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Andaluz S, Zhao B, Sinha S, Lagniton PNP, Costa DA, Ding X, Brito M, Wang SM. Using Portuguese BRCA pathogenic variation as a model to study the impact of human admixture on human health. BMC Genomics 2024; 25:416. [PMID: 38671360 PMCID: PMC11055274 DOI: 10.1186/s12864-024-10311-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
BACKGROUND Admixture occurs between different ethnic human populations. The global colonization in recent centuries by Europeans led to the most significant admixture in human history. While admixture may enhance genetic diversity for better fitness, it may also impact on human health by transmitting genetic variants for disease susceptibility in the admixture population. The admixture by Portuguese global exploration initiated in the 15th century has reached over 20 million of Portuguese-heritage population worldwide. It provides a valuable model to study the impact of admixture on human health. BRCA1 and BRCA2 (BRCA) are two of the important tumor suppressor genes. The pathogenic variation (PV) in BRCA is well determined to cause high risk of hereditary breast and ovarian cancer. Tracing the distribution of Portuguese BRCA PV in Portuguese-heritage population will help to understand the impact of admixture on cancer susceptibility in modern humans. In this study, we analyzed the distribution of the Portuguese-originated BRCA variation in Brazilian population, which has high degree Portuguese-heritage. METHODS By comprehensive data mining, standardization and annotation, we generated a Portuguese-derived BRCA variation dataset and a Brazilian-derived BRCA variation dataset. We compared the two BRCA variation datasets to identify the BRCA variants shared between the two populations. RESULTS The Portuguese-derived BRCA variation dataset consists of 220 BRCA variants including 78 PVs from 11,482 Portuguese cancer patients, 93 (42.2%) in BRCA1 and 127 (57.7%) in BRCA2. Of the 556 Portuguese BRCA PV carriers carrying the 78 PVs, 331 (59.5%) carried the three Portuguese-BRCA founder PVs of BRCA1 c.2037delinsCC, BRCA1 c.3331_3334del and BRCA2 c.156_157insAlu. The Brazilian-derived BRCA variation dataset consists of 255 BRCA PVs from 7,711 cancer patients, 136 (53.3%) in BRCA1 and 119 (46.6%) in BRCA2. We developed an open database named dbBRCA-Portuguese ( https://genemutation.fhs.um.edu.mo/dbbrca-portuguese/ ) and an open database named dbBRCA-Brazilian ( https://genemutation.fhs.um.edu.mo/dbbrca-brazilian ) to host the BRCA variation data from Portuguese and Brazilian populations. We compared the BRCA PV datasets between Portuguese and Brazilian populations, and identified 29 Portuguese-specific BRCA PVs shared between Portuguese and Brazilian populations, 14 in BRCA1 including the Portuguese founder BRCA1 c.3331_3334del and BRCA1 c.2037delinsCC, and 15 in BRCA2 including the Portuguese founder BRCA2 c.156_157insAlu. Searching the 78 Portuguese BRCA PVs in over 5,000 ancient human genomes identified evolution origin for only 8 PVs in Europeans dated between 37,470 and 3,818 years before present, confirming the Portuguese-specificity of Portuguese BRCA PVs; comparing the 78 Portuguese BRCA PVs Portuguese, 255 Brazilian BRCA PVs, and 134 African BRCA PVs showed little overlapping, ruling out the possibility that the BRCA PVs shared between Portuguese and Brazilian may also be contributed by African. CONCLUSION Our study provides evidence that the admixture in recent human history contributed to cancer susceptibility in modern humans.
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Affiliation(s)
- Stephanie Andaluz
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Center and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macao SRA, China
| | - Bojin Zhao
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Center and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macao SRA, China
| | - Siddharth Sinha
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Center and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macao SRA, China
| | - Philip Naderev Panuringan Lagniton
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Center and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macao SRA, China
| | - Diogo Alpuim Costa
- Medical Oncology Department, Hospital de Cascais, Cascais; Haematology and Oncology Department, CUF Oncologia, Lisbon; NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Lisbon, Portugal
| | - Xiaofan Ding
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Center and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macao SRA, China
| | - Miguel Brito
- Escola Superior de Tecnologia da Saúde de Lisboa, Instituto Politécnico de Lisboa, Lisbon, Portugal.
| | - San Ming Wang
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Center and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macao SRA, China.
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de Oliveira Ferreira C, Carneiro VCG, Araujo Mariz C. Germline mutations in BRCA1 and BRCA2 among Brazilian women with ovarian cancer treated in the Public Health System. BMC Cancer 2024; 24:499. [PMID: 38641594 PMCID: PMC11027424 DOI: 10.1186/s12885-024-12246-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 04/10/2024] [Indexed: 04/21/2024] Open
Abstract
BACKGROUND Germline mutations in BRCA1 and BRCA2 genes are among the main causes of hereditary ovarian cancer. Identifying these mutations may reduce cancer risk, facilitate early detection, and enable personalized treatment. However, genetic testing is limited in the Brazilian Public Health System, and data regarding germline mutations in many regions are scarce. Therefore, the study aimed to investigate the prevalence of germline mutations in BRCA1 and BRCA2 in women with ovarian cancer treated in the Public Health System in Pernambuco, Brazil. METHODS A cross-sectional study was conducted in the Hereditary Cancer Program from two reference oncological centers in Pernambuco. Women (n = 45) with high-grade serous ovarian cancer underwent genetic counseling and DNA sequencing for BRCA1 and BRCA2 genes. RESULTS The prevalence of deleterious mutations in the BRCA1 and BRCA2 genes was 33%. Of the 15 germline mutations found, 13 were in BRCA1 and 2 in BRCA2; two mutations of unknown clinical significance were also found in BRCA2. Mutations c.5266dupC and c.2215 A > T were the most frequent; each was mutation observed in three patients. Additionally, the mutations c.7645dupT and c.921dupT were reported for the first time. CONCLUSION One in three women showed a pathogenic mutation, demonstrating a significant prevalence of germline mutations in this sample. Additionally, the small sample revealed an interesting number of mutations, indicating the need to explore more regions of the country.
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Affiliation(s)
| | - Vandré Cabral Gomes Carneiro
- Hospital de Câncer de Pernambuco, Recife, Pernambuco, Brazil
- Instituto de Medicina Integral Professor Fernando Figueira, Recife, Pernambuco, Brazil
| | - Carolline Araujo Mariz
- Instituto Aggeu Magalhães, FIOCRUZ, Recife, Pernambuco, Brazil.
- Faculdade de Medicina de Olinda, Olinda, Pernambuco, Brazil.
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de Freitas Ribeiro AA, Junior NMC, Dos Santos LL. Systematic review of the molecular basis of hereditary breast and ovarian cancer syndrome in Brazil: the current scenario. Eur J Med Res 2024; 29:187. [PMID: 38504328 PMCID: PMC10953197 DOI: 10.1186/s40001-024-01767-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 03/04/2024] [Indexed: 03/21/2024] Open
Abstract
BACKGROUND A detailed understanding of the genetic basis of cancer is of great interest to public health monitoring programs. Although many studies have been conducted in Brazil, a global view on the molecular profile related to hereditary breast and ovarian cancer (HBOC) in this large and heterogeneous population is lacking. METHODS A systematic review following the PRISMA guidelines was conducted in three electronic databases (PubMed, BIREME and SciELO). Brazilian studies covering molecular analysis of genes related to HBOC, published until December 2023, were considered. RESULTS We identified 35 original studies that met all the inclusion criteria. A total of 137 distinct mutations were found in the BRCA1 gene, but four of them corresponded to 44.5% of all mutations found in this gene. The c.5266dupC BRCA1 mutation was responsible for 26.8% of all pathogenic mutations found in the BRCA1 gene in patients with clinical criteria for HBOC from the Brazilian population. Considering all studies that track this mutation in the BRCA1 gene, we found a frequency of 2% (120/6008) for this mutation in Brazilian patients. In the BRCA2 gene, the four most frequent mutations corresponded to 29.2% of pathogenic mutations. Even though it was tracked by few studies, the c.156_157insAlu mutation was responsible for 9.6% of all pathogenic mutations reported in the BRCA2 gene. Seventeen studies found pathogenic mutations in other non-BRCA genes, the c.1010G > A mutation in the TP53 gene being the most frequent one. Considering all studies that screened for this specific mutation in patients with the clinical criteria for HBOC, the frequency of c.1010G > A was estimated at 1.83% (61/3336). CONCLUSIONS Despite significant molecular heterogeneity among mutations in HBOC patients from Brazil, three mutations deserve to be highlighted, c.5266dupC, c.156_157insAlu and c.1010G > A in the BRCA1, BRCA2 and TP53 genes, respectively. With more than 200 records, these three mutations play a vital role in the pathology of breast and ovarian cancer in Brazil. The data collected shed light on the subject, but there is still not enough data from certain subpopulations.
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Affiliation(s)
| | | | - Luciana Lara Dos Santos
- Universidade Federal de São João del Rei (UFSJ), 400 Sebastião Gonçalves Coelho St, Divinópolis, MG, 35501-296, Brazil.
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Sánchez-Heras AB, Dámaso E, Castillejo A, Robledo M, Teulé A, Lázaro C, Sánchez-Martínez R, Zúñiga Á, López-Fernández A, Balmaña J, Robles L, Ramon Y Cajal T, Castillejo MI, Ibañez RP, Sevila CM, Sánchez-Mira A, Escandell I, Gómez L, Berbel P, Soto JL. Genetic and clinical characterization of a novel FH founder mutation in families with hereditary leiomyomatosis and renal cell cancer syndrome. Orphanet J Rare Dis 2024; 19:26. [PMID: 38279137 PMCID: PMC10811853 DOI: 10.1186/s13023-024-03017-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 01/11/2024] [Indexed: 01/28/2024] Open
Abstract
BACKGROUND Hereditary leiomyomatosis and renal cell cancer syndrome is a rare autosomal dominant hereditary syndrome. Previously, we published the largest cohort of FH mutation carriers in Spain and observed a highly recurrent missense heterozygous variant, FH(NM_000143.4):c.1118A > G p.(Asn373Ser), in 104 individuals from 31 apparently unrelated families. Here, we aimed to establish its founder effect and characterize the associated clinical phenotype. RESULTS Haplotype analysis confirmed that families shared a common haplotype (32/38 markers) spanning 0.61-0.82 Mb, indicating this recurrent variant was inherited from a founder ancestor. Cutaneous and uterine leiomyomatosis were diagnosed in 64.6% (64/99) and 98% (50/51) of patients, respectively, and renal cell cancer was present in 10.4% (10/96). The pathogenic FH_c.1118A > G variant is a Spanish founder mutation that originated 12-26 generations ago. We estimate that the variant may have appeared between 1370 and 1720. Individuals carrying this founder mutation had similar frequency of renal cell cancer and a higher frequency of renal cysts and leiomyomas than those in other cohorts of this syndrome. CONCLUSIONS In the Spanish province of Alicante there is a high prevalence of HLRCC because of the founder mutation FH c.1118A > G; p.(Asn373Ser). The characterization of founder mutations provides accurate and specific information regarding their penetrance and expressivity. In individuals with suspected HLRCC from the province of Alicante, genetic testing by direct analysis of the founder FH c.1118A > G; p.(Asn373Ser) mutation may be a faster and more efficient diagnostic tool compared with complete gene sequencing.
