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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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Pantaleo A, Forte G, Fasano C, Lepore Signorile M, Sanese P, De Marco K, Di Nicola E, Latrofa M, Grossi V, Disciglio V, Simone C. Understanding the Genetic Landscape of Pancreatic Ductal Adenocarcinoma to Support Personalized Medicine: A Systematic Review. Cancers (Basel) 2023; 16:56. [PMID: 38201484 PMCID: PMC10778202 DOI: 10.3390/cancers16010056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/13/2023] [Accepted: 12/15/2023] [Indexed: 01/12/2024] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is one of the most fatal malignancies worldwide. While population-wide screening recommendations for PDAC in asymptomatic individuals are not achievable due to its relatively low incidence, pancreatic cancer surveillance programs are recommended for patients with germline causative variants in PDAC susceptibility genes or a strong family history. In this study, we sought to determine the prevalence and significance of germline alterations in major genes (ATM, BRCA1, BRCA2, CDKN2A, EPCAM, MLH1, MSH2, MSH6, PALB2, PMS2, STK11, TP53) involved in PDAC susceptibility. We performed a systematic review of PubMed publications reporting germline variants identified in these genes in PDAC patients. Overall, the retrieved articles included 1493 PDAC patients. A high proportion of these patients (n = 1225/1493, 82%) were found to harbor alterations in genes (ATM, BRCA1, BRCA2, PALB2) involved in the homologous recombination repair (HRR) pathway. Specifically, the remaining PDAC patients were reported to carry alterations in genes playing a role in other cancer pathways (CDKN2A, STK11, TP53; n = 181/1493, 12.1%) or in the mismatch repair (MMR) pathway (MLH1, MSH2, MSH6, PMS2; n = 87/1493, 5.8%). Our findings highlight the importance of germline genetic characterization in PDAC patients for better personalized targeted therapies, clinical management, and surveillance.
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Affiliation(s)
- Antonino Pantaleo
- Medical Genetics, National Institute of Gastroenterology-IRCCS “Saverio de Bellis” Research Hospital, 70013 Bari, Italy; (A.P.); (G.F.); (C.F.); (M.L.S.); (P.S.); (K.D.M.); (E.D.N.); (M.L.); (V.G.)
| | - Giovanna Forte
- Medical Genetics, National Institute of Gastroenterology-IRCCS “Saverio de Bellis” Research Hospital, 70013 Bari, Italy; (A.P.); (G.F.); (C.F.); (M.L.S.); (P.S.); (K.D.M.); (E.D.N.); (M.L.); (V.G.)
| | - Candida Fasano
- Medical Genetics, National Institute of Gastroenterology-IRCCS “Saverio de Bellis” Research Hospital, 70013 Bari, Italy; (A.P.); (G.F.); (C.F.); (M.L.S.); (P.S.); (K.D.M.); (E.D.N.); (M.L.); (V.G.)
| | - Martina Lepore Signorile
- Medical Genetics, National Institute of Gastroenterology-IRCCS “Saverio de Bellis” Research Hospital, 70013 Bari, Italy; (A.P.); (G.F.); (C.F.); (M.L.S.); (P.S.); (K.D.M.); (E.D.N.); (M.L.); (V.G.)
| | - Paola Sanese
- Medical Genetics, National Institute of Gastroenterology-IRCCS “Saverio de Bellis” Research Hospital, 70013 Bari, Italy; (A.P.); (G.F.); (C.F.); (M.L.S.); (P.S.); (K.D.M.); (E.D.N.); (M.L.); (V.G.)
| | - Katia De Marco
- Medical Genetics, National Institute of Gastroenterology-IRCCS “Saverio de Bellis” Research Hospital, 70013 Bari, Italy; (A.P.); (G.F.); (C.F.); (M.L.S.); (P.S.); (K.D.M.); (E.D.N.); (M.L.); (V.G.)
| | - Elisabetta Di Nicola
- Medical Genetics, National Institute of Gastroenterology-IRCCS “Saverio de Bellis” Research Hospital, 70013 Bari, Italy; (A.P.); (G.F.); (C.F.); (M.L.S.); (P.S.); (K.D.M.); (E.D.N.); (M.L.); (V.G.)
| | - Marialaura Latrofa
- Medical Genetics, National Institute of Gastroenterology-IRCCS “Saverio de Bellis” Research Hospital, 70013 Bari, Italy; (A.P.); (G.F.); (C.F.); (M.L.S.); (P.S.); (K.D.M.); (E.D.N.); (M.L.); (V.G.)
| | - Valentina Grossi
- Medical Genetics, National Institute of Gastroenterology-IRCCS “Saverio de Bellis” Research Hospital, 70013 Bari, Italy; (A.P.); (G.F.); (C.F.); (M.L.S.); (P.S.); (K.D.M.); (E.D.N.); (M.L.); (V.G.)
| | - Vittoria Disciglio
- Medical Genetics, National Institute of Gastroenterology-IRCCS “Saverio de Bellis” Research Hospital, 70013 Bari, Italy; (A.P.); (G.F.); (C.F.); (M.L.S.); (P.S.); (K.D.M.); (E.D.N.); (M.L.); (V.G.)
| | - Cristiano Simone
- Medical Genetics, National Institute of Gastroenterology-IRCCS “Saverio de Bellis” Research Hospital, 70013 Bari, Italy; (A.P.); (G.F.); (C.F.); (M.L.S.); (P.S.); (K.D.M.); (E.D.N.); (M.L.); (V.G.)
- Medical Genetics, Department of Precision and Regenerative Medicine and Jonic Area (DiMePRe-J), University of Bari Aldo Moro, 70124 Bari, Italy
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Morales-Pison S, Tapia JC, Morales-González S, Maldonado E, Acuña M, Calaf GM, Jara L. Association of Germline Variation in Driver Genes with Breast Cancer Risk in Chilean Population. Int J Mol Sci 2023; 24:16076. [PMID: 38003265 PMCID: PMC10671568 DOI: 10.3390/ijms242216076] [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: 09/27/2023] [Revised: 11/02/2023] [Accepted: 11/04/2023] [Indexed: 11/26/2023] Open
Abstract
Cancer is a genomic disease, with driver mutations contributing to tumorigenesis. These potentially heritable variants influence risk and underlie familial breast cancer (BC). This study evaluated associations between BC risk and 13 SNPs in driver genes MAP3K1, SF3B1, SMAD4, ARID2, ATR, KMT2C, MAP3K13, NCOR1, and TBX3, in BRCA1/2-negative Chilean families. SNPs were genotyped using TaqMan Assay in 492 cases and 1285 controls. There were no associations between rs75704921:C>T (ARID2); rs2229032:A>C (ATR); rs3735156:C>G (KMT2C); rs2276738:G>C, rs2293906:C>T, rs4075943T:>A, rs13091808:C>T (MAP3K13); rs178831:G>A (NCOR1); or rs3759173:C>A (TBX3) and risk. The MAP3K1 rs832583 A allele (C/A+A/A) showed a protective effect in families with moderate BC history (OR = 0.7 [95% CI 0.5-0.9] p = 0.01). SF3B1 rs16865677-T (G/T+T/T) increased risk in sporadic early-onset BC (OR = 1.4 [95% CI 1.0-2.0] p = 0.01). SMAD4 rs3819122-C (A/C+C/C) increased risk in cases with moderate family history (OR = 2.0 [95% CI 1.3-2.9] p ≤ 0.0001) and sporadic cases diagnosed ≤50 years (OR = 1.6 [95% CI 1.1-2.2] p = 0.006). SMAD4 rs12456284:A>G increased BC risk in G-allele carriers (A/G + G/G) in cases with ≥2 BC/OC cases and early-onset cases (OR = 1.2 [95% CI 1.0-1.6] p = 0.04 and OR = 1.4 [95% CI 1.0-1.9] p = 0.03, respectively). Our study suggests that specific germline variants in driver genes MAP3K1, SF3B1, and SMAD4 contribute to BC risk in Chilean population.
