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Oosthuizen J, Van der Merwe NC, Kotze MJ. Navigating the genetic landscape of breast cancer in South Africa amidst a developing healthcare system. Front Genet 2024; 14:1330946. [PMID: 38259622 PMCID: PMC10800608 DOI: 10.3389/fgene.2023.1330946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 12/19/2023] [Indexed: 01/24/2024] Open
Abstract
Breast cancer is a significant global health issue as it represents the leading cause of death in women worldwide. In 2021, the World Health Organization established the Global Breast Cancer Initiative framework with the aim to reduce the breast cancer mortality rate by the year 2040. In countries with developing healthcare systems, such as South Africa, the implementation of first-world technologies has been slow. We provide an overview of the strides taken to improve the cost-effectiveness of genetic service delivery for breast cancer patients in South Africa - from advances in the technology utilized for BRCA founder genotyping to variant screening in moderate-to high-penetrance genes. We furthermore reflect on research undertaken to improve accessibility by means of population-directed point-of-care genetic testing that is ideal for use in a primary healthcare setting. We also report on a pilot study utilizing exome sequencing at the intersection between research and service delivery. Finally, we discuss and conclude on the controversies, research gaps, and future prospects based on the most recent developments in first-world countries that are implementable in developing countries to improve early detection of breast cancer and overall disease management.
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Affiliation(s)
- Jaco Oosthuizen
- Division of Human Genetics, National Health Laboratory Service, Bloemfontein, South Africa
- Division of Human Genetics, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
| | - Nerina C. Van der Merwe
- Division of Human Genetics, National Health Laboratory Service, Bloemfontein, South Africa
- Division of Human Genetics, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
| | - Maritha J. Kotze
- Division of Chemical Pathology, Department of Pathology, National Health Laboratory Service, Tygerberg Hospital, Cape Town, South Africa
- Division of Chemical Pathology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
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2
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Christowitz C, Olivier DW, Schneider JW, Kotze MJ, Engelbrecht AM. Incorporating functional genomics into the pathology-supported genetic testing framework implemented in South Africa: A future view of precision medicine for breast carcinomas. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2024; 793:108492. [PMID: 38631437 DOI: 10.1016/j.mrrev.2024.108492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 02/25/2024] [Accepted: 04/11/2024] [Indexed: 04/19/2024]
Abstract
A pathology-supported genetic testing (PSGT) framework was established in South Africa to improve access to precision medicine for patients with breast carcinomas. Nevertheless, the frequent identification of variants of uncertain significance (VUSs) with the use of genome-scale next-generation sequencing has created a bottleneck in the return of results to patients. This review highlights the importance of incorporating functional genomics into the PSGT framework as a proposed initiative. Here, we explore various model systems and experimental methods available for conducting functional studies in South Africa to enhance both variant classification and clinical interpretation. We emphasize the distinct advantages of using in vitro, in vivo, and translational ex vivo models to improve the effectiveness of precision oncology. Moreover, we highlight the relevance of methodologies such as protein modelling and structural bioinformatics, multi-omics, metabolic activity assays, flow cytometry, cell migration and invasion assays, tube-formation assays, multiplex assays of variant effect, and database mining and machine learning models. The selection of the appropriate experimental approach largely depends on the molecular mechanism of the gene under investigation and the predicted functional effect of the VUS. However, before making final decisions regarding the pathogenicity of VUSs, it is essential to assess the functional evidence and clinical outcomes under current variant interpretation guidelines. The inclusion of a functional genomics infrastructure within the PSGT framework will significantly advance the reclassification of VUSs and enhance the precision medicine pipeline for patients with breast carcinomas in South Africa.
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Affiliation(s)
- Claudia Christowitz
- Department of Physiological Sciences, Faculty of Science, Stellenbosch University, Stellenbosch 7600, South Africa.
