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Wang Y, He Y, Shi Y, Qian DC, Gray KJ, Winn R, Martin AR. Aspiring toward equitable benefits from genomic advances to individuals of ancestrally diverse backgrounds. Am J Hum Genet 2024; 111:809-824. [PMID: 38642557 PMCID: PMC11080611 DOI: 10.1016/j.ajhg.2024.04.002] [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: 10/05/2023] [Revised: 04/01/2024] [Accepted: 04/01/2024] [Indexed: 04/22/2024] Open
Abstract
Advancements in genomic technologies have shown remarkable promise for improving health trajectories. The Human Genome Project has catalyzed the integration of genomic tools into clinical practice, such as disease risk assessment, prenatal testing and reproductive genomics, cancer diagnostics and prognostication, and therapeutic decision making. Despite the promise of genomic technologies, their full potential remains untapped without including individuals of diverse ancestries and integrating social determinants of health (SDOHs). The NHGRI launched the 2020 Strategic Vision with ten bold predictions by 2030, including "individuals from ancestrally diverse backgrounds will benefit equitably from advances in human genomics." Meeting this goal requires a holistic approach that brings together genomic advancements with careful consideration to healthcare access as well as SDOHs to ensure that translation of genetics research is inclusive, affordable, and accessible and ultimately narrows rather than widens health disparities. With this prediction in mind, this review delves into the two paramount applications of genetic testing-reproductive genomics and precision oncology. When discussing these applications of genomic advancements, we evaluate current accessibility limitations, highlight challenges in achieving representativeness, and propose paths forward to realize the ultimate goal of their equitable applications.
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Affiliation(s)
- Ying Wang
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA.
| | - Yixuan He
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Yue Shi
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA; Reproductive Medicine Center, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - David C Qian
- Department of Thoracic Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kathryn J Gray
- Department of Obstetrics and Gynecology, University of Washington, Seattle, WA, USA
| | - Robert Winn
- Virginia Commonwealth University Massey Cancer Center, Richmond, VA, USA
| | - Alicia R Martin
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA.
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2
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de Oliveira Ferreira C, Carneiro VCG, Araujo Mariz C. Germline mutations in BRCA1 and BRCA2 among Brazilian women with ovarian cancer treated in the Public Health System. BMC Cancer 2024; 24:499. [PMID: 38641594 PMCID: PMC11027424 DOI: 10.1186/s12885-024-12246-1] [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: 02/08/2024] [Accepted: 04/10/2024] [Indexed: 04/21/2024] Open
Abstract
BACKGROUND Germline mutations in BRCA1 and BRCA2 genes are among the main causes of hereditary ovarian cancer. Identifying these mutations may reduce cancer risk, facilitate early detection, and enable personalized treatment. However, genetic testing is limited in the Brazilian Public Health System, and data regarding germline mutations in many regions are scarce. Therefore, the study aimed to investigate the prevalence of germline mutations in BRCA1 and BRCA2 in women with ovarian cancer treated in the Public Health System in Pernambuco, Brazil. METHODS A cross-sectional study was conducted in the Hereditary Cancer Program from two reference oncological centers in Pernambuco. Women (n = 45) with high-grade serous ovarian cancer underwent genetic counseling and DNA sequencing for BRCA1 and BRCA2 genes. RESULTS The prevalence of deleterious mutations in the BRCA1 and BRCA2 genes was 33%. Of the 15 germline mutations found, 13 were in BRCA1 and 2 in BRCA2; two mutations of unknown clinical significance were also found in BRCA2. Mutations c.5266dupC and c.2215 A > T were the most frequent; each was mutation observed in three patients. Additionally, the mutations c.7645dupT and c.921dupT were reported for the first time. CONCLUSION One in three women showed a pathogenic mutation, demonstrating a significant prevalence of germline mutations in this sample. Additionally, the small sample revealed an interesting number of mutations, indicating the need to explore more regions of the country.
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Affiliation(s)
| | - Vandré Cabral Gomes Carneiro
- Hospital de Câncer de Pernambuco, Recife, Pernambuco, Brazil
- Instituto de Medicina Integral Professor Fernando Figueira, Recife, Pernambuco, Brazil
| | - Carolline Araujo Mariz
- Instituto Aggeu Magalhães, FIOCRUZ, Recife, Pernambuco, Brazil.
- Faculdade de Medicina de Olinda, Olinda, Pernambuco, Brazil.
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Smith AJB, Howell EA, Ko EM. Ovarian Cancer Isn't Just a White Woman's Disease. JAMA Oncol 2024:2817119. [PMID: 38573626 DOI: 10.1001/jamaoncol.2024.0191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
This Viewpoint highlights the need for recognition that ovarian cancer affects women from racial and ethnic minority groups worldwide and that the rates of ovarian cancer are increasing in those populations while decreasing among White women.
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Affiliation(s)
- Anna Jo Bodurtha Smith
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of Pennsylvania Health Systems, Philadelphia
- Leonard Davis Institute of Health Economics, University of Pennsylvania, Philadelphia
| | - Elizabeth A Howell
- Department of Obstetrics and Gynecology, University of Pennsylvania Health Systems, Philadelphia
- Leonard Davis Institute of Health Economics, University of Pennsylvania, Philadelphia
| | - Emily M Ko
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of Pennsylvania Health Systems, Philadelphia
- Leonard Davis Institute of Health Economics, University of Pennsylvania, Philadelphia
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Martin FJ, Saffie IM, Hurtado MA, Avila-Jaque D, Lagos RA, Selman CA, Huserman JZ, Castillo VA, Chahuán BJ. Variants in BRCA1/2 in a hospital-based cohort in Chile and national literature review. Ecancermedicalscience 2024; 18:1683. [PMID: 38566764 PMCID: PMC10984842 DOI: 10.3332/ecancer.2024.1683] [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: 10/02/2023] [Indexed: 04/04/2024] Open
Abstract
Purpose The aim was to assess the diagnostic yield of next generation sequencing (NGS) multi-gene panels for breast and ovarian cancer in a high-complexity cancer centre in Chile. Additionally, our goal was to broaden the genotypic spectrum of BRCA variants already identified in Chilean families. Methods Retrospective analysis was conducted on the genetic test results of 722 individuals from Fundación Arturo López Pérez's genetic counselling unit between 2016 and 2021. A comprehensive literature review encompassing articles analysing the frequency of germinal pathogenic variants in BRCA1/2 within the Chilean population was undertaken. Results 23.5% of the panels had positive results, with 60% due to pathogenic variants in the BRCA1/2 genes. Seven previously unreported variants in BRCA1 from Chilean studies were identified.One or more variants of uncertain significance were detected in 31% of the results, and 11.5% of the families in this cohort presented copy number variants (CNVs) in BRCA1/2.8 studies analysed the frequency of pathogenic variants in BRCA1/2 in the Chilean population between 2006 and 2023, with a frequency between 7.1% and 17.1%.51 BRCA1 variants in 149 families have been reported in Chile and 38 BRCA2 variants in 132 families. Nine founder pathogenic variants identified by one study were present in 51.9% of the total Chilean families reported. Conclusion Our findings advocate for the integration of NGS multi-gene panel testing as a primary strategy within our population. This approach allows for the comprehensive assessment of single nucleotide variants and CNVs in BRCA1/2, alongside other high and moderately penetrant genes associated with breast and ovarian cancer.
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Affiliation(s)
- Fernanda J Martin
- Unidad Asesoramiento Genético Oncológico, Fundación Arturo López Pérez, Santiago 7500921, Chile
- https://orcid.org/0000-0002-7167-8850
| | - Isabel M Saffie
- Cirugía de mama, Fundación Arturo López Pérez, Santiago 7500921, Chile
- https://orcid.org/0000-0002-4723-5750
| | - Mabel A Hurtado
- Unidad Asesoramiento Genético Oncológico, Fundación Arturo López Pérez, Santiago 7500921, Chile
- Cirugía de mama, Fundación Arturo López Pérez, Santiago 7500921, Chile
| | - Diana Avila-Jaque
- Sección de Genética, Hospital San Juan de Dios, Santiago 8350488, Chile
- https://orcid.org/0009-0002-7787-6847
| | - Rodrigo A Lagos
- Unidad estadística, Fundación Arturo López Pérez, Santiago 7500921, Chile
- https://orcid.org/0000-0002-5806-6227
| | - Carolina A Selman
- Subdirección Unidades Diagnósticas, Fundación Arturo López Pérez, Santiago 7500921, Chile
| | - Jonathan Z Huserman
- Departamento Genética, Hospital Base San José Osorno, Osorno 5311523, Chile
- https://orcid.org/0000-0002-9355-3282
| | - Valentina A Castillo
- Departamento Genética, Hospital Clínico Universidad de Chile, Santiago 8380453, Chile
- Departamento Genética, Hospital Dr. Sótero del Río, Santiago 8150000, Chile
| | - Badir J Chahuán
- Unidad Asesoramiento Genético Oncológico, Fundación Arturo López Pérez, Santiago 7500921, Chile
- Cirugía de mama, Fundación Arturo López Pérez, Santiago 7500921, Chile
- https://orcid.org/0000-0003-3133-6706
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Tiscoski KA, Giacomazzi J, Rocha MS, Gössling G, Werutsky G. Real-world data on triple-negative breast cancer in Latin America and the Caribbean. Ecancermedicalscience 2023; 17:1635. [PMID: 38414969 PMCID: PMC10898885 DOI: 10.3332/ecancer.2023.1635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Indexed: 02/29/2024] Open
Abstract
Breast cancer (BC) is the most prevalent cancer in women in Latin America and the Caribbean. We compiled real-world data (RWD) on the epidemiology, diagnosis, treatment, and patient outcomes of triple-negative breast cancer (TNBC), addressing the main barriers to optimal care in Latin America. The prevalence of TNBC varies between 11% and 38.5% of all BC cases diagnosed in the region, and TNBC primarily affects young patients. Delays in BC diagnosis, with consequent advanced disease stages and barriers to access efficient therapies, particularly due to high costs, negatively impact patient outcomes. Cancer clinical trials are an opportunity to access standard and novel therapies for patients with this aggressive BC subtype and thus must be prioritised. Finally, generating RWD and cost-effectiveness studies in a region with limited resources is critical for decision-makers to define the incorporation of new technologies for the treatment of BC.
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Affiliation(s)
- Katsuki Arima Tiscoski
- Santa Casa de Misericórdia de Porto Alegre, Rua Professor Annes Dias, Porto Alegre 90020-090, Brazil
- https://orcid.org/0000-0003-0074-4272
| | - Juliana Giacomazzi
- Latin American Cooperative Oncology Group (LACOG), Av Ipiranga, Porto Alegre 90619-900, Brazil
- https://orcid.org/0000-0001-5811-5140
| | - Matheus Soares Rocha
- Latin American Cooperative Oncology Group (LACOG), Av Ipiranga, Porto Alegre 90619-900, Brazil
- https://orcid.org/0000-0001-8972-7449
| | - Gustavo Gössling
- Latin American Cooperative Oncology Group (LACOG), Av Ipiranga, Porto Alegre 90619-900, Brazil
- https://orcid.org/0000-0002-4361-2889
| | - Gustavo Werutsky
- Latin American Cooperative Oncology Group (LACOG), Av Ipiranga, Porto Alegre 90619-900, Brazil
- https://orcid.org/0000-0001-6271-105X
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Newman L. Oncologic anthropology: Global variations in breast cancer risk, biology, and outcome. J Surg Oncol 2023; 128:959-966. [PMID: 37814598 DOI: 10.1002/jso.27459] [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: 09/13/2023] [Accepted: 09/14/2023] [Indexed: 10/11/2023]
Abstract
The global breast cancer burden is growing. Of 19.3 million new cancers diagnosed in 2020, 2.26 million were breast, surpassing lung as the most commonly diagnosed worldwide. Breast cancer is the fourth most common cause of cancer deaths worldwide, and the leading cause of death in females. Incidence and mortality rates are projected to rise disproportionately in low and middle-income countries, a consequence of socioeconomic factors and differences in tumor biology related to genetic ancestry.
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Affiliation(s)
- Lisa Newman
- Division of Breast Surgery, Interdisciplinary Breast Program, International Center for theStudy of Breast Cancer, Weill Cornell Medicine/New York Presbyterian Hospital Network, New York, New York, USA
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Ferreyra Y, Rosas G, Cock-Rada AM, Araujo J, Bravo L, Doimi F, Casas J, Clavo MDLÁ, Pinto JA, Belmar-López C. Landscape of germline BRCA1/BRCA2 variants in breast and ovarian cancer in Peru. Front Oncol 2023; 13:1227864. [PMID: 37664050 PMCID: PMC10470619 DOI: 10.3389/fonc.2023.1227864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 07/27/2023] [Indexed: 09/05/2023] Open
Abstract
Background There is an increasing amount of data from Latin America on the characterization of BRCA variants; however, there is limited information from Peru. We conducted a retrospective study to describe germline pathogenic/likely pathogenic(P/LP) variants and variants of uncertain/unknown significance (VUS) in the BRCA1 and BRCA2 genes in Peru, in patients with breast and ovarian cancer, candidates for treatment with poly (adenosine diphosphate-ribose) polymerase (PARP) inhibitors. Methods The patients were evaluated during the period 2019-2021. Genomic DNA was isolated from peripheral blood samples and targeted sequencing was performed using the Ampliseq BRCA panel. Genetic variant interpretation was carried out in accordance with the recommendations of the American College of Medical Genetics and ClinVar. During this period, 525 patients (143 with breast cancer and 382 with ovarian cancer) were studied. Results We found that 14.7% (21/143) of breast cancer patients and 20.7% (79/382) of ovarian cancer patients were carriers of P/LP variants in BRCA1/2. The most frequent pathogenic variants detected in BRCA1 were c.2105dupT (BIC: 2224insT, n=12, 18.75%), c.68_69delAG (BIC: 185delAG, n=6, 9.38%), c.140G>T and c.815_824dupAGCCATGTGG (n=5, 7.81%), while in BRCA2 were c.8023A>G (n=6, 16.67%), c.6024dupG (BIC: 6252insG, n=4, 11.11%), and c.9235delG (BIC: 9463delG, n=3, 8.33%). Regarding VUS, we found that 6.99% (10/143) of breast cancer patients and 7.33% (28/382) of ovarian cancer patients were carriers of a VUS in BRCA1/2. For BRCA1, the most frequent VUS was c.93C>G (n=2), and for BRCA2, c.5465A>T (n=4), c.3101T>C (n=3), c.205C>A and c.437T>C (n=2). Conclusion We found a frequency of 14.7% germline mutations in breast cancer patients and 20.7% in ovarian cancer patients. The most recurrent mutations were BRCA1 c.2105dupT and BRCA2 c.8023A>G. We found that BRCA2 c.8023A>G, c.6024dupG, and c.9235delG were not previously reported in Peruvian patients. BRCA1 c.2344dupA is a novel mutation that has not been previously reported in any database. The frequency of VUS in our cohort was 7.2%.