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Affiliation(s)
- Sebastián Morales-Pison
- Centro de Oncología de Precisión (COP), Facultad de Medicina y Ciencias de la Salud, Universidad Mayor, Las Condes, Santiago 7560908, Chile;
| | - Julio C. Tapia
- Laboratorio de Transformación Celular, Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas (ICBM), Facultad de Medicina, Universidad de Chile, Independencia, Santiago 783090, Chile;
| | - Sarai Morales-González
- Laboratorio de Genética Humana, Programa de Genética Humana, Instituto de Ciencias Biomédicas (ICBM), Facultad de Medicina, Universidad de Chile, Independencia, Santiago 783090, Chile; (S.M.-G.); (M.A.)
| | - Edio Maldonado
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas (ICBM), Facultad de Medicina, Universidad de Chile, Independencia, Santiago 783090, Chile;
| | - Mónica Acuña
- Laboratorio de Genética Humana, Programa de Genética Humana, Instituto de Ciencias Biomédicas (ICBM), Facultad de Medicina, Universidad de Chile, Independencia, Santiago 783090, Chile; (S.M.-G.); (M.A.)
| | - Gloria M. Calaf
- Instituto de Alta Investigación, Universidad de Tarapacá, Arica 1010069, Chile;
| | - Lilian Jara
- Laboratorio de Genética Humana, Programa de Genética Humana, Instituto de Ciencias Biomédicas (ICBM), Facultad de Medicina, Universidad de Chile, Independencia, Santiago 783090, Chile; (S.M.-G.); (M.A.)
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Ziyatdinov A, Torres J, Alegre-Díaz J, Backman J, Mbatchou J, Turner M, Gaynor SM, Joseph T, Zou Y, Liu D, Wade R, Staples J, Panea R, Popov A, Bai X, Balasubramanian S, Habegger L, Lanche R, Lopez A, Maxwell E, Jones M, García-Ortiz H, Ramirez-Reyes R, Santacruz-Benítez R, Nag A, Smith KR, Damask A, Lin N, Paulding C, Reppell M, Zöllner S, Jorgenson E, Salerno W, Petrovski S, Overton J, Reid J, Thornton TA, Abecasis G, Berumen J, Orozco-Orozco L, Collins R, Baras A, Hill MR, Emberson JR, Marchini J, Kuri-Morales P, Tapia-Conyer R. Genotyping, sequencing and analysis of 140,000 adults from Mexico City. Nature 2023; 622:784-793. [PMID: 37821707 PMCID: PMC10600010 DOI: 10.1038/s41586-023-06595-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 08/31/2023] [Indexed: 10/13/2023]
Abstract
The Mexico City Prospective Study is a prospective cohort of more than 150,000 adults recruited two decades ago from the urban districts of Coyoacán and Iztapalapa in Mexico City1. Here we generated genotype and exome-sequencing data for all individuals and whole-genome sequencing data for 9,950 selected individuals. We describe high levels of relatedness and substantial heterogeneity in ancestry composition across individuals. Most sequenced individuals had admixed Indigenous American, European and African ancestry, with extensive admixture from Indigenous populations in central, southern and southeastern Mexico. Indigenous Mexican segments of the genome had lower levels of coding variation but an excess of homozygous loss-of-function variants compared with segments of African and European origin. We estimated ancestry-specific allele frequencies at 142 million genomic variants, with an effective sample size of 91,856 for Indigenous Mexican ancestry at exome variants, all available through a public browser. Using whole-genome sequencing, we developed an imputation reference panel that outperforms existing panels at common variants in individuals with high proportions of central, southern and southeastern Indigenous Mexican ancestry. Our work illustrates the value of genetic studies in diverse populations and provides foundational imputation and allele frequency resources for future genetic studies in Mexico and in the United States, where the Hispanic/Latino population is predominantly of Mexican descent.
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Affiliation(s)
| | - Jason Torres
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK.
- MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK.
| | - Jesús Alegre-Díaz
- Experimental Research Unit from the Faculty of Medicine (UIME), National Autonomous University of Mexico (UNAM), Mexico City, Mexico
| | | | | | - Michael Turner
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
- Oxford Kidney Unit, Churchill Hospital, Oxford, UK
| | | | | | - Yuxin Zou
- Regeneron Genetics Center, Tarrytown, NY, USA
| | - Daren Liu
- Regeneron Genetics Center, Tarrytown, NY, USA
| | - Rachel Wade
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
- MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | | | | | - Alex Popov
- Regeneron Genetics Center, Tarrytown, NY, USA
| | | | | | | | | | - Alex Lopez
- Regeneron Genetics Center, Tarrytown, NY, USA
| | | | | | | | - Raul Ramirez-Reyes
- Experimental Research Unit from the Faculty of Medicine (UIME), National Autonomous University of Mexico (UNAM), Mexico City, Mexico
| | - Rogelio Santacruz-Benítez
- Experimental Research Unit from the Faculty of Medicine (UIME), National Autonomous University of Mexico (UNAM), Mexico City, Mexico
| | - Abhishek Nag
- Centre for Genomics Research, Discovery Sciences, Research and Development Biopharmaceuticals, AstraZeneca, Cambridge, UK
| | - Katherine R Smith
- Centre for Genomics Research, Discovery Sciences, Research and Development Biopharmaceuticals, AstraZeneca, Cambridge, UK
| | - Amy Damask
- Regeneron Genetics Center, Tarrytown, NY, USA
| | - Nan Lin
- Regeneron Genetics Center, Tarrytown, NY, USA
| | | | | | - Sebastian Zöllner
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | | | | | - Slavé Petrovski
- Centre for Genomics Research, Discovery Sciences, Research and Development Biopharmaceuticals, AstraZeneca, Cambridge, UK
| | | | | | | | | | - Jaime Berumen
- Experimental Research Unit from the Faculty of Medicine (UIME), National Autonomous University of Mexico (UNAM), Mexico City, Mexico
| | | | - Rory Collins
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Aris Baras
- Regeneron Genetics Center, Tarrytown, NY, USA
| | - Michael R Hill
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
- MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Jonathan R Emberson
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
- MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | | | - Pablo Kuri-Morales
- Instituto Tecnológico y de Estudios Superiores de Monterrey, Monterrey, Mexico
- Faculty of Medicine, National Autonomous University of Mexico, Mexico City, Mexico
| | - Roberto Tapia-Conyer
- Faculty of Medicine, National Autonomous University of Mexico, Mexico City, Mexico.
