- Role: Senior Lecturer
- Contact Details:
- Telephone: +27 21 959 3645
- Facsimile: +27 21 959 2512
- Email: nicki at sanbi.ac.za
- generic approaches to disease gene prediction and
- genetics of host response to pathogen infection
- Lab Members:
My formal postgraduate education was in laboratory science in the field of medical genetics, particularly in genetics underlying disease. My undergraduate degree was in Biochemistry and my Honours degree was in the field of Medical Biochemistry at the University of Cape Town. I did my PhD in Paediatric Molecular Oncology at the Royal Marsden Cancer Hospital in London, UK, with the University of London. I completed a postdoctoral position in the USA at the University of California, San Francisco, specialising in genetics in the field of Paediatric Endocrinology.
In 2003 I returned to Cape Town and made the transition to bioinformatics with a Wellcome Trust Postdoctoral Fellowship at the South African National Bioinformatics Institute (SANBI), UWC, where I developed generic approaches to computational disease gene prediction.
I subsequently took a postdoctoral position in the department of Human Genetics at the University of Cape Town until the end of 2008, where I pursued methods to identify and prioritise good candidate aetiological genes for specific diseases. During 2009/2010 I continued in computational analysis of disease genetics as an independent consultant researcher.
I have also developed an interest in the genetics of the host response to infectious agents, working with the international SysCo consortium studying host response of macrophages to leishmania infection with genome-wide systems biology approaches that integrate protein, mRNA, miRNA and regulatory network data.
In July 2010 I rejoined SANBI, UWC, as a Senior Lecturer, where I will be developing my own research group and contributing to existing studies ongoing at SANBI. My interests remain in the areas of generic approaches to disease gene prediction and genetics of host response to pathogen infection. I have a keen interest in the area of translational research, aiming to bring together computational approaches, molecular biology and clinical approaches to enhance our understanding of and ability to modify the disease state
Currently, I work on human genetics underlying disease, specifically in African populations, aiming to characterise genetic diversity in South Africa patient populations within the disease context. I research generic computational disease gene prediction, candidate disease gene prioritisation for specific diseases, and genetics of host response to infectious disease.
Ongoing projects include a collaborative project establishing a registry of patients from Cape Town who have systemic lupus erythematosus (SLE). We are building a database for effective storage and data-mining of extensive clinical and biochemical patient data for these patients, and will use this data to design and implement –omics studies to further elucidate the genetic and environmental contributors to this disease, as well as to characterise the clinical characteristics of lupus in South African patients. In parallel, we are undertaking bioinformatics approaches to harness the public data available from studies on lupus genetics, and to understand gene regulatory pathways and processes that are implicated in lupus. I also work with clinical collaborators to investigate genetic factors underlying susceptibility to salt-sensitive hypertension in South African patients, and we have conducted next generation sequencing to analyse a candidate gene that may be implicated. We are also involved in exome sequencing studies of patients and controls to determine genetic factors underlying myoclonic epilepsy; and autosomal dominant kidney disease. I continue research in the area of generic approaches to computational disease gene prioritisation, with a study ongoing on the effects of genome architecture on disease gene status.
This year, we have undertaken a thorough study of the ethical and legal considerations for genomic clinical and medical research in Africa, in order to inform our own research as well as to provide a resource for other researchers undertaking such research in Africa.
Grants, funding, awards received:
Medical Research Council of South Africa – MRC Unit for Bioinformatics Capacity Development.
H3ABioNet – SANBI node of the H3A Bioinformatics Network (NIH)
H3A Kidney Disease Research Network – Bioinformatics partner (NIH)
UWC research funding – “Identification of the genetic defect in a family with progressive myoclinic epilepsy”
NRF Freestanding Postdoctoral Fellowship
A CSHL stipend was received to attend the Cold Spring Harbor Laboratory (CSHL) Conference: PERSONAL GENOMES & MEDICAL GENOMICS, Cold Spring Harbor, USA (14- 17 November 2012).
A student bursary was received to attend the Joint South African Genetics Society and South African Society for Bioinformatics and Computational Biology, Stellenbosch, South Africa (10-12 September 2012).
- Genetics underlying systemic lupus erythematosus (SLE/lupus) in South African Patients.
Collaborator: Dr Ikechi Okpechi, Department of Nephrology, University of Cape Town/Groote Schuur Hospital.
- Genetics underlying Salt Sensitive Hypertension in Black South African Patients
Collaborator: Professor Brian Rayner, Department of Nephrology, University of Cape Town/Groote Schuur Hospital.
- Establishing a bioinformatics network in Africa for bioinformatics capacity and skills development.
Collaborators: The H3Africa Bioinformatics Network (H3ABioNet). P.I. Dr Nicky Mulder, Department of Computational Biology, University of Cape Town.
- Researching genetics and environmental factors underlying kidney disease in African patients.
Collaborators: The H3Africa Kidney Disease Research Network. P.I.s Prof. Dwomoa Adu University of Ghana Medical School, and Prof. Akinololu Ojo University of Michigan.
- Genetics underlying Autosomal Dominant Kidney Disease in a South African family.
Collaborator: Dr Ikechi Okpechi, Department of Nephrology, University of Cape Town/Groote Schuur Hospital
- Genetics underlying Myoclonic Epilepsy in a South African family.
Collaborator: Professor Jonathan Carr, Division of Neurology ,University of Stellenbosch.
- Host macrophage response to infection with Leishmania major.
Collaborators: The SysCo Consortium (EU Sixth Framework); Professor Frank Brombacher and Dr Anita Schwegmann, International Center for Genetic Engineering and Biotechnology, Cape Town Component and Division of Immunology, University of Cape Town
- A study of the ethical and legal implications of whole genome and whole exome sequencing in African populations.
Collaborator: Prof Adebowale Adeyemo, Center for Research on Genomics and Global Health, National Institutes of Health/National Human Genome Research Institute, USA
- Meta-analysis of African Genomes.
Collaborators: P.I.s Professor Michèle Ramsay, Division of Human Genetics at the National Health Laboratory Service and University of the Witwatersrand; Professor Scott Hazelhurst, Department of Bioinformatics, University of the Witwatersrand; Dr Nicky Mulder, Department of Computational Biology, University of Cape Town.
- Mechanisms underlying HPV-induced inflammation in oesophageal Oesophageal Cancer.
Collaborators: Prof Iqbal Parker and Dr Marike Janse van Rensburg, International Center for Genetic Engineering and Biotechnology, Cape Town Component and Division of Medical Biochemistry, University of Cape Town