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Affiliation(s)
- Yomali Ferreyra
- Departamento de Bioingeniería, Universidad de Ingenieria y Tecnología, Lima, Peru
| | - Gina Rosas
- Departamento de Patología, Insituto Nacional de Enfermedades Neoplásicas, Lima, Peru
| | - Alicia M. Cock-Rada
- Departmento de Oncología Médica, Instituto de Cancerología Las Américas - Auna, Medellín, Colombia
| | - Jhajaira Araujo
- Centro de Investigación Básicas y traslacional, Auna Ideas, Lima, Peru
| | - Leny Bravo
- Escuela Profesional de Medicina Humana-Filial Ica, Universidad Privada San Juan Bautista, Ica, Peru
| | | | | | | | - Joseph A. Pinto
- Centro de Investigación Básicas y traslacional, Auna Ideas, Lima, Peru
| | - Carolina Belmar-López
- Escuela Profesional de Medicina Humana-Filial Ica, Universidad Privada San Juan Bautista, Ica, Peru
- Oncogenomics, Auna, Lima, Peru
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Zampiga V, Cangini I, Bandini E, Azzali I, Ravegnani M, Ravaioli A, Mancini S, Tebaldi M, Tedaldi G, Pirini F, Veneroni L, Frassineti GL, Falcini F, Danesi R, Calistri D, Arcangeli V. Prevalence of a BRCA2 Pathogenic Variant in Hereditary-Breast-and-Ovarian-Cancer-Syndrome Families with Increased Risk of Pancreatic Cancer in a Restricted Italian Area. Cancers (Basel) 2023; 15:cancers15072132. [PMID: 37046793 PMCID: PMC10093547 DOI: 10.3390/cancers15072132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 03/31/2023] [Accepted: 04/01/2023] [Indexed: 04/07/2023] Open
Abstract
PVs and LPVs in BRCA1/2 genes are correlated to a high risk of developing breast cancer and/or ovarian cancer (Hereditary Breast and Ovarian Cancer syndrome, HBOC); additionally, in recent years, an increasing number of BRCA 1/2 variants have been identified and associated with pancreatic cancer. Epidemiologic studies have highlighted that inherited factors are involved in 10% to 20% of PCs, mainly through deleterious variants of BRCA2. The frequency of BRCA1/2 germline alterations fluctuates quite a lot among different ethnic groups, and the estimated rate of PVs/LPVs variants in Italian HBOC families is not very accurate, according to different reports. The aim of our study is to describe the prevalence of a BRCA2 PV observed in a selected cohort of HBOC patients and their relatives, whose common origin is the eastern coast of Emilia Romagna, a region of Italy. This study provides insight into the frequency of the variant detected in this area and provides evidence of an increased risk of pancreatic and breast cancer, useful for genetic counseling and surveillance programs.
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Affiliation(s)
- Valentina Zampiga
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy
| | - Ilaria Cangini
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy
| | - Erika Bandini
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy
| | - Irene Azzali
- Unit of Biostatistics and Clinical Trials, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy
| | - Mila Ravegnani
- Romagna Cancer Registry, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy
| | - Alessandra Ravaioli
- Romagna Cancer Registry, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy
| | - Silvia Mancini
- Romagna Cancer Registry, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy
| | - Michela Tebaldi
- Unit of Biostatistics and Clinical Trials, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy
| | - Gianluca Tedaldi
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy
| | - Francesca Pirini
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy
| | - Luigi Veneroni
- Surgical Department, Infermi Hospital, 47923 Rimini, Italy
| | - Giovanni Luca Frassineti
- Department of Medical Oncology, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy
| | - Fabio Falcini
- Romagna Cancer Registry, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy
| | - Rita Danesi
- Romagna Cancer Registry, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy
| | - Daniele Calistri
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy
| | - Valentina Arcangeli
- Romagna Cancer Registry, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy
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Zhang Y, Wu H, Yu Z, Li L, Zhang J, Liang X, Huang Q. Germline variants profiling of BRCA1 and BRCA2 in Chinese Hakka breast and ovarian cancer patients. BMC Cancer 2022; 22:842. [PMID: 35918668 PMCID: PMC9347172 DOI: 10.1186/s12885-022-09943-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 07/25/2022] [Indexed: 12/26/2022] Open
Abstract
Objective To investigate the prevalence and spectrum of BRCA1 and BRCA2 mutations in Chinese Hakka patients with breast and ovarian cancer. Methods A total of 1,664 breast or ovarian cancer patients were enrolled for genetic testing at our hospital. Germline mutations of the BRCA gene were analysed by next-generation sequencing, including the coding regions and exon intron boundary regions. Results The 1,664 patients included 1,415 (85.04%) breast cancer patients and 245 (14.72%) ovarian cancer patients, while four (0.24%) patients had both the breast and ovarian cancers. A total of 151 variants, including 71 BRCA1 variants and 80 BRCA2 variants, were detected in the 234 (14.06%) patients. The 151 variants included 58 pathogenic variants, 8 likely pathogenic variants, and 85 variants of unknown significance (VUS). A total of 56.25% (18/32) and 65.38% (17/26) of pathogenic variants (likely pathogenic variants are not included) were distributed in exon 14 of BRCA1 and exon 11 of BRCA2, respectively. The most common pathogenic variants among this Hakka population are c.2635G > T (p.Glu879*) (n = 7) in the BRCA1 gene and c.5164_5165del (p.Ser1722Tyrfs*4) (n = 7) in the BRCA2 gene among the Hakka population. A hotspot mutation in the Chinese population, the BRCA1 c.5470_5477del variant was not found in this Hakka population. The prevalence and spectrum of variants in the BRCA genes in the Hakka patients are different from that in other ethnic groups. Conclusions The most common pathogenic variant in this population is c.2635G > T in the BRCA1 gene, and c.5164_5165delAG in the BRCA2 gene in this population. The prevalence and spectrum of variants in the BRCA1 and BRCA2 genes in the Hakka patients from southern China are different from those in other ethnic groups. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-022-09943-0.
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Affiliation(s)
- Yunuo Zhang
- Department of Medical Oncology, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, China.,Center for Precision Medicine, Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, No 63 Huangtang Road, Meijiang District, Meizhou, 514031, People's Republic of China
| | - Heming Wu
- Center for Precision Medicine, Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, No 63 Huangtang Road, Meijiang District, Meizhou, 514031, People's Republic of China.,Center for Precision Medicine, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, China.,Meizhou Municipal Engineering and Technology Research Center for Molecular Diagnostics of Major Genetic Disorders, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, China
| | - Zhikang Yu
- Center for Precision Medicine, Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, No 63 Huangtang Road, Meijiang District, Meizhou, 514031, People's Republic of China.,Center for Precision Medicine, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, China.,Meizhou Municipal Engineering and Technology Research Center for Molecular Diagnostics of Major Genetic Disorders, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, China
| | - Liang Li
- Department of Medical Oncology, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, China.,Center for Precision Medicine, Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, No 63 Huangtang Road, Meijiang District, Meizhou, 514031, People's Republic of China
| | - Jinhong Zhang
- Department of Medical Oncology, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, China.,Center for Precision Medicine, Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, No 63 Huangtang Road, Meijiang District, Meizhou, 514031, People's Republic of China
| | - Xinhong Liang
- Center for Precision Medicine, Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, No 63 Huangtang Road, Meijiang District, Meizhou, 514031, People's Republic of China.,Radiology department, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, China
| | - Qingyan Huang
- Center for Precision Medicine, Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, No 63 Huangtang Road, Meijiang District, Meizhou, 514031, People's Republic of China. .,Center for Precision Medicine, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, China. .,Meizhou Municipal Engineering and Technology Research Center for Molecular Diagnostics of Major Genetic Disorders, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, China.
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Sheth H, Naik P, Shah M, Bhavsar R, Nair A, Sheth F, Sheth J. The GALNS p.P77R variant is a probable Gujarati-Indian founder mutation causing Mucopolysaccharidosis IVA syndrome. BMC Genomics 2022; 23:458. [PMID: 35729508 PMCID: PMC9210747 DOI: 10.1186/s12864-022-08693-4] [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: 03/14/2022] [Accepted: 06/13/2022] [Indexed: 11/20/2022] Open
Abstract
Background Mucopolysaccharidosis IVA (Morquio syndrome A, MPS IVA) is an autosomal recessive lysosomal storage disorder caused due to biallelic variants in the N-acetylgalactoseamine-6-sulfate sulfatase (GALNS) gene. The mutation spectrum in this condition is determined amongst sub-populations belonging to the north, south and east India geography, however, sub-populations of west Indian origin, especially Gujarati-Indians, are yet to be studied. We aimed to analyse the variants present in the GLANS gene amongst the population of Gujarat by sequencing all exons and exon–intron boundaries of the GALNS gene in patients from 23 unrelated families. Results We report 11 variants that include eight missense variants: (p.L36R, p.D39G, p.P77R, p.C79R, pP125L, p.P151L, p.G255A and p.L350P), one splice site variant: (c.121-7C > G), one small insertion: (c.1241_1242insA, p.I416HfsTer2) and one small deletion: (c.839_841delACA). Of these, three missense variants (p.D39G, p.G255A and p.L350P), one splice site and the two indels mentioned above are novel. Interestingly, we observed a higher than anticipated prevalence of p.P77R variant in our cohort (n = 14/25, 56%). Haplotype analysis in cases with p.P77R variant and 63 ethnicity matched healthy population controls suggested a 4 SNP haplotype block present in cases compared to controls (likelihood ratio test p-value = 1.16 × 10–13), thereby suggesting p.P77R variant as a founder variant in the Gujarati-Indian population. Furthermore, age of mutation analysis suggested the variant to have arisen approximately 450 years ago in the population. Conclusion p.P77R variant in the GLANS gene is likely to be a founder variant in MPS IVA patients of Gujarati-Indian ancestry and appeared approximately 450 years ago in the population. To our knowledge, this is the first variant to be posited as a founder variant in the GLANS gene in patients with MPS IVA syndrome. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08693-4.
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Affiliation(s)
- Harsh Sheth
- FRIGE's Institute of Human Genetics, FRIGE House, Jodhpur Village Road, Satellite, Ahmedabad, Gujarat, 380015, India.
| | - Premal Naik
- Rainbow Super Speciality Hospital and Children's Orthopedic Centre, Ahmedabad, India
| | | | - Riddhi Bhavsar
- FRIGE's Institute of Human Genetics, FRIGE House, Jodhpur Village Road, Satellite, Ahmedabad, Gujarat, 380015, India
| | - Aadhira Nair
- FRIGE's Institute of Human Genetics, FRIGE House, Jodhpur Village Road, Satellite, Ahmedabad, Gujarat, 380015, India
| | - Frenny Sheth
- FRIGE's Institute of Human Genetics, FRIGE House, Jodhpur Village Road, Satellite, Ahmedabad, Gujarat, 380015, India
| | - Jayesh Sheth
- FRIGE's Institute of Human Genetics, FRIGE House, Jodhpur Village Road, Satellite, Ahmedabad, Gujarat, 380015, India.
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11
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Gallardo-Rincón D, Montes-Servín E, Alamilla-García G, Montes-Servín E, Bahena-González A, Cetina-Pérez L, Morales Vásquez F, Cano-Blanco C, Coronel-Martínez J, González-Ibarra E, Espinosa-Romero R, María Alvarez-Gómez R, Pedroza-Torres A, Castro-Eguiluz D. Clinical Benefits of Olaparib in Mexican Ovarian Cancer Patients With Founder Mutation BRCA1-Del ex9-12. Front Genet 2022; 13:863956. [PMID: 35734436 PMCID: PMC9207274 DOI: 10.3389/fgene.2022.863956] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 05/02/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Ovarian cancer (OC) is gynecologic cancer with the highest mortality rate. It is estimated that 13–17% of ovarian cancers are due to heritable mutations in BRCA1 and BRCA2. The BRCA1 (BRCA1-Del ex9-12) Mexican founder mutation is responsible for 28–35% of the cases with ovarian cancer. The aim was to describe the PFS of OC patients treated with olaparib, emphasizing patients carrying the Mexican founder mutation (BRCA1-Del ex9-12). Methods: In this observational study, of 107 patients with BRCAm, 35 patients were treated with olaparib from November 2016 to May 2021 at the Ovarian Cancer Program (COE) of Mexico; patient information was extracted from electronic medical records. Results: Of 311 patients, 107 (34.4%) were with BRCAm; 71.9% (77/107) were with BRCA1, of which 27.3% (21/77) were with BRCA1-Del ex9-12, and 28.1% (30/107) were with BRCA2 mutations. Only 35 patients received olaparib treatment, and the median follow-up was 12.87 months. The PFS of BRCA1-Del ex9-12 was NR (non-reach); however, 73% of the patients received the treatment at 36 vs. 11.59 months (95% CI; 10.43–12.75) in patients with other BRCAm (p = 0.008). Almost 50% of patients required dose reduction due to toxicity; the most frequent adverse events were hematological in 76.5% and gastrointestinal in 4%. Conclusion: Mexican OC BRCA1-Del ex9-12 patients treated with olaparib had a significant increase in PFS regardless of the line of treatment compared to other mutations in BRCA.
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Affiliation(s)
- Dolores Gallardo-Rincón
- Ovarian and Endometrial Cancer Program (COE), Instituto Nacional de Cancerología (INCan), Mexico City, Mexico
- Department of Medical Oncology, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico
- *Correspondence: Dolores Gallardo-Rincón,
| | - Edgar Montes-Servín
- Ovarian and Endometrial Cancer Program (COE), Instituto Nacional de Cancerología (INCan), Mexico City, Mexico
| | - Gabriela Alamilla-García
- Ovarian and Endometrial Cancer Program (COE), Instituto Nacional de Cancerología (INCan), Mexico City, Mexico
- Department of Medical Oncology, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico
| | - Elizabeth Montes-Servín
- Ovarian and Endometrial Cancer Program (COE), Instituto Nacional de Cancerología (INCan), Mexico City, Mexico
| | - Antonio Bahena-González
- Ovarian and Endometrial Cancer Program (COE), Instituto Nacional de Cancerología (INCan), Mexico City, Mexico
- Department of Medical Oncology, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico
| | - Lucely Cetina-Pérez
- Department of Clinical Research and Medical Oncology, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico
- Cervical Cancer Program (Micaela), Instituto Nacional de Cancerología (INCan), Mexico City, Mexico
| | - Flavia Morales Vásquez
- Department of Medical Oncology, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico
| | - Claudia Cano-Blanco
- Department of Medical Oncology, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico
| | - Jaime Coronel-Martínez
- Department of Medical Oncology, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico
| | - Ernesto González-Ibarra
- Ovarian and Endometrial Cancer Program (COE), Instituto Nacional de Cancerología (INCan), Mexico City, Mexico
| | - Raquel Espinosa-Romero
- Ovarian and Endometrial Cancer Program (COE), Instituto Nacional de Cancerología (INCan), Mexico City, Mexico
- Department of Medical Oncology, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico
| | - Rosa María Alvarez-Gómez
- Department of Clinical Research and Medical Oncology, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico
- Hereditary Cancer Clinic, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico
| | - Abraham Pedroza-Torres
- Hereditary Cancer Clinic, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico
- Catedrático CONACYT, Instituto Nacional de Cancerología, Mexico City, Mexico
| | - Denisse Castro-Eguiluz
- Cervical Cancer Program (Micaela), Instituto Nacional de Cancerología (INCan), Mexico City, Mexico
- Catedrático CONACYT, Instituto Nacional de Cancerología, Mexico City, Mexico
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12
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BRCA1 and BRCA2 screening of nine Chilean founder mutations through allelic-discrimination and real-time PCR in breast/ovarian cancer patients. Mol Biol Rep 2022; 49:7531-7539. [PMID: 35596815 PMCID: PMC9123627 DOI: 10.1007/s11033-022-07561-4] [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: 01/05/2022] [Accepted: 05/04/2022] [Indexed: 11/02/2022]
Abstract
BACKGROUND In a previous work, we identified nine founder mutations present in close to 80% of BRCA1 and BRCA2 mutation carriers, and distributed across the country. The presence of founder mutations constitutes a valuable opportunity to develop new strategies for genetic screening. Genetic tests are primarily performed by NGS sequencing, which requires sophisticated and expensive equipment, and it takes 2-3 weeks for the results to be informed to the patient. In addition, genetic tests are not covered by insurance companies in Latin American countries. In this work, we present the standardization and technical validation of a real-time PCR based methodology for allelic discrimination in order to identify the nine Chilean founder mutations in BRCA1 and BRCA2 genes. METHODS AND RESULTS We designed nine pairs of probes and nine pairs of primers to amplify synchronically nine regions of the BRCA1/BRCA2 genes by real-time PCR, in order to identify the nine founder mutations through allelic discrimination analyses. Technical validation was performed using 90 positive and 90 negative samples for each mutation. The methodology was tested in a second group of 60 patients. Our method correctly classified carriers and non-carriers of one of the nine Chilean founder mutations with a 100% specificity and 100% sensitivity, compared with Sanger sequencing performance. CONCLUSIONS We develop an inexpensive, simple, and fast mutation detection method that could be implemented locally in Hospitals from the Private to Public health system. This methodology may be useful for the screening of BRCA1 and BRCA2 mutations in other populations.