| | - Daniel W Olivier
- Department of Physiological Sciences, Faculty of Science, Stellenbosch University, Stellenbosch 7600, South Africa; Division of Chemical Pathology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa
| | - Johann W Schneider
- Division of Anatomical Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa; National Health Laboratory Service, Tygerberg Hospital, Cape Town 7505, South Africa
| | - Maritha J Kotze
- Division of Chemical Pathology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa; National Health Laboratory Service, Tygerberg Hospital, Cape Town 7505, South Africa
| | - Anna-Mart Engelbrecht
- Department of Physiological Sciences, Faculty of Science, Stellenbosch University, Stellenbosch 7600, South Africa; Department of Global Health, African Cancer Institute, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa
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3
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Okunola AO, Baatjes KJ, Zemlin AE, Torrorey-Sawe R, Conradie M, Kidd M, Erasmus RT, van der Merwe NC, Kotze MJ. Pathology-supported genetic testing for the application of breast cancer pharmacodiagnostics: family counselling, lifestyle adjustments and change of medication. Expert Rev Mol Diagn 2023; 23:431-443. [PMID: 37060281 DOI: 10.1080/14737159.2023.2203815] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2023]
Abstract
BACKGROUND Pathology-supported genetic testing (PSGT) enables transitioning of risk stratification from the study population to the individual. RESEARCH DESIGN AND METHODS We provide an overview of the translational research performed in postmenopausal breast cancer patients at increased risk of osteoporosis due to aromatase inhibitor therapy, as the indication for referral. Both tumour histopathology and blood biochemistry levels were assessed to identify actionable disease pathways using whole exome sequencing (WES). RESULTS The causes and consequences of inadequate vitamin D levels as a modifiable risk factor for bone loss were highlighted in 116 patients with hormone receptor-positive breast cancer. Comparison of lifestyle factors and WES data between cases with vitamin D levels at extreme upper and lower ranges identified obesity as a major discriminating factor, with the lowest levels recorded during winter. Functional polymorphisms in the vitamin D receptor gene contributed independently to therapy-related osteoporosis risk. In a patient with invasive lobular carcinoma, genetic counselling facilitated investigation of the potential modifying effect of a rare CDH1 variant co-occurring withBRCA1 c.66dup (p.Glu23ArgfsTer18). CONCLUSION Validation of PSGT as a three-pronged pharmacodiagnostics tool for generation of adaptive reports and data reinterpretation during follow-up represents a new paradigm in personalised medicine, exposing significant limitations to overcome.
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Affiliation(s)
- Abisola O Okunola
- Division of Chemical Pathology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Karin J Baatjes
- Department of Surgical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Annalise E Zemlin
- Division of Chemical Pathology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- Division of Chemical Pathology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University and the National Health Laboratory Service, Tygerberg Hospital, Cape Town, South Africa
| | - Rispah Torrorey-Sawe
- Division of Chemical Pathology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- Department of Immunology, School of Medicine, College of Health Sciences, Moi University, Eldoret, Kenya
| | - Magda Conradie
- Division of Endocrinology, Department of Medicine, Faculty of Medicine and Health Sciences Stellenbosch University, Cape Town, South Africa
| | - Martin Kidd
- Centre for Statistical Consultation, Stellenbosch University, South Africa
| | - Rajiv T Erasmus
- Division of Chemical Pathology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Nerina C van der Merwe
- Division of Human Genetics, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
- Division of Human Genetics, National Health Laboratory Service, Universitas Hospital, Bloemfontein, South Africa
| | - Maritha J Kotze
- Division of Chemical Pathology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- Division of Chemical Pathology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University and the National Health Laboratory Service, Tygerberg Hospital, Cape Town, South Africa
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4
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van der Merwe NC, Ntaita KS, Stofberg H, Combrink HM, Oosthuizen J, Kotze MJ. Implementation of multigene panel testing for breast and ovarian cancer in South Africa: A step towards excellence in oncology for the public sector. Front Oncol 2022; 12:938561. [PMID: 36568162 PMCID: PMC9768488 DOI: 10.3389/fonc.2022.938561] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 11/08/2022] [Indexed: 12/13/2022] Open
Abstract
Translation of genomic knowledge into public health benefits requires the implementation of evidence-based recommendations in clinical practice. In this study, we moved beyond BRCA1/2 susceptibility testing in breast and ovarian cancer patients to explore the application of pharmacogenetics across multiple genes participating in homologous recombination DNA damage repair. This involved the utilisation of next-generation sequencing (NGS) at the intersection of research and service delivery for development of a comprehensive genetic testing platform in South Africa. Lack of international consensus regarding risk categorization of established cancer susceptibility genes and the level of evidence required for prediction of drug response supported the development of a central database to facilitate clinical interpretation. Here we demonstrate the value of this approach using NGS to 1) determine the variant spectrum applicable to targeted therapy and implementation of prevention strategies using the 15-gene Oncomine™ BRCA Expanded Panel, and 2) searched for novel and known pathogenic variants in uninformative cases using whole exome sequencing (WES). Targeted NGS performed as a routine clinical service in 414 South African breast and/or ovarian cancer patients resulted in the detection of 48 actionable variants among 319 (15%) cases. BRCA1/2-associated cancers were identified in 70.8% of patients (34/48, including two double-heterozygotes), with the majority (35.3%, 12/34) representing known South African founder variants. Detection of actionable variants in established non-BRCA1/2 risk genes contributed 29% to the total percentage (14/48), distributed amongst ATM, CHEK2, BARD1, BRIP1, PALB2 and TP53. Experimental WES using a virtually constructed multi-cancer NGS panel in 16 genetically unresolved cases (and four controls) revealed novel protein truncating variants in the basal cell carcinoma gene PTCH1 (c.4187delG) and the signal transmission and transduction gene KIT (c.930delA) involved in crucial cellular processes. Based on these findings, the most cost-effective approach would be to perform BRCA1/2 founder variant testing at referral, followed by targeted multigene panel testing if clinically indicated and addition of WES in unresolved cases. This inventive step provides a constant flow of new knowledge into the diagnostic platform via a uniquely South African pathology-supported genetic approach implemented for the first time in this context to integrate research with service delivery.