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Ahmad O, Sutter C, Hirsch S, Pfister SM, Schaaf CP. BRCA1/2 potential founder variants in the Jordanian population: an opportunity for a customized screening panel. Hered Cancer Clin Pract 2023; 21:11. [PMID: 37400873 DOI: 10.1186/s13053-023-00256-2] [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: 03/01/2023] [Accepted: 06/22/2023] [Indexed: 07/05/2023] Open
Abstract
A founder variant is a genetic alteration, that is inherited from a common ancestor together with a surrounding chromosomal segment, and is observed at a high frequency in a defined population. This founder effect occurs as a consequence of long-standing inbreeding of isolated populations. For high-risk cancer predisposition genes, such as BRCA1/2, the identification of founder variants in a certain population could help designing customized cost-effective cancer screening panels. This advantage has been best utilized in designing a customized breast cancer BRCA screening panel for the Ashkenazi Jews (AJ) population, composed of the three BRCA founder variants which account for approximately 90% of identified BRCA alterations. Indeed, the high prevalence of pathogenic BRCA1/2 variants among AJ (~ 2%) has additionally contributed to make population-based screening cost-effective in comparison to family-history-based screening. In Jordan there are multiple demographic characteristics supporting the proposal of a founder effect. A high consanguinity rate of ~ 57% in the nineties of the last century and ~ 30% more recently is a prominent factor, in addition to inbreeding which is often practiced by different sub-populations of the country.This review explains the concept of founder effect, then applies it to analyze published Jordanian BRCA variants, and concludes that nine pathogenic (P) and likely pathogenic (LP) BRCA2 variants together with one pathogenic BRCA1 variant are potential founder variants. Together they make up 43% and 55% of all identified BRCA1/2 alterations in the two largest studied cohorts of young patients and high-risk patients respectively. These variants were identified based on being recurrent and either specific to ethnic groups or being novel. In addition, the report highlights the required testing methodologies to validate these findings, and proposes a health economic evaluation model to test cost-effectiveness of a population-based customized BRCA screening panel for the Jordanian population. The aim of this report is to highlight the potential utilization of founder variants in establishing customized cancer predisposition services, in order to encourage more population-based genomic studies in Jordan and similar populations.
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Affiliation(s)
- Olfat Ahmad
- Division of Pediatric Neurooncology, Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
- University of Oxford, Oxford, UK
- King Hussein Cancer Center (KHCC), Amman, Jordan
| | - Christian Sutter
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Steffen Hirsch
- Division of Pediatric Neurooncology, Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Stefan M Pfister
- Division of Pediatric Neurooncology, Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Christian P Schaaf
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany.
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Acevedo F, Walbaum B, Camus M, Manzor M, Muñiz S, Medina L, Petric M, Reyes P, Domínguez F, Puschel K, Merino T, Bravo ML, Pinto MP, Ibáñez C, Hughes K, Sánchez C. Access disparities and underutilization of germline genetic testing in Chilean breast cancer patients. Breast Cancer Res Treat 2023; 199:363-370. [PMID: 36988750 DOI: 10.1007/s10549-023-06909-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 03/04/2023] [Indexed: 03/30/2023]
Abstract
PURPOSE Latin American reports on genetic cancer risk assessments are scarce. In Chile, current breast cancer (BC) guidelines do not define strategies for germline genetic testing. Our study sought to quantify the disparities in access to genetic testing in Chilean BC patients, according to international standards and their clinical characteristics to explore improvement strategies. METHODS Retrospective analysis of invasive BC databases including patients treated in a Public Hospital (PH) and in an Academic Private Center (AC) in Santiago, Chile between 2012 and 2021. RESULTS Of 5438 BC patients, 3955 had enough data for National Comprehensive Cancer Network (NCCN) categorization. From these, 1911 (48.3%) fulfilled NCCN criteria for germline testing, of whom, 300 were tested for germline mutations and 268 with multigene panels. A total of 65 pathogenic variants were found in this subset. As expected, BRCA1/2 mutations were the most frequent (17.7%). Access to genetic testing was higher in AC versus PH (19.6% vs. 10.3%, p = 0.0001). Other variables associated with germline genetic testing were BC diagnosis after 2018, being 45 years old or younger at diagnosis, BC family history (FH), FH of ovarian cancer, non-metastatic disease, and triple-negative subtype. CONCLUSION In our cohort, 15% of BC patients who met NCCN criteria for germline testing were effectively tested. This percentage was even lower at the PH. Current recommendations encourage universal genetic testing for BC patients; however, our findings suggest that Chile is far from reaching such a goal and national guidelines in this regard are urgently needed. To our knowledge, this is the first study of its kind in Chile and Latin America.
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Affiliation(s)
- Francisco Acevedo
- Departamento de Hematología-Oncología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Diagonal Paraguay 362, 8330077, Santiago, Chile
- Fundación Chile Sin Cáncer, Santiago, Chile
| | - Benjamín Walbaum
- Departamento de Hematología-Oncología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Diagonal Paraguay 362, 8330077, Santiago, Chile
- Fundación Chile Sin Cáncer, Santiago, Chile
| | - Mauricio Camus
- Departamento de Cirugía Oncológica, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Manuel Manzor
- Cirugía Oncológica, Hospital Dr. Sótero del Río, Santiago, Chile
| | - Sabrina Muñiz
- Departamento de Hematología-Oncología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Diagonal Paraguay 362, 8330077, Santiago, Chile
| | - Lidia Medina
- Centro de Cáncer, Red de Salud UC Christus, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Militza Petric
- Cirugía Oncológica, Hospital Gustavo Fricke, Valparaíso, Chile
| | - Paula Reyes
- Departamento de Hematología-Oncología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Diagonal Paraguay 362, 8330077, Santiago, Chile
| | - Francisco Domínguez
- Departamento de Cirugía Oncológica, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Klaus Puschel
- Departamento de Medicina Familiar, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Tomas Merino
- Departamento de Hematología-Oncología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Diagonal Paraguay 362, 8330077, Santiago, Chile
| | - M Loreto Bravo
- Support Team for Oncological Research and Medicine (STORM), Providencia, Santiago, Chile
| | - Mauricio P Pinto
- Support Team for Oncological Research and Medicine (STORM), Providencia, Santiago, Chile
| | - Carolina Ibáñez
- Departamento de Hematología-Oncología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Diagonal Paraguay 362, 8330077, Santiago, Chile
| | - Kevin Hughes
- Division of Oncologic & Endocrine Surgery, Medical University of South Carolina, Charleston, SC, USA
| | - César Sánchez
- Departamento de Hematología-Oncología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Diagonal Paraguay 362, 8330077, Santiago, Chile.