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13
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Discovery of BRCA1/BRCA2 Founder Variants by Haplotype Analysis. Cancer Genet 2022; 266-267:19-27. [DOI: 10.1016/j.cancergen.2022.05.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 05/22/2022] [Accepted: 05/26/2022] [Indexed: 11/20/2022]
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14
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Nunez SE, Ariza-Hutchinson A, Fields RA, Vondenberg JA, Patel RA, Emil NS, Muruganandam M, Gibb JI, Poole JL, Sibbitt WL. Systemic sclerosis manifestations and clinical outcomes in Hispanics/Latinos of the American Southwest. JOURNAL OF SCLERODERMA AND RELATED DISORDERS 2022; 7:135-143. [DOI: 10.1177/23971983221086214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 02/16/2022] [Indexed: 11/16/2022]
Abstract
Objective: Certain Hispanic/Latino (Hispanic) populations have been reported to have higher rates and severity of systemic sclerosis; however, little is known of systemic sclerosis in the American Southwest. This study compared manifestations of systemic sclerosis in Hispanics with non-Hispanics of New Mexico. Methods: This cross-sectional longitudinal study included 109 systemic sclerosis patients followed over a mean of 12.6 ± 8.9 years. Subjects were repetitively evaluated including physical examination, echocardiography, chest imaging, and serologic testing and observed for complications. Disease characteristics and long-term outcomes were statistically compared between self-identified Hispanic and non-Hispanic subjects. Results: A total of 73 (67%) systemic sclerosis subjects were Hispanic and 36 (33%) were non-Hispanic. The cohorts were similar in mean age, age of systemic sclerosis onset, limited versus diffuse cutaneous systemic sclerosis, telangiectases, gastroesophageal reflux disease, Raynaud’s phenomenon, autoantibody profile, interstitial lung disease, pulmonary hypertension, scleroderma renal crisis, mortality, and comorbid malignancy (all p > 0.05). However, the standardized mortality ratio was increased in both cohorts relative to age-adjusted mortality: Hispanic: 2.08, confidence interval (1.94–2.24); non-Hispanic: 1.56, confidence interval (1.46–1.68). Furthermore, the standardized incidence ratio for malignancy was increased in both cohorts: Hispanic: 1.45, confidence interval (1.35–1.56); non-Hispanic: 1.24, confidence interval (1.16–1.34). The mean age of cancer diagnosis occurred at a significantly younger age in Hispanics (Hispanics: 53.1 ± 9.7 years; non-Hispanics 63.7 ± 7.9 years; 95% confidence interval: −19 ⩽ 10.6 ⩽ 2.2; p = 0.016). Conclusion: Systemic sclerosis phenotype, autoantibodies, complications, outcomes, malignancy rates, and mortality are generally similar between Hispanics and non-Hispanics with systemic sclerosis in the American Southwest. However, age-adjusted comorbid malignancy and mortality rates are significantly increased in both groups.
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Affiliation(s)
- Sharon E Nunez
- Department of Internal Medicine, Division of Rheumatology, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Angie Ariza-Hutchinson
- Department of Internal Medicine, Division of Rheumatology, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Roderick A Fields
- Department of Internal Medicine, Division of Rheumatology, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Jaime A Vondenberg
- Department of Medicine, Rheumatology/Immunology, Cleveland Clinic, Cleveland, OH, USA
| | - Rosemina A Patel
- Department of Internal Medicine, Division of Rheumatology, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - N Suzanne Emil
- Department of Internal Medicine, Division of Rheumatology, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Maheswari Muruganandam
- Department of Internal Medicine, Division of Rheumatology, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - James I Gibb
- Department of Internal Medicine, Division of Rheumatology, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Janet L Poole
- Department of Internal Medicine, Division of Rheumatology, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Wilmer L Sibbitt
- Department of Internal Medicine, Division of Rheumatology, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
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15
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ElBiad O, Laraqui A, El Boukhrissi F, Mounjid C, Lamsisi M, Bajjou T, Elannaz H, Lahlou AI, Kouach J, Benchekroune K, Oukabli M, Chahdi H, Ennaji MM, Tanz R, Sbitti Y, Ichou M, Ennibi K, Badaoui B, Sekhsokh Y. Prevalence of specific and recurrent/founder pathogenic variants in BRCA genes in breast and ovarian cancer in North Africa. BMC Cancer 2022; 22:208. [PMID: 35216584 PMCID: PMC8876448 DOI: 10.1186/s12885-022-09181-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 11/24/2021] [Indexed: 12/11/2022] Open
Abstract
Background Elucidation of specific and recurrent/founder pathogenic variants (PVs) in BRCA (BRCA1 and BRCA2) genes can make the genetic testing, for breast cancer (BC) and/or ovarian cancer (OC), affordable for developing nations. Methods To establish the knowledge about BRCA PVs and to determine the prevalence of the specific and recurrent/founder variants in BRCA genes in BC and/or OC women in North Africa, a systematic review was conducted in Morocco, Algeria, and Tunisia. Results Search of the databases yielded 25 relevant references, including eleven studies in Morocco, five in Algeria, and nine in Tunisia. Overall, 15 studies investigated both BRCA1 and BRCA2 genes, four studies examined the entire coding region of the BRCA1 gene, and six studies in which the analysis was limited to a few BRCA1 and/or BRCA2 exons. Overall, 76 PVs (44 in BRCA1 and32 in BRCA2) were identified in 196 BC and/or OC patients (129 BRCA1 and 67 BRCA2 carriers). Eighteen of the 76 (23.7%) PVs [10/44 (22.7%) in BRCA1 and 8/32 (25%) in BRCA2] were reported for the first time and considered to be novel PVs. Among those identified as unlikely to be of North African origin, the BRCA1 c.68_69del and BRCA1 c.5266dupC Jewish founder alleles and PVs that have been reported as recurrent/founder variants in European populations (ex: BRCA1 c.181T>G, BRCA1 c1016dupA). The most well characterized PVs are four in BRCA1 gene [c.211dupA (14.7%), c.798_799detTT (14%), c.5266dup (8.5%), c.5309G>T (7.8%), c.3279delC (4.7%)] and one in BRCA2 [c.1310_1313detAAGA (38.9%)]. The c.211dupA and c.5309G>T PVs were identified as specific founder variants in Tunisia and Morocco, accounting for 35.2% (19/54) and 20.4% (10/49) of total established BRCA1 PVs, respectively. c.798_799delTT variant was identified in 14% (18/129) of all BRCA1 North African carriers, suggesting a founder allele. A broad spectrum of recurrent variants including BRCA1 3279delC, BRCA1 c.5266dup and BRCA2 c.1310_1313detAAGA was detected in 42 patients. BRCA1 founder variants explain around 36.4% (47/129) of BC and outnumber BRCA2 founder variants by a ratio of ≈3:1. Conclusions Testing BC and/or OC patients for the panel of specific and recurrent/founder PVs might be the most cost-effective molecular diagnosis strategy.
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Affiliation(s)
- Oubaida ElBiad
- Laboratoire de Recherche et de Biosécurité P3, Hôpital Militaire d'Instruction Mohammed V, Rabat, Maroc. .,Unité de séquençage, Laboratoire de Virologie, Centre de Virologie, des Maladies Infectieuses et Tropicales, Hôpital Militaire d'Instruction Mohammed V, Faculté de Médecine et de Pharmacie, Université Mohammed V, Rabat, Maroc. .,Laboratoire de Biodiversité, Ecologie et Génome, Faculté des Sciences, Université Mohammed V, Rabat, Maroc.
| | - Abdelilah Laraqui
- Laboratoire de Recherche et de Biosécurité P3, Hôpital Militaire d'Instruction Mohammed V, Rabat, Maroc.,Unité de séquençage, Laboratoire de Virologie, Centre de Virologie, des Maladies Infectieuses et Tropicales, Hôpital Militaire d'Instruction Mohammed V, Faculté de Médecine et de Pharmacie, Université Mohammed V, Rabat, Maroc.,Centre de virologie, des maladies infectieuses et tropicales, Hôpital militaire d'Instruction Mohammed V, Faculté de Médecine et de Pharmacie, Université Mohammed V, Rabat, Maroc
| | - Fatima El Boukhrissi
- Laboratoire de Biochimie-Toxicologie, Hôpital Militaire Moulay Ismail Meknès, Faculté de Médecine et de Pharmacie, Université Sidi Mohamed Ben Abdellah, Fès, Maroc
| | - Chaimaa Mounjid
- Laboratoire de Recherche et de Biosécurité P3, Hôpital Militaire d'Instruction Mohammed V, Rabat, Maroc
| | - Maryame Lamsisi
- Laboratoire de Virologie, Microbiologie, Qualité, Biotechnologies/Ecotoxicologie et Biodiversité, Faculté des sciences et techniques, Mohammadia, Université Hassan II, Casa, Maroc
| | - Tahar Bajjou
- Laboratoire de Recherche et de Biosécurité P3, Hôpital Militaire d'Instruction Mohammed V, Rabat, Maroc
| | - Hicham Elannaz
- Unité de séquençage, Laboratoire de Virologie, Centre de Virologie, des Maladies Infectieuses et Tropicales, Hôpital Militaire d'Instruction Mohammed V, Faculté de Médecine et de Pharmacie, Université Mohammed V, Rabat, Maroc.,Centre de virologie, des maladies infectieuses et tropicales, Hôpital militaire d'Instruction Mohammed V, Faculté de Médecine et de Pharmacie, Université Mohammed V, Rabat, Maroc
| | - Amine Idriss Lahlou
- Unité de séquençage, Laboratoire de Virologie, Centre de Virologie, des Maladies Infectieuses et Tropicales, Hôpital Militaire d'Instruction Mohammed V, Faculté de Médecine et de Pharmacie, Université Mohammed V, Rabat, Maroc.,Centre de virologie, des maladies infectieuses et tropicales, Hôpital militaire d'Instruction Mohammed V, Faculté de Médecine et de Pharmacie, Université Mohammed V, Rabat, Maroc
| | - Jaouad Kouach
- Service de Gynécologie Obstétrique, Hôpital militaire d'Instruction Mohammed V, Faculté de Médecine et de Pharmacie, Université Mohammed V, Rabat, Maroc
| | - Khadija Benchekroune
- Service de Gynécologie Obstétrique, Hôpital militaire d'Instruction Mohammed V, Faculté de Médecine et de Pharmacie, Université Mohammed V, Rabat, Maroc
| | - Mohammed Oukabli
- Laboratoire d'Anatomopathologie, Hôpital militaire d'Instruction Mohammed V, Faculté de Médecine et de Pharmacie, Université Mohammed V, Rabat, Maroc
| | - Hafsa Chahdi
- Laboratoire d'Anatomopathologie, Hôpital militaire d'Instruction Mohammed V, Faculté de Médecine et de Pharmacie, Université Mohammed V, Rabat, Maroc
| | - Moulay Mustapha Ennaji
- Laboratoire de Virologie, Microbiologie, Qualité, Biotechnologies/Ecotoxicologie et Biodiversité, Faculté des sciences et techniques, Mohammadia, Université Hassan II, Casa, Maroc
| | - Rachid Tanz
- Service d'Oncologie Médicale, Hôpital militaire d'Instruction Mohammed V, Faculté de Médecine et de Pharmacie, Université Mohammed V, Rabat, Maroc
| | - Yassir Sbitti
- Service d'Oncologie Médicale, Hôpital militaire d'Instruction Mohammed V, Faculté de Médecine et de Pharmacie, Université Mohammed V, Rabat, Maroc
| | - Mohammed Ichou
- Service d'Oncologie Médicale, Hôpital militaire d'Instruction Mohammed V, Faculté de Médecine et de Pharmacie, Université Mohammed V, Rabat, Maroc
| | - Khalid Ennibi
- Unité de séquençage, Laboratoire de Virologie, Centre de Virologie, des Maladies Infectieuses et Tropicales, Hôpital Militaire d'Instruction Mohammed V, Faculté de Médecine et de Pharmacie, Université Mohammed V, Rabat, Maroc.,Centre de virologie, des maladies infectieuses et tropicales, Hôpital militaire d'Instruction Mohammed V, Faculté de Médecine et de Pharmacie, Université Mohammed V, Rabat, Maroc
| | - Bouabid Badaoui
- Laboratoire de Biodiversité, Ecologie et Génome, Faculté des Sciences, Université Mohammed V, Rabat, Maroc
| | - Yassine Sekhsokh
- Laboratoire de Recherche et de Biosécurité P3, Hôpital Militaire d'Instruction Mohammed V, Rabat, Maroc
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16
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Douglas MP, Lin GA, Trosman JR, Phillips KA. Hereditary cancer panel testing challenges and solutions for the latinx community: costs, access, and variants. J Community Genet 2022; 13:75-80. [PMID: 34743282 PMCID: PMC8799811 DOI: 10.1007/s12687-021-00563-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 10/28/2021] [Indexed: 11/29/2022] Open
Abstract
Hereditary breast and ovarian cancers (HBOCs) are common among the Latinx population, and risk testing is recommended using multi-gene hereditary cancer panels (HCPs). However, little is known about how payer reimbursement and out-of-pocket expenses impact provider ordering of HCP in the Latinx population. Our objective is to describe key challenges and possible solutions for HCP testing in the Latinx population. As part of a larger study, we conducted semi-structured interviews with key provider informants (genetic counselors, oncologist, nurse practitioner) from safety-net institutions in the San Francisco Bay Area. We used a deductive thematic analysis approach to summarize themes around challenges and possible solutions to facilitating HCP testing in Latinx patients. We found few financial barriers for HCP testing for the Latinx population due to laboratory patient assistance programs that cover testing at low or no cost to patients. However, we found potential challenges related to the sustainability of low-cost testing and out-of-pocket expenses for patients, access to cascade testing for family members, and pathogenic variants specific to Latinx. Providers questioned whether current laboratory payment programs that decrease barriers to testing are sustainable and suggested solutions for accessing cascade testing and ensuring variants specific to the Latinx population were included in testing. The use of laboratories with payment assistance programs reduces barriers to HCP testing among the US population; however, other barriers are present that may impact testing use in the Latinx population and must be addressed to ensure equitable access to HCP testing for this population.
