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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] [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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Sun Z, Bai C, Su M, Tang H, Wu X, Wang Y, Bao H, Liu X, Wu X, Shao Y, Xu B. Comprehensive profiling of pathogenic germline large genomic rearrangements in a pan-cancer analysis. Mol Oncol 2023; 17:1917-1929. [PMID: 37013911 PMCID: PMC10483597 DOI: 10.1002/1878-0261.13430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 03/07/2023] [Accepted: 04/03/2023] [Indexed: 04/05/2023] Open
Abstract
The presence of large genomic rearrangements (LGRs) has been heavily investigated in breast and ovarian cancer. However, correlations between LGRs and cancer types beyond these two have not been extensively profiled, likely due to the highly inefficient methods of detecting these types of alterations. This study utilized next-generation sequencing (NGS) to analyze and classify the germline LGR profile in 17 025 cancer patients across 22 cancer types. We characterized newly identified LGRs based on predicted pathogenicity and took a closer look at genes that acquire both germline and somatic mutations within our samples. The detection method for LGRs was validated using droplet digital polymerase chain reaction (ddPCR) assay of commonly investigated LGR genes. In total, 15 659 samples from across 22 cancer types were retained for analysis after filtering. We observed that, in our cohort, the cancer types with the highest proportion of germline LGRs were ovarian cancer (4.7%), renal cell carcinoma (2.5%), breast cancer (2%), glioma (1.8%) and thyroid carcinoma (1.8%). Annotation of detected germline variants revealed several genes-MSH2, FANCA and PMS2-that contain novel LGRs. We observed co-occurrences between germline LGRs in MSH2 and somatic single nucleotide variants/insertion and deletions (SNVs/InDels) in BRCA2, KTM2B, KDM5A, CHD8, and HNF1A. Furthermore, our analysis showed that samples with pathogenic and likely pathogenic germline LGRs tended to also have higher mutational burden, chromosomal instability, and microsatellite instability ratio compared to samples with pathogenic germline SNVs/InDels. In this study, we demonstrated the prevalence of pathogenic germline LGRs beyond breast and ovarian cancer. The profiles of these pathogenic or likely pathogenic alterations will fuel further investigations and highlight new understanding of LGRs across multiple cancer types.
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Affiliation(s)
- Zhe Sun
- The First Clinical Medical CollegeGuangzhou University of Chinese MedicineGuangdongChina
| | - Chujie Bai
- Department of Bone and Soft Tissue Tumor, Key Laboratory of Carcinogenesis and Translational ResearchPeking University Cancer Hospital and InstituteBeijingChina
| | - Miaoyi Su
- Department of Radiation OncologyGuangqian HospitalQuanzhouChina
| | - Haimeng Tang
- Geneseeq Research InstituteNanjing Geneseeq Technology Inc.China
| | - Xiaoying Wu
- Geneseeq Research InstituteNanjing Geneseeq Technology Inc.China
| | - Yue Wang
- Geneseeq Research InstituteNanjing Geneseeq Technology Inc.China
| | - Hua Bao
- Geneseeq Research InstituteNanjing Geneseeq Technology Inc.China
| | - Xunbiao Liu
- Geneseeq Research InstituteNanjing Geneseeq Technology Inc.China
| | - Xue Wu
- Geneseeq Research InstituteNanjing Geneseeq Technology Inc.China
| | - Yang Shao
- Geneseeq Research InstituteNanjing Geneseeq Technology Inc.China
- School of Public HealthNanjing Medical UniversityChina
| | - Bei Xu
- Department of Medical OncologyZhongshan HospitalShanghaiChina
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Iwai Y, Toumbou K, Zuze T, Morgan JS, Simwinga L, Wright ST, Fedoriw Y, Oladeru OT, Balogun OD, Roberson ML, Olopade OI, Tomoka T, Elmore SN. Breast Cancer Germline Genetic Counseling and Testing for Populations of African Heritage Globally: A Scoping Review on Research, Practice, and Bioethical Considerations. JCO Glob Oncol 2023; 9:e2300154. [PMID: 37944088 PMCID: PMC10645409 DOI: 10.1200/go.23.00154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/05/2023] [Accepted: 09/05/2023] [Indexed: 11/12/2023] Open
Abstract