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7
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Yanus GA, Savonevich EL, Sokolenko AP, Romanko AA, Ni VI, Bakaeva EK, Gorustovich OA, Bizin IV, Imyanitov EN. Founder vs. non-founder BRCA1/2 pathogenic alleles: the analysis of Belarusian breast and ovarian cancer patients and review of other studies on ethnically homogenous populations. Fam Cancer 2023; 22:19-30. [PMID: 35596902 DOI: 10.1007/s10689-022-00296-y] [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: 04/20/2022] [Accepted: 05/08/2022] [Indexed: 01/13/2023]
Abstract
The spectrum of BRCA1/2 mutations demonstrates significant interethnic variations. We analyzed for the first time the entire BRCA1/2 coding region in 340 Belarusian cancer patients with clinical signs of BRCA1/2-related disease, including 168 women with bilateral and/or early-onset breast cancer (BC), 104 patients with ovarian cancer and 68 subjects with multiple primary malignancies involving BC and/or OC. BRCA1/2 pathogenic alleles were detected in 98 (29%) women, with 67 (68%) of these being represented by founder alleles. Systematic comparison with other relevant studies revealed that the founder effect observed in Belarus is among the highest estimates observed worldwide. These findings are surprising, given that the population of Belarus did not experience geographic or cultural isolation throughout history.
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Affiliation(s)
- G A Yanus
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, Saint-Petersburg, Russia
| | - E L Savonevich
- Department of Obstetrics and Gynecology, Grodno State Medical University, Grodno, Belarus
| | - A P Sokolenko
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, Saint-Petersburg, Russia. .,Department of Medical Genetics, St.-Petersburg Pediatric Medical University, Saint-Petersburg, Russia.
| | - A A Romanko
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, Saint-Petersburg, Russia.,Department of Medical Genetics, St.-Petersburg Pediatric Medical University, Saint-Petersburg, Russia
| | - V I Ni
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, Saint-Petersburg, Russia
| | - E Kh Bakaeva
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, Saint-Petersburg, Russia
| | - O A Gorustovich
- Department of Obstetrics and Gynecology, Grodno State Medical University, Grodno, Belarus
| | - I V Bizin
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, Saint-Petersburg, Russia
| | - E N Imyanitov
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, Saint-Petersburg, Russia.,Department of Medical Genetics, St.-Petersburg Pediatric Medical University, Saint-Petersburg, Russia.,Department of Oncology, I.I. Mechnikov North-Western Medical University, St.-Petersburg, Russia
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8
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Dalby A, Mezzano D, Rivera J, Watson SP, Morgan NV. Introduction of an ancient founder glycoprotein VI mutation into the Chilean population. Blood Adv 2022; 6:5866-5869. [PMID: 35994634 PMCID: PMC9647427 DOI: 10.1182/bloodadvances.2022008531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 08/10/2022] [Indexed: 11/27/2022] Open
Affiliation(s)
- Amanda Dalby
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Diego Mezzano
- Laboratorio de Hemostasia, Pontificia Universidad de Chile, Santiago, Chile
| | - José Rivera
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, IMIB-Arrixaca, CIBERER-U765, Grupo Español de Alteraciones Plaquetarias Congénitas (GEAPC), Murcia, Spain
| | - Steve P. Watson
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Neil V. Morgan
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
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9
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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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10
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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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11
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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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12
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Kozlov AP. Mammalian tumor-like organs. 1. The role of tumor-like normal organs and atypical tumor organs in the evolution of development (carcino-evo-devo). Infect Agent Cancer 2022; 17:2. [PMID: 35012580 PMCID: PMC8751115 DOI: 10.1186/s13027-021-00412-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 12/23/2021] [Indexed: 12/24/2022] Open
Abstract
Background Earlier I hypothesized that hereditary tumors might participate in the evolution of multicellular organisms. I formulated the hypothesis of evolution by tumor neofunctionalization, which suggested that the evolutionary role of hereditary tumors might consist in supplying evolving multicellular organisms with extra cell masses for the expression of evolutionarily novel genes and the origin of new cell types, tissues, and organs. A new theory—the carcino-evo-devo theory—has been developed based on this hypothesis. Main text My lab has confirmed several non-trivial predictions of this theory. Another non-trivial prediction is that evolutionarily new organs if they originated from hereditary tumors or tumor-like structures, should recapitulate some tumor features in their development. This paper reviews the tumor-like features of evolutionarily novel organs. It turns out that evolutionarily new organs such as the eutherian placenta, mammary gland, prostate, the infantile human brain, and hoods of goldfishes indeed have many features of tumors. I suggested calling normal organs, which have many tumor features, the tumor-like organs. Conclusion Tumor-like organs might originate from hereditary atypical tumor organs and represent the part of carcino-evo-devo relationships, i.e., coevolution of normal and neoplastic development. During subsequent evolution, tumor-like organs may lose the features of tumors and the high incidence of cancer and become normal organs without (or with almost no) tumor features.
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Affiliation(s)
- A P Kozlov
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 3, Gubkina Street, Moscow, Russia, 117971. .,Peter the Great St. Petersburg Polytechnic University, 29, Polytekhnicheskaya Street, St. Petersburg, Russia, 195251.
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13
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Luo X, Liu Q, Jiang J, Tang W, Ding Y, Zhou L, Yu J, Tang X, An Y, Zhao X. Characterization of a Cohort of Patients With LIG4 Deficiency Reveals the Founder Effect of p.R278L, Unique to the Chinese Population. Front Immunol 2021; 12:695993. [PMID: 34630384 PMCID: PMC8498043 DOI: 10.3389/fimmu.2021.695993] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 09/06/2021] [Indexed: 01/13/2023] Open
Abstract
DNA ligase IV (LIG4) deficiency is an extremely rare autosomal recessive primary immunodeficiency disease caused by mutations in LIG4. Patients suffer from a broad spectrum of clinical problems, including microcephaly, growth retardation, developmental delay, dysmorphic facial features, combined immunodeficiency, and a predisposition to autoimmune diseases and malignancy. In this study, the clinical, molecular, and immunological characteristics of 15 Chinese patients with LIG4 deficiency are summarized in detail. p.R278L (c.833G>T) is a unique mutation site present in the majority of Chinese cases. We conducted pedigree and haplotype analyses to examine the founder effect of this mutation site in China. This suggests that implementation of protocols for genetic diagnosis and for genetic counseling of affected pedigrees is essential. Also, the search might help determine the migration pathways of populations with Asian ancestry.