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Affiliation(s)
- Michael P Douglas
- UCSF Center for Translational and Policy Research On Personalized Medicine (TRANSPERS), Department of Clinical Pharmacy, University of California San Francisco, 490 Illinois Street, 3rd Floor, Box 0613, San Francisco, CA, 94143, USA.
| | - Grace A Lin
- UCSF Center for Translational and Policy Research On Personalized Medicine (TRANSPERS), Department of Clinical Pharmacy, University of California San Francisco, 490 Illinois Street, 3rd Floor, Box 0613, San Francisco, CA, 94143, USA
- Department of Medicine, University of California, San Francisco, CA, USA
- Philip R. Lee Institute for Health Policy Studies, University of California, San Francisco, CA, USA
| | - Julia R Trosman
- UCSF Center for Translational and Policy Research On Personalized Medicine (TRANSPERS), Department of Clinical Pharmacy, University of California San Francisco, 490 Illinois Street, 3rd Floor, Box 0613, San Francisco, CA, 94143, USA
- Center for Business Models in Healthcare, Glencoe, IL, USA
| | - Kathryn A Phillips
- UCSF Center for Translational and Policy Research On Personalized Medicine (TRANSPERS), Department of Clinical Pharmacy, University of California San Francisco, 490 Illinois Street, 3rd Floor, Box 0613, San Francisco, CA, 94143, USA
- Philip R. Lee Institute for Health Policy Studies, University of California, San Francisco, CA, USA
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California-San Francisco, San Francisco, CA, USA
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17
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Identification of potential immunotherapy biomarkers for breast cancer by bioinformatics analysis. Biosci Rep 2022; 42:230663. [PMID: 35037689 PMCID: PMC8819662 DOI: 10.1042/bsr20212035] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 12/28/2021] [Accepted: 01/06/2022] [Indexed: 11/17/2022] Open
Abstract
Breast cancer is a serious malignancy with a high incidence worldwide and a tendency to relapse. We used integrated bioinformatics analysis to identify potential biomarkers in breast carcinoma in the present study. Microarray data, 127breast tumor samples and 23 non-tumor samples, received from the Gene Expression Omnibus (GEO) dataset; 121 differentially expressed genes (DEGs) were selected. Functional analysis using DAVID revealed that these DEGs were highly gathered in endodermal cell differentiation and proteinaceous extracellular matrix. Five bioactive compounds (prostaglandin J2, tanespimycin, semustine, 5182598, and flunarizine) were identified using Connectivity Map. We used Cytoscape software and STRING dataset to structure a protein–protein interaction (PPI) network. The expression of CD24, MMP1, SDC1, and SPP1 was much higher in breast carcinoma tissue than in Para cancerous tissues analyzed by Gene Expression Profiling Interactive Analysis (GEPIA) and ONCOMINE. Overexpression ofCD24, MMP1, SDC1, and SPP1 indicated the poor prognosis in breast carcinoma patients analyzed by Kaplan–Meier (KM) Plotter. Immunohistochemistry microarray was used to further confirm that protein expression of CD24, MMP1, SDC1, and SPP1 was much higher in tumor sections than in Para cancerous tissues. Hub genes expression at the protein level was correlated tothe breast cancer subtype and grade. Furthermore, immunity analysis showed that CD24, MMP1, SDC1, and SPP1 were potentially associated with five immune cell types infiltration (CD8+ T cells, CD4+ T cells, neutrophils, macrophages,and dendritic cells) by TIMER. Thus, this study indicates potential biomarkers that could have applications in the development of immune therapy for breast cancer. However, further studies are required for verifying these results in vivo and vitro.
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Double heterozygous pathogenic variants in the BRCA1 and BRCA2 genes in a patient with bilateral metachronous breast cancer. Cancer Genet 2021; 260-261:14-17. [PMID: 34801929 DOI: 10.1016/j.cancergen.2021.11.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 08/24/2021] [Accepted: 11/08/2021] [Indexed: 12/20/2022]
Abstract
Double heterozygosity pathogenic variants in BRCA1 and BRCA2 genes are a very rare finding, particularly in non-Ashkenazi individuals. We described the first case of double heterozygosity variants in a non-Ashkenazi Argentinean woman with metachronous bilateral breast cancer. The proband is a 65-year-old female diagnosed with invasive ductal carcinoma in the left breast at 45 years old and invasive carcinoma in the right breast at 65 years old. She underwent a multi-gene panel testing indicating the presence of two concurrent heterozygous germline deleterious variants NM_007300.4(BRCA1):c.4201C>T (p.Gln1401Ter), and NM_000059.3(BRCA2):c.5146_5149del (p.Tyr1716fs). . The patient's son (40 years-old) was found to have the inherited pathogenic variant in BRCA2 gene. There are few reports of double heterozygosity variants in BRCA1 and BRCA2 genes in Latin America. The two pathogenic variants identified in our patient have not been described together so far.
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19
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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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20
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Integrative analysis of DNA methylation and gene expression profiles identified potential breast cancer-specific diagnostic markers. Biosci Rep 2021; 40:224161. [PMID: 32412047 PMCID: PMC7263199 DOI: 10.1042/bsr20201053] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/13/2020] [Accepted: 05/14/2020] [Indexed: 12/14/2022] Open
Abstract
Breast cancer is a common malignant tumor among women whose prognosis is largely determined by the period and accuracy of diagnosis. We here propose to identify a robust DNA methylation-based breast cancer-specific diagnostic signature. Genome-wide DNA methylation and gene expression profiles of breast cancer patients along with their adjacent normal tissues from the Cancer Genome Atlas (TCGA) were obtained as the training set. CpGs that with significantly elevated methylation level in breast cancer than not only their adjacent normal tissues and the other ten common cancers from TCGA but also the healthy breast tissues from the Gene Expression Omnibus (GEO) were finally remained for logistic regression analysis. Another independent breast cancer DNA methylation dataset from GEO was used as the testing set. Lots of CpGs were hyper-methylated in breast cancer samples compared with adjacent normal tissues, which tend to be negatively correlated with gene expressions. Eight CpGs located at RIIAD1, ENPP2, ESPN, and ETS1, were finally retained. The diagnostic model was reliable in separating BRCA from normal samples. Besides, chromatin accessibility status of RIIAD1, ENPP2, ESPN and ETS1 showed great differences between MCF-7 and MDA-MB-231 cell lines. In conclusion, the present study should be helpful for breast cancer early and accurate diagnosis.
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21
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Jain A, Sharma D, Bajaj A, Gupta V, Scaria V. Founder variants and population genomes-Toward precision medicine. ADVANCES IN GENETICS 2021; 107:121-152. [PMID: 33641745 DOI: 10.1016/bs.adgen.2020.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Human migration and community specific cultural practices have contributed to founder events and enrichment of the variants associated with genetic diseases. While many founder events in isolated populations have remained uncharacterized, the application of genomics in clinical settings as well as for population scale studies in the recent years have provided an unprecedented push towards identification of founder variants associated with human health and disease. The discovery and characterization of founder variants could have far reaching implications not only in understanding the history or genealogy of the disease, but also in implementing evidence based policies and genetic testing frameworks. This further enables precise diagnosis and prevention in an attempt towards precision medicine. This review provides an overview of founder variants along with methods and resources cataloging them. We have also discussed the public health implications and examples of prevalent disease associated founder variants in specific populations.
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Affiliation(s)
- Abhinav Jain
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Disha Sharma
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Anjali Bajaj
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Vishu Gupta
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Vinod Scaria
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India.
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22
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Giornelli G, Gallardo D, Hegg R, Abuin GG, La Vega MD, Lim-Law M, Caceres V, Trujillo L, Pilar Estevez-Diz MD, Pacheco C, Sganga L, Goncalves S. FLABRA, frontline approach for BRCA testing in an ovarian cancer population: a Latin America epidemiologic study. Future Oncol 2021; 17:1601-1609. [PMID: 33415992 DOI: 10.2217/fon-2020-1152] [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: 11/21/2022] Open
Abstract
Aim: FLABRA evaluated the prevalence of BRCA mutations, genetic counseling and management approaches in patients with ovarian cancer in Latin America. Patients & methods: Patients with ovarian cancer from six Latin-American countries were enrolled. Tumor samples were tested for BRCA mutations (BRCAmut). In cases with BRCAmut, blood samples were analyzed to determine germline versus somatic mutations. Medical records were reviewed for counseling approach and treatment plan. Results: From 472 patients enrolled, 406 samples yielded conclusive results: 282 were BRCA wild-type (BRCAwt), 115 were BRCAmut and nine were variants of uncertain significance. In total, 110/115 were tested for germline mutations (77 germline and 33 somatic). Conclusion: Tumor testing to identify mutations in BRCA1/2 in ovarian cancer can help optimize treatment choices, meaning fewer patients require germline testing and genetic counseling, a scant resource in Latin America. Clinical trial registration: NCT02984423 (ClinicalTrials.gov).
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Affiliation(s)
- Gonzalo Giornelli
- Department of Oncology, Instituto Alexander Fleming, Buenos Aires, Argentina
| | - Dolores Gallardo
- Department of Medical Oncology, Hospital Nacional de Cancerología, Ciudad de México, México
| | | | | | - Maximo De La Vega
- Department of Internal Medicine, CEMIC (Centro de Educación Médica e Investigaciones Clínicas), Buenos Aires, Argentina
| | - Maria Lim-Law
- Centro Oncológico de Panamá, Hospital Santa Fe, Panamá, República de Panamá
| | - Valeria Caceres
- Department of Clinical Oncology, Instituto de Oncología Ángel H. Roffo, Buenos Aires, Argentina
| | - Lina Trujillo
- Clínica de Ginecología, Instituto Nacional de Cancerología, Bogotá, Colombia
| | - Maria Del Pilar Estevez-Diz
- Instituto do Câncer do Estado de São Paulo, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brasil
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23
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Five Italian Families with Two Mutations in BRCA Genes. Genes (Basel) 2020; 11:genes11121451. [PMID: 33287145 PMCID: PMC7761639 DOI: 10.3390/genes11121451] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 11/27/2020] [Accepted: 12/01/2020] [Indexed: 02/07/2023] Open
Abstract
Double heterozygosity (DH) in BRCA1 and BRCA2 genes and double mutation (DM) in BRCA1 or BRCA2 are extremely rare events in the general population, and few cases have been reported worldwide so far. Here, we describe five probands, all women, with breast and/or ovarian cancer and their families. Particularly, we identified two probands with DH in the BRCA1/2 genes with a frequency of 0.3% and three probands with DM in the BRCA2 gene with a frequency of 0.5%. The DH BRCA1 c.547+2T>A (IVS8+2T>A)/BRCA2 c.2830A>T (p.Lys944Ter) and BRCA1 c.3752_3755GTCT (p.Ser1253fs)/BRCA2 c.425+2T>C (IVS4+2T>C) have not been described together so far. The DM in BRCA2, c.631G>A (p.Val211Ile) and c.7008-2A>T (IVS13-2A>T), found in three unrelated probands, was previously reported in further unrelated patients. Due to its peculiarity, it is likely that both pathogenic variants descend from a common ancestor and, therefore, are founder mutations. Interestingly, analyzing the tumor types occurring in DH and DM families, we observed ovarian cancer only in DH families, probably due to the presence in DH patients of BRCA1 pathogenic variants, which predispose one more to ovarian cancer onset. Furthermore, male breast cancer and pancreatic cancer ensued in families with DM but not with DH. These data confirm that BRCA2 pathogenic variants have greater penetrance to develop breast cancer in men and are associated with an increased risk of pancreatic cancer.
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Shaw T, Chan SH, Teo JX, Chong ST, Li ST, Courtney E, Ishak D, Sankar H, Ang ZLT, Chiang J, Loh M, Zhou L, Lee SC, Yeh HY, Kolinjivadi AM, Lim WK, Ngeow J. Investigation into the origins of an ancient BRCA1 founder mutation identified among Chinese families in Singapore. Int J Cancer 2020; 148:637-645. [PMID: 32745242 DOI: 10.1002/ijc.33241] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 07/03/2020] [Accepted: 07/13/2020] [Indexed: 11/07/2022]
Abstract
Identification of ancestry-specific pathogenic variants is imperative for diagnostic, treatment, management and prevention strategies, and to understand penetrance/modifiers on risk. Our study aimed to determine the clinical significance of a recurrent BRCA1 c.442-22_442-13del variant of unknown significance identified among 13 carriers from six Chinese families, all with a significant history of breast and/or ovarian cancer. We further aimed to establish whether this was due to a founder effect and explore its origins. Haplotype analysis, using nine microsatellite markers encompassing 2.5 megabase pairs around the BRCA1 locus, identified a common haploblock specific to the variant carriers, confirming a founder effect. Variant age was estimated to date back 77.9 generations to 69 bc using the Gamma approach. On principal component analysis using single nucleotide polymorphisms merged with 1000 Genomes dataset, variant carriers were observed to overlap predominantly with the southern Han Chinese population. To determine pathogenicity of the variant, we assessed the functional effect on RAD51 foci formation as well as replication fork stability upon induction of DNA damage and observed an impaired DNA repair response associated with the variant. In summary, we identified an ancient Chinese founder mutation dating back 77.9 generations, possibly common among individuals of southern Han Chinese descent. Using evidence from phenotypic/family history studies, segregation analysis and functional characterization, the BRCA1 variant was reclassified from uncertain significance to pathogenic.
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Affiliation(s)
- Tarryn Shaw
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Sock Hoai Chan
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Jing Xian Teo
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore
| | - Siao Ting Chong
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Shao-Tzu Li
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Eliza Courtney
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Diana Ishak
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Haresh Sankar
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Zoe Li Ting Ang
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Jianbang Chiang
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Marie Loh
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore.,Department of Epidemiology and Biostatistics, Imperial College London, London, UK
| | - Li Zhou
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Soo Chin Lee
- Department of Haematology-Oncology, National University Cancer Institute Singapore, Singapore
| | - Hui-Yuan Yeh
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | | | - Weng Khong Lim
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore
| | - Joanne Ngeow
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore.,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
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25
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Tian Z, He W, Tang J, Liao X, Yang Q, Wu Y, Wu G. Identification of Important Modules and Biomarkers in Breast Cancer Based on WGCNA. Onco Targets Ther 2020; 13:6805-6817. [PMID: 32764968 PMCID: PMC7367932 DOI: 10.2147/ott.s258439] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 06/17/2020] [Indexed: 12/12/2022] Open
Abstract
Introduction Breast cancer (BRCA) has the highest incidence among female malignancies, and the prognosis for these patients remains poor. Materials and Methods In this study, core modules and central genes related to BRCA were identified through a weighted gene co-expression network analysis (WGCNA). Gene expression profiles and clinical data of GSE25066 were obtained from the Gene Expression Omnibus (GEO) database. The result was validated with RNA-seq data from The Cancer Genome Atlas (TCGA) and Oncomine database. The top 30 key module genes with the highest intramodule connectivity were selected as the core genes (R2 = 0.40). Results According to TCGA and Oncomine datasets, seven genes were selected as candidate hub genes. Following further experimental verification, four hub genes (FAM171A1, NDFIP1, SKP1, and REEP5) were retained. Conclusion We identified four hub genes as candidate biomarkers for BRCA. These hub genes may provide a theoretical basis for targeted therapy against BRCA.
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Affiliation(s)
- Zelin Tian
- Department of Thyroid and Breast Surgery, Zhongnan Hospital of Wuhan University, Wuhan, People's Republic of China
| | - Weixiang He
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, People's Republic of China
| | - Jianing Tang
- Department of Thyroid and Breast Surgery, Zhongnan Hospital of Wuhan University, Wuhan, People's Republic of China
| | - Xing Liao
- Department of Thyroid and Breast Surgery, Zhongnan Hospital of Wuhan University, Wuhan, People's Republic of China
| | - Qian Yang
- Department of Thyroid and Breast Surgery, Zhongnan Hospital of Wuhan University, Wuhan, People's Republic of China
| | - Yumin Wu
- Department of Thyroid and Breast Surgery, Zhongnan Hospital of Wuhan University, Wuhan, People's Republic of China
| | - Gaosong Wu
- Department of Thyroid and Breast Surgery, Zhongnan Hospital of Wuhan University, Wuhan, People's Republic of China
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26
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Gomes R, Soares BL, Felicio PS, Michelli R, Netto CBO, Alemar B, Ashton-Prolla P, Palmero EI, Moreira MÂM. Haplotypic characterization of BRCA1 c.5266dupC, the prevailing mutation in Brazilian hereditary breast/ovarian cancer. Genet Mol Biol 2020. [PMID: 32453342 PMCID: PMC7250276 DOI: 10.1590//1678-4685-gmb-2019-0072] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Specific pathogenic mutations associated with breast cancer development can vary between ethnical groups. One example is BRCA1 c.5266dupC that was first described as a founder mutation in the Ashkenazi Jewish population, but was later also found in other populations. In Brazil, this mutation corresponds to 20% of pathogenic BRCA1 variants reported. Our objective was to investigate the haplotype component of a group of Brazilian families who inherited c.5266dupC in the BRCA1 gene and to verify the ancestry contribution from European, African, and Amerindian origins. Fourteen probands carrying c.5266dupC and 16 relatives (carriers and non-carriers) were investigated. The same haplotype was observed segregating within all the families analyzed, revealing no recombinants in a region of 0.68 Mb. Ancestry analysis demonstrated that the European component was predominant among probands. The BRCA1 c.5266dupC analysis indicates that there was a founder effect in the Brazilian population.