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Affiliation(s)
- Ana Beatriz Sánchez-Heras
- Cancer Genetic Counselling Unit, Medical Oncology Department, Hospital General Universitario de Elche, 03203, Elche, Alicante, Spain.
| | - Estela Dámaso
- Molecular Genetics Laboratory, Hospital General Universitario de Elche, Elche, Alicante, Spain
- Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO), FISABIO-Elche Health Department, Elche, Spain
| | - Adela Castillejo
- Molecular Genetics Laboratory, Hospital General Universitario de Elche, Elche, Alicante, Spain
- Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO), FISABIO-Elche Health Department, Elche, Spain
| | - Mercedes Robledo
- Hereditary Endocrine Cancer, Human Cancer Genetics Programme Spanish National Cancer Centre (CNIO), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras, CIBERER, 28029, Madrid, Spain
| | - Alexandre Teulé
- Hereditary Cancer Program, Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Catalan Institute of Oncology, L'Hospitalet del Llobregat, Barcelona, Spain
| | - Conxi Lázaro
- Hereditary Cancer Program, Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Catalan Institute of Oncology, L'Hospitalet del Llobregat, Barcelona, Spain
| | - Rosario Sánchez-Martínez
- Multidisciplinary Rare Disease Unit, Internal Medicine Department, Alicante University General Hospital, Alicante Institute for Health and Biomedical Research (ISABIAL), Alicante, Spain
| | - Ángel Zúñiga
- Clinical Genetics Unit, Hospital Politécnico y Universitario La Fe, Valencia, Spain
| | - Adrià López-Fernández
- Hereditary Cancer Genetics Group, VHIO, and Medical Oncology Department, Hospital Vall D'Hebron, Barcelona, Spain
| | - Judith Balmaña
- Hereditary Cancer Genetics Group, VHIO, and Medical Oncology Department, Hospital Vall D'Hebron, Barcelona, Spain
| | - Luis Robles
- Medical Oncology Department. Hospital 12 de Octubre, Madrid, Spain
| | - Teresa Ramon Y Cajal
- Familiar Cancer Clinic, Medical Oncology Department, Santa Creu i Sant Pau Hospital, Barcelona, Spain
| | - M Isabel Castillejo
- Molecular Genetics Laboratory, Hospital General Universitario de Elche, Elche, Alicante, Spain
- Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO), FISABIO-Elche Health Department, Elche, Spain
| | - Raquel Perea Ibañez
- Cancer Genetic Counselling Unit, Medical Oncology Department, Hospital General Universitario de Elche, 03203, Elche, Alicante, Spain
| | - Carmen Martínez Sevila
- Cancer Genetic Counselling Unit, Medical Oncology Department, Hospital General Universitario de Elche, 03203, Elche, Alicante, Spain
| | - Andrea Sánchez-Mira
- Molecular Genetics Laboratory, Hospital General Universitario de Elche, Elche, Alicante, Spain
- Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO), FISABIO-Elche Health Department, Elche, Spain
| | - Inés Escandell
- Servicio de Dermatología, Hospital General Universitario de Elda, Elda, Alicante, Spain
| | - Luís Gómez
- Urology Department, Hospital General Universitario de Elche, Elche, Alicante, Spain
| | - Pere Berbel
- Departamento de Histología y Anatomía, Facultad de Medicina, Universidad Miguel Hernández, Sant Joan d'Alacant, Alicante, Spain
| | - José Luis Soto
- Molecular Genetics Laboratory, Hospital General Universitario de Elche, Elche, Alicante, Spain
- Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO), FISABIO-Elche Health Department, Elche, Spain
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Eyries M, Ariste O, Legrand G, Basset N, Guillerm E, Perrier A, Duros C, Cohen-Haguenauer O, de la Grange P, Coulet F. Detection of a pathogenic Alu element insertion in PALB2 gene from targeted NGS diagnostic data. Eur J Hum Genet 2022; 30:1187-1190. [PMID: 35277653 PMCID: PMC9553905 DOI: 10.1038/s41431-022-01064-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 01/11/2022] [Accepted: 02/01/2022] [Indexed: 12/15/2022] Open
Abstract
Despite routine analysis of a large panel of genes, pathogenic variants are only detected in approximately 20% of families with hereditary breast and/or ovarian cancer. Mobile element insertions (MEI) are known to cause genetic diseases in humans, but remain challenging to detect. Retrospective analysis of targeted next-generation sequencing (NGS) data from 359 patients was performed using a dedicated MEI detection pipeline. We detected one MEI in exon 9 of the PALB2 gene in a woman with a family history of breast cancer. The pathogenic variant, c.2872_2888delins114AluL2, disrupts the PALB2 coding sequence and leads to the production of a truncated protein, p.(Gln958Valfs*38). This is the first report of a pathogenic MEI in PALB2. This study illustrates that MEI analysis may help to improve molecular diagnostic yield and can be performed from targeted NGS data used for routine diagnosis.
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Affiliation(s)
- Mélanie Eyries
- Sorbonne Université, Département de génétique, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, F-75013, Paris, France.
| | | | - Gaelle Legrand
- Sorbonne Université, Département de génétique, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, F-75013, Paris, France
| | - Noémie Basset
- Sorbonne Université, Département de génétique, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, F-75013, Paris, France
| | - Erell Guillerm
- Sorbonne Université, Département de génétique, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, F-75013, Paris, France
| | - Alexandre Perrier
- Sorbonne Université, Département de génétique, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, F-75013, Paris, France
| | - Caroline Duros
- Hôpital Saint-Louis-Lariboisière-Fernand-Widal, Service d'oncologie médicale Assistance Publique-Hôpitaux de Paris, F-75010, Paris, France
| | - Odile Cohen-Haguenauer
- Hôpital Saint-Louis-Lariboisière-Fernand-Widal, Service d'oncologie médicale Assistance Publique-Hôpitaux de Paris, F-75010, Paris, France
| | | | - Florence Coulet
- Sorbonne Université, Département de génétique, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, F-75013, Paris, France
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Vicente R, Alpuim Costa D, Vitorino M, Mendes AD, Santos C, Fontes-sousa M. Mutation Patterns in Portuguese Families with Hereditary Breast and Ovarian Cancer Syndrome. Cancers (Basel) 2022; 14:4717. [PMID: 36230639 PMCID: PMC9564125 DOI: 10.3390/cancers14194717] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 09/25/2022] [Accepted: 09/25/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary The pattern of Breast Cancer Genes 1 (BRCA1) and 2 (BRCA2) mutations in Hereditary Breast Ovarian Cancer (HBOC) families varies widely among different populations. About 30% of Portuguese HBOC can be associated with inherited cancer caused by BRCA1 or BRCA2 mutations. Three variants were identified (c.156_157insAlu in the BRCA2 gene and c.3331_3334del and c.2037delinsCC in the BRCA1 gene), accounting for about 50% of all Portuguese pathogenic mutations. Characterising the mutational spectrum in specific populations allows for a more efficient and cost-saving screening approach. Abstract Germline pathogenic variants in the Breast Cancer Genes 1 (BRCA1) and 2 (BRCA2) are responsible for Hereditary Breast and Ovarian Cancer (HBOC) syndrome. Genetic susceptibility to breast cancer accounts for 5–10% of all cases, phenotypically presenting with characteristics such as an autosomal dominant inheritance pattern, earlier age of onset, bilateral tumours, male breast cancer, and ovarian tumours, among others. BRCA2 pathogenic variant is usually associated with other cancers such as melanoma, prostate, and pancreatic cancers. Many rearrangements of different mutations were found in both genes, with some ethnic groups having higher frequencies of specific mutations due to founder effects. Despite the heterogeneity of germline BRCA1/BRCA2 mutations in Portuguese breast or/and ovarian cancer families, the first described founder mutation in the BRCA2 gene (c.156_157insAlu) and two other variants in the BRCA1 gene (c.3331_3334del and c.2037delinsCC) contribute to about 50% of all pathogenic mutations. Furthermore, the families with the BRCA1 c.3331_3334del or the c.2037delinsCC mutations share a common haplotype, suggesting that these may also be founder mutations in the Portuguese population. Identifying specific and recurrent/founder mutations plays an important role in increasing the efficiency of genetic testing since it allows the use of more specific, cheaper and faster strategies to screen HBOC families. Therefore, this review aims to describe the mutational rearrangements of founder mutations and evaluate their impact on the genetic testing criteria for HBOC families of Portuguese ancestry.
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Bastos Lopes CE, Reis AC, dos Santos Carneiro Lacerda M, Coelho Lopes M, Oliveira dos Santos D, Vilardo Lóes Moreira M, Dantas Cassali G, Ferreira E, Ecco R. Metastatic mammary tubulopapillary carcinoma in a captive black jaguar (
Panthera onca
). Vet Record Case Reports 2022. [DOI: 10.1002/vrc2.472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Carlos Eduardo Bastos Lopes
- Sector of Animal Pathology, Department of Clinic and Surgery, Veterinary School Universidade Federal de Minas Gerais Belo Horizonte Brazil
| | - Ana Carolina Reis
- Sector of Animal Pathology, Department of Clinic and Surgery, Veterinary School Universidade Federal de Minas Gerais Belo Horizonte Brazil
| | - Maira dos Santos Carneiro Lacerda
- Sector of Animal Pathology, Department of Clinic and Surgery, Veterinary School Universidade Federal de Minas Gerais Belo Horizonte Brazil
| | - Marcelo Coelho Lopes
- Sector of Animal Pathology, Department of Clinic and Surgery, Veterinary School Universidade Federal de Minas Gerais Belo Horizonte Brazil
| | - Daniel Oliveira dos Santos
- Sector of Animal Pathology, Department of Clinic and Surgery, Veterinary School Universidade Federal de Minas Gerais Belo Horizonte Brazil
| | - Matheus Vilardo Lóes Moreira
- Sector of Animal Pathology, Department of Clinic and Surgery, Veterinary School Universidade Federal de Minas Gerais Belo Horizonte Brazil
| | - Geovani Dantas Cassali
- Department of General Pathology Institute of Biological Sciences Universidade Federal de Minas Gerais Belo Horizonte Brazil
| | - Enio Ferreira
- Department of General Pathology Institute of Biological Sciences Universidade Federal de Minas Gerais Belo Horizonte Brazil
| | - Roselene Ecco
- Sector of Animal Pathology, Department of Clinic and Surgery, Veterinary School Universidade Federal de Minas Gerais Belo Horizonte Brazil
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Arancio W, Coronnello C. Repetitive Sequence Transcription in Breast Cancer. Cells 2022; 11:2522. [PMID: 36010599 DOI: 10.3390/cells11162522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/05/2022] [Accepted: 08/12/2022] [Indexed: 11/17/2022] Open
Abstract
Repetitive sequences represent about half of the human genome. They are actively transcribed and play a role during development and in epigenetic regulation. The altered activity of repetitive sequences can lead to genomic instability and they can contribute to the establishment or the progression of degenerative diseases and cancer transformation. In this work, we analyzed the expression profiles of DNA repetitive sequences in the breast cancer specimens of the HMUCC cohort. Satellite expression is generally upregulated in breast cancers, with specific families upregulated per histotype: in HER2-enriched cancers, they are the human satellite II (HSATII), in luminal A and B, they are part of the ALR family and in triple-negative, they are part of SAR and GSAT families, together with a perturbation in the transcription from endogenous retroviruses and their LTR sequences. We report that the background expression of repetitive sequences in healthy tissues of cancer patients differs from the tissues of non-cancerous controls. To conclude, peculiar patterns of expression of repetitive sequences are reported in each specimen, especially in the case of transcripts arising from satellite repeats.
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Abstract
BACKGROUND Transposable elements (TEs) are powerful creators of genotypic and phenotypic diversity due to their inherent mutagenic capabilities and in this way they serve as a deep reservoir of sequences for genomic variation. As agents of genetic disruption, a TE's potential to impact phenotype is partially a factor of its location in the genome. Previous research has shown TEs' ability to impact the expression of neighboring genes, however our understanding of this trend is hampered by the exceptional amount of diversity in the TE world, and a lack of publicly available computational methods that quantify the presence of TEs relative to genes. RESULTS Here, we have developed a tool to more easily quantify TE presence relative to genes through the use of only a gene and TE annotation, yielding a new metric we call TE Density. Briefly defined as the proportion of TE-occupied base-pairs relative to a window-size of the genome. This new pipeline reports TE density for each gene in the genome, for each type descriptor of TE (order and superfamily), and for multiple positions and distances relative to the gene (upstream, intragenic, and downstream) over sliding, user-defined windows. In this way, we overcome previous limitations to the study of TE-gene relationships by focusing on all TE types present in the genome, utilizing flexible genomic distances for measurement, and reporting a TE presence metric for every gene in the genome. CONCLUSIONS Together, this new tool opens up new avenues for studying TE-gene relationships, genome architecture, comparative genomics, and the tremendous diversity present of the TE world. TE Density is open-source and freely available at: https://github.com/sjteresi/TE_Density .
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Affiliation(s)
- Scott J Teresi
- Department of Horticulture, Michigan State University, East Lansing, Michigan, USA
- Genetics and Genome Sciences Program, Michigan State University, East Lansing, Michigan, USA
| | | | - Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, Michigan, USA.
- Genetics and Genome Sciences Program, Michigan State University, East Lansing, Michigan, USA.