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Affiliation(s)
- Xianze Luo
- National Clinical Research Center for Child Health and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Child Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Qing Liu
- National Clinical Research Center for Child Health and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Child Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Jinqiu Jiang
- National Clinical Research Center for Child Health and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Child Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Wenjing Tang
- National Clinical Research Center for Child Health and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Child Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, China.,Department of Rheumatism and Immunology, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Yuan Ding
- National Clinical Research Center for Child Health and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Child Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, China.,Department of Healthy Examination Center, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Lina Zhou
- National Clinical Research Center for Child Health and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Child Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Jie Yu
- National Clinical Research Center for Child Health and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,Department of Hematological Oncology, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Xuemei Tang
- National Clinical Research Center for Child Health and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Child Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, China.,Department of Rheumatism and Immunology, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Yunfei An
- National Clinical Research Center for Child Health and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Child Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, China.,Department of Rheumatism and Immunology, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Xiaodong Zhao
- National Clinical Research Center for Child Health and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Child Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, China.,Department of Rheumatism and Immunology, Children's Hospital of Chongqing Medical University, Chongqing, China
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14
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Ben Ayed-Guerfali D, Ben Kridis-Rejab W, Ammous-Boukhris N, Ayadi W, Charfi S, Khanfir A, Sellami-Boudawara T, Frikha M, Daoud J, Mokdad-Gargouri R. Novel and recurrent BRCA1/BRCA2 germline mutations in patients with breast/ovarian cancer: a series from the south of Tunisia. J Transl Med 2021; 19:108. [PMID: 33726785 PMCID: PMC7962399 DOI: 10.1186/s12967-021-02772-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 02/26/2021] [Indexed: 12/14/2022] Open
Abstract
Background The incidence of breast cancer (BC) and/or ovarian cancer (OC) is increasing in Tunisia especially in young women and mostly those with family history. However, the spectrum of BRCA mutations remains little explored in Tunisian patients in particular in the southern region. Methods We sequenced the entire coding regions of BRCA1and BRCA2 genes using next generation sequencing (NGS) in 134 selected patients with BC and/or OC. Results Among the 134 patients, 19 (14.17%) carried pathogenic mutations (10 are BRCA1 mutation carriers and 9 are BRCA2 mutation carriers) that are mainly frameshift index (76.9%). Interestingly, 5 out of the 13 variants (38.46%) were found at least twice in unrelated patients, as the c.1310-1313 delAAGA in BRCA2 and the c.5030_5033 delCTAA that has been identified in 4/98 BC patients and in 3/15 OC patients from unrelated families with strong history of cancer. Besides recurrent mutations, 6 variant (4 in BRCA1 and 2 in BRCA2) were not reported previously. Furthermore, 3 unrelated patients carried the VUS c.9976A > T, (K3326*) in BRCA2 exon 27. BRCA carriers correlated significantly with tumor site (p = 0.029) and TNBC cases (p = 0.008). In the groups of patients aged between 31 and 40, and 41–50 years, BRCA1 mutations occurred more frequently in patients with OC than those with BC, and conversely BRCA2 carriers are mostly affected with BC (p = 0.001, and p = 0.044 respectively). Conclusions The overall frequency of the BRCA germline mutations was 14.17% in patients with high risk of breast/ovarian cancer. We identified recurrent mutations as the c.1310_1313 delAAGA in BRCA2 gene and the c.5030_5033 delCTAA in BRCA1 gene that were found in 4% and 20% of familial BC and OC respectively. Our data will contribute in the implementation of genetic counseling and testing for families with high-risk of BC and/or OC.
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Affiliation(s)
- Dorra Ben Ayed-Guerfali
- Center of Biotechnology of Sfax, University of Sfax, Sidi Mansour Street Km 6, BP 1177, 3038, Sfax, Tunisia
| | | | - Nihel Ammous-Boukhris
- Center of Biotechnology of Sfax, University of Sfax, Sidi Mansour Street Km 6, BP 1177, 3038, Sfax, Tunisia
| | - Wajdi Ayadi
- Center of Biotechnology of Sfax, University of Sfax, Sidi Mansour Street Km 6, BP 1177, 3038, Sfax, Tunisia
| | - Slim Charfi
- Department of Anatomo-pathology, Habib Bourguiba Hospital, Sfax, Tunisia
| | - Afef Khanfir
- Department of Oncology, Habib Bourguiba Hospital, Sfax, Tunisia
| | | | - Mounir Frikha
- Department of Oncology, Habib Bourguiba Hospital, Sfax, Tunisia
| | - Jamel Daoud
- Department of Radiotherapy, Habib Bourguiba Hospital, Sfax, Tunisia
| | - Raja Mokdad-Gargouri
- Center of Biotechnology of Sfax, University of Sfax, Sidi Mansour Street Km 6, BP 1177, 3038, Sfax, Tunisia.
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15
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Tuazon AMDA, Lott P, Bohórquez M, Benavides J, Ramirez C, Criollo A, Estrada-Florez A, Mateus G, Velez A, Carmona J, Olaya J, Garcia E, Polanco-Echeverry G, Stultz J, Alvarez C, Tapia T, Ashton-Prolla P, Vega A, Lazaro C, Tornero E, Martinez-Bouzas C, Infante M, De La Hoya M, Diez O, Browning BL, Rannala B, Teixeira MR, Carvallo P, Echeverry M, Carvajal-Carmona LG. Haplotype analysis of the internationally distributed BRCA1 c.3331_3334delCAAG founder mutation reveals a common ancestral origin in Iberia. Breast Cancer Res 2020; 22:108. [PMID: 33087180 PMCID: PMC7579869 DOI: 10.1186/s13058-020-01341-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 09/16/2020] [Indexed: 12/02/2022] Open
Abstract
Background The BRCA1 c.3331_3334delCAAG founder mutation has been reported in hereditary breast and ovarian cancer families from multiple Hispanic groups. We aimed to evaluate BRCA1 c.3331_3334delCAAG haplotype diversity in cases of European, African, and Latin American ancestry. Methods BC mutation carrier cases from Colombia (n = 32), Spain (n = 13), Portugal (n = 2), Chile (n = 10), Africa (n = 1), and Brazil (n = 2) were genotyped with the genome-wide single nucleotide polymorphism (SNP) arrays to evaluate haplotype diversity around BRCA1 c.3331_3334delCAAG. Additional Portuguese (n = 13) and Brazilian (n = 18) BC mutation carriers were genotyped for 15 informative SNPs surrounding BRCA1. Data were phased using SHAPEIT2, and identical by descent regions were determined using BEAGLE and GERMLINE. DMLE+ was used to date the mutation in Colombia and Iberia. Results The haplotype reconstruction revealed a shared 264.4-kb region among carriers from all six countries. The estimated mutation age was ~ 100 generations in Iberia and that it was introduced to South America early during the European colonization period. Conclusions Our results suggest that this mutation originated in Iberia and later introduced to Colombia and South America at the time of Spanish colonization during the early 1500s. We also found that the Colombian mutation carriers had higher European ancestry, at the BRCA1 gene harboring chromosome 17, than controls, which further supported the European origin of the mutation. Understanding founder mutations in diverse populations has implications in implementing cost-effective, ancestry-informed screening.
