Publications by authors named "Carmen Swanepoel"

8 Publications

  • Page 1 of 1

Between a rock and a hard place: COVID-19 and South Africa's response.

J Law Biosci 2020 Jan-Jun;7(1):lsaa052. Epub 2020 Jul 7.

Department of Jurisdprudence, School of Law, University of South Africa, South Africa.

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http://dx.doi.org/10.1093/jlb/lsaa052DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7454702PMC
July 2020

Ethical and practical issues to consider in the governance of genomic and human research data and data sharing in South Africa: a meeting report.

AAS Open Res 2019 May 22;2:15. Epub 2019 May 22.

Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.

Genomic research and biobanking has undergone exponential growth in Africa and at the heart of this research is the sharing of biospecimens and associated clinical data amongst researchers in Africa and across the world. While this move towards open science is progressing, there has been a strengthening internationally of data protection regulations that seek to safeguard the rights of data subjects while promoting the movement of data for the benefit of research. In line with this global shift, many jurisdictions in Africa are introducing data protection regulations, but there has been limited consideration of the regulation of data sharing for genomic research and biobanking in Africa. South Africa (SA) is one country that has sought to regulate the international sharing of data and has enacted the Protection of Personal Information Act (POPIA) 2013 that will change the governance and regulation of data in SA, including health research data, once it is in force. To identify and discuss challenges and opportunities in the governance of data sharing for genomic and health research data in SA, a two-day meeting was convened in February 2019 in Cape Town, SA with over 30 participants with expertise in law, ethics, genomics and biobanking science, drawn from academia, industry, and government. This report sets out some of the key challenges identified during the workshop and the opportunities and limitations of the current regulatory framework in SA.
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http://dx.doi.org/10.12688/aasopenres.12968.1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7118803PMC
May 2019

Differential Diagnosis of Malignant Lymphadenopathy Using Flow Cytometry on Fine Needle Aspirate: Report on 269 Cases.

J Clin Med 2020 Jan 20;9(1). Epub 2020 Jan 20.

National Health Laboratory Services, Tygerberg Hospital, Cape Town 7505, South Africa.

Introduction: Fine needle aspiration (FNA) is frequently the first noninvasive test used for the diagnostic workup of lymphadenopathy. There have been many studies showing its usefulness, especially in conjunction with other techniques for the diagnosis of lymphoma, but it remains inferior to histological examination. The data regarding this subject have mostly been reported mostly from first-world countries, but are scarce for emerging economies. Thus, the current study assesses the agreement between fine needle aspiration flow cytometry (FNA FC) and histology in the aforementioned region.

Material And Methods: We conducted a retrospective study including the FNA FC adenopathy diagnoses made between January 2011 and December 2016 at the Tygerberg Hospital, Cape Town, South Africa. Additional variables included were the histological diagnosis, sex and age of the included patients.

Results: In the descriptive part of the current study, 269 FNA FC samples were included. The most frequent diagnoses made on these were represented by B-cell lymphoma, reactive adenopathy, no abnormality detected (NAD), and non-hematological malignancy. In the analytical part of the current study, there were 115 cases included that had both valid FNA FC and histological diagnoses. It could be observed that FNA FC can correctly diagnose B-cell lymphoma in most cases, but it is a poor diagnostic tool especially for Hodgkin lymphoma in this setting as only a four-color flow cytometer was available for diagnosis. Moreover, FNA FC diagnosis of reactive adenopathy and of no abnormalities detected was shown to frequently hide a malignant disease.

Conclusion: In countries with scarce resources, FNA FC represents a useful diagnostic tool in the case of B-cell lymphoma, but may misdiagnose reactive adenopathy. Thus, FNA FC should be used in a case-specific manner, in addition to as a screening tool, with the knowledge that in cases with a high clinical suspicion of lymphoma, histological diagnosis is a necessity.
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http://dx.doi.org/10.3390/jcm9010283DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7019747PMC
January 2020

Baobab Laboratory Information Management System: Development of an Open-Source Laboratory Information Management System for Biobanking.

Biopreserv Biobank 2017 Apr 4;15(2):116-120. Epub 2017 Apr 4.

1 South African National Bioinformatics Institute, SA Medical Research Council Unit, University of the Western Cape , Bellville, South Africa .

A laboratory information management system (LIMS) is central to the informatics infrastructure that underlies biobanking activities. To date, a wide range of commercial and open-source LIMSs are available and the decision to opt for one LIMS over another is often influenced by the needs of the biobank clients and researchers, as well as available financial resources. The Baobab LIMS was developed by customizing the Bika LIMS software ( www.bikalims.org ) to meet the requirements of biobanking best practices. The need to implement biobank standard operation procedures as well as stimulate the use of standards for biobank data representation motivated the implementation of Baobab LIMS, an open-source LIMS for Biobanking. Baobab LIMS comprises modules for biospecimen kit assembly, shipping of biospecimen kits, storage management, analysis requests, reporting, and invoicing. The Baobab LIMS is based on the Plone web-content management framework. All the system requirements for Plone are applicable to Baobab LIMS, including the need for a server with at least 8 GB RAM and 120 GB hard disk space. Baobab LIMS is a server-client-based system, whereby the end user is able to access the system securely through the internet on a standard web browser, thereby eliminating the need for standalone installations on all machines.
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http://dx.doi.org/10.1089/bio.2017.0014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5397207PMC
April 2017

The role of microRNAs in the pathogenesis of HIV-related lymphomas.