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Custódio N, Savisaar R, Carvalho C, Bak-Gordon P, Ribeiro MI, Tavares J, Nunes PB, Peixoto A, Pinto C, Escudeiro C, Teixeira MR, Carmo-Fonseca M. Expression Profiling in Ovarian Cancer Reveals Coordinated Regulation of BRCA1/2 and Homologous Recombination Genes. Biomedicines 2022; 10:biomedicines10020199. [PMID: 35203410 PMCID: PMC8868827 DOI: 10.3390/biomedicines10020199] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/09/2022] [Accepted: 01/13/2022] [Indexed: 02/04/2023] Open
Abstract
Predictive biomarkers are crucial in clarifying the best strategy to use poly(ADP-ribose) polymerase inhibitors (PARPi) for the greatest benefit to ovarian cancer patients. PARPi are specifically lethal to cancer cells that cannot repair DNA damage by homologous recombination (HR), and HR deficiency is frequently associated with BRCA1/2 mutations. Genetic tests for BRCA1/2 mutations are currently used in the clinic, but results can be inconclusive due to the high prevalence of rare DNA sequence variants of unknown significance. Most tests also fail to detect epigenetic modifications and mutations located deep within introns that may alter the mRNA. The aim of this study was to investigate whether quantitation of BRCA1/2 mRNAs in ovarian cancer can provide information beyond the DNA tests. Using the nCounter assay from NanoString Technologies, we analyzed RNA isolated from 38 ovarian cancer specimens and 11 normal fallopian tube samples. We found that BRCA1/2 expression was highly variable among tumors. We further observed that tumors with lower levels of BRCA1/2 mRNA showed downregulated expression of 12 additional HR genes. Analysis of 299 ovarian cancer samples from The Cancer Genome Atlas (TCGA) confirmed the coordinated expression of BRCA1/2 and HR genes. To facilitate the routine analysis of BRCA1/2 mRNA in the clinical setting, we developed a targeted droplet digital PCR approach that can be used with FFPE samples. In conclusion, this study underscores the potential clinical benefit of measuring mRNA levels in tumors when BRCA1/2 DNA tests are negative or inconclusive.
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Affiliation(s)
- Noélia Custódio
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal; (R.S.); (C.C.); (P.B.-G.); (M.I.R.); (M.C.-F.)
- Correspondence: ; Tel.: +35-121-799-9411
| | - Rosina Savisaar
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal; (R.S.); (C.C.); (P.B.-G.); (M.I.R.); (M.C.-F.)
| | - Célia Carvalho
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal; (R.S.); (C.C.); (P.B.-G.); (M.I.R.); (M.C.-F.)
| | - Pedro Bak-Gordon
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal; (R.S.); (C.C.); (P.B.-G.); (M.I.R.); (M.C.-F.)
| | - Maria I. Ribeiro
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal; (R.S.); (C.C.); (P.B.-G.); (M.I.R.); (M.C.-F.)
| | - Joana Tavares
- Serviço de Anatomia Patológica, Hospital de Santa Maria, Centro Hospitalar Universitário Lisboa Norte, 1649-028 Lisboa, Portugal;
| | - Paula B. Nunes
- Hospital CUF Descobertas, 1998-018 Lisboa, Portugal;
- Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Ana Peixoto
- Serviço de Genética, Instituto Português de Oncologia do Porto Francisco Gentil, 4200-072 Porto, Portugal; (A.P.); (C.P.); (C.E.); (M.R.T.)
| | - Carla Pinto
- Serviço de Genética, Instituto Português de Oncologia do Porto Francisco Gentil, 4200-072 Porto, Portugal; (A.P.); (C.P.); (C.E.); (M.R.T.)
| | - Carla Escudeiro
- Serviço de Genética, Instituto Português de Oncologia do Porto Francisco Gentil, 4200-072 Porto, Portugal; (A.P.); (C.P.); (C.E.); (M.R.T.)
| | - Manuel R. Teixeira
- Serviço de Genética, Instituto Português de Oncologia do Porto Francisco Gentil, 4200-072 Porto, Portugal; (A.P.); (C.P.); (C.E.); (M.R.T.)
| | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal; (R.S.); (C.C.); (P.B.-G.); (M.I.R.); (M.C.-F.)
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11
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Miguel I, Rodrigues F, Fragoso S, Freixo J, Clara A, Luís A, Bento S, Fernandes M, Bacelar F, Câmara S, Parreira J, Duarte T, Rodrigues P, Santos S, Vaz F. Hereditary breast cancer and ancestry in the Madeira archipelago: an exploratory study. Ecancermedicalscience 2021; 15:1261. [PMID: 34567246 PMCID: PMC8426025 DOI: 10.3332/ecancer.2021.1261] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Indexed: 11/30/2022] Open
Abstract
Access to genetic testing and counselling in remote areas such as the Madeira archipelago, in the Northern Atlantic Ocean, may be complex. Different counselling methods, including telegenetics, should be explored. In this study, we characterise the Hereditary Breast/Ovarian Cancer (HBOC) families with Madeira ancestry enrolled in our programme. Of a total of 3,566 index patients tested between January 2000 and June 2018, 68 had Madeira ancestry and 22 were diagnosed with a pathogenic germline variant (PV). As in the whole group, BRCA2 PV were more frequent in Madeira patients (68.4%: c.9382C>T (26.3%), c.658_659del (21%), c.156_157insAlu (10.5%), c.793+1G>A (5.3%) and c.298A>T (5.3%). However, the most frequently diagnosed PV in Madeira patients was the BRCA1 c.3331_3334del (31.6%). BRCA1/2 detection rates were 27.9% and 10.5% for Madeira and the whole group, respectively. This study is the first characterisation of HBOC patients with Madeira ancestry. A distinct pattern of BRCA1/2 variants was observed, and the geographic clustering of BRCA1 c.3331_3334del variant may support the possibility of a founder mutation previously described in Northern Portugal. The high detection rate observed reinforces the need to reduce gaps in access to genetic testing in Madeira and other remote areas. According to current guidelines, timely identification of HBOC patients can contribute to their ongoing care and treatment.
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Affiliation(s)
- Isália Miguel
- Instituto Português de Oncologia de Lisboa Francisco Gentil, EPE, Rua Prof. Lima Basto 1099-023 Lisboa, Portugal
| | - Fátima Rodrigues
- Instituto Português de Oncologia de Lisboa Francisco Gentil, EPE, Rua Prof. Lima Basto 1099-023 Lisboa, Portugal
| | - Sofia Fragoso
- Instituto Português de Oncologia de Lisboa Francisco Gentil, EPE, Rua Prof. Lima Basto 1099-023 Lisboa, Portugal
| | - João Freixo
- CGPP-IBMC-i3S - Centro de Genética Preditiva e Preventiva, Instituto de Biologia Molecular e Celular, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Júlio Amaral de Carvalho 45, 4200-135 Porto, Portugal
| | - Ana Clara
- Instituto Português de Oncologia de Lisboa Francisco Gentil, EPE, Rua Prof. Lima Basto 1099-023 Lisboa, Portugal
| | - Ana Luís
- Instituto Português de Oncologia de Lisboa Francisco Gentil, EPE, Rua Prof. Lima Basto 1099-023 Lisboa, Portugal
| | - Sandra Bento
- Instituto Português de Oncologia de Lisboa Francisco Gentil, EPE, Rua Prof. Lima Basto 1099-023 Lisboa, Portugal
| | - Mariana Fernandes
- Hospital Dr Nélio Mendonça, SESARAM, EPE, Avenida Luís de Camões 57, 9004-514 Funchal, Portugal
| | - Filipe Bacelar
- Hospital Dr Nélio Mendonça, SESARAM, EPE, Avenida Luís de Camões 57, 9004-514 Funchal, Portugal
| | - Sara Câmara
- Hospital Dr Nélio Mendonça, SESARAM, EPE, Avenida Luís de Camões 57, 9004-514 Funchal, Portugal
| | - Joana Parreira
- Instituto Português de Oncologia de Lisboa Francisco Gentil, EPE, Rua Prof. Lima Basto 1099-023 Lisboa, Portugal
| | - Teresa Duarte
- Instituto Português de Oncologia de Lisboa Francisco Gentil, EPE, Rua Prof. Lima Basto 1099-023 Lisboa, Portugal
| | - Paula Rodrigues
- Instituto Português de Oncologia de Lisboa Francisco Gentil, EPE, Rua Prof. Lima Basto 1099-023 Lisboa, Portugal
| | - Sidónia Santos
- Instituto Português de Oncologia de Lisboa Francisco Gentil, EPE, Rua Prof. Lima Basto 1099-023 Lisboa, Portugal
| | - Fátima Vaz
- Instituto Português de Oncologia de Lisboa Francisco Gentil, EPE, Rua Prof. Lima Basto 1099-023 Lisboa, Portugal
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12
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Pires C, Marques IJ, Dias D, Saramago A, Leite V, Cavaco BM. A pathogenic variant in CHEK2 shows a founder effect in Portuguese Roma patients with thyroid cancer. Endocrine 2021; 73:588-597. [PMID: 33683595 DOI: 10.1007/s12020-021-02660-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 02/10/2021] [Indexed: 01/04/2023]
Abstract
PURPOSE Germline mutations in DNA repair-related genes have been recently reported in cases with familial non-medullary thyroid carcinoma (FNMTC). A Portuguese family from the Roma ethnic group with four members affected with papillary thyroid carcinoma (PTC), and three members with multinodular goiter (MNG) was identified. The aim of this study was to investigate the involvement of DNA repair-related genes in the etiology of FNMTC in this family and in the Roma ethnic group. METHODS Ninety-four hereditary cancer predisposition genes were analyzed through next-generation sequencing. Sanger sequencing was used for variant confirmation and screening. Twelve polymorphic markers were genotyped for haplotype analysis in the CHEK2 locus. RESULTS A germline pathogenic frameshift variant in the CHEK2 gene [c.596dupA, p.(Tyr199Ter)] was detected in homozygosity in the proband (PTC) and in his brother (MNG), being heterozygous in his mother (PTC), two sisters (PTC), and one nephew (MNG). This variant was absent in 100 general population controls. The screening of the CHEK2 variant was extended to other Roma individuals, being detected in 2/33 Roma patients with thyroid cancer, and in 1/15 Roma controls. Haplotype segregation analysis identified a common ancestral core haplotype (Hcac), covering 10 Mb in the CHEK2 locus, shared by affected CHEK2 variant carriers. Analysis of 62 individuals CHEK2 wild-type indicated that none presented the Hcac haplotype. The estimated age for this variant suggested that it was transmitted by a relatively recent common ancestor. CONCLUSIONS We identified a founder CHEK2 pathogenic variant, which is likely to underlie thyroid cancer and other cancer manifestations in the Roma population.
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Affiliation(s)
- Carolina Pires
- Unidade de Investigação em Patobiologia Molecular (UIPM), Instituto Português de Oncologia de Lisboa Francisco Gentil, Lisboa, Portugal
| | - Inês Jorge Marques
- Unidade de Investigação em Patobiologia Molecular (UIPM), Instituto Português de Oncologia de Lisboa Francisco Gentil, Lisboa, Portugal
- Chronic Diseases Research Centre (CEDOC), Universidade Nova de Lisboa, Lisboa, Portugal
- Nova Medical School/Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Daniela Dias
- Serviço de Endocrinologia, Instituto Português de Oncologia de Lisboa Francisco Gentil, Lisboa, Portugal
| | - Ana Saramago
- Unidade de Investigação em Patobiologia Molecular (UIPM), Instituto Português de Oncologia de Lisboa Francisco Gentil, Lisboa, Portugal
| | - Valeriano Leite
- Serviço de Endocrinologia, Instituto Português de Oncologia de Lisboa Francisco Gentil, Lisboa, Portugal
| | - Branca Maria Cavaco
- Unidade de Investigação em Patobiologia Molecular (UIPM), Instituto Português de Oncologia de Lisboa Francisco Gentil, Lisboa, Portugal.