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Affiliation(s)
| | - Paul Lott
- Genome Center, University of California Davis, Davis, CA, USA
| | | | | | | | | | | | | | - Alejandro Velez
- Hospital Pablo Tobon Uribe, Medellín, Colombia.,Dinamica IPS, Medellín, Colombia
| | | | - Justo Olaya
- Hospital Universitario Hernando Moncaleano Perdomo, Neiva, Colombia
| | - Elisha Garcia
- Genome Center, University of California Davis, Davis, CA, USA
| | | | - Jacob Stultz
- Genome Center, University of California Davis, Davis, CA, USA
| | | | - Teresa Tapia
- Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Patricia Ashton-Prolla
- Department of Genetics, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.,Post-graduate Course in Genetics and Molecular Biology, UFRGS, Porto Alegre, Brazil.,Medical Genetics Service, Hospital de Clinicas de Porto Alegre (HCPA), Porto Alegre, Brazil
| | | | - Ana Vega
- Fundación Pública Galega de Medicina Xenómica, Grupo de Medicina Xenómica-USC, CIBERER, IDIS, Santiago de Compostela, Spain
| | - Conxi Lazaro
- Hereditary Cancer Program, Catalan Institute of Oncology, Oncobell Program-IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Eva Tornero
- Hereditary Cancer Program, Catalan Institute of Oncology, Oncobell Program-IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | | | - Mar Infante
- Cancer Genetics Group, Institute of Genetics and Molecular Biology (UVa-CSIC), Valladolid, Spain
| | - Miguel De La Hoya
- Laboratorio de Oncología Molecular, Hospital Clínico San Carlos. IdISSC (Instituto de Investigación Sanitaria San Carlos), Madrid, Spain
| | - Orland Diez
- Grupo de Cáncer Hereditario, Instituto Oncológico Vall d'Hebron (VHIO), Madrid, Spain
| | - Brian L Browning
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA, USA
| | | | - Bruce Rannala
- Department of Evolution and Ecology, University of California Davis, Davis, CA, USA
| | - Manuel R Teixeira
- Portuguese Oncology Institute of Porto (IPO Porto) and Biomedical Sciences Institute (ICBAS), University of Porto, Porto, Portugal
| | - Pilar Carvallo
- Pontificia Universidad Católica de Chile, Santiago, Chile
| | | | - Luis G Carvajal-Carmona
- Genome Center, University of California Davis, Davis, CA, USA. .,Division de Investigaciones, Fundacion de Genética y Genómica, Ibague, Colombia. .,University of California Davis Comprehensive Cancer Center, Sacramento, CA, USA. .,Department of Biochemistry and Molecular Medicine, University of California Davis, Sacramento, CA, USA.
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Foglietta J, Ludovini V, Bianconi F, Pistola L, Reda MS, Al-Refaie A, Tofanetti FR, Mosconi A, Minenza E, Anastasi P, Molica C, Stracci F, Roila F. Prevalence and Spectrum of BRCA Germline Variants in Central Italian High Risk or Familial Breast/Ovarian Cancer Patients: A Monocentric Study. Genes (Basel) 2020; 11:E925. [PMID: 32806537 PMCID: PMC7464094 DOI: 10.3390/genes11080925] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/05/2020] [Accepted: 08/06/2020] [Indexed: 01/04/2023] Open
Abstract
Hereditary breast and ovarian cancers are mainly linked to variants in BRCA1/2 genes. Recently, data has shown that identification of BRCA variants has an immediate impact not only in cancer prevention but also in targeted therapeutic approaches. This prospective observational study characterized the overall germline BRCA variant and variant of uncertain significance (VUS) frequency and spectrum in individuals affected by breast (BC) or ovarian cancer (OC) and in healthy individuals at risk by sequencing the entire BRCA genes. Of the 363 probands analyzed, 50 (13.8%) were BRCA1/2 mutated, 28 (7.7%) at BRCA1 and 23 (6.3%) at BRCA2 gene. The variant c.5266dupC p.(Gln1756Profs) was the most frequent alteration, representing 21.4% of the BRCA1 variants and 12.0% of all variants identified. The variant c.6313delA p.(Ile2105Tyrfs) of BRCA2 was the most frequent alteration observed in 6 patients. Interestingly, two new variants were identified in BRCA2. In addition, 25 different VUS were identified; two were reported for the first time in BRCA1 and two in BRCA2. The number of triple-negative BCs was significantly higher in patients with the pathogenic BRCA1/2-variant (36.4%) than in BRCA1/2 VUS (16.0%) and BRCA1/2 wild-type patients (10.7%) (p < 0.001). Our study reveals that the overall frequency of BRCA germline variants in the selected high-risk Italian population is about 13.8%. We believe that our results could have significant implications for preventive strategies for unaffected BRCA-carriers and effective targeted treatments such as PARP inhibitors for patients with BC or OC.
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Affiliation(s)
| | - Vienna Ludovini
- Medical Oncology Division, S. Maria della Misericordia Hospital, 06132 Perugia, Italy; (L.P.); (M.S.R.); (A.A.-R.); (F.R.T.); (A.M.); (E.M.); (P.A.); (C.M.); (F.R.)
| | | | - Lorenza Pistola
- Medical Oncology Division, S. Maria della Misericordia Hospital, 06132 Perugia, Italy; (L.P.); (M.S.R.); (A.A.-R.); (F.R.T.); (A.M.); (E.M.); (P.A.); (C.M.); (F.R.)
| | - Maria Sole Reda
- Medical Oncology Division, S. Maria della Misericordia Hospital, 06132 Perugia, Italy; (L.P.); (M.S.R.); (A.A.-R.); (F.R.T.); (A.M.); (E.M.); (P.A.); (C.M.); (F.R.)
| | - Antonella Al-Refaie
- Medical Oncology Division, S. Maria della Misericordia Hospital, 06132 Perugia, Italy; (L.P.); (M.S.R.); (A.A.-R.); (F.R.T.); (A.M.); (E.M.); (P.A.); (C.M.); (F.R.)
