be pre-arranged)
4. Digital photograph of light microscopy of histology slides
5. Histological evidence may be dated up to 5 years back, as long as it is still clear and undisputable.

Exclusion Criteria

1. Secondary glomerular diseases, such as lupus nephritis, IgA nephropathy, Henoch–Schönlein purpura.
2. Lack of clinical data and histological evidence to track the phenotype.

Study Procedures for Subjects

Only a single collection of blood or saliva is required and this can be performed during visits to their doctors. Saliva will be collected either by asking the subject to spit into a cup, or by using absorbent sponges.

Possible Benefits

By possibly identifying genetic causes of the disease, it may lead to more directed treatment strategies, which may translate to decreased side effects and lower healthcare costs. Identification of risk alleles for the FSGS in Asia may allow estimation of lifetime risks for kidney disease, as well as possibility of response to therapy and risk of disease progression.

Possible Risks, Inconvenience or Discomfort

Apart from the standard risks involved in blood-taking, there are no additional risks involved.

We welcome collaborators from healthcare institutions in Asia. If you are a clinician or researcher and would like to find out more about this study, please email Dr Ng Kar Hui at paenkh@nus.edu.sg for more details.

We cover shipping costs, and provide co-authorship in all publications.

Main Coordinating Centres

Khoo Teck Puat – National University Children's Medical Institute

Level 12 NUHS Tower Block, 1E Kent Ridge Road, Singapore 119228

National University of Singapore

Department of Paediatrics

Tahir Foundation Building, MD1 Level 15, 12 Science Drive 2, Singapore 117549

Investigators

• Dr Ng Kar Hui
• Professor Yap Hui Kim

Research Support Staff

• Dr U Mya Than
• Ms Ng Jun Li

Our research focuses on understanding the molecular basis of human genetics disorders in children. The Human Genetics Laboratory (HUMGEN Lab) was established in 1989 to develop molecular diagnostic methods for single gene disorders such as Duchenne muscular dystrophy (DMD), retinoblastoma (RB), spinal muscular atrophy (SMA), haemophilia and glucose-6-phosphate dehydrogenase (G6PD) deficiency. This subsequently expanded to cover other disorders such as Alagille syndrome, Wilson's disease, Hirschsprung's disease, Wilm's tumor, neurofibromatosis, myotonic dystrophy, charcot-marie tooth disease, limb girdle muscular dystrophies, Marfan's syndrome and Tarui's disease. Mutation screening of rare disorders can contribute towards early detection and improved clinical management in patients.

As part of the clinical interface with research, the lab had developed genetic tests for applications in molecular analysis, prenatal diagnosis and genetic counselling of various congenital disorders in Singapore. We have been actively engaged in the areas of molecular diagnostics and therapeutics, as well as in providing an understanding of the mechanisms underlying normal and disease states in subjects. Our current interest is in the application of techniques and strategies in studying disease susceptibility and elucidating the molecular architecture of genetic traits in specific conditions. We also conduct multidisciplinary collaborations with other departments and institutions to infuse innovative insights into our research programme.

The ultimate goals of our research are to provide clinically relevant outcomes in the form of:

1. Diagnostic molecular tests for a variety of genetic conditions
2. Customised genetic screening algorithms for molecular and predictive diagnosis that are specific to our populations
3. Identification of novel drug targets or therapeutic strategies

Our Team

• Professor Low Poh Sim
• Associate Professor Lai Poh San
• Associate Professor Stacey Tay
• Associate Professor Ong Hian Tat

Research Areas

Ongoing research interests of our group include:

• Elucidating the genetic and clinical heterogeneity of neuromuscular disorders
• Identifying novel genes and mechanisms underlying tumorigenesis in RB beyond the loss of RB1
• Diagnostic evaluation in neurogenetic disorders including mitochondrial disorders
• Detection of molecular abnormalities in non-syndromic mental retardation, and genetic conditions associated with developmental delays and learning disabilities
• Epigenetic mechanisms underlying autism spectrum disorders
• Genetics of human behaviour and decision making
• The role of phenotype and genetic determinants in determining human telomere length
• The Pan-Asian SNP Initiative (PASNPI) and the Pan-Asian Population Genomics Initiative (PAPGI)

Our group is interested in leveraging on genetic and genomic knowledge and technological advances to improve the diagnosis and prevention of heritable disorders, in the process developing novel and innovative molecular tests using technology platforms.