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13
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Silva TP, Pereira CA, Raposo AC, Oliveira AR, Arez M, Cabral JMS, Milagre I, Carmo-Fonseca M, Rocha STD. Generation and characterization of induced pluripotent stem cells heterozygous for the Portuguese BRCA2 founder mutation. Stem Cell Res 2021; 53:102364. [PMID: 34087993 DOI: 10.1016/j.scr.2021.102364] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 04/05/2021] [Accepted: 04/18/2021] [Indexed: 10/21/2022] Open
Abstract
Women who inherit heterozygous mutations in the BRCA2 gene have an increased risk of developing cancer, mainly breast and ovarian tumors. A particular BRCA2 mutation (c.156_157insAlu) is exclusively found in families of Portuguese ancestry and is present in approximately 30% of all Portuguese families with hereditary breast and ovarian cancers. We report the generation and characterization of the first iPSC line from a female donor harboring the Portuguese BRCA2 founder mutation. Skin fibroblasts were reprogrammed using a non-integrative Sendai virus. These iPSCs are a valuable tool to study the origin of BRCA2-associated cancer in its earliest phases.
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Affiliation(s)
- Teresa P Silva
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Portugal; Departamento de Bioengenharia e Instituto de Bioengenharia e Biociências, Instituto Superior Técnico, Universidade de Lisboa, Portugal; Associate Laboratory i4HB - Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Portugal
| | | | - Ana Cláudia Raposo
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Portugal; Departamento de Bioengenharia e Instituto de Bioengenharia e Biociências, Instituto Superior Técnico, Universidade de Lisboa, Portugal; Associate Laboratory i4HB - Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Portugal
| | - Ana Rita Oliveira
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Portugal
| | - Maria Arez
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Portugal; Departamento de Bioengenharia e Instituto de Bioengenharia e Biociências, Instituto Superior Técnico, Universidade de Lisboa, Portugal; Associate Laboratory i4HB - Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Portugal
| | - Joaquim M S Cabral
- Departamento de Bioengenharia e Instituto de Bioengenharia e Biociências, Instituto Superior Técnico, Universidade de Lisboa, Portugal; Associate Laboratory i4HB - Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Portugal
| | - Inês Milagre
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Portugal
| | - Simão Teixeira da Rocha
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Portugal; Departamento de Bioengenharia e Instituto de Bioengenharia e Biociências, Instituto Superior Técnico, Universidade de Lisboa, Portugal; Associate Laboratory i4HB - Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Portugal.
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14
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Pócza T, Grolmusz VK, Papp J, Butz H, Patócs A, Bozsik A. Germline Structural Variations in Cancer Predisposition Genes. Front Genet 2021; 12:634217. [PMID: 33936164 PMCID: PMC8081352 DOI: 10.3389/fgene.2021.634217] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 03/08/2021] [Indexed: 12/14/2022] Open
Abstract
In addition to single nucleotide variations and small-scale indels, structural variations (SVs) also contribute to the genetic diversity of the genome. SVs, such as deletions, duplications, amplifications, or inversions may also affect coding regions of cancer-predisposing genes. These rearrangements may abrogate the open reading frame of these genes or adversely affect their expression and may thus act as germline mutations in hereditary cancer syndromes. With the capacity of disrupting the function of tumor suppressors, structural variations confer an increased risk of cancer and account for a remarkable fraction of heritability. The development of sequencing techniques enables the discovery of a constantly growing number of SVs of various types in cancer predisposition genes (CPGs). Here, we provide a comprehensive review of the landscape of germline SV types, detection methods, pathomechanisms, and frequency in CPGs, focusing on the two most common cancer syndromes: hereditary breast- and ovarian cancer and gastrointestinal cancers. Current knowledge about the possible molecular mechanisms driving to SVs is also summarized.
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Affiliation(s)
- Tímea Pócza
- Department of Molecular Genetics, National Institute of Oncology, Budapest, Hungary
| | - Vince Kornél Grolmusz
- Department of Molecular Genetics, National Institute of Oncology, Budapest, Hungary.,Hereditary Cancers Research Group, Hungarian Academy of Sciences, Semmelweis University, Budapest, Hungary
| | - János Papp
- Department of Molecular Genetics, National Institute of Oncology, Budapest, Hungary.,Hereditary Cancers Research Group, Hungarian Academy of Sciences, Semmelweis University, Budapest, Hungary
| | - Henriett Butz
- Department of Molecular Genetics, National Institute of Oncology, Budapest, Hungary.,Hereditary Cancers Research Group, Hungarian Academy of Sciences, Semmelweis University, Budapest, Hungary.,Department of Laboratory Medicine, Semmelweis University, Budapest, Hungary
| | - Attila Patócs
- Department of Molecular Genetics, National Institute of Oncology, Budapest, Hungary.,Hereditary Cancers Research Group, Hungarian Academy of Sciences, Semmelweis University, Budapest, Hungary.,Department of Laboratory Medicine, Semmelweis University, Budapest, Hungary
| | - Anikó Bozsik
- Department of Molecular Genetics, National Institute of Oncology, Budapest, Hungary.,Hereditary Cancers Research Group, Hungarian Academy of Sciences, Semmelweis University, Budapest, Hungary
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15
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Watson CM, Crinnion LA, Lindsay H, Mitchell R, Camm N, Robinson R, Joyce C, Tanteles GA, Halloran DJO, Pena SDJ, Carr IM, Bonthron DT. Assessing the utility of long-read nanopore sequencing for rapid and efficient characterization of mobile element insertions. J Transl Med 2021; 101:442-449. [PMID: 32989232 DOI: 10.1038/s41374-020-00489-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 09/09/2020] [Accepted: 09/10/2020] [Indexed: 12/16/2022] Open
Abstract
Short-read next generation sequencing (NGS) has become the predominant first-line technique used to diagnose patients with rare genetic conditions. Inherent limitations of short-read technology, notably for the detection and characterization of complex insertion-containing variants, are offset by the ability to concurrently screen many disease genes. "Third-generation" long-read sequencers are increasingly being deployed as an orthogonal adjunct technology, but their full potential for molecular genetic diagnosis has yet to be exploited. Here, we describe three diagnostic cases in which pathogenic mobile element insertions were refractory to characterization by short-read sequencing. To validate the accuracy of the long-read technology, we first used Sanger sequencing to confirm the integration sites and derive curated benchmark sequences of the variant-containing alleles. Long-read nanopore sequencing was then performed on locus-specific amplicons. Pairwise comparison between these data and the previously determined benchmark alleles revealed 100% identity of the variant-containing sequences. We demonstrate a number of technical advantages over existing wet-laboratory approaches, including in silico size selection of a mixed pool of amplification products, and the relative ease with which an automated informatics workflow can be established. Our findings add to a growing body of literature describing the diagnostic utility of long-read sequencing.
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Affiliation(s)
- Christopher M Watson
- Yorkshire and North East Genomic Laboratory Hub, Central Lab, St. James's University Hospital, Leeds, LS9 7TF, UK.
- Leeds Institute of Medical Research, University of Leeds, St. James's University Hospital, Leeds, LS9 7TF, UK.
| | - Laura A Crinnion
- Yorkshire and North East Genomic Laboratory Hub, Central Lab, St. James's University Hospital, Leeds, LS9 7TF, UK
- Leeds Institute of Medical Research, University of Leeds, St. James's University Hospital, Leeds, LS9 7TF, UK
| | - Helen Lindsay
- Yorkshire and North East Genomic Laboratory Hub, Central Lab, St. James's University Hospital, Leeds, LS9 7TF, UK
| | - Rowena Mitchell
- Yorkshire and North East Genomic Laboratory Hub, Central Lab, St. James's University Hospital, Leeds, LS9 7TF, UK
| | - Nick Camm
- Yorkshire and North East Genomic Laboratory Hub, Central Lab, St. James's University Hospital, Leeds, LS9 7TF, UK
| | - Rachel Robinson
- Yorkshire and North East Genomic Laboratory Hub, Central Lab, St. James's University Hospital, Leeds, LS9 7TF, UK
| | - Caroline Joyce
- Department of Endocrinology, Cork University Hospital, Wilton, Cork, Ireland
| | - George A Tanteles
- Department of Clinical Genetics, The Cyprus Institute of Neurology and Genetics, 6 International Airport Avenue, PO Box 23462, CY1683, Nicosia, Cyprus
| | | | | | - Ian M Carr
- Leeds Institute of Medical Research, University of Leeds, St. James's University Hospital, Leeds, LS9 7TF, UK
| | - David T Bonthron
- Leeds Institute of Medical Research, University of Leeds, St. James's University Hospital, Leeds, LS9 7TF, UK
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16
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Abstract
PURPOSE OF REVIEW Male breast cancer (MaBC) is a rare disease, and some challenges exist in its management because current treatment recommendations are extrapolated from trials that mostly excluded men. This review will revise all available data that could improve the treatment of MaBC, with a special focus on adjuvant systemic treatments. RECENT FINDINGS To date, men with hormone receptor-positive breast cancer, who are candidates for adjuvant endocrine therapy, should be offered tamoxifen (TAM) for five years. Additional five years are possible, according to tolerance and recurrence risk. If TAM is contraindicated, a gonadotropin-releasing hormone (GnRH) agonist or antagonist and aromatase inhibitor should be proposed. Chemotherapy and targeted therapy in the other breast cancer subtypes should be used with the same indications offered to women with breast cancer. All men with breast cancer should be offered genetic counseling and germline genetic testing of cancer predisposition genes. SUMMARY For decades, men with breast cancer have been treated suboptimally and denied the participation in clinical trials. Recently, many clinical trials started enrolling both genders, as strongly endorsed by the Food and Drug Administration. Hopefully, this turnaround will help subdue the disparities in the quality of care.
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Affiliation(s)
- Chiara Corti
- Department of Oncology and Haematology (DIPO), University of Milan.,Division of Early Drug Development for Innovative Therapy, European Institute of Oncology, IRCCS, Milan, Italy
| | - Edoardo Crimini
- Department of Oncology and Haematology (DIPO), University of Milan.,Division of Early Drug Development for Innovative Therapy, European Institute of Oncology, IRCCS, Milan, Italy
| | - Carmen Criscitiello
- Division of Early Drug Development for Innovative Therapy, European Institute of Oncology, IRCCS, Milan, Italy
| | - Dario Trapani
- Division of Early Drug Development for Innovative Therapy, European Institute of Oncology, IRCCS, Milan, Italy
| | - Giuseppe Curigliano
- Department of Oncology and Haematology (DIPO), University of Milan.,Division of Early Drug Development for Innovative Therapy, European Institute of Oncology, IRCCS, Milan, Italy
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17
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Deuitch N, Li ST, Courtney E, Shaw T, Dent R, Tan V, Yackowski L, Torene R, Berkofsky-Fessler W, Ngeow J. Early-onset breast cancer in a woman with a germline mobile element insertion resulting in BRCA2 disruption: a case report. Hum Genome Var 2020; 7:24. [PMID: 32884827 PMCID: PMC7447638 DOI: 10.1038/s41439-020-00111-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 08/03/2020] [Accepted: 08/03/2020] [Indexed: 11/24/2022] Open
Abstract
Mobile element insertions (MEIs) contribute to genomic diversity, but they can be responsible for human disease in some cases. Initial clinical testing (BRCA1, BRCA2 and PALB2) in a 40-year-old female with unilateral breast cancer did not detect any pathogenic variants. Subsequent reanalysis for MEIs detected a novel likely pathogenic insertion of the retrotransposon element (RE) c.7894_7895insSVA in BRCA2. This case highlights the importance of bioinformatic pipeline optimization for the detection of MEIs in genes associated with hereditary cancer, as early detection can significantly impact clinical management.
