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Dix-Peek T, Dickens C, Augustine TN, Phakathi BP, Van Den Berg EJ, Joffe M, Ayeni OA, Cubasch H, Nietz S, Mathew CG, Hayat M, Neugut AI, Jacobson JS, Ruff P, Duarte RA. FGFR2 genetic variants in women with breast cancer. Mol Med Rep 2023; 28:226. [PMID: 37830168 PMCID: PMC10619128 DOI: 10.3892/mmr.2023.13113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 05/11/2023] [Indexed: 10/14/2023] Open
Abstract
Black African populations are more genetically diverse than others, but genetic variants have been studied primarily in European populations. The present study examined the association of four single nucleotide polymorphisms (SNPs) of the fibroblast growth factor receptor 2, associated with breast cancer in non‑African populations, with breast cancer in Black, southern African women. Genomic DNA was extracted from whole blood samples of 1,001 patients with breast cancer and 1,006 controls (without breast cancer), and the rs2981582, rs35054928, rs2981578, and rs11200014 polymorphisms were analyzed using allele‑specific Kompetitive allele‑specific PCR™, and the χ2 or Fisher's exact tests were used to compare the genotype frequencies. There was no association between those SNPs and breast cancer in the studied cohort, although an association was identified between the C/C homozygote genotype for rs2981578 and invasive lobular carcinoma. These results show that genetic biomarkers of breast cancer risk in European populations are not necessarily associated with risk in sub‑Saharan African populations. African populations are more heterogenous than other populations, and the information from this population can help focus genetic risks of cancer in this understudied population.
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Affiliation(s)
- Thérèse Dix-Peek
- Department of Internal Medicine, School of Clinical Medicine, Faculty of Health Sciences, University of The Witwatersrand, Johannesburg 2193, South Africa
| | - Caroline Dickens
- Department of Internal Medicine, School of Clinical Medicine, Faculty of Health Sciences, University of The Witwatersrand, Johannesburg 2193, South Africa
| | - Tanya N. Augustine
- School of Anatomical Sciences, Faculty of Health Sciences, University of The Witwatersrand, Johannesburg 2193, South Africa
| | - Boitumelo P. Phakathi
- Department of Surgery, School of Clinical Medicine, Faculty of Health Sciences, University of Kwa-Zulu Natal, Durban 4001, South Africa
| | - Eunice J. Van Den Berg
- Department of Histopathology, National Health Laboratory Services, Chris Hani Baragwanath Hospital, Johannesburg 1864, South Africa
- Department of Anatomical Pathology, Faculty of Health Sciences, University of The Witwatersrand, Johannesburg 2193, South Africa
| | - Maureen Joffe
- Strengthening Oncology Services Research Unit, Faculty of Health Sciences, University of The Witwatersrand, Johannesburg 2193, South Africa
- South African Medical Research Council Common Epithelial Cancer Research Centre, Faculty of Health Sciences, University of The Witwatersrand, Johannesburg 2193, South Africa
- Non-Communicable Diseases Research Division, Wits Health Consortium (PTY) Ltd., Faculty of Health Sciences, University of The Witwatersrand, Johannesburg 2193, South Africa
| | - Oluwatosin A. Ayeni
- Strengthening Oncology Services Research Unit, Faculty of Health Sciences, University of The Witwatersrand, Johannesburg 2193, South Africa
- South African Medical Research Council Common Epithelial Cancer Research Centre, Faculty of Health Sciences, University of The Witwatersrand, Johannesburg 2193, South Africa
- Non-Communicable Diseases Research Division, Wits Health Consortium (PTY) Ltd., Faculty of Health Sciences, University of The Witwatersrand, Johannesburg 2193, South Africa
- Division of Radiation Oncology, Department of Radiation Sciences, Faculty of Health Sciences, University of The Witwatersrand, Johannesburg 2193, South Africa
| | - Herbert Cubasch
- South African Medical Research Council Common Epithelial Cancer Research Centre, Faculty of Health Sciences, University of The Witwatersrand, Johannesburg 2193, South Africa
- Non-Communicable Diseases Research Division, Wits Health Consortium (PTY) Ltd., Faculty of Health Sciences, University of The Witwatersrand, Johannesburg 2193, South Africa
- Batho Pele Breast Unit, Chris Hani Baragwanath Academic Hospital, Soweto 1860, South Africa
- Department of Surgery, Faculty of Health Sciences, University of The Witwatersrand, Johannesburg 2193, South Africa
| | - Sarah Nietz
- South African Medical Research Council Common Epithelial Cancer Research Centre, Faculty of Health Sciences, University of The Witwatersrand, Johannesburg 2193, South Africa
- Department of Surgery, Faculty of Health Sciences, University of The Witwatersrand, Johannesburg 2193, South Africa
| | - Christopher G. Mathew
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of The Witwatersrand, Johannesburg 2193, South Africa
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King's College London, London, WC2R 2LS, United Kingdom
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of The Witwatersrand, Johannesburg 2193, South Africa
| | - Mahtaab Hayat
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of The Witwatersrand, Johannesburg 2193, South Africa
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of The Witwatersrand, Johannesburg 2193, South Africa
| | - Alfred I. Neugut
- Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians and Surgeons, New York 10032, United States of America
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York 10032, United States of America
| | - Judith S. Jacobson
- Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians and Surgeons, New York 10032, United States of America
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York 10032, United States of America
| | - Paul Ruff
- Department of Internal Medicine, School of Clinical Medicine, Faculty of Health Sciences, University of The Witwatersrand, Johannesburg 2193, South Africa
- South African Medical Research Council Common Epithelial Cancer Research Centre, Faculty of Health Sciences, University of The Witwatersrand, Johannesburg 2193, South Africa
- Non-Communicable Diseases Research Division, Wits Health Consortium (PTY) Ltd., Faculty of Health Sciences, University of The Witwatersrand, Johannesburg 2193, South Africa
| | - Raquel A.B. Duarte
- Department of Internal Medicine, School of Clinical Medicine, Faculty of Health Sciences, University of The Witwatersrand, Johannesburg 2193, South Africa
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Shain J, Michel A, May MS, Qunaj L, El-Sadr W, Chung WK, Appelbaum PS, Jacobson JS, Justman J, Neugut AI. Cancer genetic mutation prevalence in sub-Saharan Africa: A review of existing data. Semin Oncol 2023; 50:123-130. [PMID: 38171987 DOI: 10.1053/j.seminoncol.2023.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 12/15/2023] [Accepted: 12/16/2023] [Indexed: 01/05/2024]
Abstract
BACKGROUND Cancer represents a leading cause of death worldwide. Germline mutations in several genes increase the risk of developing several cancers, including cancers of the breast, ovary, pancreas, colorectum, and melanoma. An understanding of the population prevalence of pathogenic germline variants can be helpful in the design of public health interventions, such as genetic testing, which has downstream implications for cancer screening, prevention, and treatment. While population-based studies of pathogenic germline variants exist, most such studies have been conducted in White populations. Limited data exist regarding the prevalence of germline mutations within sub-Saharan African populations. MATERIALS AND METHODS We identified countries defined as sub-Saharan Africa by the World Bank and conducted a scoping literature review using PubMed. For each country, we identified and summarized studies that focused on the prevalence of germline genetic mutations with sample sizes >10 and in a population directly from sub-Saharan Africa, either with or without diseases associated with the relevant genetic mutations. Studies that evaluated the prevalence of somatic or likely benign variants were excluded. RESULTS Within the 48 countries in sub-Saharan Africa, we identified 34 studies which meet the inclusion criteria. Twenty studies were conducted in South Africa, Nigeria, or Burkina Faso; four countries had more than two published papers. We found that 33 of 48 countries in sub-Saharan Africa lacked any genetic studies. Notably, there has been an increase in relevant studies starting in 2020. Importantly, of the 34 studies identified, 29 included data on BRCA1 or BRCA2. Data on the prevalence of mutations contributing to familial cancer syndromes other than BRCA1 and BRCA2 was limited. CONCLUSIONS While some progress has been made towards understanding the prevalence of germline mutations in cancer susceptibility genes, the characterization of genetic mutations among sub-Saharan African populations remains strikingly incomplete. Given the genetic diversity in the region, there remains a great need for large-scale, population-based studies to understand the prevalence of germline pathogenic variants and adequately capture all the subpopulations in this part of the world.
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Affiliation(s)
- Joshua Shain
- Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY
| | - Alissa Michel
- Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY
| | - Michael S May
- Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY
| | - Lindor Qunaj
- Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY
| | - Wafaa El-Sadr
- Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY; Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY; Department of Epidemiology and ICAP, Mailman School of Public Health, Columbia University, New York, NY
| | - Wendy K Chung
- Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY; Department of Psychiatry, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY; Department of Epidemiology and ICAP, Mailman School of Public Health, Columbia University, New York, NY
| | - Paul S Appelbaum
- Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY; Department of Epidemiology and ICAP, Mailman School of Public Health, Columbia University, New York, NY
| | - Judith S Jacobson
- Department of Epidemiology and ICAP, Mailman School of Public Health, Columbia University, New York, NY
| | - Jessica Justman
- Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY; Department of Epidemiology and ICAP, Mailman School of Public Health, Columbia University, New York, NY
| | - Alfred I Neugut
- Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY; Department of Epidemiology and ICAP, Mailman School of Public Health, Columbia University, New York, NY.
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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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