PURPOSE Despite the disproportionately high risk of breast cancer among women of African heritage, little is known about the facilitators and barriers to implementing germline genetic testing and counseling (GT/C). METHODS This scoping review followed guidelines recommended by the Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for scoping reviews. Published manuscripts from database inception through 2021 were sourced from PubMed, Cumulative Index to Nursing and Allied Health Literature via EBSCO, Embase, Cochrane Library, and Scopus. Search terms were used to retrieve articles addressing (1) African heritage, (2) breast cancer, and (3) GT or GC. The screening involved abstract and title review and full-text review. Data were extracted for all articles meeting the inclusion criteria. RESULTS A total of 154 studies were included. Most studies that took place were conducted in the United States (71.4%), and most first authors (76.9%) were from the United States. GT was conducted in 73 (49.7%) studies. BRCA1/BRCA2 were the most commonly studied genes for germline mutations. GC was conducted in 49 studies (33.3%), and perspectives on GC were evaluated in 43 (29.3%). The use of racial/ethnic categories varied broadly, although African American was most common (40.1%). Racism was mentioned in three studies (2.0%). CONCLUSION There is a growing body of literature on GT/C for breast cancer in women of African heritage. Future studies on GT/C of African populations should consider increased clarity around racial/ethnic categorizations, continued community engagement, and intentional processes for informed consent.
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Affiliation(s)
- Yoshiko Iwai
- University of North Carolina School of Medicine, Chapel Hill, NC
| | | | | | - Jenny S. Morgan
- Department of Medicine, University of North Carolina School of Medicine, Chapel Hill, NC
- Department of Clinical Medicine, Indiana University School of Medicine, Indianapolis, IN
- Department of Global Health, Indiana University School of Medicine, Indianapolis, IN
| | | | - Sarah T. Wright
- UNC Health Sciences Library, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Yuri Fedoriw
- Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill, NC
| | - Oluwadamilola T. Oladeru
- Department of Radiation Oncology, University of Florida, Gainesville, FL
- Department of Radiation Oncology, Mayo Clinic in Florida, Jacksonville, FL
| | | | - Mya L. Roberson
- Department of Health Policy, University of North Carolina Gillings School of Global Public Health, Chapel Hill, NC
| | | | | | - Shekinah N.C. Elmore
- Department of Radiation Oncology, University of North Carolina School of Medicine, Chapel Hill, NC
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Lei H, Zhang M, Zhang L, Hemminki K, Wang XJ, Chen T. Overview on population screening for carriers with germline BRCA mutation in China. Front Oncol 2022; 12:1002360. [PMID: 36439508 PMCID: PMC9682265 DOI: 10.3389/fonc.2022.1002360] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 10/24/2022] [Indexed: 12/01/2023] Open
Abstract
Carriers with BRCA1/2 germline pathogenic variants are associated with a high risk of breast and ovarian cancers (also pancreatic and prostate cancers). While the spectrum on germline BRCA mutations among the Chinese population shows ethnic specificity, the identification of carriers with germline BRCA mutation before cancer onset is the most effective approach to protect them. This review focused on the current status of BRCA1/2 screening, the surveillance and prevention measures, and discussed the issues and potential impact of BRCA1/2 population screening in China. We conducted literature research on databases PubMed and Google Scholar, as well as Chinese databases CNKI and Wangfang Med Online database (up to 31 March 2022). Latest publications on germline BRCA1/2 prevalence, spectrum, genetic screening as well as carrier counseling, surveillance and prevention were captured where available. While overall 15,256 records were retrieved, 72 publications using germline BRCA1/2 testing were finally retained for further analyses. Germline BRCA1/2 mutations are common in Chinese patients with hereditary breast, ovarian, prostate and pancreatic cancers. Within previous studies, a unique BRCA mutation spectrum in China was revealed. Next-generation sequencing panel was considered as the most common method for BRCA1/2 screening. Regular surveillance and preventive surgeries were tailored to carriers with mutated-BRCA1/2. We recommend that all Chinese diagnosed with breast, ovarian, pancreatic or prostate cancers and also healthy family members, shall undergo BRCA1/2 gene test to provide risk assessment. Subsequently, timely preventive measures for mutation carriers are recommended after authentic genetic counseling.