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Affiliation(s)
- Natalie Deuitch
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre, Singapore, Singapore
- Department of Genetics, Stanford University School of Medicine, Stanford, CA USA
| | - Shao-Tzu Li
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre, Singapore, Singapore
| | - Eliza Courtney
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre, Singapore, Singapore
| | - Tarryn Shaw
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre, Singapore, Singapore
| | - Rebecca Dent
- Division of Medical Oncology, National Cancer Centre, Singapore, Singapore
| | - Veronique Tan
- Division of Breast Surgical Oncology, National Cancer Centre, Singapore, Singapore
| | | | | | | | - Joanne Ngeow
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
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18
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Tubeuf H, Caputo SM, Sullivan T, Rondeaux J, Krieger S, Caux-Moncoutier V, Hauchard J, Castelain G, Fiévet A, Meulemans L, Révillion F, Léoné M, Boutry-Kryza N, Delnatte C, Guillaud-Bataille M, Cleveland L, Reid S, Southon E, Soukarieh O, Drouet A, Di Giacomo D, Vezain M, Bonnet-Dorion F, Bourdon V, Larbre H, Muller D, Pujol P, Vaz F, Audebert-Bellanger S, Colas C, Venat-Bouvet L, Solano AR, Stoppa-Lyonnet D, Houdayer C, Frebourg T, Gaildrat P, Sharan SK, Martins A. Calibration of Pathogenicity Due to Variant-Induced Leaky Splicing Defects by Using BRCA2 Exon 3 as a Model System. Cancer Res 2020; 80:3593-3605. [PMID: 32641407 DOI: 10.1158/0008-5472.can-20-0895] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/14/2020] [Accepted: 07/02/2020] [Indexed: 12/25/2022]
Abstract
BRCA2 is a clinically actionable gene implicated in breast and ovarian cancer predisposition that has become a high priority target for improving the classification of variants of unknown significance (VUS). Among all BRCA2 VUS, those causing partial/leaky splicing defects are the most challenging to classify because the minimal level of full-length (FL) transcripts required for normal function remains to be established. Here, we explored BRCA2 exon 3 (BRCA2e3) as a model for calibrating variant-induced spliceogenicity and estimating thresholds for BRCA2 haploinsufficiency. In silico predictions, minigene splicing assays, patients' RNA analyses, a mouse embryonic stem cell (mESC) complementation assay and retrieval of patient-related information were combined to determine the minimal requirement of FL BRCA2 transcripts. Of 100 BRCA2e3 variants tested in the minigene assay, 64 were found to be spliceogenic, causing mild to severe RNA defects. Splicing defects were also confirmed in patients' RNA when available. Analysis of a neutral leaky variant (c.231T>G) showed that a reduction of approximately 60% of FL BRCA2 transcripts from a mutant allele does not cause any increase in cancer risk. Moreover, data obtained from mESCs suggest that variants causing a decline in FL BRCA2 with approximately 30% of wild-type are not pathogenic, given that mESCs are fully viable and resistant to DNA-damaging agents in those conditions. In contrast, mESCs producing lower relative amounts of FL BRCA2 exhibited either null or hypomorphic phenotypes. Overall, our findings are likely to have broader implications on the interpretation of BRCA2 variants affecting the splicing pattern of other essential exons. SIGNIFICANCE: These findings demonstrate that BRCA2 tumor suppressor function tolerates substantial reduction in full-length transcripts, helping to determine the pathogenicity of BRCA2 leaky splicing variants, some of which may not increase cancer risk.
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Affiliation(s)
- Hélène Tubeuf
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France.,Interactive Biosoftware, Rouen, France
| | - Sandrine M Caputo
- Department of Genetics, Institut Curie, Paris, France.,PSL Research University, Paris, France
| | - Teresa Sullivan
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland
| | - Julie Rondeaux
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Sophie Krieger
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France.,Laboratory of Cancer Biology and Genetics, Centre François Baclesse, Caen, France - Normandie University, UNICAEN, Caen, France
| | | | - Julie Hauchard
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Gaia Castelain
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Alice Fiévet
- Department of Genetics, Institut Curie, Paris, France.,INSERM U830, University Paris Descartes, Paris, France.,Service Génétique des Tumeurs, Gustave Roussy, Villejuif, France
| | - Laëtitia Meulemans
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | | | | | | | | | | | - Linda Cleveland
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland
| | - Susan Reid
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland
| | - Eileen Southon
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland
| | - Omar Soukarieh
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Aurélie Drouet
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Daniela Di Giacomo
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Myriam Vezain
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | | | - Violaine Bourdon
- Department of Genetics, Institut Paoli-Calmettes, Marseille, France
| | - Hélène Larbre
- Laboratoire d'Oncogénétique Moléculaire, Institut Godinot, Reims, France
| | - Danièle Muller
- Unité d'Oncogénétique, Centre Paul Strauss, Strasbourg, France
| | - Pascal Pujol
- Unité d'Oncogénétique, CHU Arnaud de Villeneuve, Montpellier, France
| | - Fátima Vaz
- Breast Cancer Risk Evaluation Clinic, Portuguese Institute of Oncology of Lisbon, Lisbon, Portugal
| | | | - Chrystelle Colas
- Department of Genetics, Institut Curie, Paris, France.,PSL Research University, Paris, France
| | | | - Angela R Solano
- Genotipificacion y Cancer Hereditario, Departmento de Analisis Clinicos, Centro de Educacion Medica e Investigaciones Clinicas (CEMIC), Ciudad Autonoma de Buenos Aires, Argentina
| | - Dominique Stoppa-Lyonnet
- Department of Genetics, Institut Curie, Paris, France.,INSERM U830, University Paris Descartes, Paris, France
| | - Claude Houdayer
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France.,Department of Genetics, University Hospital, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Thierry Frebourg
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France.,Department of Genetics, University Hospital, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Pascaline Gaildrat
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Shyam K Sharan
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland
| | - Alexandra Martins
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France.
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Dawson LM, Smith KN, Werdyani S, Ndikumana R, Penney C, Wiede LL, Smith KL, Pater JA, MacMillan A, Green J, Drover S, Young TL, O'Rielly DD. A dominant RAD51C pathogenic splicing variant predisposes to breast and ovarian cancer in the Newfoundland population due to founder effect. Mol Genet Genomic Med 2019; 8:e1070. [PMID: 31782267 PMCID: PMC7005661 DOI: 10.1002/mgg3.1070] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 11/01/2019] [Accepted: 11/11/2019] [Indexed: 12/20/2022] Open
Abstract
Background RAD51C is important in DNA repair and individuals with pathogenic RAD51C variants have increased risk of hereditary breast and ovarian cancer syndrome (HBOC), an autosomal dominant genetic predisposition to early onset breast and/or ovarian cancer. Methods Five female HBOC probands sequenced negative for moderate‐ and high‐risk genes but shared a recurrent variant of uncertain significance in RAD51C (NM_058216.3: c.571 + 4A > G). Participant recruitment was followed by haplotype and case/control analyses, RNA splicing analysis, gene and protein expression assays, and Sanger sequencing of tumors. Results The RAD51C c.571 + 4A > G variant segregates with HBOC, with heterozygotes sharing a 5.07 Mbp haplotype. RAD51C c.571 + 4A > G is increased ~52‐fold in the Newfoundland population compared with the general Caucasian population and positive population controls share disease‐associated alleles, providing evidence of a founder effect. Splicing analysis confirmed in silico predictions that RAD51C c.571 + 4A > G causes exon 3 skipping, creating an immediate premature termination codon. Gene and protein expression were significantly reduced in a RAD51C c.571 + 4G > A heterozygote compared with a wild‐type relative. Sanger sequencing of tumors from two probands indicates loss‐of‐heterozygosity, suggesting loss of function. Conclusion The RAD51C c.571 + 4A > G variant affects mRNA splicing and should be re‐classified as pathogenic according to American College of Medical Genetics and Genomics guidelines.
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Affiliation(s)
- Lesa M Dawson
- Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada.,Eastern Health Authority, St. John's, NL, Canada
| | - Kerri N Smith
- Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Salem Werdyani
- Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Robyn Ndikumana
- Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Cindy Penney
- Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Louisa L Wiede
- Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Kendra L Smith
- Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Justin A Pater
- Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | | | - Jane Green
- Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Sheila Drover
- Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Terry-Lynn Young
- Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada.,Eastern Health Authority, St. John's, NL, Canada.,Centre for Translational Genomics, St. John's, NL, Canada
| | - Darren D O'Rielly
- Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada.,Eastern Health Authority, St. John's, NL, Canada.,Centre for Translational Genomics, St. John's, NL, Canada
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20
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Kim DH, Cho CH, Kwon SY, Ryoo NH, Jeon DS, Lee W, Ha JS. BRCA1/2 mutations, including large genomic rearrangements, among unselected ovarian cancer patients in Korea. J Gynecol Oncol 2019; 29:e90. [PMID: 30207098 PMCID: PMC6189434 DOI: 10.3802/jgo.2018.29.e90] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 06/19/2018] [Accepted: 07/18/2018] [Indexed: 12/18/2022] Open
Abstract
Objective We performed small-scale mutation and large genomic rearrangement (LGR) analysis of BRCA1/2 in ovarian cancer patients to determine the prevalence and the characteristics of the mutations. Methods All ovarian cancer patients who visited a single institution between September 2015 and April 2017 were included. Sanger sequencing, multiplex ligation-dependent probe amplification (MLPA), and long-range polymerase chain reaction (PCR) were performed to comprehensively study BRCA1/2. The genetic risk models BRCAPRO, Myriad, and BOADICEA were used to evaluate the mutation analysis. Results In total, 131 patients were enrolled. Of the 131 patients, Sanger sequencing identified 16 different BRCA1/2 small-scale mutations in 20 patients (15.3%). Two novel nonsense mutations were detected in 2 patients with a serous borderline tumor and a large-cell neuroendocrine carcinoma. MLPA analysis of BRCA1/2 in Sanger-negative patients revealed 2 LGRs. The LGRs accounted for 14.3% of all identified BRCA1 mutations, and the prevalence of LGRs identified in this study was 1.8% in 111 Sanger-negative patients. The genetic risk models showed statistically significant differences between mutation carriers and non-carriers. The 2 patients with LGRs had at least one blood relative with breast or ovarian cancer. Conclusion Twenty-two (16.8%) of the unselected ovarian cancer patients had BRCA1/2 mutations that were detected through comprehensive BRCA1/2 genetic testing. Ovarian cancer patients with Sanger-negative results should be considered for LGR detection if they have one blood relative with breast or ovarian cancer. The detection of more BRCA1/2 mutations in patients is important for efforts to provide targeted therapy to ovarian cancer patients.
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Affiliation(s)
- Do Hoon Kim
- Department of Laboratory Medicine, Keimyung University School of Medicine, Daegu, Korea
| | - Chi Heum Cho
- Department of Obstetrics and Gynecology, Keimyung University School of Medicine, Daegu, Korea
| | - Sun Young Kwon
- Department of Pathology, Keimyung University School of Medicine, Daegu, Korea
| | - Nam Hee Ryoo
- Department of Laboratory Medicine, Keimyung University School of Medicine, Daegu, Korea
| | - Dong Seok Jeon
- Department of Laboratory Medicine, Keimyung University School of Medicine, Daegu, Korea
| | - Wonmok Lee
- Department of Laboratory Medicine, Keimyung University School of Medicine, Daegu, Korea
| | - Jung Sook Ha
- Department of Laboratory Medicine, Keimyung University School of Medicine, Daegu, Korea.
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21
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André S, Pereira T, Silva F, Machado P, Vaz F, Aparício M, Silva GL, Pinto AE. Male breast cancer: Specific biological characteristics and survival in a Portuguese cohort. Mol Clin Oncol 2019; 10:644-654. [PMID: 31031981 PMCID: PMC6482395 DOI: 10.3892/mco.2019.1841] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 03/29/2019] [Indexed: 12/12/2022] Open
Abstract
Male breast cancer (BC) represents an individual subtype of BC, with therapeutic procedures based on female BC therapy results. The present study evaluated the parameters currently used for the characterization and therapy of male BC, and their association with disease-free (DFS) and overall survival (OS), aiming to obtain a comprehensive basis to improve the personalized care of male BC. A total of 196 patients from March 1970 to March 2018 (mean follow-up, 84.9 months) were profiled, using clinicopathological review, molecular assessment [BRCA1/2, DNA repair associated (BRCA1/2) status, immunohistochemistry, fluorescence in situ hybridization and DNA flow cytometry] and Cox regression statistical analysis. The median age of patients was 66.5 years. At presentation, 39.2% of patients with invasive carcinomas were in anatomic stage (AS) I. Patients exhibited primarily invasive carcinomas of no special type, histological grade 2, estrogen receptor α-(ERα) and progesterone receptor (PR)-positive, receptor tyrosine kinase erbB-2-negative, high Ki-67, Luminal B-like and aneuploid tumors. A total of 13 of the 44 (29.5%) BRCA-evaluated patients exhibited BRCA2 mutations, significantly associated with family history (FH), bilaterality, high Ki-67 expression, absence of PR and Luminal B-like tumors. Bilaterality was associated with the occurrence of non-breast primary neoplasms (NBPN). The 5 and 10-year DFS rates, excluding patients with distant metastasis, NBPN and in situ carcinomas (n=145) were 65.9 and 58.2%, respectively, and the 5 and 10-year OS rates were 77.5 and 59.2%, respectively. In the univariate analysis, Luminal B-like subtype, BRCA2 mutations, high Ki-67 expression, and AS II and III were significantly associated with shorter DFS and OS. In addition, age >70 years was associated with low OS. In the multivariate analysis, FH, AS II and III, and Luminal B-like subtypes were associated with poorer OS. In conclusion, the data from the present study emphasize the high incidence of BRCA2 mutation in male BC, and its association with FH, bilaterality, high Ki-67 expression, negative PR expression and Luminal B-like subtypes, and with shorter DFS and OS in univariate analysis.