Our Team

• Associate Professor Samuel Chong
• Associate Professor Denise Goh
• Dr Felicia Cheah

Research Areas

Translational Research

Translational research is focused on developing novel and innovative DNA-based diagnostics for application to preimplantation genetic testing (PGT), prenatal diagnosis (PND) and postnatal genetic testing and screening of inherited disorders that are common (alpha-thalassemia, beta-thalassemia, spinal muscular atrophy), rare (Prader-Willi and Angelman syndromes), or diagnostically challenging (fragile X-related and other trinucleotide repeat disorders). We aim to develop elegant solutions to practical barriers that hinder widespread adoption of genetic testing and screening for these disorders.

Consistent with this goal, our group has developed a molecular toolbox for the analysis of the fragile X-related disorders, which includes a novel single-step screening assay for rapid high throughput identification of affected and at-risk individuals, a fluorescent PCR assay capable of accurately sizing all normal and premutation FMR1 alleles and detecting all full mutation alleles, and a single-tube assay for detecting and sizing all unmethylated and methylated normal and premutation FMR1 alleles and determining methylation status of full mutation alleles. Each assay can be performed at a fraction of existing screening and diagnostic test costs.

A USPTO patent has been awarded for this screening concept, and the FMR1 molecular analysis toolkit has been licensed and is now available commercially. The innovative testing and screening strategy employed here is potentially applicable to other disorders caused by expansion of simple sequence repeats within a gene. Similar screening and testing assays for other trinucleotide repeat disorders based on the same strategy used in the FMR1 molecular analysis toolkit are being developed gradually. We will also be exploring the use of third generation sequencing platforms for accurate sizing of trinucleotide repeat hyperexpansions in affected individuals.

Our efforts have also been directed towards the simplification of preimplantation genetic testing of monogenic disorders (PGT-M). Generally in PGT-M, considerable assay customisation is required for each couple's specific gene mutation(s), and for identifying informative linked markers, even if the disease gene is the same. Linked markers serve an important role to independently corroborate mutation genotype results, which are vulnerable to misdiagnosis from allele dropout or exogenous DNA contamination. In situations where the mutation(s) is/are unknown or cannot be genotyped, or where an at-risk parent does not wish to know his/her mutation status, linked markers provide the only means for PGT-M of that disorder.

To address these issues, we have been gradually developing panels of highly multiplexed microsatellite markers adjacent to various disease genes, starting with the most common inherited disorders. We have developed a panel of 11 STR/STS (short tandem repeats / sequence tagged site) markers within and flanking the alpha-globin gene cluster, for PGT-M of all common deletional determinants of alpha-thalassemia. This single-tube assay tests for all common alpha-globin gene deletions and simultaneously generates multi-marker diplotypes for independent corroboration of the deletional status of embryos. The high heterozygosity of every STR marker in the panel ensures sufficient panel informativity for the assay to be used in virtually all alpha-thalassemia PGT-M cases without modification. Similar multi-marker panels flanking other common disease gene loci have been developed, including those for beta-thalassemia, haemophilia A, and trinucleotide repeat disorders such as fragile X syndrome, myotonic dystrophy type 1, and Huntington disease.

We are now expanding our translational research into PGT for whole chromosome aneuploidy (PGT-A) and other structural rearrangements (PGT-SR), both of which can be performed using next-generation sequencing (NGS) platforms. Although performing PGT-M for an inherited disease simultaneously with PGT-A to screen for chromosome aneuploidy is possible, the few reported strategies are inefficient, one contributing factor being the incompatibility of whole genome amplification methods required for PGT-M and PGT-A. Furthermore, while low-coverage NGS methods are sufficient to detect aneuploidy clearly most of the time, a significant fraction of ambiguous results of unknown cause are observed. Rather than a low-coverage shotgun sequencing of random fragments, massively-multiplexed targeted SNP amplicon sequencing may produce more consistent chromosome copy number in PGT-A. Such a strategy may also be equally applicable to PGT-SR of reciprocal and Robertsonian translocations. Finally, this PGT-A strategy can be easily combined with mutation-carrying amplicons for simultaneous PGT-M for inherited diseases.