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Affiliation(s)
- Huijun Lei
- Department of Cancer Prevention/Zhejiang Cancer Institute, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China
- Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
| | - Min Zhang
- School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Luyao Zhang
- Department of Cancer Epidemiology and Prevention, Henan Engineering Research Center of Cancer Prevention and Control, Henan International Joint Laboratory of Cancer Prevention, The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Kari Hemminki
- Biomedical Center, Faculty of Medicine, Charles University in Pilsen, Pilsen, Czechia
- Division of Cancer Epidemiology, German Cancer Research Center Deutsches Krebsforschungszentrum (DKFZ), Im Neuenheimer Feld, Heidelberg, Germany
| | - Xiao-jia Wang
- Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
- Department of Breast Medical Oncology, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China
| | - Tianhui Chen
- Department of Cancer Prevention/Zhejiang Cancer Institute, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China
- Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
- Department of Preventive Medicine, School of Medicine, Ningbo University, Ningbo, China
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Increased Co-Occurrence of Pathogenic Variants in Hereditary Breast and Ovarian Cancer and Lynch Syndromes: A Consequence of Multigene Panel Genetic Testing? Int J Mol Sci 2022; 23:ijms231911499. [PMID: 36232793 PMCID: PMC9570103 DOI: 10.3390/ijms231911499] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 09/20/2022] [Accepted: 09/23/2022] [Indexed: 11/16/2022] Open
Abstract
The probability of carrying two pathogenic variants (PVs) in dominant cancer-predisposing genes for hereditary breast and ovarian cancer and lynch syndromes in the same patient is uncommon, except in populations where founder effects exist. Two breast cancer women that are double heterozygotes (DH) for both BRCA1/BRCA2, one ovarian cancer case DH for BRCA1/RAD51C, and another breast and colorectal cancer who is DH for BRCA2/PMS2 were identified in our cohort. Ages at diagnosis and severity of disease in BRCA1/BRCA2 DH resembled BRCA1 single-carrier features. Similarly, the co-existence of the BRCA2 and PMS2 mutations prompted the development of breast and colorectal cancer in the same patient. The first BRCA1/BRCA2 DH was identified by HA-based and Sanger sequencing (1 of 623 families with BRCA PVs). However, this ratio has increased up to 2.9% (1 DH carrier vs. 103 single PV carriers) since using a custom 35-cancer gene on-demand panel. The type of cancer developed in each DH patient was consistent with the independently inherited condition, and the clinical outcome was no worse than in patients with single BRCA1 mutations. Therefore, the clinical impact, especially in patients with two hereditary syndromes, lies in genetic counseling tailor-made for each family based on the clinical guidelines for each syndrome. The number of DH is expected to be increased in the future as a result of next generation sequencing routines.