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Affiliation(s)
- Saudade André
- Department of Pathology, Portuguese Institute of Oncology of Lisbon, 1099-023 Lisbon, Portugal
| | - Teresa Pereira
- Department of Pathology, Portuguese Institute of Oncology of Lisbon, 1099-023 Lisbon, Portugal
| | - Fernanda Silva
- NOVA Medical School, NOVA University, 1169-056 Lisbon, Portugal
| | - Patrícia Machado
- Breast Cancer Risk Evaluation Clinic, Portuguese Institute of Oncology of Lisbon, 1099-023 Lisbon, Portugal
| | - Fátima Vaz
- Breast Cancer Risk Evaluation Clinic, Portuguese Institute of Oncology of Lisbon, 1099-023 Lisbon, Portugal
| | - Mariana Aparício
- Department of Mathematics of Higher Technical Institute, University of Lisbon, Portugal
| | - Giovani L. Silva
- Department of Mathematics of Higher Technical Institute, University of Lisbon, Portugal
- Statistics and Applications Center of University of Lisbon, 1049-001 Lisbon, Portugal
| | - António E. Pinto
- Department of Pathology, Portuguese Institute of Oncology of Lisbon, 1099-023 Lisbon, Portugal
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22
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Abstract
Cancer is a common non-communicable disease worldwide, although it exhibits differential population trends in incidence and mortality rates. The differences relate to population structure, environmental risk factors as well as health system organization. This article discusses the potential impact of genetic testing on population health, focusing in particular on the mutational spectrum of breast cancer susceptibility genes in diverse populations. We identify the need for improved access to, and increased investment in, comprehensive cancer risk assessment and genetic testing as well as cancer control measures that take into account lifestyle, environmental, and social factors in understudied minority groups.
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23
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Palmero EI, Carraro DM, Alemar B, Moreira MAM, Ribeiro-Dos-Santos Â, Abe-Sandes K, Galvão HCR, Reis RM, de Pádua Souza C, Campacci N, Achatz MI, Brianese RC, da Cruz Formiga MN, Makdissi FB, Vargas FR, Evangelista Dos Santos AC, Seuanez HN, Lobo de Souza KR, Netto CBO, Santos-Silva P, da Silva GS, Burbano RMR, Santos S, Assumpção PP, Bernardes IMM, Machado-Lopes TMB, Bomfim TF, Toralles MBP, Nascimento I, Garicochea B, Simon SD, Noronha S, de Lima FT, Chami AM, Bittar CM, Bines J, Artigalas O, Esteves-Diz MDP, Lajus TBP, Gifoni ACLVC, Guindalini RSC, Cintra TS, Schwartz IVD, Bernardi P, Miguel D, Nogueira STDS, Herzog J, Weitzel JN, Ashton-Prolla P. The germline mutational landscape of BRCA1 and BRCA2 in Brazil. Sci Rep 2018; 8:9188. [PMID: 29907814 DOI: 10.1038/s41598-018-27315-2] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 05/23/2018] [Indexed: 02/08/2023] Open
Abstract
The detection of germline mutations in BRCA1 and BRCA2 is essential to the formulation of clinical management strategies, and in Brazil, there is limited access to these services, mainly due to the costs/availability of genetic testing. Aiming at the identification of recurrent mutations that could be included in a low-cost mutation panel, used as a first screening approach, we compiled the testing reports of 649 probands with pathogenic/likely pathogenic variants referred to 28 public and private health care centers distributed across 11 Brazilian States. Overall, 126 and 103 distinct mutations were identified in BRCA1 and BRCA2, respectively. Twenty-six novel variants were reported from both genes, and BRCA2 showed higher mutational heterogeneity. Some recurrent mutations were reported exclusively in certain geographic regions, suggesting a founder effect. Our findings confirm that there is significant molecular heterogeneity in these genes among Brazilian carriers, while also suggesting that this heterogeneity precludes the use of screening protocols that include recurrent mutation testing only. This is the first study to show that profiles of recurrent mutations may be unique to different Brazilian regions. These data should be explored in larger regional cohorts to determine if screening with a panel of recurrent mutations would be effective.
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24
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Fernandes GC, Michelli RAD, Galvão HCR, Paula AE, Pereira R, Andrade CE, Felicio PS, Souza CP, Mendes DRP, Volc S, Berardinelli GN, Grasel RS, Sabato CS, Viana DV, Mauad EC, Scapulatempo-Neto C, Arun B, Reis RM, Palmero EI. Prevalence of BRCA1/BRCA2 mutations in a Brazilian population sample at-risk for hereditary breast cancer and characterization of its genetic ancestry. Oncotarget 2018; 7:80465-80481. [PMID: 27741520 PMCID: PMC5348334 DOI: 10.18632/oncotarget.12610] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 10/01/2016] [Indexed: 11/25/2022] Open
Abstract
Background There are very few data about the mutational profile of families at-risk for hereditary breast and ovarian cancer (HBOC) from Latin America (LA) and especially from Brazil, the largest and most populated country in LA. Results Of the 349 probands analyzed, 21.5% were BRCA1/BRCA2 mutated, 65.3% at BRCA1 and 34.7% at BRCA2 gene. The mutation c.5266dupC (former 5382insC) was the most frequent alteration, representing 36.7% of the BRCA1 mutations and 24.0% of all mutations identified. Together with the BRCA1 c.3331_3334delCAAG mutation, these mutations constitutes about 35% of the identified mutations and more than 50% of the BRCA1 pathogenic mutations. Interestingly, six new mutations were identified. Additionally, 39 out of the 44 pathogenic mutations identified were not previously reported in the Brazilian population. Besides, 36 different variants of unknown significance (VUS) were identified. Regarding ancestry, average ancestry proportions were 70.6% European, 14.5% African, 8.0% Native American and 6.8% East Asian. Materials and methods This study characterized 349 Brazilian families at-risk for HBOC regarding their germline BRCA1/BRCA2 status and genetic ancestry. Conclusions This is the largest report of BRCA1/BRCA2 assessment in an at-risk HBOC Brazilian population. We identified 21.5% of patients harboring BRCA1/BRCA2 mutations and characterized the genetic ancestry of a sample group at-risk for hereditary breast cancer showing once again how admixed is the Brazilian population. No association was found between genetic ancestry and mutational status. The knowledge of the mutational profile in a population can contribute to the definition of more cost-effective strategies for the identification of HBOC families.
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Affiliation(s)
- Gabriela C Fernandes
- Center of Molecular Diagnosis, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | | | - Henrique C R Galvão
- Oncogenetics Department, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - André E Paula
- Center of Molecular Diagnosis, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - Rui Pereira
- Institute of Research and Innovation in Health, University of Porto, Porto, Portugal.,Institute of Molecular Pathology and Immunology at the University of Porto (IPATIMUP), Porto, Portugal
| | - Carlos E Andrade
- Oncogenetics Department, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - Paula S Felicio
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - Cristiano P Souza
- Oncogenetics Department, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - Deise R P Mendes
- Center of Molecular Diagnosis, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - Sahlua Volc
- Oncogenetics Department, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | | | - Rebeca S Grasel
- Oncogenetics Department, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - Cristina S Sabato
- Center of Molecular Diagnosis, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - Danilo V Viana
- Oncogenetics Department, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - Edmundo C Mauad
- Oncogenetics Department, Barretos Cancer Hospital, Barretos, São Paulo, Brazil.,Prevention Department, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - Cristovam Scapulatempo-Neto
- Center of Molecular Diagnosis, Barretos Cancer Hospital, Barretos, São Paulo, Brazil.,Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil.,Pathology Department, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - Banu Arun
- MD Anderson Cancer Center, Houston, Texas, USA
| | - Rui M Reis
- Center of Molecular Diagnosis, Barretos Cancer Hospital, Barretos, São Paulo, Brazil.,Oncogenetics Department, Barretos Cancer Hospital, Barretos, São Paulo, Brazil.,Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil.,Life and Health Sciences Research Institute (ICVS), Health Sciences School, University of Minho, Braga, Portugal.,ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Edenir I Palmero
- Center of Molecular Diagnosis, Barretos Cancer Hospital, Barretos, São Paulo, Brazil.,Oncogenetics Department, Barretos Cancer Hospital, Barretos, São Paulo, Brazil.,Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil.,Barretos School of Health Sciences, Dr. Paulo Prata-FACISB, São Paulo, Brazil
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25
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Freitas AC, Opinião A, Fragoso S, Nunes H, Santos M, Clara A, Bento S, Luis A, Silva J, Moura C, Filipe B, Machado P, Santos S, André S, Rodrigues P, Parreira J, Vaz F. Men seeking counselling in a Breast Cancer Risk Evaluation Clinic. Ecancermedicalscience 2018; 12:804. [PMID: 29456621 PMCID: PMC5813915 DOI: 10.3332/ecancer.2018.804] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Hereditary breast and ovary cancer syndrome affects both genders but little is known about the uptake of genetic services by men. The objective of this study is to characterise the male population counselled through a multidisciplinary breast/ovarian program. METHODS Descriptive analysis of male patients counselled from January 2000 to December 2015. Data in this analysis include new cancer diagnoses during prospective follow up. RESULTS From 4,320 families registered, 362 male patients were identified: 236 (65.2%) from hereditary cancer families (HCF) and 126 (34.8%) from non-HCF. In HCF, 121 patients (51.3%) were mutation carriers (MC): BRCA2 - 102 (84.3%), BRCA1 - 16 (13.2%), CHEK2 - 1 (0.8%) and TP53 - 2 (1.7%). Non-HCF included 126 patients: 85 (67.5%) belonged to families without pathogenic mutations or with variants of unknown clinical significance; 22 (17.5%) refused testing after counselling and 19 (15.0%) did not meet criteria for testing. Both HCF and non-HCF included patients with previous cancer diagnoses: HCF- Breast Cancer (BC) - 18; prostate cancer (PC) - 13; melanoma - 1; others - 7) and non-HCF (BC - 77; PC - 20; gastric cancer (GC) - 1; melanoma - 8; bladder cancer - 1; others - 22). From the 121 MC identified (including the TP53 and CHEK2 carriers), 97 patients (80.2%) adhered to prospective surveillance. With a median follow-up of 36.9 months, 17 cancers were diagnosed in 14 patients, PC being the most frequently diagnosed neoplasia (5 cases). Eleven patients (78.6%) are alive and three patients died of advanced cancer (2 with GC, 1 with disseminated adenocarcinoma). CONCLUSION We observed a high adherence to counselling, genetic testing and active surveillance by men belonging to hereditary BC families. Male carriers of pathogenic DNA variants are at risk for several cancers and should be included in prospective follow-up studies.