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Affiliation(s)
- Nerina C. van der Merwe
- Division of Human Genetics, National Health Laboratory Service, Universitas Hospital, Bloemfontein, South Africa,Division of Human Genetics, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa,*Correspondence: Nerina C. van der Merwe,
| | - Kholiwe S. Ntaita
- Division of Human Genetics, National Health Laboratory Service, Universitas Hospital, Bloemfontein, South Africa,Division of Human Genetics, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
| | - Hanri Stofberg
- Division of Human Genetics, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
| | - Herkulaas MvE. Combrink
- Office of the Dean, Economic and Management Sciences, University of the Free State, Bloemfontein, South Africa,Interdisciplinary Centre for Digital Futures, University of the Free State, Bloemfontein, South Africa
| | - Jaco Oosthuizen
- Division of Human Genetics, National Health Laboratory Service, Universitas Hospital, Bloemfontein, South Africa,Division of Human Genetics, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
| | - Maritha J. Kotze
- Division of Chemical Pathology, Department of Pathology, National Health Laboratory Service, Tygerberg Hospital, Cape Town, South Africa,Division of Chemical Pathology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
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5
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Milambo JPM, Ndirangu J, Nyasulu PS, Akudugu JM. Feasibility of point of care testing for prevention and management of breast cancer therapy associated comorbidities in 6 African countries: short communication. BMC Res Notes 2022; 15:328. [PMID: 36273209 PMCID: PMC9588212 DOI: 10.1186/s13104-022-06204-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 09/15/2022] [Indexed: 11/10/2022] Open
Abstract
Objective: Obesity and mediators of inflammation have been identified as the most important risk and predictive factors in postmenopausal breast cancer (BC) survivors using aromatase inhibitors (AIs). This study was conducted to assess the impact of point of care technology (PCOT) as part of pathology supported genetic testing (PSGT) to prevent BC therapy-associated comorbidities in African settings. Results The study revealed that high sensitivity C-reactive protein (hs-CRP) and body mass index (BMI) are predictors of cardiovascular (CVD) related adverse events in obese postmenopausal patients subjected to AIs. There were statistically significant variations in total body fat (TBF), weight, hs-CRP, body mass index (BMI), homocysteine, ferritin, and calcium between baseline and after 24 months of follow-up. The above inflammatory markers can be incorporated in pathology supported genetic testing (PSGT) using HyBeacon® probe technology at POC for prediction and management of AI-associated adverse events among postmenopausal breast cancer survivors and associated comorbidities. The barriers for implementation of POCT application among six African countries for diagnosis of breast cancer were documented as insufficient of BC diagnosis and management capacity at different levels of health system.
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Affiliation(s)
- Jean Paul Muambngu Milambo
- Department of Public health, Faculty of Medicine and Health Sciences, University of Free State, Florence Street, 7530, Bellville, Cape Town, South Africa.