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Van der Merwe NC, Combrink HM, Ntaita KS, Oosthuizen J. Prevalence of Clinically Relevant Germline BRCA Variants in a Large Unselected South African Breast and Ovarian Cancer Cohort: A Public Sector Experience. Front Genet 2022; 13:834265. [PMID: 35464868 PMCID: PMC9024354 DOI: 10.3389/fgene.2022.834265] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 02/23/2022] [Indexed: 01/14/2023] Open
Abstract
Breast cancer is a multifaceted disease that currently represents a leading cause of death in women worldwide. Over the past two decades (1998–2020), the National Health Laboratory Service’s Human Genetics Laboratory in central South Africa screened more than 2,974 breast and/or ovarian cancer patients for abnormalities characteristic of the widely known familial breast cancer genes, Breast Cancer gene 1 (BRCA1) and Breast Cancer gene 2 (BRCA2). Patients were stratified according to the presence of family history, age at onset, stage of the disease, ethnicity and mutation status relative to BRCA1/2. Collectively, 481 actionable (likely-to pathogenic) variants were detected in this cohort among the different ethnic/racial groups. A combination of old (pre-2014) and new (post-2014) laboratory techniques was used to identify these variants. Additionally, targeted genotyping was performed as translational research revealed the first three recurrent South African pathogenic variants, namely BRCA1 c.1374del (legacy name 1493delC), BRCA1 c.2641G>T (legacy name E881X) and BRCA2 c.7934del (legacy name 8162delG). This initial flagship study resulted in a cost-effective diagnostic test that enabled screening of a particular ethnic group for these variants. Since then, various non-Afrikaner frequent variants were identified that were proven to represent recurrent variants. These include BRCA2 c.5771_5774del (legacy name 5999del4) and BRCA2 c.582G>A, both Black African founder mutations. By performing innovative translational research, medical science in South Africa can adopt first-world technologies into its healthcare context as a developing country. Over the past two decades, the progress made in the public sector enabled a pivotal shift away from population-directed genetic testing to the screening of potentially all breast and ovarian cancer patients, irrespective of ethnicity, family history or immunohistochemical status. The modifications over the years complied with international standards and guidelines aimed at universal healthcare for all. This article shares all the cohort stratifications and the likely-to pathogenic variants detected.
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Affiliation(s)
- 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
- *Correspondence: Nerina C. Van der Merwe,
| | - Herkulaas MvE Combrink
- 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
| | - Kholiwe S. Ntaita
- 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
| | - 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
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Leite Rocha D, Ashton-Prolla P, Rosset C. Reviewing the occurrence of large genomic rearrangements in patients with inherited cancer predisposing syndromes: importance of a comprehensive molecular diagnosis. Expert Rev Mol Diagn 2022; 22:319-346. [PMID: 35234551 DOI: 10.1080/14737159.2022.2049247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Hereditary cancer predisposition syndromes are caused by germline pathogenic or likely pathogenic variants in cancer predisposition genes (CPG). The majority of pathogenic variants in CPGs are point mutations, but large gene rearrangements (LGRs) are present in several CPGs. LGRs can be much more difficult to characterize and perhaps they may have been neglected in molecular diagnoses. AREAS COVERED We aimed to evaluate the frequencies of germline LGRs in studies conducted in different populations worldwide through a qualitative systematic review based on an online literature research in PubMed. Two reviewers independently extracted data from published studies between 2009 and 2020. In total, 126 studies from 37 countries and 5 continents were included in the analysis. The number of studies in different continents ranged from 3 to 48 and for several countries there was an absolute lack of information. Asia and Europe represented most of the studies, and LGR frequencies varied from 3.04 to 15.06% in different continents. MLPA was one of the methods of choice in most studies (93%). EXPERT OPINION The LGR frequencies found in this review reinforce the need for comprehensive molecular testing regardless of the population of origin and should be considered by genetic counseling providers.