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Affiliation(s)
- Ana Catarina Freitas
- Service of Medical Oncology, Instituto Português de Oncologia de Lisboa Francisco Gentil, Rua Professor Lima Bastos, 1099-023 Lisboa, Portugal
| | - Ana Opinião
- Service of Medical Oncology, Instituto Português de Oncologia de Lisboa Francisco Gentil, Rua Professor Lima Bastos, 1099-023 Lisboa, Portugal
- Breast Cancer Risk Evaluation Clinic, Instituto Português de Oncologia de Lisboa Francisco Gentil, Rua Professor Lima Bastos, 1099-023 Lisboa, Portugal
| | - Sofia Fragoso
- Molecular Pathobiology Research Unit, Instituto Português de Oncologia de Lisboa Francisco Gentil, Rua Professor Lima Bastos, 1099-023 Lisboa, Portugal
| | - Hugo Nunes
- Service of Medical Oncology, Instituto Português de Oncologia de Lisboa Francisco Gentil, Rua Professor Lima Bastos, 1099-023 Lisboa, Portugal
| | - Madalena Santos
- Service of Medical Oncology, Instituto Português de Oncologia de Lisboa Francisco Gentil, Rua Professor Lima Bastos, 1099-023 Lisboa, Portugal
| | - Ana Clara
- Service of Medical Oncology, Instituto Português de Oncologia de Lisboa Francisco Gentil, Rua Professor Lima Bastos, 1099-023 Lisboa, Portugal
- Breast Cancer Risk Evaluation Clinic, Instituto Português de Oncologia de Lisboa Francisco Gentil, Rua Professor Lima Bastos, 1099-023 Lisboa, Portugal
| | - Sandra Bento
- Breast Cancer Risk Evaluation Clinic, Instituto Português de Oncologia de Lisboa Francisco Gentil, Rua Professor Lima Bastos, 1099-023 Lisboa, Portugal
| | - Ana Luis
- Service of Medical Oncology, Instituto Português de Oncologia de Lisboa Francisco Gentil, Rua Professor Lima Bastos, 1099-023 Lisboa, Portugal
- Breast Cancer Risk Evaluation Clinic, Instituto Português de Oncologia de Lisboa Francisco Gentil, Rua Professor Lima Bastos, 1099-023 Lisboa, Portugal
| | - Jorge Silva
- Breast Cancer Risk Evaluation Clinic, Instituto Português de Oncologia de Lisboa Francisco Gentil, Rua Professor Lima Bastos, 1099-023 Lisboa, Portugal
- Service of Urology, Instituto Português de Oncologia de Lisboa Francisco Gentil, Rua Professor Lima Bastos, 1099-023 Lisboa, Portugal
| | - Cecília Moura
- Service of Dermatology, Instituto Português de Oncologia de Lisboa Francisco Gentil, Rua Professor Lima Bastos, 1099-023 Lisboa, Portugal
| | - Bruno Filipe
- Molecular Pathobiology Research Unit, Instituto Português de Oncologia de Lisboa Francisco Gentil, Rua Professor Lima Bastos, 1099-023 Lisboa, Portugal
| | - Patrícia Machado
- Molecular Pathobiology Research Unit, Instituto Português de Oncologia de Lisboa Francisco Gentil, Rua Professor Lima Bastos, 1099-023 Lisboa, Portugal
| | - Sidónia Santos
- Molecular Pathobiology Research Unit, Instituto Português de Oncologia de Lisboa Francisco Gentil, Rua Professor Lima Bastos, 1099-023 Lisboa, Portugal
| | - Saudade André
- Laboratorial Diagnosis Department, Instituto Português de Oncologia de Lisboa Francisco Gentil, Rua Professor Lima Bastos, 1099-023 Lisboa, Portugal
| | - Paula Rodrigues
- Breast Cancer Risk Evaluation Clinic, Instituto Português de Oncologia de Lisboa Francisco Gentil, Rua Professor Lima Bastos, 1099-023 Lisboa, Portugal
| | - Joana Parreira
- Breast Cancer Risk Evaluation Clinic, Instituto Português de Oncologia de Lisboa Francisco Gentil, Rua Professor Lima Bastos, 1099-023 Lisboa, Portugal
| | - Fátima Vaz
- Service of Medical Oncology, Instituto Português de Oncologia de Lisboa Francisco Gentil, Rua Professor Lima Bastos, 1099-023 Lisboa, Portugal
- Breast Cancer Risk Evaluation Clinic, Instituto Português de Oncologia de Lisboa Francisco Gentil, Rua Professor Lima Bastos, 1099-023 Lisboa, Portugal
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Hoorntje ET, Bollen IA, Barge-Schaapveld DQ, van Tienen FH, Te Meerman GJ, Jansweijer JA, van Essen AJ, Volders PG, Constantinescu AA, van den Akker PC, van Spaendonck-Zwarts KY, Oldenburg RA, Marcelis CL, van der Smagt JJ, Hennekam EA, Vink A, Bootsma M, Aten E, Wilde AA, van den Wijngaard A, Broers JL, Jongbloed JD, van der Velden J, van den Berg MP, van Tintelen JP. Lamin A/C-Related Cardiac Disease: Late Onset With a Variable and Mild Phenotype in a Large Cohort of Patients With the Lamin A/C p.(Arg331Gln) Founder Mutation. ACTA ACUST UNITED AC 2018; 10:CIRCGENETICS.116.001631. [PMID: 28790152 DOI: 10.1161/circgenetics.116.001631] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Accepted: 05/08/2017] [Indexed: 11/16/2022]
Abstract
BACKGROUND Interpretation of missense variants can be especially difficult when the variant is also found in control populations. This is what we encountered for the LMNA c.992G>A (p.(Arg331Gln)) variant. Therefore, to evaluate the effect of this variant, we combined an evaluation of clinical data with functional experiments and morphological studies. METHODS AND RESULTS Clinical data of 23 probands and 35 family members carrying this variant were retrospectively collected. A time-to-event analysis was performed to compare the course of the disease with carriers of other LMNA mutations. Myocardial biopsies were studied with electron microscopy and by measuring force development of the sarcomeres. Morphology of the nuclear envelope was assessed with immunofluorescence on cultured fibroblasts. The phenotype in probands and family members was characterized by atrioventricular conduction disturbances (61% and 44%, respectively), supraventricular arrhythmias (69% and 52%, respectively), and dilated cardiomyopathy (74% and 14%, respectively). LMNA p.(Arg331Gln) carriers had a significantly better outcome regarding the composite end point (malignant ventricular arrhythmias, end-stage heart failure, or death) compared with carriers of other pathogenic LMNA mutations. A shared haplotype of 1 Mb around LMNA suggested a common founder. The combined logarithm of the odds score was 3.46. Force development in membrane-permeabilized cardiomyocytes was reduced because of decreased myofibril density. Structural nuclear LMNA-associated envelope abnormalities, that is, blebs, were confirmed by electron microscopy and immunofluorescence microscopy. CONCLUSIONS Clinical, morphological, functional, haplotype, and segregation data all indicate that LMNA p.(Arg331Gln) is a pathogenic founder mutation with a phenotype reminiscent of other LMNA mutations but with a more benign course.
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Affiliation(s)
| | - Ilse A Bollen
- For the author affiliations, please see the Appendix
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Aryan Vink
- For the author affiliations, please see the Appendix
| | | | - Emmelien Aten
- For the author affiliations, please see the Appendix
| | | | | | - Jos L Broers
- For the author affiliations, please see the Appendix
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Ferrer-Avargues R, Díez-Obrero V, Martín-Tomás E, Hernández-Illán E, Castillejo MI, Codoñer-Alejos A, Barberá VM, Sánchez-Heras AB, Segura Á, Juan MJ, Tena I, Castillejo A, Soto JL. Characterization of a novel POLD1 missense founder mutation in a Spanish population. J Gene Med 2017; 19. [PMID: 28306219 DOI: 10.1002/jgm.2951] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 03/14/2017] [Accepted: 03/14/2017] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND We identified a new and a recurrent POLD1 mutation associated with predisposition to colorectal cancer (CRC). We characterized the molecular and clinical nature of the potential POLD1 founder mutation in families from Valencia (Spain). METHODS Clinical and molecular data were collected from four independent families known to have a POLD1 Leu474Pro mutation. To establish its founder effect, haplotype construction was performed using 14 flanking POLD1 polymorphic markers. We calculated penetrance estimates and clinical expressivity, globally and stratified by age and sex. RESULTS We included 32 individuals from the four families: 20 carriers and 12 noncarriers. A common haplotype was identified in these families in a region comprising 2,995 Mb, confirming L474P as the first founder POLD1 mutation identified. Thirteen tumors diagnosed in 10 POLD1 carriers: eight CRC, three endometrial and two other tumors were considered. The median age of cancer onset for POLD1 mutation carriers was 48 years. The observed penetrance was 50% and the cumulative risk at age of 50 years was 30%. CONCLUSIONS The findings of the present study contribute to a better understanding of CRC genetics in the Spanish population. The clinical phenotype for this mutation is similar to that in Lynch syndrome. Future studies using next generation sequencing with large gene panels for any hereditary cancer condition will offer the possibility of detecting POLE/POLD1 mutations in unsuspected clinical situations, demonstrating a more real and unbiased picture of the associated phenotype.
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Affiliation(s)
| | | | | | - Eva Hernández-Illán
- Instituto Investigación Sanitaria y Biomédica Alicante (ISABIAL), Alicante, Spain.,Unidad Investigación, Hospital Universitario Alicante, Alicante, Spain
| | | | | | - Víctor-Manuel Barberá
- Unidad Genética Molecular, Hospital Universitario Elche, Elche, Spain.,Instituto Investigación Sanitaria y Biomédica Alicante (ISABIAL), Alicante, Spain
| | | | - Ángel Segura
- Consejo Genético en Cáncer, Hospital Universitario La Fe, Valencia, Spain
| | - María-José Juan
- Consejo Genético en Cáncer, Fundación Instituto Valenciano Oncología, Valencia, Spain
| | - Isabel Tena
- Consejo Genético en Cáncer, Hospital Provincial Castellón, Castellón, Spain
| | - Adela Castillejo
- Unidad Genética Molecular, Hospital Universitario Elche, Elche, Spain
| | - José-Luis Soto
- Unidad Genética Molecular, Hospital Universitario Elche, Elche, Spain.,Instituto Investigación Sanitaria y Biomédica Alicante (ISABIAL), Alicante, Spain
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Llanos AAM, Warner WA, Luciani S, Lee TY, Bajracharya S, Slovacek S, Roach V, Lamont-Greene M. Gynecologic cancer mortality in Trinidad and Tobago and comparisons of mortality-to-incidence rate ratios across global regions. Cancer Causes Control 2017; 28:1251-1263. [PMID: 28917021 PMCID: PMC5909810 DOI: 10.1007/s10552-017-0961-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 09/08/2017] [Indexed: 12/30/2022]
Abstract
PURPOSE To examine the factors associated with gynecologic cancer mortality risks, to estimate the mortality-to-incidence rate ratios (MIR) in Trinidad and Tobago (TT), and to compare the MIRs to those of select countries. METHODS Data on 3,915 incident gynecologic cancers reported to the National Cancer Registry of TT from 1 January 1995 to 31 December 2009 were analyzed using proportional hazards models to determine factors associated with mortality. MIRs for cervical, endometrial, and ovarian cancers were calculated using cancer registry data (TT), GLOBOCAN 2012 incidence data, and WHO Mortality Database 2012 data (WHO regions and select countries). RESULTS Among the 3,915 incident gynecologic cancers diagnosed in TT during the study period, 1,795 (45.8%) were cervical, 1,259 (32.2%) were endometrial, and 861 (22.0%) were ovarian cancers. Older age, African ancestry, geographic residence, tumor stage, and treatment non-receipt were associated with increased gynecologic cancer mortality in TT. Compared to GLOBOCAN 2012 data, TT MIR estimates for cervical (0.49 vs. 0.53), endometrial (0.61 vs. 0.65), and ovarian cancers (0.32 vs. 0.48) were elevated. While the Caribbean region had intermediate gynecologic cancer MIRs, MIRs in TT were among the highest of the countries examined in the Caribbean region. CONCLUSIONS Given its status as a high-income economy, the relatively high gynecologic cancer MIRs observed in TT are striking. These findings highlight the urgent need for improved cancer surveillance, screening, and treatment for these (and other) cancers in this Caribbean nation.
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Affiliation(s)
- Adana A M Llanos
- Department of Epidemiology, Rutgers School of Public Health and Division of Population Science, Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, USA.