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Affiliation(s)
- Renan Gomes
- Instituto Nacional de Câncer, Programa de Genética, Rio de Janeiro, RJ, Brazil
| | | | - Paula Silva Felicio
- Hospital de Cancer de Barretos, Centro de Pesquisa em Oncologia Molecular, Barretos, SP, Brazil
| | - Rodrigo Michelli
- Hospital de Cancer de Barretos, Centro de Pesquisa em Oncologia Molecular, Barretos, SP, Brazil
| | - Cristina B O Netto
- Hospital de Clínicas de Porto Alegre, Serviço de Genética Médica, Porto Alegre, RS, Brazil
| | - Barbara Alemar
- Hospital de Clínicas de Porto Alegre, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil.,Universidade Federal do Rio Grande do Sul (UFRGS), Departamento de Genética, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
| | - Patrícia Ashton-Prolla
- Hospital de Clínicas de Porto Alegre, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil.,Universidade Federal do Rio Grande do Sul (UFRGS), Departamento de Genética, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
| | - Edenir Inêz Palmero
- Hospital de Cancer de Barretos, Centro de Pesquisa em Oncologia Molecular, Barretos, SP, Brazil.,Faculdade de Ciências de Saúde de Barretos Dr. Paulo Prata (FACISB), Barretos, SP, Brazil
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27
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Gomes R, Soares BL, Felicio PS, Michelli R, Netto CBO, Alemar B, Ashton-Prolla P, Palmero EI, Moreira MÂM. Haplotypic characterization of BRCA1 c.5266dupC, the prevailing mutation in Brazilian hereditary breast/ovarian cancer. Genet Mol Biol 2020; 43:e20190072. [PMID: 32453342 PMCID: PMC7250276 DOI: 10.1590/1678-4685-gmb-2019-0072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 07/23/2019] [Indexed: 06/11/2023] Open
Abstract
Specific pathogenic mutations associated with breast cancer development can vary between ethnical groups. One example is BRCA1 c.5266dupC that was first described as a founder mutation in the Ashkenazi Jewish population, but was later also found in other populations. In Brazil, this mutation corresponds to 20% of pathogenic BRCA1 variants reported. Our objective was to investigate the haplotype component of a group of Brazilian families who inherited c.5266dupC in the BRCA1 gene and to verify the ancestry contribution from European, African, and Amerindian origins. Fourteen probands carrying c.5266dupC and 16 relatives (carriers and non-carriers) were investigated. The same haplotype was observed segregating within all the families analyzed, revealing no recombinants in a region of 0.68 Mb. Ancestry analysis demonstrated that the European component was predominant among probands. The BRCA1 c.5266dupC analysis indicates that there was a founder effect in the Brazilian population.
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Affiliation(s)
- Renan Gomes
- Instituto Nacional de Câncer, Programa de Genética, Rio de Janeiro,
RJ, Brazil
| | | | - Paula Silva Felicio
- Hospital de Cancer de Barretos, Centro de Pesquisa em Oncologia
Molecular, Barretos, SP, Brazil
| | - Rodrigo Michelli
- Hospital de Cancer de Barretos, Centro de Pesquisa em Oncologia
Molecular, Barretos, SP, Brazil
| | - Cristina B. O. Netto
- Hospital de Clínicas de Porto Alegre, Serviço de Genética Médica,
Porto Alegre, RS, Brazil
| | - Barbara Alemar
- Hospital de Clínicas de Porto Alegre, Laboratório de Medicina
Genômica, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul (UFRGS), Departamento de
Genética, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre,
RS, Brazil
| | - Patrícia Ashton-Prolla
- Hospital de Clínicas de Porto Alegre, Laboratório de Medicina
Genômica, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul (UFRGS), Departamento de
Genética, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre,
RS, Brazil
| | - Edenir Inêz Palmero
- Hospital de Cancer de Barretos, Centro de Pesquisa em Oncologia
Molecular, Barretos, SP, Brazil
- Faculdade de Ciências de Saúde de Barretos Dr. Paulo Prata (FACISB),
Barretos, SP, Brazil
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28
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Biancolella M, Testa B, Baghernajad Salehi L, D'Apice MR, Novelli G. Genetics and Genomics of Breast Cancer: update and translational perspectives. Semin Cancer Biol 2020; 72:27-35. [PMID: 32259642 DOI: 10.1016/j.semcancer.2020.03.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 03/12/2020] [Accepted: 03/24/2020] [Indexed: 02/07/2023]
Abstract
In the recent years the rapid scientific innovation in the evaluation of the individual's genome have allowed the identification of variants associated with the onset, treatment and prognosis of various pathologies including cancer, and with a potential impact in the assessment of therapy responses. Despite the analysis and interpretation of genomic information is considered incomplete, in many cases the identification of specific genomic profile has allowed the stratification of subgroups of patients characterized by a better response to drug therapies. Individual genome analysis has changed profoundly the diagnostic and therapeutic approach of breast cancer in the last 15 years by identifying selective molecular lesions that drive the development of neoplasms, showing that each tumor has its own genomic signature, with some specific features and some features common to several sub-types. Several personalized therapies have been (and still are being) developed showing a remarkable efficacy in the treatment of breast cancer.
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Affiliation(s)
| | - Barbara Testa
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, 00133, Rome, Italy
| | | | | | - Giuseppe Novelli
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, 00133, Rome, Italy; IRCCS Neuromed, Pozzilli, IS, Italy; Department of Pharmacology, School of Medicine, University of Nevada, Reno, NV, 89557, USA
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29
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Breast cancer in six families from Tolima and Huila: BRCA1 3450del4 mutation. ACTA ACUST UNITED AC 2020; 40:185-194. [PMID: 32220173 PMCID: PMC7357381 DOI: 10.7705/biomedica.4673] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Indexed: 12/22/2022]
Abstract
Introducción. El cáncer de mama es un problema mundial de salud pública; entre el 5 y el 10 % de los casos presentan agregación familiar, lo que se explicaría por la presencia de mutaciones en genes de alto riesgo como el BRCA1 y el BRCA2. El origen fundador de la deleción BRCA1 3450del4 en Colombia ya fue reportado. Objetivo. Hacer un análisis descriptivo de seis familias del del Tolima y del Huila con la deleción BRCA1 3450del4 de la asociación de la mutación germinal, con el cáncer de mama y la agregación familiar. Materiales y métodos. Se hizo un estudio descriptivo y transversal de seis casos índice con cáncer de mama positivos para BRCA1 3450del4, que cumplían tres de los criterios establecidos por Jalkh, et al. A partir de la información de las entrevistas, se realizaron los árboles genealógicos (GenoPro™, versión 2016). Se tipificó la mutación en familiares sanos y afectados que aceptaron participar. Resultados. De los 78 individuos seleccionados por conveniencia en las seis familias, 30 presentaron la mutación BRCA1 3450del4; de ellos, seis tenían cáncer de mama, uno, cáncer de ovario, uno, cáncer de mama y ovario, y otro, cáncer de próstata; 21 no presentaban neoplasias. De los 30 individuos portadores de la variante patogénica, seis eran hombres y 24 mujeres, 13 de ellas menores de 30 años. Conclusiones. En este estudio se confirmó la asociación de la deleción BRCA1 3450del4 con el cáncer de mama de agregación familiar.
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30
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Gomaa Mogahed SH, Hamed YS, Ibrahim Moursy YE, Mahomoud Saied MH. Analysis of Heterozygous BRCA1 5382ins Founder Mutation in a Cohort of Egyptian Breast Cancer Female Patients Using Pyrosequencing Technique. Asian Pac J Cancer Prev 2020; 21:431-438. [PMID: 32102521 PMCID: PMC7332123 DOI: 10.31557/apjcp.2020.21.2.431] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Up to half of the heritable mutations in breast cancer (BC) are attributed to BRCA1 and BRCA2 genes. The mutation prevalence is variable based on ethnicity and may be influenced by founder mutations. The aim of this pilot study is to determine for the first time, the prevalence of BRCA1 5382insC founder mutation in a cohort of Egyptian familial breast cancer patients (FBC). METHODS Female patients were selected to have familial type of breast cancer. Twenty healthy females were included as a control group. Peripheral blood samples were withdrawn from all studied females and were analyzed for BRCA1 5382insC founder mutation detection using pyrosequencing technique. RESULTS Eighty Egyptian FBC females were eligible to be enrolled in the study with a mean age of 48.31 ± 10.97years.We found a BRCA1 5382insC mutation carrier frequency of 5% of total studied FBC patients (4 out of 80 patients) with 95% confidence interval (1.61-12.99). There was a high statistical significant difference between carriers and non-carriers concerning the number of affected family members by BC, (p=0.001). Conclusion: BRCA1 5382insC founder mutation is not uncommon among Egyptian FBC females. The carrier frequency is comparable to that reported worldwide; however it is lower than those from previous Egyptian studies using different molecular techniques. The strong association between the mutation and the number of affected family members suggest wider screening of the mutation among high risk families using the reliable pyrosequencing technique.
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Affiliation(s)
- Salwa H Gomaa Mogahed
- Department of Chemical Pathology, Medical Research Institute, Alexandria University, Egypt
| | - Yasser S Hamed
- Department of Experimental and Clinical Surgery, Medical Research Institute, Alexandria University, Egypt
| | | | - Marwa H Mahomoud Saied
- Department of Chemical and Clinical Pathology, Faculty of Medicine, Alexandria University, Egypt
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Park HS, Ryu JM, Park JS, Im SA, Jung SY, Kim EK, Park WC, Min JW, Lee J, You JY, Lee JE, Kim SW. Clinicopathological Features of Patients with the BRCA1 c.5339T>C (p.Leu1780Pro) Variant. Cancer Res Treat 2020; 52:680-688. [PMID: 32019279 PMCID: PMC7373877 DOI: 10.4143/crt.2019.351] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 01/27/2020] [Indexed: 01/27/2023] Open
Abstract
PURPOSE Recent studies revealed the BRCA1 c.5339T>C, p.Leu1780Pro variant (L1780P) is highly suggested as a likely pathogenic. The aim of this study was to evaluate clinicopathologic features of L1780P with breast cancer (BC) using multicenter data from Korea to reinforce the evidence as a pathogenic mutation and to compare L1780P and other BRCA1/2mutations using Korean Hereditary Breast Cancer (KOHBRA) study data. Materials and Methods The data of 54 BC patients with L1780P variant from 10 institutions were collected and the clinicopathologic characteristics of the patients were reviewed. The hereditary breast and/or ovarian cancer-related characteristics of the L1780P variant were compared to those of BC patients in the KOHBRA study. RESULTS The median age of all patients was 38 years, and 75.9% of cases showed triple-negative breast cancer. Comparison of cases with L1780P to carriers from the KOHBRA study revealed that the L1780P patients group was more likely to have family history (FHx) of ovarian cancer (OC) (24.1% vs. 19.6% vs. 11.2%, p < 0.001 and p=0.001) and a personal history of OC (16.7% vs. 2.9% vs. 1.3%, p=0.003 and p=0.001) without significant difference in FHx of BC and bilateral BC. The cumulative risk of contralateral BC at 10 years after diagnosis was 31.9%, while the cumulative risk of OC at 50 years of age was 20.0%. Patients with L1780P showed similar features with BRCA1 carriers and showed higher penetrance of OC than patients with other BRCA1 mutations. CONCLUSION L1780P should be considered as a pathogenic mutation. Risk-reducing salpingo-oophorectomy is highly recommended for women with L1780P.
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Affiliation(s)
- Hyung Seok Park
- Department of Surgery, Yonsei University College of Medicine, Seoul, Korea
| | - Jai Min Ryu
- Department of Surgery, Samsung Comprehensive Cancer Center, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Ji Soo Park
- Cancer Prevention Center, Yonsei Cancer Center, Seoul, Korea
| | - Seock-Ah Im
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea.,Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - So-Youn Jung
- Center for Breast Cancer, National Cancer Center, Goyang, Korea
| | - Eun-Kyu Kim
- Department of Surgery, Seoul National University College of Medicine, Seoul, Korea.,Breast Care Center, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Woo-Chan Park
- Department of Surgery, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Jun Won Min
- Department of Surgery, Dankook University College of Medicine, Cheonan, Korea
| | - Jeeyeon Lee
- Department of Surgery, School of Medicine, Kyungpook National University, Daegu, Korea
| | - Ji Young You
- Division of Breast and Endocrine Surgery, Department of Surgery, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Korea
| | - Jeong Eon Lee
- Department of Surgery, Samsung Comprehensive Cancer Center, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Sung-Won Kim
- Department of Surgery, Breast Care Center, Daerim St. Mary's Hospital, Seoul, Korea
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Abul-Husn NS, Soper ER, Odgis JA, Cullina S, Bobo D, Moscati A, Rodriguez JE, Loos RJF, Cho JH, Belbin GM, Suckiel SA, Kenny EE. Exome sequencing reveals a high prevalence of BRCA1 and BRCA2 founder variants in a diverse population-based biobank. Genome Med 2019; 12:2. [PMID: 31892343 PMCID: PMC6938627 DOI: 10.1186/s13073-019-0691-1] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 11/13/2019] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Pathogenic variants in BRCA1 and BRCA2 (BRCA1/2) lead to increased risk of breast, ovarian, and other cancers, but most variant-positive individuals in the general population are unaware of their risk, and little is known about prevalence in non-European populations. We investigated BRCA1/2 prevalence and impact in the electronic health record (EHR)-linked BioMe Biobank in New York City. METHODS Exome sequence data from 30,223 adult BioMe participants were evaluated for pathogenic variants in BRCA1/2. Prevalence estimates were made in population groups defined by genetic ancestry and self-report. EHR data were used to evaluate clinical characteristics of variant-positive individuals. RESULTS There were 218 (0.7%) individuals harboring expected pathogenic variants, resulting in an overall prevalence of 1 in 139. The highest prevalence was in individuals with Ashkenazi Jewish (AJ; 1 in 49), Filipino and other Southeast Asian (1 in 81), and non-AJ European (1 in 103) ancestry. Among 218 variant-positive individuals, 112 (51.4%) harbored known founder variants: 80 had AJ founder variants (BRCA1 c.5266dupC and c.68_69delAG, and BRCA2 c.5946delT), 8 had a Puerto Rican founder variant (BRCA2 c.3922G>T), and 24 had one of 19 other founder variants. Non-European populations were more likely to harbor BRCA1/2 variants that were not classified in ClinVar or that had uncertain or conflicting evidence for pathogenicity (uncertain/conflicting). Within mixed ancestry populations, such as Hispanic/Latinos with genetic ancestry from Africa, Europe, and the Americas, there was a strong correlation between the proportion of African genetic ancestry and the likelihood of harboring an uncertain/conflicting variant. Approximately 28% of variant-positive individuals had a personal history, and 45% had a personal or family history of BRCA1/2-associated cancers. Approximately 27% of variant-positive individuals had prior clinical genetic testing for BRCA1/2. However, individuals with AJ founder variants were twice as likely to have had a clinical test (39%) than those with other pathogenic variants (20%). CONCLUSIONS These findings deepen our knowledge about BRCA1/2 variants and associated cancer risk in diverse populations, indicate a gap in knowledge about potential cancer-related variants in non-European populations, and suggest that genomic screening in diverse patient populations may be an effective tool to identify at-risk individuals.