| | - Francesca Romana Tofanetti
- Medical Oncology Division, S. Maria della Misericordia Hospital, 06132 Perugia, Italy; (L.P.); (M.S.R.); (A.A.-R.); (F.R.T.); (A.M.); (E.M.); (P.A.); (C.M.); (F.R.)
| | - Annamaria Mosconi
- Medical Oncology Division, S. Maria della Misericordia Hospital, 06132 Perugia, Italy; (L.P.); (M.S.R.); (A.A.-R.); (F.R.T.); (A.M.); (E.M.); (P.A.); (C.M.); (F.R.)
| | - Elisa Minenza
- Medical Oncology Division, S. Maria della Misericordia Hospital, 06132 Perugia, Italy; (L.P.); (M.S.R.); (A.A.-R.); (F.R.T.); (A.M.); (E.M.); (P.A.); (C.M.); (F.R.)
| | - Paola Anastasi
- Medical Oncology Division, S. Maria della Misericordia Hospital, 06132 Perugia, Italy; (L.P.); (M.S.R.); (A.A.-R.); (F.R.T.); (A.M.); (E.M.); (P.A.); (C.M.); (F.R.)
| | - Carmen Molica
- Medical Oncology Division, S. Maria della Misericordia Hospital, 06132 Perugia, Italy; (L.P.); (M.S.R.); (A.A.-R.); (F.R.T.); (A.M.); (E.M.); (P.A.); (C.M.); (F.R.)
| | - Fabrizio Stracci
- Department of Experimental Medicine, Public Health Section, University of Perugia, 06129 Perugia, Italy;
| | - Fausto Roila
- Medical Oncology Division, S. Maria della Misericordia Hospital, 06132 Perugia, Italy; (L.P.); (M.S.R.); (A.A.-R.); (F.R.T.); (A.M.); (E.M.); (P.A.); (C.M.); (F.R.)
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Liao Y, Tu C, Song X, Cai L. Case report: Analysis of BRCA1 and BRCA2 gene mutations in a hereditary ovarian cancer family. J Assist Reprod Genet 2020; 37:1489-1495. [PMID: 32356124 PMCID: PMC7311593 DOI: 10.1007/s10815-020-01783-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 04/14/2020] [Indexed: 12/14/2022] Open
Abstract
OBJECTIVE Breast cancer susceptibility gene 1/2 (BRCA1/2) is the most important susceptibility gene associated with hereditary ovarian cancer (HOC). We aimed to screen BRAC1 and BRAC2 gene mutations in a member of a hereditary ovarian cancer family in China, and to analyze the structure and function of the mutant protein. METHODS A typical HOC family was selected. Blood samples and pathological tissue samples were taken from the female members of the family. Blood samples from two patients with sporadic ovaries of the same pathological type were taken as a control group. After RNA extraction, PCR amplification was applied and the PCR products were directly sequenced and aligned, prediction and analysis of protein structure and molecular conformation that may be caused by BRCA1/2 mutation. RESULTS The whole gene analysis of BRCA1 and BRCA2 in ovarian cancer patients in the family showed that there were 8 mutations in BRCA1 whole gene sequencing, including 3 nonsense mutations (2314C>T, 2543T>C, 4540T>C); two mutations have been recorded, which are associated with cervical cancer (2844C>T) and endometriosis (3345A>G); three newly discovered mutations (3780A>G, 5069A>G, 3326A>T). Among them, 3780A>G and 5069A>G caused amino acid changes, while 3326A>T mutation caused Arg mutation to stop codon. A total of 7 mutations were detected in BRCA2 whole-genome sequencing, including 5 non-significant mutations (3623A>G, 4034T>C, 4790A>G, 6740G>C, 7469A>G); one no-record mutation (1716T>A), and 1 recorded mutation (1342A>C), which was associated with breast cancer and ovarian cancer. BRCA1 (3326A>T) and BRCA2 (1342A>C) mutations were co-existing in patients (II1, II3, and II5) identified as serous adenocarcinoma grade II. Two cases of ovarian serous cystadenocarcinoma with no history of family tumors were normalized for BRCA1/2 gene sequencing. In the gene detection of III generation female, four females with BRCA2 (1342A>C) mutation were found, and one of them also carried the BRCA1 (3326A>T) mutation, who can be considered a high-risk group of HOC in this family. Online protein structure predictions revealed that BRCA1 (3326A>T) mutations mutated AGA at this site to TGA resulting in a translated Arg (arginine) mutation as a stop codon, while BRCA2 (1342A>C) mutated AAT at this site to CAT resulting in a translated Asn mutation to His. CONCLUSION The BRCA1 (3326A>T) and BRCA2 (1342A>C) were detected in the HOC family, which may be the susceptibility gene of the family's HOC. The BRCA1/2 gene screening may be possible to obtain high-risk populations in this family.
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Affiliation(s)
- Ying Liao
- Department of Gynecology, Xinyu People's Hospital, Xinyu, 338000, Jiangxi, China
| | - Chunhua Tu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Nanchang University, No. 17 Yongwai Zhengjie, Nanchang, 330000, Jiangxi, China
| | - Xiaoxia Song
- Department of Gynecology, Xinyu People's Hospital, Xinyu, 338000, Jiangxi, China
| | - Liping Cai
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Nanchang University, No. 17 Yongwai Zhengjie, Nanchang, 330000, Jiangxi, China.