| | - James Ndirangu
- Department of Public health, Faculty of Medicine and Health Sciences, University of Free State, Florence Street, 7530, Bellville, Cape Town, South Africa
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6
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Van Der Merwe N, Ramesar R, De Vries J. Whole Exome Sequencing in South Africa: Stakeholder Views on Return of Individual Research Results and Incidental Findings. Front Genet 2022; 13:864822. [PMID: 35754817 PMCID: PMC9216214 DOI: 10.3389/fgene.2022.864822] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 03/30/2022] [Indexed: 11/17/2022] Open
Abstract
The use of whole exome sequencing (WES) in medical research is increasing in South Africa (SA), raising important questions about whether and which individual genetic research results, particularly incidental findings, should be returned to patients. Whilst some commentaries and opinions related to the topic have been published in SA, there is no qualitative data on the views of professional stakeholders on this topic. Seventeen participants including clinicians, genomics researchers, and genetic counsellors (GCs) were recruited from the Western Cape in SA. Semi-structured interviews were conducted, and the transcripts analysed using the framework approach for data analysis. Current roadblocks for the clinical adoption of WES in SA include a lack of standardised guidelines; complexities relating to variant interpretation due to lack of functional studies and underrepresentation of people of African ancestry in the reference genome, population and variant databases; lack of resources and skilled personnel for variant confirmation and follow-up. Suggestions to overcome these barriers include obtaining funding and buy-in from the private and public sectors and medical insurance companies; the generation of a locally relevant reference genome; training of health professionals in the field of genomics and bioinformatics; and multidisciplinary collaboration. Participants emphasised the importance of upscaling the accessibility to and training of GCs, as well as upskilling of clinicians and genetic nurses for return of genetic data in collaboration with GCs and medical geneticists. Future research could focus on exploring the development of stakeholder partnerships for increased access to trained specialists as well as community engagement and education, alongside the development of guidelines for result disclosure.
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Affiliation(s)
- Nicole Van Der Merwe
- UCT/MRC Genomic and Precision Medicine Research Unit, Division of Human Genetics, Institute for Infectious Diseases and Molecular Medicine, Department of Pathology, Faculty of Medicine and Health Sciences, University of Cape Town, Cape Town, South Africa.,Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Raj Ramesar
- UCT/MRC Genomic and Precision Medicine Research Unit, Division of Human Genetics, Institute for Infectious Diseases and Molecular Medicine, Department of Pathology, Faculty of Medicine and Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Jantina De Vries
- Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,Neuroscience Institute, Faculty of Health Sciences, University of Cape Town, Observatory, South Africa
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7
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Vafaei R, Samadi M, Hosseinzadeh A, Barzaman K, Esmailinejad M, Khaki Z, Farahmand L. Comparison of mucin-1 in human breast cancer and canine mammary gland tumor: a review study. Cancer Cell Int 2022; 22:14. [PMID: 35000604 PMCID: PMC8744232 DOI: 10.1186/s12935-021-02398-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 12/08/2021] [Indexed: 11/10/2022] Open
Abstract
Mucin-1 (MUC-1) is a transmembrane glycoprotein, which bears many similarities between dogs and humans. Since the existence of animal models is essential to understand the significant factors involved in breast cancer mechanisms, canine mammary tumors (CMTs) could be used as a spontaneously occurring tumor model for human studies. Accordingly, this review assessed the comparison of canine and human MUC-1 based on their diagnostic and therapeutic aspects and showed how comparative oncology approaches could provide insights into translating pre-clinical trials from human to veterinary oncology and vice versa which could benefit both humans and dogs.
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Affiliation(s)
- Rana Vafaei
- Recombinant Proteins Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, No.146, South Gandi Ave, Vanak Sq, Tehran, Iran
| | - Mitra Samadi
- Recombinant Proteins Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, No.146, South Gandi Ave, Vanak Sq, Tehran, Iran
| | - Aysooda Hosseinzadeh
- Recombinant Proteins Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, No.146, South Gandi Ave, Vanak Sq, Tehran, Iran
| | - Khadijeh Barzaman
- Recombinant Proteins Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, No.146, South Gandi Ave, Vanak Sq, Tehran, Iran
- Department of Immunology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - MohammadReza Esmailinejad
- Department of Surgery and Radiology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Zohreh Khaki
- Recombinant Proteins Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, No.146, South Gandi Ave, Vanak Sq, Tehran, Iran.
- Department of Clinical Pathology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran.
| | - Leila Farahmand
- Recombinant Proteins Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, No.146, South Gandi Ave, Vanak Sq, Tehran, Iran.