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Affiliation(s)
- Noura S Abul-Husn
- The Center for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Emily R Soper
- The Center for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jacqueline A Odgis
- The Center for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sinead Cullina
- The Center for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Dean Bobo
- The Center for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Arden Moscati
- The Center for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jessica E Rodriguez
- The Center for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Judy H Cho
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gillian M Belbin
- The Center for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sabrina A Suckiel
- The Center for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eimear E Kenny
- The Center for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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Oliver J, Quezada Urban R, Franco Cortés CA, Díaz Velásquez CE, Montealegre Paez AL, Pacheco-Orozco RA, Castro Rojas C, García-Robles R, López Rivera JJ, Gaitán Chaparro S, Gómez AM, Suarez Obando F, Giraldo G, Maya MI, Hurtado-Villa P, Sanchez AI, Serrano N, Orduz Galvis AI, Aruachan S, Nuñez Castillo J, Frecha C, Riggi C, Jauk F, Gómez García EM, Carranza CL, Zamora V, Torres Mejía G, Romieu I, Castañeda CA, Castillo M, Gitler R, Antoniano A, Rojas Jiménez E, Romero Cruz LE, Vallejo Lecuona F, Delgado Enciso I, Martínez Rizo AB, Flores Carranza A, Benites Godinez V, Méndez Catalá CF, Herrera LA, Chirino YI, Terrazas LI, Perdomo S, Vaca Paniagua F. Latin American Study of Hereditary Breast and Ovarian Cancer LACAM: A Genomic Epidemiology Approach. Front Oncol 2019; 9:1429. [PMID: 31921681 PMCID: PMC6933010 DOI: 10.3389/fonc.2019.01429] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 12/02/2019] [Indexed: 12/29/2022] Open
Abstract
Purpose: Hereditary Breast and Ovarian Cancer (HBOC) syndrome is responsible for ~5-10% of all diagnosed breast and ovarian cancers. Breast cancer is the most common malignancy and the leading cause of cancer-related mortality among women in Latin America (LA). The main objective of this study was to develop a comprehensive understanding of the genomic epidemiology of HBOC throughout the establishment of The Latin American consortium for HBOC-LACAM, consisting of specialists from 5 countries in LA and the description of the genomic results from the first phase of the study. Methods: We have recruited 403 individuals that fulfilled the criteria for HBOC from 11 health institutions of Argentina, Colombia, Guatemala, Mexico and Peru. A pilot cohort of 222 individuals was analyzed by NGS gene panels. One hundred forty-three genes were selected on the basis of their putative role in susceptibility to different hereditary cancers. Libraries were sequenced in MiSeq (Illumina, Inc.) and PGM (Ion Torrent-Thermo Fisher Scientific) platforms. Results: The overall prevalence of pathogenic variants was 17% (38/222); the distribution spanned 14 genes and varied by country. The highest relative prevalence of pathogenic variants was found in patients from Argentina (25%, 14/57), followed by Mexico (18%, 12/68), Guatemala (16%, 3/19), and Colombia (13%, 10/78). Pathogenic variants were found in BRCA1 (20%) and BRCA2 (29%) genes. Pathogenic variants were found in other 12 genes, including high and moderate risk genes such as MSH2, MSH6, MUTYH, and PALB2. Additional pathogenic variants were found in HBOC unrelated genes such as DCLRE1C, WRN, PDE11A, and PDGFB. Conclusion: In this first phase of the project, we recruited 403 individuals and evaluated the germline genetic alterations in an initial cohort of 222 patients among 4 countries. Our data show for the first time in LA the distribution of pathogenic variants in a broad set of cancer susceptibility genes in HBOC. Even though we used extended gene panels, there was still a high proportion of patients without any detectable pathogenic variant, which emphasizes the larger, unexplored genetic nature of the disease in these populations.
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Affiliation(s)
- Javier Oliver
- Medical Oncology Service, Hospitales Universitarios Regional y Virgen de la Victoria, Institute of Biomedical Research in Malaga, CIMES, University of Málaga, Málaga, Spain
- Laboratorio de Secuenciación, Instituto de Medicina Traslacional e Ingeniería Biomédica, Hospital Italiano de Buenos Aires, Buenos Aires, Argentina
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla de Baz, Mexico
| | - Rosalía Quezada Urban
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla de Baz, Mexico
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, Tlalnepantla de Baz, Mexico
| | - Claudia Alejandra Franco Cortés
- Laboratorio de Secuenciación, Instituto de Medicina Traslacional e Ingeniería Biomédica, Hospital Italiano de Buenos Aires, Buenos Aires, Argentina
| | - Clara Estela Díaz Velásquez
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla de Baz, Mexico
| | - Ana Lorena Montealegre Paez
- Instituto de Nutrición, Genética y Metabolismo, Facultad de Medicina, Universidad El Bosque, Bogota, Colombia
| | | | - Carlos Castro Rojas
- Instituto de Nutrición, Genética y Metabolismo, Facultad de Medicina, Universidad El Bosque, Bogota, Colombia
| | - Reggie García-Robles
- Instituto de Nutrición, Genética y Metabolismo, Facultad de Medicina, Universidad El Bosque, Bogota, Colombia
| | - Juan Javier López Rivera
- Grupo INPAC, Organización Keralty, Departamento de Genética, Clínica Universitaria Colombia, Bogotá, Colombia
| | - Sandra Gaitán Chaparro
- Grupo INPAC, Organización Keralty, Facultad de Medicina, Fundación Universitaria Sanitas, Bogotá, Colombia
| | - Ana Milena Gómez
- Servicio de Genética, Hospital Universitario San Ignacio, Bogotá, Colombia
| | - Fernando Suarez Obando
- Servicio de Genética, Hospital Universitario San Ignacio, Bogotá, Colombia
- Instituto de Genética Humana, Facultad de Medicina, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Gustavo Giraldo
- Clínica Universitaria Bolivariana, Pontificia Universidad Bolivariana, Medellín, Colombia
| | - Maria Isabel Maya
- Clínica Universitaria Bolivariana, Pontificia Universidad Bolivariana, Medellín, Colombia
| | - Paula Hurtado-Villa
- Departamento Ciencias Básicas de Salud, Facultad de Ciencias de la Salud, Pontificia Universidad Javeriana Cali, Cali, Colombia
- Centro Médico Imbanaco, Cali, Colombia
| | - Ana Isabel Sanchez
- Centro Médico Imbanaco, Cali, Colombia
- Departamento Materno Infantil, Facultad de Ciencias de la Salud, Pontificia Universidad Javeriana Cali, Cali, Colombia
| | - Norma Serrano
- Fundación Cardiovascular de Colombia, Centro de Investigaciones, Floridablanca, Colombia
| | | | - Sandra Aruachan
- Departamento de Investigación y Estudios Clínicos, IMAT - Oncomédica S.A., Montería, Colombia
| | - Johanna Nuñez Castillo
- Departamento de Investigación y Estudios Clínicos, IMAT - Oncomédica S.A., Montería, Colombia
| | - Cecilia Frecha
- Instituto de Medicina Traslacional e Ingeniería Biomédica, CONICET-Instituto Universitario del Hospital Italiano-Hospital Italiano de Buenos Aires, Buenos Aires, Argentina
| | - Cecilia Riggi
- Servicio de Ginecología, Hospital Italiano de Buenos Aires, Buenos Aires, Argentina
| | - Federico Jauk
- Laboratorio de Secuenciación, Instituto de Medicina Traslacional e Ingeniería Biomédica, Hospital Italiano de Buenos Aires, Buenos Aires, Argentina
| | | | | | | | | | - Isabelle Romieu
- Instituto Nacional de Salud Pública, Cuernavaca, Mexico
- Hubert Department of Global Health, Emory University, Atlanta, GA, United States
| | - Carlos Arturo Castañeda
- Departamento de Oncología Médica, Instituto Nacional de Enfermedades Neoplásicas, Lima, Peru
| | - Miluska Castillo
- Departamento de Investigación, Instituto Nacional de Enfermedades Neoplásicas, Lima, Peru
| | | | | | - Ernesto Rojas Jiménez
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla de Baz, Mexico
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, Tlalnepantla de Baz, Mexico
| | - Luis Enrique Romero Cruz
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla de Baz, Mexico
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, Tlalnepantla de Baz, Mexico
| | - Fernando Vallejo Lecuona
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla de Baz, Mexico
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, Tlalnepantla de Baz, Mexico
| | | | | | | | | | - Claudia Fabiola Méndez Catalá
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla de Baz, Mexico
| | - Luis Alonso Herrera
- Unidad de Investigación Biomédica en Cáncer, Instituto de Investigaciones Biomédicas-Instituto Nacional de Cancerología, Ciudad de México, Mexico
| | - Yolanda Irasema Chirino
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, Tlalnepantla de Baz, Mexico
| | - Luis Ignacio Terrazas
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla de Baz, Mexico
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, Tlalnepantla de Baz, Mexico
| | - Sandra Perdomo
- Instituto de Nutrición, Genética y Metabolismo, Facultad de Medicina, Universidad El Bosque, Bogota, Colombia
- Departamento de Patología, Hospital Universitario Fundación Santa Fe de Bogotá, Bogota, Colombia
| | - Felipe Vaca Paniagua
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla de Baz, Mexico
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, Tlalnepantla de Baz, Mexico
- Instituto Nacional de Cancerología, Ciudad de México, Mexico
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Ivanov M, Ivanov M, Kasianov A, Rozhavskaya E, Musienko S, Baranova A, Mileyko V. Novel bioinformatics quality control metric for next-generation sequencing experiments in the clinical context. Nucleic Acids Res 2019; 47:e135. [PMID: 31511888 PMCID: PMC6868350 DOI: 10.1093/nar/gkz775] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 07/22/2019] [Accepted: 08/29/2019] [Indexed: 11/23/2022] Open
Abstract
As the use of next-generation sequencing (NGS) for the Mendelian diseases diagnosis is expanding, the performance of this method has to be improved in order to achieve higher quality. Typically, performance measures are considered to be designed in the context of each application and, therefore, account for a spectrum of clinically relevant variants. We present EphaGen, a new computational methodology for bioinformatics quality control (QC). Given a single NGS dataset in BAM format and a pre-compiled VCF-file of targeted clinically relevant variants it associates this dataset with a single arbiter parameter. Intrinsically, EphaGen estimates the probability to miss any variant from the defined spectrum within a particular NGS dataset. Such performance measure virtually resembles the diagnostic sensitivity of given NGS dataset. Here we present case studies of the use of EphaGen in context of BRCA1/2 and CFTR sequencing in a series of 14 runs across 43 blood samples and 504 publically available NGS datasets. EphaGen is superior to conventional bioinformatics metrics such as coverage depth and coverage uniformity. We recommend using this software as a QC step in NGS studies in the clinical context. Availability: https://github.com/m4merg/EphaGen or https://hub.docker.com/r/m4merg/ephagen.
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Affiliation(s)
- Maxim Ivanov
- Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russian Federation
| | - Mikhail Ivanov
- Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russian Federation
| | - Artem Kasianov
- Vavilov Institute of General Genetics, Moscow, Russian Federation
| | - Ekaterina Rozhavskaya
- Vavilov Institute of General Genetics, Moscow, Russian Federation.,Atlas Oncology Diagnostics, Ltd, Moscow, Russian Federation
| | | | - Ancha Baranova
- Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russian Federation.,Atlas Oncology Diagnostics, Ltd, Moscow, Russian Federation.,Research Centre for Medical Genetics, Moscow, Russian Federation.,School of Systems Biology, George Mason University, Fairfax, VA 22030, USA
| | - Vladislav Mileyko
- Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russian Federation.,Atlas Oncology Diagnostics, Ltd, Moscow, Russian Federation
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Urbina-Jara LK, Rojas-Martinez A, Martinez-Ledesma E, Aguilar D, Villarreal-Garza C, Ortiz-Lopez R. Landscape of Germline Mutations in DNA Repair Genes for Breast Cancer in Latin America: Opportunities for PARP-Like Inhibitors and Immunotherapy. Genes (Basel) 2019; 10:E786. [PMID: 31658756 PMCID: PMC6827033 DOI: 10.3390/genes10100786] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 09/28/2019] [Accepted: 10/04/2019] [Indexed: 12/24/2022] Open
Abstract
Germline mutations in BRCA1 and BRCA2 (BRCA1/2) genes are present in about 50% of cases of hereditary breast cancer. Proteins encoded by these genes are key players in DNA repair by homologous recombination (HR). Advances in next generation sequencing and gene panels for breast cancer testing have generated a large amount of data on gene variants implicated in hereditary breast cancer, particularly in genes such as PALB2, ATM, CHEK2, RAD51, MSH2, and BARD1. These genes are involved in DNA repair. Most of these variants have been reported for Caucasian, Jewish, and Asian population, with few reports for other communities, like those in Latin American (LA) countries. We reviewed 81 studies from 11 LA countries published between 2000 and 2019 but most of these studies focused on BRCA1/2 genes. In addition to these genes, breast cancer-related variants have been reported for PALB2, ATM, CHEK2, BARD1, MLH1, BRIP1, MSH2, NBN, MSH6, and PMS2 genes. Some of these variants are unique to LA populations. This analysis may contribute to enhance breast cancer variant characterization, and thus to find therapies and implement precision medicine for LA communities.
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Affiliation(s)
- Laura Keren Urbina-Jara
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey 64710, Mexico.
| | - Augusto Rojas-Martinez
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey 64710, Mexico.
| | | | - Dione Aguilar
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey 64710, Mexico.
- Tecnologico de Monterrey, Centro de Cancer de Mama, Hospital Zambrano Hellion, San Pedro Garza Garcia 66278, Mexico.
| | - Cynthia Villarreal-Garza
- Tecnologico de Monterrey, Centro de Cancer de Mama, Hospital Zambrano Hellion, San Pedro Garza Garcia 66278, Mexico.
- Instituto Nacional de Cancerologia, Departamento de Investigacion, Av. San Fernando #22, Tlalpan, Ciudad de Mexico 14080, Mexico.
| | - Rocio Ortiz-Lopez
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey 64710, Mexico.
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Fragoso-Ontiveros V, Velázquez-Aragón JA, Nuñez-Martínez PM, de la Luz Mejía-Aguayo M, Vidal-Millán S, Pedroza-Torres A, Sánchez-Contreras Y, Ramírez-Otero MA, Muñiz-Mendoza R, Domínguez-Ortíz J, Wegman-Ostrosky T, Bargalló-Rocha JE, Gallardo-Rincón D, Reynoso-Noveron N, Arriaga-Canon C, Meneses-García A, Herrera-Montalvo LA, Alvarez-Gomez RM. Mexican BRCA1 founder mutation: Shortening the gap in genetic assessment for hereditary breast and ovarian cancer patients. PLoS One 2019; 14:e0222709. [PMID: 31545835 PMCID: PMC6756553 DOI: 10.1371/journal.pone.0222709] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 09/05/2019] [Indexed: 12/19/2022] Open
Abstract
The deletion of exons 9 to 12 of BRCA1 (9-12 del BRCA1) is considered a founder mutation in the Mexican population. We evaluate the usefulness of the target detection of 9-12 del BRCA1 as the first molecular diagnostic strategy in patients with Hereditary Breast and Ovarian Cancer (HBOC). We performed the genetic assessment of 637 patients with suspected HBOC. The region corresponding to the breakpoints for the 9-12 del BRCA1 was amplified by polymerase chain reaction (PCR). An analysis of the clinical data of the carriers and non-carriers was done, searching for characteristics that correlated with the deletion. The 9-12 del BRCA1 was detected in 5% of patients with suspected HBOC (30/637). In patients diagnosed with ovarian cancer, 13 of 30 were 9-12 del BRCA1 carriers, which represents 43%. We found a significant association between the 9-12 del BRCA1 carriers with triple negative breast cancer and high-grade papillary serous ovarian cancer. We concluded that the detection of the 9-12 del BRCA1 is useful as a first molecular diagnostic strategy in the Mexican population. In particular, it shortens the gap in genetic assessment in patients with triple negative breast cancer and ovarian cancer.