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18
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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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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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Bisgin A, Boga I, Yalav O, Sonmezler O, Tug Bozdogan S. BRCAmutation characteristics in a series of index cases of breast cancer selected independent of family history. Breast J 2019; 25:1029-1033. [DOI: 10.1111/tbj.13400] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 12/24/2018] [Accepted: 01/03/2019] [Indexed: 11/26/2022]
Affiliation(s)
- Atil Bisgin
- Faculty of Medicine, Medical Genetics Department of Balcali Clinic and Hospital Cukurova University Adana Turkey
- Cukurova University AGENTEM (Adana Genetic Disease Diagnosis and Treatment Center) Adana Turkey
| | - Ibrahim Boga
- Cukurova University AGENTEM (Adana Genetic Disease Diagnosis and Treatment Center) Adana Turkey
- Department of Biotehnology, Institute of Science Cukurova University Adana Turkey
| | - Orcun Yalav
- General Surgey Department of Balcali Clinis and Hospital, Faculty of Medicine Cukurova Unversity Adana Turkey
| | - Ozge Sonmezler
- Cukurova University AGENTEM (Adana Genetic Disease Diagnosis and Treatment Center) Adana Turkey
- Department of Biotehnology, Institute of Science Cukurova University Adana Turkey
| | - Sevcan Tug Bozdogan
- Faculty of Medicine, Medical Genetics Department of Balcali Clinic and Hospital Cukurova University Adana Turkey
- Cukurova University AGENTEM (Adana Genetic Disease Diagnosis and Treatment Center) Adana Turkey
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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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Lu L, Huang H, Zhou J, Ma W, Mackay S, Wang Z. BRCA1 mRNA expression modifies the effect of T cell activation score on patient survival in breast cancer. BMC Cancer 2019; 19:387. [PMID: 31023256 PMCID: PMC6482542 DOI: 10.1186/s12885-019-5595-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 04/09/2019] [Indexed: 12/30/2022] Open
Abstract
Background Effector CD8+ T cell activation and its cytotoxic function to eradicate tumor cells depend on the T cell recognition of tumor neoantigens, and are positively associated with improved survival in breast cancer. Tumor suppressor BRCA1 and cell cycle regulator CCND1 play a critical role in maintaining genome integrity and tumorigenesis, respectively. However, it is still unclear how BRCA1 and CCND1 expression levels affect the effect of T cell activation on breast cancer patient survival. Methods The interactions between T cell activation status and either BRCA1 or CCND1 expression were evaluated using Kaplan-Meier survival curves and multivariate Cox regression models in a public dataset with 1088 breast cancer patients. Results Among the patients with low BRCA1 or CCND1 expression, the Activation group showed better overall survival than the Exhaustion group. Adjusted hazards ratios were 0.43 (95% CI: 0.20–0.93) in patients with a low BRCA1 level, and 0.39 (95% CI: 0.19–0.81) in patients with a low CCND1 level, respectively. There was a significant trend in both subgroups (p-trend = 0.011 in the low BRCA1 group, and p-trend = 0.009 in the low CCND1 group). In contrast, there is no significant association in patients with either high BRCA1 or high CCND1 levels. There is a significant interaction between T cell activation status and BRCA1 level (p = 0.009), but not between T cell activation status and CCND1 level (p = 0.135). Conclusions BRCA1 expression modified the effect of T cell activation status on patient survival in breast cancer, suggesting that the existence of neoantigens and the enhancement of neoantigen presentation in combination with immune checkpoint blockade may have synergistic effects on patient outcome.
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Affiliation(s)
- Lingeng Lu
- Department of Chronic Disease Epidemiology, Yale School of Public Health, School of Medicine, Center for Biomedical Data Science, Yale Cancer Center, Yale University, 60 College Street, New Haven, CT, 06520-8034, USA.
| | - Huatian Huang
- Guizhou Qianxinan People's Hospital, Xingyi, 652400, Guizhou, China
| | - Jing Zhou
- Isoplexis Corporation, 35 NE Industrial Road, Branford, CT, 06405, USA
| | - Wenxue Ma
- Moores Cancer Center, University of California San Diego, La Jolla, CA, 92093, USA
| | - Sean Mackay
- Isoplexis Corporation, 35 NE Industrial Road, Branford, CT, 06405, USA
| | - Zuoheng Wang
- Department of Biostatistics, Yale School of Public Health, School of Medicine, Center for Biomedical Data Science, Yale Cancer Center, Yale University, 60 College Street, New Haven, CT, 06520-8034, USA.
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23
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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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24
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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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25
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Sharma-Oates A, Shaaban AM, Tomlinson I, Wynne L, Cazier JB, Sundar S. Heterogeneity of germline variants in high risk breast and ovarian cancer susceptibility genes in India. PRECISION CLINICAL MEDICINE 2018; 1:75-87. [PMID: 35693198 PMCID: PMC8985795 DOI: 10.1093/pcmedi/pby010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Revised: 07/17/2018] [Accepted: 07/23/2018] [Indexed: 12/15/2022] Open
Abstract
Breast and ovarian cancers now account for one in three cancers in Indian women and their incidence is rising. Major differences in the clinical presentation of breast and ovarian cancers exist between India and the United Kingdom. For example, Indian patients with breast cancer typically present a decade earlier than in the UK. Reasons for this could be multifactorial, including differences in underlying biology, environmental risks, and other systematic factors including access to screening. One possible explanation lies in variable incidence or penetrance of germline mutations in genes such as BRCA1 and BRCA2. We performed a methodical database and literature review to investigate the prevalence and spectrum of high-risk cancer susceptibility genes in Indian patients with breast and ovarian cancers. We identified 148 articles, but most studies were small, with inconsistent inclusion criteria and based on heterogeneous technologies, so that mutation frequency could not be reliably ascertained. Data were also often lacking on penetrance, histopathology, and survival outcomes. After filtering out unsuitable studies, only 13 remained, comprising 1028 patients. Large-scale research studies are urgently needed to determine mutation prevalence, spectra, and clinico-pathological features, and hence derive guidelines for screening, treatment, and prevention specific to the Indian population.
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Affiliation(s)
- Archana Sharma-Oates
- Centre for Computational Biology, Haworth Building, University of Birmingham, Edgbaston, Birmingham, UK
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, Haworth Building, University of Birmingham, Edgbaston, Birmingham, UK
| | - Abeer M Shaaban
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, Haworth Building, University of Birmingham, Edgbaston, Birmingham, UK
- Department of Cellular Pathology, University Hospitals Birmingham NHS Foundation Trust, Queen Elizabeth Hospital Birmingham, Mindelsohn Way, Birmingham, UK
| | - Ian Tomlinson
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, Haworth Building, University of Birmingham, Edgbaston, Birmingham, UK
| | - Luke Wynne
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, Haworth Building, University of Birmingham, Edgbaston, Birmingham, UK
| | - Jean-Baptiste Cazier
- Centre for Computational Biology, Haworth Building, University of Birmingham, Edgbaston, Birmingham, UK
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, Haworth Building, University of Birmingham, Edgbaston, Birmingham, UK
| | - Sudha Sundar
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, Haworth Building, University of Birmingham, Edgbaston, Birmingham, UK
- Pan-Birmingham Gynaecological Cancer Centre, City Hospital, Dudley Road, Birmingham, West Midlands, UK
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26
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Genetic diversity in populations across Latin America: implications for population and medical genetic studies. Curr Opin Genet Dev 2018; 53:98-104. [PMID: 30125792 DOI: 10.1016/j.gde.2018.07.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 07/22/2018] [Indexed: 01/03/2023]
Abstract
Hispanic/Latino (H/L) populations, although linked by culture and aspects of shared history, reflect the complexity of history and migration influencing the Americas. The original settlement by indigenous Americans, followed by postcolonial admixture from multiple continents, has yielded localized genetic patterns. In addition, numerous H/L populations appear to have signatures of pre-colonization and post-colonization bottlenecks, indicating that tens of millions of H/Ls may harbor signatures of founder effects today. Based on both population and medical genetic findings we highlight the extreme differentiation across the Americas, providing evidence for why H/Ls should not be considered a single population in modern human genetics. We highlight the need for additional sampling of understudied H/L groups, and ramifications of these findings for genomic medicine in one-tenth of the world's population.
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