Crit Rev Clin Lab Sci 2015 28;52(5):232-41. Epub 2015 Jul 28.

a Division of Hematopathology , Tygerberg Academic Hospital , Tygerberg , South Africa .

The incidence of HIV-related lymphomas (HRLs) is increased by 60-100 times in patients with HIV. When compared to the general population, patients with HRLs often present with extranodal lymphoid proliferation, most frequently of the gastrointestinal tract, central nervous system, liver and bone marrow. MicroRNAs (miRs) are non-coding double-stranded RNA molecules of 18-25 nucleotides that regulate post-translational gene expression by inhibiting translation or promoting degradation of messenger RNA complementary sequences. Before their discovery, tumorigenesis was thought to have been caused by the alteration of protein-coding oncogenes and tumor-suppressor genes, but once identified in B-cell chronic lymphocytic leukemia, miRs function as either oncogenes or tumor-suppressor genes was confirmed in different types of malignancies. Since miRs are clearly involved in tumorigenesis in many cancers, their role in HRLs is now receiving attention. A few studies have been conducted thus far in some HRLs on the involvement of miR in the pathogenesis of lymphoid malignancies. Since B-cell lymphomas arise from various stages of B-cell development in both HIV-infected and HIV-naïve patients, investigators have tried to determine the different miR signatures in B-cell development. As classic immunohistochemistry staining is sometimes not enough for the differential diagnosis of HRLs, in the present review, we have described the potential use of miRs in the prognosis and diagnosis of these diseases.
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http://dx.doi.org/10.3109/10408363.2015.1030063DOI Listing
May 2016

Challenges of biobanking in South Africa to facilitate indigenous research in an environment burdened with human immunodeficiency virus, tuberculosis, and emerging noncommunicable diseases.

Biopreserv Biobank 2013 Dec 22;11(6):347-54. Epub 2013 Nov 22.

1 Division of Haematology, Stellenbosch University Faculty of Medicine and Health Sciences , Tygerberg, South Africa .

The high burden of infectious diseases and the growing problem of noncommunicable and metabolic disease syndromes in South Africa (SA) forces a more focused research approach to facilitate cutting-edge scientific growth and public health development. Increased SA research on these diseases and syndromes and the collection of associated biospecimens has ensured a plethora of biobanks created by individuals, albeit without the foresight of prospective and collective use by other local and international researchers. As the need for access to high-quality specimens in statistically relevant numbers has increased, so has the necessity for the development of national human biobanks in SA and across the Continent. The prospects of achieving sustainable centralized biobanks are still an emerging and evolving concept, primarily and recently driven by the launch of the H3Africa consortium, which includes the development of harmonized and standardized biobanking operating procedures. This process is hindered by a myriad of complex societal considerations and ethico-legal challenges. Efforts to consolidate and standardize biological sample collections are further compromised by the lack of full appreciation by national stakeholders of the biological value inherent in these collections, and the availability of high quality human samples with well-annotated data for future scientific research and development. Inadequate or nonexistent legislative structures that specifically regulate the storage, use, dispersal, and disposal of human biological samples are common phenomena and pose further challenges. Furthermore, concerns relating to consent for unspecified future uses, as well as access to information and data protection, are all new paradigms that require further consideration and public engagement. This article reviews important fundamental issues such as governance, ethics, infrastructure, and bioinformatics that are important foundational prerequisites for the establishment and evolution of successful human biobanking in South Africa.
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http://dx.doi.org/10.1089/bio.2013.0049DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4076990PMC
December 2013

The human immunodeficiency virus, (HIV-1), pandemic: cellular therapies, stem cells and biobanking.

Transfus Apher Sci 2013 Aug 13;49(1):9-11. Epub 2013 Jun 13.

Department of Pathology, Tygerberg Academic Hospital, Faculty of Health Sciences, University of Stellenbosch, Tygerberg, South Africa.

The Human Immunodeficiency Virus, (HIV-1), has become a major global health threat with recent estimates suggesting that 68% of people living with HIV (PLWH) reside in Sub-Saharan Africa. The current strategies for containment of this disease in the absence of an effective vaccine are of concern in terms of long-term fiscal sustainability and cost effectiveness. HIV prevalence rates are set to rise, not because of increasing incidence but rather because of the effort involved in implementing the anti-retroviral (ARV) programmes, especially on the African continent. Even when sub-optimally delivered, these therapies will lead to a decrease in mortality rates and prevent early death from opportunistic infections. However, evidence is emerging for long-term systemic effects of chronic HIV infection in persons on ARV therapy, including increased incidence of Haematological abnormalities and malignancies.
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http://dx.doi.org/10.1016/j.transci.2013.05.017DOI Listing
August 2013