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Zayas-Villanueva OA, Campos-Acevedo LD, Lugo-Trampe JDJ, Hernández-Barajas D, González-Guerrero JF, Noriega-Iriondo MF, Ramírez-Sánchez IA, Martínez-de-Villarreal LE. Analysis of the pathogenic variants of BRCA1 and BRCA2 using next-generation sequencing in women with familial breast cancer: a case-control study. BMC Cancer 2019; 19:722. [PMID: 31331294 PMCID: PMC6647062 DOI: 10.1186/s12885-019-5950-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 07/17/2019] [Indexed: 11/13/2022] Open
Abstract
Background Pathogenic variants (PVs) of BRCA genes entail a lifetime risk of developing breast cancer in 50–85% of carriers. Their prevalence in different populations has been previously reported. However, there is scarce information regarding the most common PVs of these genes in Latin-Americans. This study identified BRCA1 and BRCA2 PV frequency in a high-risk female population from Northeastern Mexico and determined the association of these mutations with the patients’ clinical and pathological characteristics. Methods Women were divided into three groups: aged ≤ 40 years at diagnosis and/or risk factors for hereditary breast cancer (n = 101), aged > 50 years with sporadic breast cancer (n = 22), and healthy women (n = 72). Their DNA was obtained from peripheral blood samples and the variants were examined by next-generation sequencing with Ion AmpliSeq BRCA1 and BRCA2 Panel using next-generation sequencing. Results PVs were detected in 13.8% group 1 patients (BRCA1, 12 patients; BRCA2, 2 patients). Only two patients in group 2 and none in group 3 exhibited BRCA1 PVs. Variants of uncertain significance were reported in 15.8% patients (n = 16). In group 1, patients with the triple-negative subtype, PV frequency was 40% (12/30). Breast cancer prevalence in young women examined in this study was higher than that reported by the National Cancer Institute Surveillance, Epidemiology (15.5% vs. 5.5%, respectively). Conclusions The detected BRCA1 and BRCA2 PV frequency was similar to that reported in other populations. Our results indicate that clinical data should be evaluated before genetic testing and highly recommend genetic testing in patients with the triple-negative subtype and other clinical aspects. Electronic supplementary material The online version of this article (10.1186/s12885-019-5950-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | - David Hernández-Barajas
- Department of Medical Oncology, Hospital Universitario "José E. González", Monterrey, Mexico
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Novel BRCA2 pathogenic variant c.5219 T > G; p.(Leu1740Ter) in a consanguineous Senegalese family with hereditary breast cancer. BMC MEDICAL GENETICS 2019; 20:73. [PMID: 31060517 PMCID: PMC6501405 DOI: 10.1186/s12881-019-0814-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 04/24/2019] [Indexed: 01/07/2023]
Abstract
Background Pathogenic variants associated with hereditary breast cancer have been reported for BRCA1 and BRCA2 (BRCA1/2) genes in patients from multiple ethnicities, but limited information is available from sub-Saharan African populations. We report a BRCA2 pathogenic variant in a Senegalese family with hereditary breast cancer. Methods An index case from a consanguineous family and nineteen healthy female relatives were recruited after informed consent. Along with this family, 14 other index cases with family history of breast cancer were also recruited. For the control populations we recruited 48 healthy women with no cancer diagnosis and 48 women diagnosed with sporadic breast cancer without family history. Genomic DNA was extracted from peripheral blood. All BRCA2 exons were amplified by PCR and sequenced. Sequences were compared to the BRCA2 GenBank reference sequence (NM_000059.3) using Alamut Software. Results We identified a novel nonsense pathogenic variant c.5219 T > G; p.(Leu1740Ter) in exon 11 of BRCA2 in the index case. The pathogenic variant was also identified in three sisters and one daughter, but was absent in the controls and unrelated cases. Conclusions This is the first report of a novel BRCA2 pathogenic variant in a Senegalese family with hereditary breast cancer. This result confirms the diversity of hereditary breast cancer pathogenic variants across populations and extends our knowledge of genetic susceptibility to breast cancer in Africa. Electronic supplementary material The online version of this article (10.1186/s12881-019-0814-y) contains supplementary material, which is available to authorized users.
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Adaniel C, Salinas F, Donaire JM, Bravo ME, Peralta O, Paredes H, Aliaga N, Sola A, Neira P, Behnke C, Rodriguez T, Torres S, Lopez F, Hurtado C. Non- BRCA1/2 Variants Detected in a High-Risk Chilean Cohort With a History of Breast and/or Ovarian Cancer. J Glob Oncol 2019; 5:1-14. [PMID: 31125277 PMCID: PMC6550094 DOI: 10.1200/jgo.18.00163] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/19/2019] [Indexed: 12/13/2022] Open
Abstract
METHODS Data were retrospectively collected from the registry of the High-Risk Breast and Ovarian Cancer Program at Clínica Las Condes, Santiago, Chile. Data captured included index case diagnosis, ancestry, family history, and genetic test results. RESULTS Three hundred fifteen individuals underwent genetic testing during the study period. The frequency of germline pathogenic and likely pathogenic variants in a breast or ovarian cancer predisposition gene was 20.3%. Of those patients who underwent testing with a panel of both high- and moderate-penetrance genes, 10.5% were found to have pathogenic or likely pathogenic variants in non-BRCA1/2 genes. CONCLUSION Testing for non-BRCA1 and -2 mutations may be clinically relevant for individuals who are suspected to have a hereditary breast or ovarian cancer syndrome in Chile. Comprehensive genetic testing of individuals who are at high risk is necessary to further characterize the genetic susceptibility to cancer in Chile.
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Affiliation(s)
- Christina Adaniel
- Programa de Alto Riesgo de Cáncer de Mama y Ovario, Clínica Las Condes, Santiago, Chile
| | - Francisca Salinas
- Programa de Alto Riesgo de Cáncer de Mama y Ovario, Clínica Las Condes, Santiago, Chile
| | - Juan Manuel Donaire
- Programa de Alto Riesgo de Cáncer de Mama y Ovario, Clínica Las Condes, Santiago, Chile
| | - Maria Eugenia Bravo
- Programa de Alto Riesgo de Cáncer de Mama y Ovario, Clínica Las Condes, Santiago, Chile
| | - Octavio Peralta
- Programa de Alto Riesgo de Cáncer de Mama y Ovario, Clínica Las Condes, Santiago, Chile
| | - Hernando Paredes
- Programa de Alto Riesgo de Cáncer de Mama y Ovario, Clínica Las Condes, Santiago, Chile
| | - Nuvia Aliaga
- Programa de Alto Riesgo de Cáncer de Mama y Ovario, Clínica Las Condes, Santiago, Chile
| | - Antonio Sola
- Programa de Alto Riesgo de Cáncer de Mama y Ovario, Clínica Las Condes, Santiago, Chile
| | - Paulina Neira
- Programa de Alto Riesgo de Cáncer de Mama y Ovario, Clínica Las Condes, Santiago, Chile
| | - Carolina Behnke
- Programa de Alto Riesgo de Cáncer de Mama y Ovario, Clínica Las Condes, Santiago, Chile
| | - Tulio Rodriguez
- Programa de Alto Riesgo de Cáncer de Mama y Ovario, Clínica Las Condes, Santiago, Chile
| | - Soledad Torres
- Programa de Alto Riesgo de Cáncer de Mama y Ovario, Clínica Las Condes, Santiago, Chile
| | - Francisco Lopez
- Programa de Alto Riesgo de Cáncer de Mama y Ovario, Clínica Las Condes, Santiago, Chile
| | - Claudia Hurtado
- Programa de Alto Riesgo de Cáncer de Mama y Ovario, Clínica Las Condes, Santiago, Chile
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Germline Missense Variants in BRCA1: New Trends and Challenges for Clinical Annotation. Cancers (Basel) 2019; 11:cancers11040522. [PMID: 31013702 PMCID: PMC6520942 DOI: 10.3390/cancers11040522] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 03/13/2019] [Accepted: 03/30/2019] [Indexed: 12/24/2022] Open
Abstract
Genetic testing allows for the identification of germline DNA variations, which are associated with a significant increase in the risk of developing breast cancer (BC) and ovarian cancer (OC). Detection of a BRCA1 or BRCA2 pathogenic variant triggers several clinical management actions, which may include increased surveillance and prophylactic surgery for healthy carriers or treatment with the PARP inhibitor therapy for carriers diagnosed with cancer. Thus, standardized validated criteria for the annotation of BRCA1 and BRCA2 variants according to their pathogenicity are necessary to support clinical decision-making and ensure improved outcomes. Upon detection, variants whose pathogenicity can be inferred by the genetic code are typically classified as pathogenic, likely pathogenic, likely benign, or benign. Variants whose impact on function cannot be directly inferred by the genetic code are labeled as variants of uncertain clinical significance (VUS) and are evaluated by multifactorial likelihood models that use personal and family history of cancer, segregation data, prediction tools, and co-occurrence with a pathogenic BRCA variant. Missense variants, coding alterations that replace a single amino acid residue with another, are a class of variants for which determination of clinical relevance is particularly challenging. Here, we discuss current issues in the missense variant classification by following a typical life cycle of a BRCA1 missense variant through detection, annotation and information dissemination. Advances in massively parallel sequencing have led to a substantial increase in VUS findings. Although the comprehensive assessment and classification of missense variants according to their pathogenicity remains the bottleneck, new developments in functional analysis, high throughput assays, data sharing, and statistical models are rapidly changing this scenario.
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Zavala VA, Serrano-Gomez SJ, Dutil J, Fejerman L. Genetic Epidemiology of Breast Cancer in Latin America. Genes (Basel) 2019; 10:E153. [PMID: 30781715 PMCID: PMC6410045 DOI: 10.3390/genes10020153] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 02/13/2019] [Accepted: 02/14/2019] [Indexed: 12/20/2022] Open
Abstract
The last 10 years witnessed an acceleration of our understanding of what genetic factors underpin the risk of breast cancer. Rare high- and moderate-penetrance variants such as those in the BRCA genes account for a small proportion of the familial risk of breast cancer. Low-penetrance alleles are expected to underlie the remaining heritability. By now, there are about 180 genetic polymorphisms that are associated with risk, most of them of modest effect. In combination, they can be used to identify women at the lowest or highest ends of the risk spectrum, which might lead to more efficient cancer prevention strategies. Most of these variants were discovered in populations of European descent. As a result, we might be failing to discover additional polymorphisms that could explain risk in other groups. This review highlights breast cancer genetic epidemiology studies conducted in Latin America, and summarizes the information that they provide, with special attention to similarities and differences with studies in other populations. It includes studies of common variants, as well as moderate- and high-penetrance variants. In addition, it addresses the gaps that need to be bridged in order to better understand breast cancer genetic risk in Latin America.
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Affiliation(s)
- Valentina A Zavala
- Department of Medicine, Division of General Internal Medicine, University of California San Francisco, San Francisco, CA 94143-1793, USA.
| | - Silvia J Serrano-Gomez
- Grupo de investigación en biología del cáncer, Instituto Nacional de Cancerología, Bogotá 11001000, Colombia.
| | - Julie Dutil
- Cancer Biology Division, Ponce Research Institute, Ponce Health Sciences University, Ponce, PR 00732, USA.
| | - Laura Fejerman
- Department of Medicine, Division of General Internal Medicine, University of California San Francisco, San Francisco, CA 94143-1793, USA.
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Pinto JA, Saravia CH, Flores C, Araujo JM, Martínez D, Schwarz LJ, Casas A, Bravo L, Zavaleta J, Chuima B, Alvarado H, Fujita R, Gómez HL. Precision medicine for locally advanced breast cancer: frontiers and challenges in Latin America. Ecancermedicalscience 2019; 13:896. [PMID: 30792813 PMCID: PMC6372295 DOI: 10.3332/ecancer.2019.896] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Indexed: 12/18/2022] Open
Abstract
Advances in high-throughput technologies and their involvement in the 'omics' of cancer have made possible the identification of hundreds of biomarkers and the development of predictive and prognostic platforms that model the management of cancer from evidence-based medicine to precision medicine. Latin America (LATAM) is a region characterised by fragmented healthcare, high rates of poverty and disparities to access to a basic standard of care not only for cancer but also for other complex diseases. Patients from the public setting cannot afford targeted therapy, the facilities offering genomic platforms are scarce and the use of high-precision radiotherapy is limited to few facilities. Despite the fact that LATAM oncologists are well-trained in the use of genomic platforms and constantly participate in genomic projects, a medical practice based in precision oncology is a great challenge and frequently limited to private practice. In breast cancer, we are waiting for the results of large basket trials to incorporate the detection of actionable mutations to select targeted treatments, in a similar way to the management of lung cancer. On the other hand and paradoxically, in the 'one fit is not for all' era, clinical and genomic studies continue grouping our patients under the single label 'Latin American' or 'Hispanic' despite the different ancestries and genomic backgrounds seen in the region. More regional cancer genomic initiatives and public availability of this data are needed in order to develop more precise oncology in locally advanced breast cancer.
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Affiliation(s)
- Joseph A Pinto
- Unidad de Investigación Básica y Traslacional, Oncosalud-AUNA, Lima 15036, Perú
| | - César H Saravia
- Unidad de Investigación Básica y Traslacional, Oncosalud-AUNA, Lima 15036, Perú
| | - Claudio Flores
- Unidad de Investigación Básica y Traslacional, Oncosalud-AUNA, Lima 15036, Perú
| | - Jhajaira M Araujo
- Unidad de Investigación Básica y Traslacional, Oncosalud-AUNA, Lima 15036, Perú
| | - David Martínez
- Departamento de Radioterapia, Oncosalud-AUNA, Lima 15036, Perú
| | - Luis J Schwarz
- Departamento de Medicina Oncológica, Oncosalud-AUNA, Lima 15036, Perú
| | - Alberto Casas
- Escuela Profesional de Medicina Humana, Universidad Privada San Juan Bautista, Lima 15067, Perú
| | - Leny Bravo
- Escuela Profesional de Medicina Humana, Universidad Privada San Juan Bautista, Lima 15067, Perú
| | - Jenny Zavaleta
- Escuela Profesional de Medicina Humana, Universidad Privada San Juan Bautista, Lima 15067, Perú
| | | | - Hober Alvarado
- Facultad de Ciencias Biológicas, Universidad Nacional San Luis Gonzaga de Ica, Ica 11004, Perú
| | - Ricardo Fujita
- Centro de Genética y Biología Molecular, Universidad de San Martín de Porres, Lima 15024, Perú
| | - Henry L Gómez
- Departamento de Medicina Oncológica, Oncosalud-AUNA, Lima 15036, Perú.,Departamento de Medicina Oncológica, Instituto Nacional de Enfermedades Neoplásicas, 15038, Perú
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Fernández-Lopez JC, Romero-Córdoba S, Rebollar-Vega R, Alfaro-Ruiz LA, Jiménez-Morales S, Beltrán-Anaya F, Arellano-Llamas R, Cedro-Tanda A, Rios-Romero M, Ramirez-Florencio M, Bautista-Piña V, Dominguez-Reyes C, Villegas-Carlos F, Tenorio-Torres A, Hidalgo-Miranda A. Population and breast cancer patients' analysis reveals the diversity of genomic variation of the BRCA genes in the Mexican population. Hum Genomics 2019; 13:3. [PMID: 30630528 PMCID: PMC6327376 DOI: 10.1186/s40246-018-0188-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 12/18/2018] [Indexed: 01/08/2023] Open
Abstract
Interpretation of variants of unknown significance (VUS) in genetic tests is complicated in ethnically diverse populations, given the lack of information regarding the common spectrum of genetic variation in clinically relevant genes. Public availability of data obtained from high-throughput genotyping and/or exome massive parallel sequencing (MPS)-based projects from several thousands of outbred samples might become useful tools to evaluate the pathogenicity of a VUS, based on its frequency in different populations. In the case of the Mexican and other Latino populations, several thousands of samples have been genotyped or sequenced during the last few years as part of different efforts to identify common variants associated to common diseases. In this report, we analyzed Mexican population data from a sample of 3985 outbred individuals, and additional 66 hereditary breast cancer patients were analyzed in order to better define the spectrum of common genomic variation of the BRCA1 and BRCA2 genes. Our analyses identified the most common genetic variants in these clinically relevant genes as well as the presence and frequency of specific pathogenic mutations present in the Mexican population. Analysis of the 3985 population samples by MPS identified three pathogenic mutations in BRCA1, only one population sample showed a BRCA1 exon 16-17 deletion by MLPA. This resulted in a basal prevalence of deleterious mutations of 0.10% (1:996) for BRCA1 and 11 pathogenic mutations in BRCA2, resulting in a basal prevalence of deleterious mutations of 0.276% (1:362) for BRCA2, combined of 0.376% (1:265). Separate analysis of the breast cancer patients identified the presence of pathogenic mutations in 18% (12 pathogenic mutations in 66 patients) of the samples by MPS and 13 additional alterations by MLPA. These results will support a better interpretation of clinical studies focused on the detection of BRCA mutations in Mexican and Latino populations and will help to define the general prevalence of deleterious mutations within these populations.