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8
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Baatjes K, Peeters A, McCaul M, Conradie MM, Apffelstaedt J, Conradie M, Kotze MJ. CYP19A1 rs10046 Pharmacogenetics in Postmenopausal Breast Cancer Patients Treated with Aromatase Inhibitors: One-year Follow-up. Curr Pharm Des 2021; 26:6007-6012. [PMID: 32900345 DOI: 10.2174/1381612826666200908141858] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 08/07/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Significant individual variation in bone loss associated with aromatase inhibitors (AIs) emphasizes the importance of identifying postmenopausal breast cancer patients at high risk for this adverse effect. The study explores the clinical relevance of genetic variation in the Cytochrome P450 19A1 (CYP19A1) gene in a subset of South African patients during the first year of taking AIs for estrogen receptor (ER)-positive breast cancer. METHODS The study population consisted of ER-positive breast cancer patients on AIs, followed in real-life clinical practice. Body mass index was measured and bone mineral density (BMD) was determined at baseline and at month 12. CYP19A1 genotyping was performed using real-time polymerase chain reaction analysis of rs10046, extended to Sanger sequencing and whole exome sequencing in 10 patients with more than 5% bone loss at month 12 at the lumbar spine. RESULTS After 12 months of AI treatment, 72 patients had completed BMD and were successfully genotyped. Ten patients (14%) experienced more than 5% bone loss at the lumbar spine over the study period. Genotyping for CYP19A1 rs10046 revealed that patients with two copies of the A-allele were 10.79 times more likely to have an ordinal category change of having an increased percentage of bone loss or no increase at the lumbar spine, compared to patients with the GA or GG genotypes (CI of 1.771- 65.830, p=0.01). None of the 34 patients without lumbar spine bone loss at month 12 were homozygous for the functional CYP19A1 polymorphism. At the total hip region, patients with the AA genotype were 7. 37 times more likely to have an ordinal category change of having an increased percentage of bone loss or no increase (CI of 1.101- 49.336, p=0.04). CONCLUSION Homozygosity for the CYP19A1 rs10046 A-allele may provide information, in addition to clinical and biochemical factors that may be considered in risk stratification to optimize bone health in postmenopausal breast cancer women on AIs. Further investigation is required to place the clinical effect observed for a single CYP19A1 gene variant in a genomic context.
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Affiliation(s)
- Karin Baatjes
- Department Surgical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Armand Peeters
- Division of Chemical Pathology, Department of Pathology Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Micheal McCaul
- Division of Epidemiology and Biostatistics, Department of Global Health, Stellenbosch University, South Africa
| | - Maria M Conradie
- Division of Endocrinology, Department of Medicine, Faculty of Medicine and Health Sciences Stellenbosch University, Tygerberg, South Africa
| | - Justus Apffelstaedt
- Department Surgical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Magda Conradie
- Division of Chemical Pathology, Department of Pathology Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Maritha J Kotze
- Division of Chemical Pathology, Department of Pathology Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
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9
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Oosthuizen J, Kotze MJ, Van Der Merwe N, Myburgh EJ, Bester P, van der Merwe NC. Globally Rare BRCA2 Variants With Founder Haplotypes in the South African Population: Implications for Point-of-Care Testing Based on a Single-Institution BRCA1/2 Next-Generation Sequencing Study. Front Oncol 2021; 10:619469. [PMID: 33643918 PMCID: PMC7908826 DOI: 10.3389/fonc.2020.619469] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 12/23/2020] [Indexed: 12/16/2022] Open
Abstract
Breast cancer patients historically benefitted from population-based genetic research performed in South Africa, which led to the development of founder-based BRCA1/2 diagnostic tests. With the advent of next-generation sequencing (NGS) technologies, the clinical utility of limited, targeted genetic assays were questioned. The study focused on mining NGS data obtained from an extensive single-institution NGS series (n=763). The aims were to determine (i) the prevalence of the most common recurrent/founder variants in patients referred for NGS directly; and (ii) to explore the data for inferred haplotypes associated with previous and potential new recurrent/founder variants. The identification of additional founder variants was essential for promoting and potentially advancing to rapid founder-based BRCA1/2 point-of-care (POC) technology as a time- and cost-effective alternative. NGS revealed actionable BRCA1/2 variants in 11.1% of patients tested (BRCA1 - 4.7%; BRCA2 - 6.4%), of which 22.4% represented variants currently screened for using first-tier targeted genetic testing. A retrospective investigation into the overall mutation-positive rate for an extended cohort (n=1906), which included first-tier test results, revealed that targeted genetic testing identified 74% of all pathogenic variants. This percentage justified the use of targeted genetic testing as a first-tier assay. Inferred haplotype analysis confirmed the founder status of BRCA2 c.5771_5774del (rs80359535) and c.7934del (rs80359688) and revealed an additional African founder variant (BRCA2 c.582G>A - rs80358810). A risk-benefit analysis using a questionnaire-based survey was performed in parallel to determine genetic professionals' views regarding POC testing. This was done to bridge the clinical implementation gap between haplotype analysis and POC testing as a first-tier screen during risk stratification of breast and ovarian cancer patients. The results reflected high acceptance (94%) of BRCA1/2 POC testing when accompanied by genetic counselling. Establishing the founder status for several recurrent BRCA2 variants across ethnic groups supports unselected use of the BRCA POC assay in all SA breast/ovarian cancer patients by recent local and international public health recommendations. Incorporating POC genotyping into the planned NGS screening algorithm of the Department of Health will ensure optimal use of the country's recourses to adhere to the set standards for optimal care and management for all breast cancer patients.