In the course of our diagnostic development work, we have also made interesting observations that have led to identification of novel gene rearrangements at the alpha-globin gene cluster, as well as nucleotide variants within trinucleotide repeats. These findings are important as they may have significant implications for diagnostic test accuracy and correct results interpretation.

Basic Research

Our group's current basic research efforts have been focused on elucidating the function of genes implicated in developmental disorders, in particular oral clefting. Oral clefts rank among the most common congenital malformations globally, and represent a major public health burden especially in Third World countries. The etiology of oral clefts is complex, with strong evidence that multiple genes control risk to oral clefts, some of which may interact with common environmental risk factors such as maternal smoking, alcohol consumption, and vitamin supplementation. As part of an international collaborative group aiming to identify genetic factors predisposing to idiopathic oral clefting, several genes that increase risk for oral clefting were identified, either directly or through interaction with environmental factors.

We have utilised the zebrafish Danio rerio, an established vertebrate model, to study the effects of gene function and dysfunction on normal and abnormal development. In particular, we examined an interesting maternal zygotic transcription factor Interferon Regulatory Factor 6 (IRF6), which appears to activate different genes at different stages of embryonic and fetal development. We have been focusing on its function in the zygote and early embryo. Deletion of its protein interaction domain, but not its DNA binding domain, leads to early developmental arrest at gastrulation followed by embryo rupture at the animal pole. Using transcriptome analysis of such perturbed embryos, we identified two very highly down-regulated direct target genes of this transcription factor. We have shown that they are directly bound and activated by IRF6. Future work will involve characterisation of other highly dysregulated genes identified from the microarray analysis.

Our research focuses on many different aspects of neonatology, as our work involve both well infants and sick premature infants.

For well infants, we are experienced in developing the cord thyroid-stimulating hormone (TSH) screening for detecting congenital hypothyroidism. It is now translated from bench to clinical care nationwide. We collaborated with the Audiology Department in development of Universal Newborn Hearing Screening and establishing protocols for various at-risk groups. We also worked with the National Expanded Newborn Screening committee in developing national norms for metabolic screening with tandem mass spectrometry. We continue to research novel screening technologies to improve the health of newborns through early screening.

Working with collaborators, we had also performed studies looking at common neonatal diseases like neonatal jaundice and its genetic predisposition as well as early detection and treatment.

In the field of maternal and neonatal medicine, we had won grants studying the effect of maternal chronic hepatitis B infections on immunoprophylaxis failure of the hepatitis B vaccination programme.

For premature infants, we had won grants studying the clinical applicability of cranial and vascular ultrasonography. We also have animal studies in the field of neonatal haemodynamics.

In collaboration with Duke University, we completed a pilot trial on the safety and feasibility of autologous cord blood cell infusion for term infants with hypoxic-ischemic encephalopathy in Singapore.

The ultimate aim of our research is to translate basic research into further understanding of the common neonatal diseases and developing better care for our fragile patients.

Our Team

• Associate Professor Lee Jiun
• Associate Professor Roy Joseph
• Dr Lee Le Ye
• Dr Chinnadurai Amutha
• Dr Krishnamoorthy Niduvaje
  

Research Areas

Ongoing research of our group includes:

1. Reduction in Serum Bilirubin before and after Introduction of Transcutaneous Bilirubinometry
2. Neonatal infections in NICU
3. Neonatal hemodynamics
4. Feeding behaviours in ex-premature infants
5. Zika infections in Singapore mothers
6. Survey maternal knowledge and practice in mothers with chronic hepatitis B carriage