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Affiliation(s)
- Débora Leite Rocha
- Laboratório de Medicina Genômica, Serviço de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre (HCPA), Rua Ramiro Barcelos, 2350, CEP: 90035-930, Porto Alegre, Rio Grande do Sul, Brazil
| | - Patrícia Ashton-Prolla
- Laboratório de Medicina Genômica, Serviço de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre (HCPA), Rua Ramiro Barcelos, 2350, CEP: 90035-930, Porto Alegre, Rio Grande do Sul, Brazil.,Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil. Av. Bento Gonçalves, 9500 - Prédio 43312 M, CEP: 91501-970, Caixa Postal 1505, Porto Alegre, Rio Grande do Sul, Brazil.,Serviço de Genética Médica, HCPA, Rio Grande do Sul, Brazil. Rua Ramiro Barcelos, 2350, CEP: 90035-930, Porto Alegre, Rio Grande do Sul, Brazil
| | - Clévia Rosset
- Laboratório de Medicina Genômica, Serviço de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre (HCPA), Rua Ramiro Barcelos, 2350, CEP: 90035-930, Porto Alegre, Rio Grande do Sul, Brazil
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Combrink HM, Oosthuizen J, Visser B, Chabilal N, Buccimazza I, Foulkes WD, van der Merwe NC. Mutations in BRCA-related breast and ovarian cancer in the South African Indian population: A descriptive study. Cancer Genet 2021; 258-259:1-6. [PMID: 34218100 DOI: 10.1016/j.cancergen.2021.06.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 02/07/2021] [Accepted: 06/06/2021] [Indexed: 10/21/2022]
Abstract
Knowledge of the genetic landscape of a specific population group is vital for population-specific diagnosis and treatment of familial breast cancer. Although BRCA-related diagnostic testing has long been implemented in South Africa, the genotyping approach previously failed for the SA Indian population as it was based on other SA population groups. Because this population is uniquely admixed, the lack of population-specific data resulted in the implementation of comprehensive mutation screens for BRCA1/2. A total of 223 female patients were screened for clinically actionable variants. High-resolution melting analysis (HRMA) was used to screen 88 patients for DNA alterations in the coding and splice site boundaries of BRCA1 exons 2-9, BRCA1 exons 11-23, BRCA2 exons 2-9 and BRCA2 exons 12-27. The protein truncation test (PTT) was used to screen the three larger exons (BRCA1 exon 10 and BRCA2 exons 10 and 11) for protein termination changes. Multiplex ligation-dependent probe amplification (MLPA) was used to determine the presence of larger indels and possible copy number differences. Next Generation Sequencing (NGS) was performed on the remaining 135 samples. All potential variants were confirmed by performing Sanger DNA sequencing. The search revealed 28 different pathogenic heterozygotic variants, together with nine variants of unknown significance (VUS). The results suggested that the SA Indian population represents a different genetic admixture compared to that of mainland India, as only five pathogenic variants corresponded to those reported for mainland India. Familial breast cancer testing for SA Indian patients should therefore be performed as comprehensively as possible as the pathogenic variants seem to be family- rather than population-specific. Furthermore, predictive testing of family members will contribute to relieve the financial burden on the country's healthcare system, as increased surveillance and appropriate management could prevent disease.
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Affiliation(s)
- Herkulaas Mve Combrink
- Division of Human Genetics, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa; Division of Human Genetics, National Health Laboratory Services, Universitas Hospital, Bloemfontein, South Africa.
| | - 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 Services, Universitas Hospital, Bloemfontein, South Africa
| | - Botma Visser
- Department of Plant Sciences, Faculty of Natural and Agricultural Sciences, University of the Free State, Bloemfontein, South Africa
| | - Namitha Chabilal
- Genetics Unit, Inkosi Albert Luthuli General Hospital, Durban, South Africa
| | - Ines Buccimazza
- Department of Surgery, Faculty of Medicine, Inkosi Albert Luthuli General Hospital, Durban, South Africa
| | - William D Foulkes
- Lady Davis Institute and Segal Cancer Centre, Jewish General Hospital, Montréal, QC, Canada; Research Institute of the McGill University Health Centre, Montréal, QC, Canada; Program in Cancer Genetics, Departments of Oncology and Human Genetics, McGill University, Montréal, QC, Canada
| | - 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 Services, Universitas Hospital, Bloemfontein, South Africa
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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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