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Affiliation(s)
- Jaco Oosthuizen
- Division of Human Genetics, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa.,Division of Human Genetics, National Health Laboratory Service, Universitas Hospital, Bloemfontein, South Africa
| | - Maritha J Kotze
- Department of Pathology, Division of Chemical Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa.,Division of Chemical Pathology, National Health Laboratory Service, Tygerberg Hospital, Cape Town, South Africa
| | - Nicole Van Der Merwe
- Department of Pathology, Division of Chemical Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | | | - Phillip Bester
- Division of Virology, National Health Laboratory Service, Universitas Hospital, Bloemfontein, South Africa
| | - Nerina C van der Merwe
- Division of Human Genetics, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa.,Division of Human Genetics, National Health Laboratory Service, Universitas Hospital, Bloemfontein, South Africa
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10
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Glanzmann B, Jooste T, Ghoor S, Gordon R, Mia R, Mao J, Li H, Charls P, Douman C, Kotze MJ, Peeters AV, Loots G, Esser M, Tiemessen CT, Wilkinson RJ, Louw J, Gray G, Warren RM, Möller M, Kinnear C. Human whole genome sequencing in South Africa. Sci Rep 2021; 11:606. [PMID: 33436733 PMCID: PMC7803990 DOI: 10.1038/s41598-020-79794-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 12/08/2020] [Indexed: 12/26/2022] Open
Abstract
The advent and evolution of next generation sequencing has considerably impacted genomic research. Until recently, South African researchers were unable to access affordable platforms capable of human whole genome sequencing locally and DNA samples had to be exported. Here we report the whole genome sequences of the first six human DNA samples sequenced and analysed at the South African Medical Research Council’s Genomics Centre. We demonstrate that the data obtained is of high quality, with an average sequencing depth of 36.41, and that the output is comparable to data generated internationally on a similar platform. The Genomics Centre creates an environment where African researchers are able to access world class facilities, increasing local capacity to sequence whole genomes as well as store and analyse the data.
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Affiliation(s)
- Brigitte Glanzmann
- Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Stellenbosch University, Cape Town, South Africa.,Genomics Centre, South African Medical Research Council, Tygerberg, Cape Town, South Africa
| | - Tracey Jooste
- Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg, Cape Town, South Africa.,Division of Medical Physiology Faculty of Medicine and Health Sciences, Tygerberg Hospital, Stellenbosch University, Cape Town, South Africa.,Genomics Centre, South African Medical Research Council, Tygerberg, Cape Town, South Africa
| | - Samira Ghoor
- Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg, Cape Town, South Africa.,Genomics Centre, South African Medical Research Council, Tygerberg, Cape Town, South Africa
| | - Richard Gordon
- Grants, Innovation and Product Development, South African Medical Research Council, Tygerberg, Cape Town, South Africa
| | - Rizwana Mia
- Grants, Innovation and Product Development, South African Medical Research Council, Tygerberg, Cape Town, South Africa.,Genomics Centre, South African Medical Research Council, Tygerberg, Cape Town, South Africa
| | - Jun Mao
- BGI-Shenzhen, Beishan Industrial Zone, Building 11, Yantian District, Shenzhen, 518083, China.,Genomics Centre, South African Medical Research Council, Tygerberg, Cape Town, South Africa
| | - Hao Li
- BGI-Shenzhen, Beishan Industrial Zone, Building 11, Yantian District, Shenzhen, 518083, China
| | - Patrick Charls
- Information Technology Services Division, South African Medical Research Council, Cape Town, South Africa
| | - Craig Douman
- Information Technology Services Division, South African Medical Research Council, Cape Town, South Africa
| | - Maritha J Kotze
- Division of Chemical Pathology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.,Division of Chemical Pathology, Department of Pathology, National Health Laboratory Service, Tygerberg Hospital, Cape Town, South Africa
| | - Armand V Peeters
- Division of Chemical Pathology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Glaudina Loots
- South African National Department of Science and Innovation, Pretoria, South Africa
| | - Monika Esser
- Department of Pathology, Division Medical Microbiology and Immunology, Faculty of Medicine and Health Sciences, Tygerberg Hospital, Stellenbosch University, Cape Town, South Africa
| | - Caroline T Tiemessen
- Centre for HIV and STIs, National Institute for Communicable Diseases, and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Robert J Wilkinson
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, 7925, South Africa.,Department of Infectious Diseases, Imperial College London, London, W12 0NN, UK.,The Francis Crick Institute, London, NW1 1AT, UK
| | - Johan Louw
- Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg, Cape Town, South Africa
| | - Glenda Gray
- Office of the President, South African Medical Research Council, Cape Town, South Africa.,Perinatal HIV Research Unit, Faculty of Clinical Medicine, Chris Hani Baragwanath Academic Hospital, University of the Witwatersrand, Johannesburg, South Africa
| | - Robin M Warren
- Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Stellenbosch University, Cape Town, South Africa
| | - Marlo Möller
- Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Stellenbosch University, Cape Town, South Africa.,Genomics Centre, South African Medical Research Council, Tygerberg, Cape Town, South Africa
| | - Craig Kinnear
- Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Stellenbosch University, Cape Town, South Africa. .,Genomics Centre, South African Medical Research Council, Tygerberg, Cape Town, South Africa.
