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Nicki Tiffin

  • Role:  Senior Lecturer
  • Contact Details:
    • Telephone: +27 21 959 3645
    • Facsimile: +27 21 959 2512
    • Email: nicki at sanbi ac
  • Research:

Overview

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.

Papers published:

Rabhi I, Rabhi S, Ben-Othman R, Rasche A, The Sysco Consortium*, Daskalaki A, Trentin B, Piquemal D, Regnault B, Descoteaux A, Guizani-Tabbane L. Transcriptomic signature of Leishmania infected mice macrophages: a metabolic point of view. PLoS Negl Trop Dis. 2012 Aug;6(8):e1763 (link to Rabhi et al. 2012) * includes N Tiffin

Okpechi I, Swanepoel CR, Tiffin N, Duffield M, Rayner B. Clinicopathological insights into lupus nephritis in South Africans: A study of 251 patients. Lupus 2012, March 26, 2012.(link to Okpechi, I et al. 2012)

Tiffin N, Adeyemo A, Okpechi I. A diverse array of genetic factors contribute to the pathogenesis of Systemic Lupus Erythematosus. Orphanet J Rare Dis. 2013 Jan 7;8(1):2. (link to Tiffin et al. 2013)

 

Conference outputs:

Poster: 62nd American Society of Human Genetics (ASHG) Annual Meeting, San Francisco, USA (6-10 November 2012).Wright GEB, Koornhof PGJ, Tiffin N (2012) Ethical and legal considerations regarding participant privacy in the genomic era of research on the African continent.

Poster: Cold Spring Harbor Laboratory (CSHL) Conference: PERSONAL GENOMES & MEDICAL GENOMICS, Cold Spring Harbor, USA (14- 17 November 2012). Wright GEB, Koornhof PGJ, Tiffin N (2012) Ethical and legal considerations regarding participant privacy in the genomic era of research on the African continent.

Talk: A computational characterisation of the relationship between genome structure and disease genes. T Kibler, N Tiffin and A Christoffels South African Genetics & Bioinformatics and Computational Biology Society Conference. 2012, Stellenbosch, South Africa (10-12 September)

Poster: Effects of single nucleotide polymorphisms on putative transcription factor binding sites and gene expression. M Maqungo, S Schmeier, U Schaefer, N Tiffin, A Christoffels and V Bajic. South African Genetics & Bioinformatics and Computational Biology Society Conference. 2012, Stellenbosch, South Africa (10-12 September).

Poster: Legal considerations regarding participant privacy in the genomic era of research on the African continent. G Wright, P Koornhof and N Tiffin. South African Genetics & Bioinformatics and Computational Biology Society Conference. 2012, Stellenbosch, South Africa (10-12 September).

 

Meetings:

N. Tiffin: The AfriCRAN Craniofacial Anomalies Network Meeting. Lagos, 22-25th February, 2012. Presentation: Tiffin,N. SANBI’s role in AfriCRAN – bioinformatics analysis of genomic data.

N. Tiffin: The Inaugural Meeting of the H3Africa Consortium, Addis Ababa, 8-10 October 2012.

N. Tiffin: The Inaugural meeting of the H3Africa Kidney Disease Research Network. Accra, Ghana, January 9-11, 2013. Presentation: The role of the South African National Bioinformatics Network in the H3Africa Kidney Disease Research Network.

 

Invited Talks:

N Tiffin: Rheumatology Department, Groote Schuur Hospital/University of Cape Town. “Genetics underlying susceptibility to Lupus”. February 2012

N Tiffin: Neurology Department, Groote Schuur Hospital/University of Cape Town. “Clinical Applications of Exome Sequencing”. 8 June 2012

 

Grants, funding, awards received:

N.Tiffin:

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”

G. Wright: NRF Freestanding Postdoctoral Fellowship

G.Wright: 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).

G.Wright: 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).

 

Journal review editor positions:

N Tiffin: Review Editor, Frontiers in Bioinformatics and Computational Biology

Journals reviewed for in 2012:

Orphanet Journal of Rare Diseases, Personalized Medicine (Future Medicine), Nature Reviews Genetics, BMC Systems Biology, Frontiers in Genetics, Nucleic Acids Research

Conference review panels:

N Tiffin: ISCB/ASBCB 2013 Abstract reviews

 

Collaborations ongoing:

Projects

  1. 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.

  1. Genetics underlying Salt Sensitive Hypertension in Black South African Patients

Collaborator: Professor Brian Rayner, Department of Nephrology, University of Cape Town/Groote Schuur Hospital.

  1. 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.

  1. 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.

  1. 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

  1. Genetics underlying Myoclonic Epilepsy in a South African family.

Collaborator: Professor Jonathan Carr, Division of Neurology ,University of Stellenbosch.

  1. 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

  1. 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

Additional Collaborations

  1. 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.

  1. 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

 

Courses attended:

N. Tiffin: Next generation sequencing and bioinformatics. SANBI/Roche, Cape Town ,17-19 April 2012.

G. Wright: Seven week “National Bioinformatics Workshop” hosted by the South African National Bioinformatics Institute, University of the Western Cape, Cape Town, South Africa (2012). Modules included biological databases, genomics, next generation sequencing, phylogenetics, Python programming, sequence analysis, statistics, and systems biology.

G. Wright: “Ensembl Browser Workshop” hosted by Dr B Overduin (European Bioinformatics Institute) at South African National Bioinformatics Institute, University of the Western Cape, Cape Town, South Africa (2012).

G. Wright: “Galaxy Workshop” presented by Dr D Clements (Emory University) Stellenbosch University, Stellenbosch, South Africa (2012).

T. Kibler: “Workshop on Population Genetics and Genomics” (June 2012). CBio, UCT, Cape Town) June 2012

 

Teaching (including courses presented or organised):

N Tiffin: University of Mauritius, SANBio Masters Programme. Module: Identifying candidate genes for human disease. 24-28 January 2012.

N Tiffin: University of the Western Cape, 3rd Year Bioinformatics Module BTN323, “Evaluating candidate disease genes”.

 

Thesis examined:

N Tiffin, Masters (2): University of the Western Cape

N Tiffin, Ph D: University of New South Wales, Australia (1)
Community Outreach:

City Press Article, November 2012 (need to scan but not sure how, as it is a large article – Samantha has it)

 

Visiting scientists to SANBI:

Dr Tobias Karakach. November 2012. Associate Professor, Department of Biochemistry and Molecular Biology, Dalhousie University, Nova Scotia, Canada.

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