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Affiliation(s)
- J C Fernández-Lopez
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Perfiérico Sur, 4809, Arenal Tepepan, 14610, Mexico City, CP, Mexico
| | - S Romero-Córdoba
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Perfiérico Sur, 4809, Arenal Tepepan, 14610, Mexico City, CP, Mexico
| | - R Rebollar-Vega
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Perfiérico Sur, 4809, Arenal Tepepan, 14610, Mexico City, CP, Mexico
| | - L A Alfaro-Ruiz
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Perfiérico Sur, 4809, Arenal Tepepan, 14610, Mexico City, CP, Mexico
| | - S Jiménez-Morales
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Perfiérico Sur, 4809, Arenal Tepepan, 14610, Mexico City, CP, Mexico
| | - F Beltrán-Anaya
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Perfiérico Sur, 4809, Arenal Tepepan, 14610, Mexico City, CP, Mexico
| | - R Arellano-Llamas
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Perfiérico Sur, 4809, Arenal Tepepan, 14610, Mexico City, CP, Mexico
| | - A Cedro-Tanda
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Perfiérico Sur, 4809, Arenal Tepepan, 14610, Mexico City, CP, Mexico
| | - M Rios-Romero
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Perfiérico Sur, 4809, Arenal Tepepan, 14610, Mexico City, CP, Mexico
| | - M Ramirez-Florencio
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Perfiérico Sur, 4809, Arenal Tepepan, 14610, Mexico City, CP, Mexico
| | - V Bautista-Piña
- Instituto de Enfermedades la Mama FUCAM, Avenida El Bordo 100, Santa Ursula Coapa, 04980, Mexico City, CP, Mexico
| | - C Dominguez-Reyes
- Instituto de Enfermedades la Mama FUCAM, Avenida El Bordo 100, Santa Ursula Coapa, 04980, Mexico City, CP, Mexico
| | - F Villegas-Carlos
- Instituto de Enfermedades la Mama FUCAM, Avenida El Bordo 100, Santa Ursula Coapa, 04980, Mexico City, CP, Mexico
| | - A Tenorio-Torres
- Instituto de Enfermedades la Mama FUCAM, Avenida El Bordo 100, Santa Ursula Coapa, 04980, Mexico City, CP, Mexico
| | - A Hidalgo-Miranda
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Perfiérico Sur, 4809, Arenal Tepepan, 14610, Mexico City, CP, Mexico.
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Abstract
Germline mutations in BRCA1 and BRCA2 account for approximately 50% of inherited breast and ovarian cancers. Three founder mutations in BRCA1/2 have been reported in Colombia, but the pattern of mutations in other cancer susceptibility genes is unknown. This study describes the frequency and type of germline mutations in hereditary breast and/or ovarian cancer genes in a referral cancer center in Colombia. Eighty-five women referred to the oncogenetics unit of the Instituto de Cancerologia Las Americas in Medellin (Colombia), meeting testing criteria for hereditary breast and ovarian cancer syndrome (NCCN 2015), who had germline testing with a commercial 25-gene hereditary cancer panel, were included in the analysis. Nineteen patients (22.4%) carried a deleterious germline mutation in a cancer susceptibility gene: BRCA1 (7), BRCA2 (8), PALB2 (1), ATM (1), MSH2 (1) and PMS2 (1). The frequency of mutations in BRCA1/2 was 17.6%. One BRCA2 mutation (c.9246dupG) was recurrent in five non-related individuals and is not previously reported in the country. Seventeen mutation-carriers had a diagnosis of breast cancer (median age of diagnosis of 36 years) and two of ovarian cancer. All BRCA1 mutation-carriers with breast cancer had triple negative tumors (median age of diagnosis of 31 years). Variants of unknown significance were reported in 35% of test results. This is the first report of a multi-gene study for hereditary breast and/or ovarian cancer in a Latin American country. We found a high frequency and a wide spectrum of germline mutations in cancer susceptibility genes in Colombian patients, some of which were not previously reported in the country. We observed a very low frequency of known Colombian founder BRCA1/2 mutations (1.2%) and we found mutations in other genes such as PALB2, ATM, MSH2 and PMS2. Our results highlight the importance of performing multi-gene panel testing, including comprehensive BRCA1/2 analysis (full gene sequencing and large rearrangement analysis), in high-risk breast and/or ovarian cancer patients in Colombia.
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Cotrim DP, Ribeiro ARG, Paixão D, de Queiroz Soares DC, Jbili R, Pandolfi NC, Cezana C, de Cássia Mauro C, Mantoan H, Bovolim G, de Brot L, Torrezan GT, Carraro DM, Baiocchi G, da Cruz Formiga MN, da Costa AABA. Prevalence of BRCA1 and BRCA2 pathogenic and likely pathogenic variants in non-selected ovarian carcinoma patients in Brazil. BMC Cancer 2019; 19:4. [PMID: 30606148 PMCID: PMC6319008 DOI: 10.1186/s12885-018-5235-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 12/19/2018] [Indexed: 11/30/2022] Open
Abstract
Background BRCA1/2 pathogenic (P) and likely pathogenic (LP) germline variants are frequent among patients with ovarian carcinoma. However, these variants have not been extensively characterized in patients with ovarian cancer in Brazil. Methods In this retrospective study we evaluated clinical characteristics and BRCA1/2 genetic test results from patients with ovarian carcinoma who underwent genetic counseling at A.C.Camargo Cancer Center (Brazil) between 2015 and 2017 and had performed germline genetic testing of BRCA1/2 genes. Results Among 158 patients, 33 P and LP variants and were found (20.8%), 27 in BRCA1 and six in BRCA2, and six variants of unknown clinical significance (VUS). Thirteen percent of the patients did not have Multiplex Ligation-dependent Probe Amplification (MLPA) results. Three P variants in BRCA1 were found in more than one patient: c.5266dupC (p.Gln1756Profs*74), c.3331_3334delCAAG (p.Gln1111Asnfs5*), and c.211A > G (p.Arg71Gly). One LP variant in BRCA1 had not been previously described, c.4153_4154delCT (p.Leu1385Ilefs*5). Patients with previous diagnosis of breast cancer were carriers of P or LP variant in 8 of 12 cases (66.7%), and patients with a family history of ovarian or breast cancer in first- or second-degree relatives were carriers of P or LP variant in 26.7% of cases compared to 16.9% for patients without family history (p = 0.166). Conclusion Prevalence of BRCA1/2 germline P and LP variants is slightly higher than previously described by the largest occidental studies, with a high prevalence of variant c.5266dupC (p.Gln1756Profs*74) in BRCA1 observed. Moreover, we identified a new LP variant.
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Affiliation(s)
- Deborah Porto Cotrim
- Department of Medical Oncology, AC Camargo Cancer Center, Rua Professor Antonio Prudente 211, São Paulo, CEP: 01509-900, Brazil
| | | | - Daniele Paixão
- Department of Oncogenetics, AC Camargo Cancer Center, Rua Professor Antonio Prudente 211, São Paulo, CEP: 01509-900, Brazil
| | | | - Rima Jbili
- Department of Oncogenetics, AC Camargo Cancer Center, Rua Professor Antonio Prudente 211, São Paulo, CEP: 01509-900, Brazil
| | - Natasha Carvalho Pandolfi
- Department of Medical Oncology, AC Camargo Cancer Center, Rua Professor Antonio Prudente 211, São Paulo, CEP: 01509-900, Brazil
| | - Camila Cezana
- Department of Medical Oncology, AC Camargo Cancer Center, Rua Professor Antonio Prudente 211, São Paulo, CEP: 01509-900, Brazil
| | - Carine de Cássia Mauro
- Department of Medical Oncology, AC Camargo Cancer Center, Rua Professor Antonio Prudente 211, São Paulo, CEP: 01509-900, Brazil
| | - Henrique Mantoan
- Department of Gynecologic Oncology, AC Camargo Cancer Center, São Paulo, Brazil
| | - Graziele Bovolim
- Department of Pathology, AC Camargo Cancer Center, São Paulo, Brazil
| | - Louise de Brot
- Department of Pathology, AC Camargo Cancer Center, São Paulo, Brazil
| | | | - Dirce Maria Carraro
- Genomics and Molecular Biology Laboratory, AC Camargo Cancer Center, São Paulo, Brazil
| | - Glauco Baiocchi
- Department of Gynecologic Oncology, AC Camargo Cancer Center, São Paulo, Brazil
| | - Maria Nirvana da Cruz Formiga
- Department of Medical Oncology, AC Camargo Cancer Center, Rua Professor Antonio Prudente 211, São Paulo, CEP: 01509-900, Brazil.,Department of Oncogenetics, AC Camargo Cancer Center, Rua Professor Antonio Prudente 211, São Paulo, CEP: 01509-900, Brazil
| | - Alexandre A B A da Costa
- Department of Medical Oncology, AC Camargo Cancer Center, Rua Professor Antonio Prudente 211, São Paulo, CEP: 01509-900, Brazil. .,Department of Oncogenetics, AC Camargo Cancer Center, Rua Professor Antonio Prudente 211, São Paulo, CEP: 01509-900, Brazil.
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46
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Barrett R, Neben CL, Zimmer AD, Mishne G, McKennon W, Zhou AY, Ginsberg J. A scalable, aggregated genotypic-phenotypic database for human disease variation. Database (Oxford) 2019; 2019:5316668. [PMID: 30759220 PMCID: PMC6372842 DOI: 10.1093/database/baz013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 01/04/2019] [Accepted: 01/18/2019] [Indexed: 12/19/2022]
Abstract
Next generation sequencing multi-gene panels have greatly improved the diagnostic yield and cost effectiveness of genetic testing and are rapidly being integrated into the clinic for hereditary cancer risk. With this technology comes a dramatic increase in the volume, type and complexity of data. This invaluable data though is too often buried or inaccessible to researchers, especially to those without strong analytical or programming skills. To effectively share comprehensive, integrated genotypic-phenotypic data, we built Color Data, a publicly available, cloud-based database that supports broad access and data literacy. The database is composed of 50 000 individuals who were sequenced for 30 genes associated with hereditary cancer risk and provides useful information on allele frequency and variant classification, as well as associated phenotypic information such as demographics and personal and family history. Our user-friendly interface allows researchers to easily execute their own queries with filtering, and the results of queries can be shared and/or downloaded. The rapid and broad dissemination of these research results will help increase the value of, and reduce the waste in, scientific resources and data. Furthermore, the database is able to quickly scale and support integration of additional genes and human hereditary conditions. We hope that this database will help researchers and scientists explore genotype-phenotype correlations in hereditary cancer, identify novel variants for functional analysis and enable data-driven drug discovery and development.
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Affiliation(s)
- Ryan Barrett
- Color Genomics, 831 Mitten Road, Suite 100, Burlingame, CA, USA
| | - Cynthia L Neben
- Color Genomics, 831 Mitten Road, Suite 100, Burlingame, CA, USA
| | - Anjali D Zimmer
- Color Genomics, 831 Mitten Road, Suite 100, Burlingame, CA, USA
| | - Gilad Mishne
- Color Genomics, 831 Mitten Road, Suite 100, Burlingame, CA, USA
| | - Wendy McKennon
- Color Genomics, 831 Mitten Road, Suite 100, Burlingame, CA, USA
| | - Alicia Y Zhou
- Color Genomics, 831 Mitten Road, Suite 100, Burlingame, CA, USA
| | - Jeremy Ginsberg
- Color Genomics, 831 Mitten Road, Suite 100, Burlingame, CA, USA
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47
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Marques AM, Ananina G, Costa VP, de Vasconcellos JPC, de Melo MB. Estimating the age of the p.Cys433Arg variant in the MYOC gene in patients with primary open-angle glaucoma. PLoS One 2018; 13:e0207409. [PMID: 30444892 PMCID: PMC6239314 DOI: 10.1371/journal.pone.0207409] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 10/30/2018] [Indexed: 11/24/2022] Open
Abstract
The aim of this study was to estimate the age of the Cys433Arg (c.1297T>C, p.Cys433Arg) variant by comparing the genotypes of individuals affected and not affected by primary open angle glaucoma juvenile onset (JOAG). Our sample consisted of 35 JOAG-affected individuals from three families, 16 unrelated patients with the MYOC p.Cys433Arg variant and 16 unaffected individuals. Genomic DNA was amplified by PCR; nine short tandem repeats were genotyped through automated electrophoresis and three single nucleotide polymorphisms through Sanger sequencing. The determination of haplotypes was performed using Arlequin software and age estimation was performed using DMLE+ 2.3 and BDMC21 softwares. Four markers constituted the haplotypes associated with the p.Cys433Arg variant. The software DMLE+2.3 predicted an age of 43 generations for this variant with a 95% confidence interval ranging from 28 to 76 generations (560-1520 years) and BDMC21 predicted an age of 59 generations (1180 years) (95% CI: 40 to 100).
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Affiliation(s)
- Ana Maria Marques
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Galina Ananina
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Vital Paulino Costa
- Department of Ophthalmology and Otorhinolaryngology, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - José Paulo Cabral de Vasconcellos
- Department of Ophthalmology and Otorhinolaryngology, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Mônica Barbosa de Melo
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
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48
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Capillary electrophoresis as alternative method to detect tumor genetic mutations: the model built on the founder BRCA1 c.4964_4982del19 variant. Fam Cancer 2018; 18:29-35. [DOI: 10.1007/s10689-018-0094-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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49
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The germline mutational landscape of BRCA1 and BRCA2 in Brazil. Sci Rep 2018; 8:9188. [PMID: 29907814 PMCID: PMC6003960 DOI: 10.1038/s41598-018-27315-2] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 05/23/2018] [Indexed: 02/08/2023] Open
Abstract
The detection of germline mutations in BRCA1 and BRCA2 is essential to the formulation of clinical management strategies, and in Brazil, there is limited access to these services, mainly due to the costs/availability of genetic testing. Aiming at the identification of recurrent mutations that could be included in a low-cost mutation panel, used as a first screening approach, we compiled the testing reports of 649 probands with pathogenic/likely pathogenic variants referred to 28 public and private health care centers distributed across 11 Brazilian States. Overall, 126 and 103 distinct mutations were identified in BRCA1 and BRCA2, respectively. Twenty-six novel variants were reported from both genes, and BRCA2 showed higher mutational heterogeneity. Some recurrent mutations were reported exclusively in certain geographic regions, suggesting a founder effect. Our findings confirm that there is significant molecular heterogeneity in these genes among Brazilian carriers, while also suggesting that this heterogeneity precludes the use of screening protocols that include recurrent mutation testing only. This is the first study to show that profiles of recurrent mutations may be unique to different Brazilian regions. These data should be explored in larger regional cohorts to determine if screening with a panel of recurrent mutations would be effective.
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50
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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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