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11
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Torrorey-Sawe R, van der Merwe N, Mining SK, Kotze MJ. Pioneering Informed Consent for Return of Research Results to Breast Cancer Patients Facing Barriers to Implementation of Genomic Medicine: The Kenyan BRCA1/2 Testing Experience Using Whole Exome Sequencing. Front Genet 2020; 11:170. [PMID: 32231682 PMCID: PMC7089032 DOI: 10.3389/fgene.2020.00170] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 02/12/2020] [Indexed: 12/13/2022] Open
Abstract
INTRODUCTION Obtaining informed consent from study participants and disseminating the findings responsibly is a key principle required for ethically conducted clinical and genetic research. Reports from African researchers providing feedback on insights gained during the return of whole exome sequencing (WES) results to breast cancer patients treated in resource-limited settings is lacking. AIM The empirical process used to fill this gap in relation to BRCA1/2 variant detection using WES provided unique insights incorporated into a pathology-supported genetic testing algorithm for return of research results to Kenyan breast cancer patients. METHODS The Informed consent form approved by the Moi Teaching and Referral Hospital in Kenya was adopted from a translational research study conducted in South Africa. Initially, the informed consent process was piloted in 16 Kenyan female patients referred for breast surgery, following a community-based awareness campaign. A total of 95 female and two male breast cancer patients were enrolled in the study from 2013 to 2016. Immunohistochemistry (IHC) results of estrogen receptor (ER), progesterone receptor (PR) and human epidermal growth factor receptor-2 (HER2) status were obtained from hospital records. DNA of patients with a family history of cancer was extracted from saliva and screened for pathogenic variants in the BRCA1/2 genes as the first step using WES. RESULTS Ten patients approached for participation in this study declined to sign the informed consent form. Data on IHC used as a proxy for molecular subtype were available in 8 of 13 breast cancer patients (62%) with a family history of cancer. Five BRCA1/2 variants of uncertain clinical significance were detected, as well as a pathogenic BRCA2 variant (c.5159C > A; S1720∗) in a female patient eligible for return of WES results. CONCLUSION Experience gained during the qualitative pilot phase was essential to overcome challenges associated with the translation of sophisticated genetic terms into native African languages. Detection of a pathogenic BRCA2 variant in a patient with familial breast cancer, frequently associated with hormone receptor-positive breast carcinoma as reported in this case, led to a high level of confidence on which to base risk management in future. Implementation of new technologies alongside standard pathology provides a practical approach to the application of genomic medicine in Africa.
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Affiliation(s)
- Rispah Torrorey-Sawe
- Division of Chemical Pathology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
- Department of Immunology, School of Medicine, College of Health Sciences, Moi University, Eldoret, Kenya
| | - Nicole van der Merwe
- Division of Chemical Pathology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Simeon Kipkoech Mining
- Department of Immunology, School of Medicine, College of Health Sciences, Moi University, Eldoret, Kenya
| | - Maritha J Kotze
- Division of Chemical Pathology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
- National Health Laboratory Service, Tygerberg Hospital, Cape Town, South Africa
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12
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Identification of an iron-responsive subtype in two children diagnosed with relapsing-remitting multiple sclerosis using whole exome sequencing. Mol Genet Metab Rep 2019; 19:100465. [PMID: 30963028 PMCID: PMC6434495 DOI: 10.1016/j.ymgmr.2019.100465] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 03/16/2019] [Accepted: 03/16/2019] [Indexed: 12/26/2022] Open
Abstract
Background Multiple sclerosis is a disorder related to demyelination of axons. Iron is an essential cofactor in myelin synthesis. Previously, we described two children (males of mixed ancestry) with relapsing-remitting multiple sclerosis (RRMS) where long-term remission was achieved by regular iron supplementation. A genetic defect in iron metabolism was postulated, suggesting that more advanced genetic studies could shed new light on disease pathophysiology related to iron. Methods Whole exome sequencing (WES) was performed to identify causal pathways. Blood tests were performed over a 10 year period to monitor the long-term effect of a supplementation regimen. Clinical wellbeing was assessed quarterly by a pediatric neurologist and regular feedback was obtained from the schoolteachers. Results WES revealed gene variants involved in iron absorption and transport, in the transmembrane protease, serine 6 (TMPRSS6) and transferrin (TF) genes; multiple genetic variants in CUBN, which encodes cubilin (a receptor involved in the absorption of vitamin B12 as well as the reabsorption of transferrin-bound iron and vitamin D in the kidneys); SLC25A37 (involved in iron transport into mitochondria) and CD163 (a scavenger receptor involved in hemorrhage resolution). Variants were also found in COQ3, involved with synthesis of Coenzyme Q10 in mitochondria. Neither of the children had the HLA-DRB1*1501 allele associated with increased genetic risk for MS, suggesting that the genetic contribution of iron-related genetic variants may be instrumental in childhood MS. In both children the RRMS has remained stable without activity over the last 10 years since initiation of nutritional supplementation and maintenance of normal iron levels, confirming the role of iron deficiency in disease pathogenesis in these patients. Conclusion Our findings highlight the potential value of WES to identify heritable risk factors that could affect the reabsorption of transferrin-bound iron in the kidneys causing sustained iron loss, together with inhibition of vitamin B12 absorption and vitamin D reabsorption (CUBN) and iron transport into mitochondria (SLC25A37) as the sole site of heme synthesis. This supports a model for RRMS in children with an apparent iron-deficient biochemical subtype of MS, with oligodendrocyte cell death and impaired myelination possibly caused by deficits of energy- and antioxidant capacity in mitochondria.
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Key Words
- CNS, central nervous system
- CoQ, Coenzyme Q
- DFO, desferroxamine mesylate
- DIS, dissemination in space
- DIT, dissemination in time
- DMT, disease modifying therapy
- EDSS, Expanded Disability Status Scale
- ETC, electron transport chain
- GWAS, genome-wide association study
- Genetic variants
- HDL, high density lipoprotein
- HERV-W, human endogenous retrovirus W
- HLA, human leukocyte antigen
- HREC, human research ethics committee
- IPMSSG, International Pediatric Multiple Sclerosis Study Group
- IRE, iron-response element
- Iron deficiency
- MGA1, juvenile hereditary megaloblastic anemia 1
- MRI, magnetic resonance imaging
- MS, Multiple sclerosis
- MSRV, MS-associated retrovirus
- MST1R, macrophage stimulating-1 receptor
- Mitochondria
- Oxidative stress
- PSGT, pathology supported genetic testing
- Pediatric onset multiple sclerosis
- ROS, reactive oxygen species
- RRMS, relapsing-remitting MS
- SAMe, S-adenosyl methionine
- SDHB, iron-protein subunit of Complex II
- TF, transferrin
- TMPRSS6, transmembrane protease, serine 6
- WES, whole exome sequencing
- Whole exome sequencing
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Genetics of breast cancer in African populations: a literature review. GLOBAL HEALTH EPIDEMIOLOGY AND GENOMICS 2018; 3:e8. [PMID: 30263132 PMCID: PMC6152487 DOI: 10.1017/gheg.2018.8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 03/19/2018] [Accepted: 03/19/2018] [Indexed: 12/25/2022]
Abstract
Breast cancer (BC) is one of the most complex, diverse and leading cause of death in women worldwide. The present investigation aims to explore genes panel associated with BC in different African regions, and compare them to those studied worldwide. We extracted relevant information from 43 studies performed in Africa using the following criteria: case-control study, association between genetic variations and BC risk. Data were provided on mutations and polymorphisms associated with BC without fixing a specific date. Case-only studies and clinical trials were excluded. Our study revealed that the majority of African BC genetic studies remain restricted to the investigation of BRCA1 and BRCA2 genes and differences in their mutations spectrum. Therefore, it is necessary to encourage African researchers to characterize more genes involved in BC using methods generating global information such as next-generation sequencing in order to guide specific and more effective therapeutic strategies for the African community.
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