- Department of Epidemiology, Rutgers School of Public Health, 683 Hoes Lane West, Room 211, Piscataway, NJ, 08854, USA.
| | - Wayne A Warner
- Oncology Division, Department of Cell Biology and Physiology, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Silvana Luciani
- Cancer Prevention and Control, Pan American Health Organization, Washington, DC, USA
| | - Tammy Y Lee
- Division of Applied and Advanced Studies in Education, California State University, Los Angeles, CA, USA
| | - Smriti Bajracharya
- Center for Public Health Systems Science, George Warren Brown School of Social Work, Washington University, St. Louis, MO, USA
| | - Simeon Slovacek
- Division of Applied and Advanced Studies in Education, California State University, Los Angeles, CA, USA
| | - Veronica Roach
- Dr. Elizabeth Quamina Cancer Registry, Eric Williams Medical Sciences Complex, Mt. Hope, Trinidad and Tobago
| | - Marjorie Lamont-Greene
- Dr. Elizabeth Quamina Cancer Registry, Eric Williams Medical Sciences Complex, Mt. Hope, Trinidad and Tobago
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Hoorntje ET, van Spaendonck-Zwarts KY, Te Rijdt WP, Boven L, Vink A, van der Smagt JJ, Asselbergs FW, van Wijngaarden J, Hennekam EA, Pinto YM, Lekanne Deprez RH, Barge-Schaapveld DQCM, Bootsma M, Regieli J, Hoedemaekers YM, Jongbloed JDH, van den Berg MP, van Tintelen JP. The first titin (c.59926 + 1G > A) founder mutation associated with dilated cardiomyopathy. Eur J Heart Fail 2017; 20:803-806. [PMID: 29057560 PMCID: PMC5993291 DOI: 10.1002/ejhf.1030] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 09/04/2017] [Indexed: 11/12/2022] Open
Affiliation(s)
- Edgar T Hoorntje
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands.,Netherlands Heart Institute, Utrecht, the Netherlands
| | | | - Wouter P Te Rijdt
- Department of Cardiology, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - Ludolf Boven
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - Aryan Vink
- Department of Pathology, University Medical Centre Utrecht, Utrecht, the Netherlands
| | | | - Folkert W Asselbergs
- Department of Cardiology, Division Heart & Lungs, University Medical Centre Utrecht, Utrecht, the Netherlands.,Durrer Centre for Cardiovascular Research, Netherlands Heart Institute, Utrecht, the Netherlands.,Institute of Cardiovascular Science, Faculty of Population Health Sciences, University College London, London, UK
| | | | - Eric A Hennekam
- Department of Genetics, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Yigal M Pinto
- Department of Cardiology, Academic Medical Centre, Amsterdam, the Netherlands
| | - Ronald H Lekanne Deprez
- Department of Clinical Genetics, Academic Medical Centre, University of Amsterdam, Amsterdam, the Netherlands
| | | | - Marianne Bootsma
- Department of Cardiology, Leiden University Medical Centre, Leiden, the Netherlands
| | - Jakub Regieli
- Department of Cardiology, Isala Clinics, Zwolle, the Netherlands.,Heart Clinic, Amsterdam, the Netherlands
| | - Yvonne M Hoedemaekers
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - Jan D H Jongbloed
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - Maarten P van den Berg
- Department of Cardiology, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - J Peter van Tintelen
- Netherlands Heart Institute, Utrecht, the Netherlands.,Department of Clinical Genetics, Academic Medical Centre, University of Amsterdam, Amsterdam, the Netherlands
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van der Linde IHM, Hiemstra YL, Bökenkamp R, van Mil AM, Breuning MH, Ruivenkamp C, Ten Broeke SW, Veldkamp RF, van Waning JI, van Slegtenhorst MA, van Spaendonck-Zwarts KY, Lekanne Deprez RH, Herkert JC, Boven L, van der Zwaag PA, Jongbloed JDH, Bootsma M, Barge-Schaapveld DQCM. A Dutch MYH7 founder mutation, p.(Asn1918Lys), is associated with early onset cardiomyopathy and congenital heart defects. Neth Heart J 2017; 25:675-681. [PMID: 28864942 PMCID: PMC5691818 DOI: 10.1007/s12471-017-1037-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 08/22/2017] [Indexed: 02/07/2023] Open
Abstract
Background Mutations in the myosin heavy chain 7 (MYH7) gene commonly cause cardiomyopathy but are less frequently associated with congenital heart defects. Methods In this study, we describe a mutation in the MYH7 gene, c. 5754C > G; p. (Asn1918Lys), present in 15 probands and 65 family members. Results Of the 80 carriers (age range 0–88 years), 46 (57.5%) had cardiomyopathy (mainly dilated cardiomyopathy (DCM)) and seven (8.8%) had a congenital heart defect. Childhood onset of cardiomyopathy was present in almost 10% of carriers. However, in only a slight majority (53.7%) was the left ventricular ejection fraction reduced and almost no arrhythmias or conduction disorders were noted. Moreover, only one carrier required heart transplantation and nine (11.3%) an implantable cardioverter defibrillator. In addition, the standardised mortality ratio for MYH7 carriers was not significantly increased. Whole exome sequencing in several cases with paediatric onset of DCM and one with isolated congenital heart defects did not reveal additional known disease-causing variants. Haplotype analysis suggests that the MYH7 variant is a founder mutation, and is therefore the first Dutch founder mutation identified in the MYH7 gene. The mutation appears to have originated in the western region of the province of South Holland between 500 and 900 years ago. Conclusion Clinically, the p. (Asn1918Lys) mutation is associated with congenital heart defects and/or cardiomyopathy at young age but with a relatively benign course. Electronic supplementary material The online version of this article (10.1007/s12471-017-1037-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- I H M van der Linde
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Y L Hiemstra
- Department of Cardiology, Leiden University Medical Centre, Leiden, The Netherlands
| | - R Bökenkamp
- Department of Paediatric Cardiology, Leiden University Medical Centre, Leiden, The Netherlands
| | - A M van Mil
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - M H Breuning
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - C Ruivenkamp
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - S W Ten Broeke
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - R F Veldkamp
- Department of Cardiology, Haaglanden Medical Centre, The Hague, The Netherlands
| | - J I van Waning
- Department of Clinical Genetics, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - M A van Slegtenhorst
- Department of Clinical Genetics, Erasmus Medical Centre, Rotterdam, The Netherlands
| | | | - R H Lekanne Deprez
- Department of Clinical Genetics, Academic Medical Centre, Amsterdam, The Netherlands
| | - J C Herkert
- University Medical Centre Groningen, Department of Genetics, University of Groningen, Groningen, The Netherlands
| | - L Boven
- University Medical Centre Groningen, Department of Genetics, University of Groningen, Groningen, The Netherlands
| | - P A van der Zwaag
- University Medical Centre Groningen, Department of Genetics, University of Groningen, Groningen, The Netherlands
| | - J D H Jongbloed
- University Medical Centre Groningen, Department of Genetics, University of Groningen, Groningen, The Netherlands
| | - M Bootsma
- Department of Cardiology, Leiden University Medical Centre, Leiden, The Netherlands
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31
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Qian Y, Mancini-DiNardo D, Judkins T, Cox HC, Brown K, Elias M, Singh N, Daniels C, Holladay J, Coffee B, Bowles KR, Roa BB. Identification of pathogenic retrotransposon insertions in cancer predisposition genes. Cancer Genet 2017; 216-217:159-169. [PMID: 29025590 DOI: 10.1016/j.cancergen.2017.08.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 08/09/2017] [Accepted: 08/11/2017] [Indexed: 12/31/2022]
Abstract
Cancer risks have been previously reported for some retrotransposon element (RE) insertions; however, detection of these insertions is technically challenging and very few oncogenic RE insertions have been reported. Here we evaluate RE insertions identified during hereditary cancer genetic testing using a comprehensive testing strategy. Individuals who had single-syndrome or pan-cancer hereditary cancer genetic testing from February 2004 to March 2017 were included. RE insertions were identified using Sanger sequencing, Next Generation Sequencing, or multiplex quantitative PCR, and further characterized using targeted PCR and sequencing analysis. Personal cancer history, ancestry, and haplotype were evaluated. A total of 37 unique RE insertions were identified in 10 genes, affecting 211 individuals. BRCA2 accounted for 45.9% (17/37) of all unique RE insertions. Several RE insertions were detected with high frequency in populations of conserved ancestry wherein up to 100% of carriers shared a high degree of haplotype conservation, suggesting founder effects. Our comprehensive testing strategy resulted in a substantial increase in the number of reported oncogenic RE insertions, several of which may have possible founder effects. Collectively, these data show that the detection of RE insertions is an important component of hereditary cancer genetic testing and may be more prevalent than previously reported.
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Affiliation(s)
- Yaping Qian
- Myriad Genetic Laboratories, Inc., 320 Wakara Way, Salt Lake City, UT 84108, USA
| | | | - Thaddeus Judkins
- Myriad Genetic Laboratories, Inc., 320 Wakara Way, Salt Lake City, UT 84108, USA
| | - Hannah C Cox
- Myriad Genetic Laboratories, Inc., 320 Wakara Way, Salt Lake City, UT 84108, USA
| | - Krystal Brown
- Myriad Genetic Laboratories, Inc., 320 Wakara Way, Salt Lake City, UT 84108, USA
| | - Maria Elias
- Myriad Genetic Laboratories, Inc., 320 Wakara Way, Salt Lake City, UT 84108, USA
| | - Nanda Singh
- Myriad Genetic Laboratories, Inc., 320 Wakara Way, Salt Lake City, UT 84108, USA
| | - Courtney Daniels
- Myriad Genetic Laboratories, Inc., 320 Wakara Way, Salt Lake City, UT 84108, USA
| | - Jayson Holladay
- Myriad Genetic Laboratories, Inc., 320 Wakara Way, Salt Lake City, UT 84108, USA
| | - Bradford Coffee
- Myriad Genetic Laboratories, Inc., 320 Wakara Way, Salt Lake City, UT 84108, USA
| | - Karla R Bowles
- Myriad Genetic Laboratories, Inc., 320 Wakara Way, Salt Lake City, UT 84108, USA
| | - Benjamin B Roa
- Myriad Genetic Laboratories, Inc., 320 Wakara Way, Salt Lake City, UT 84108, USA.
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Davy G, Rousselin A, Goardon N, Castéra L, Harter V, Legros A, Muller E, Fouillet R, Brault B, Smirnova AS, Lemoine F, de la Grange P, Guillaud-Bataille M, Caux-Moncoutier V, Houdayer C, Bonnet F, Blanc-Fournier C, Gaildrat P, Frebourg T, Martins A, Vaur D, Krieger S. Detecting splicing patterns in genes involved in hereditary breast and ovarian cancer. Eur J Hum Genet 2017; 25:1147-1154. [PMID: 28905878 DOI: 10.1038/ejhg.2017.116] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 05/13/2017] [Accepted: 06/13/2017] [Indexed: 12/15/2022] Open
Abstract
Interpretation of variants of unknown significance (VUS) is a major challenge for laboratories performing molecular diagnosis of hereditary breast and ovarian cancer (HBOC), especially considering that many genes are now known to be involved in this syndrome. One important way these VUS can have a functional impact is through their effects on RNA splicing. Here we present a custom RNA-Seq assay plus bioinformatics and biostatistics pipeline to analyse specifically alternative and abnormal splicing junctions in 11 targeted HBOC genes. Our pipeline identified 14 new alternative splices in BRCA1 and BRCA2 in addition to detecting the majority of known alternative spliced transcripts therein. We provide here the first global splicing pattern analysis for the other nine genes, which will enable a comprehensive interpretation of splicing defects caused by VUS in HBOC. Previously known splicing alterations were consistently detected, occasionally with a more complex splicing pattern than expected. We also found that splicing in the 11 genes is similar in blood and breast tissue, supporting the utility and simplicity of blood splicing assays. Our pipeline is ready to be integrated into standard molecular diagnosis for HBOC, but it could equally be adapted for an integrative analysis of any multigene disorder.
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Affiliation(s)
- Grégoire Davy
- Department of Cancer Biology and Genetics, CLCC François Baclesse, Normandy Centre for Genomic and Personalized Medicine, Caen, France.,Inserm U1079-IRIB, Normandy Centre for Genomic and Personalized Medicine, University of Rouen, Rouen, France
| | - Antoine Rousselin
- Department of Cancer Biology and Genetics, CLCC François Baclesse, Normandy Centre for Genomic and Personalized Medicine, Caen, France.,Inserm U1079-IRIB, Normandy Centre for Genomic and Personalized Medicine, University of Rouen, Rouen, France
| | - Nicolas Goardon
- Department of Cancer Biology and Genetics, CLCC François Baclesse, Normandy Centre for Genomic and Personalized Medicine, Caen, France.,Inserm U1079-IRIB, Normandy Centre for Genomic and Personalized Medicine, University of Rouen, Rouen, France
| | - Laurent Castéra
- Department of Cancer Biology and Genetics, CLCC François Baclesse, Normandy Centre for Genomic and Personalized Medicine, Caen, France.,Inserm U1079-IRIB, Normandy Centre for Genomic and Personalized Medicine, University of Rouen, Rouen, France
| | - Valentin Harter
- Cancéropôle Nord-Ouest Data Processing Centre, CLCC François Baclesse, Caen, France
| | - Angelina Legros
- Department of Cancer Biology and Genetics, CLCC François Baclesse, Normandy Centre for Genomic and Personalized Medicine, Caen, France
| | - Etienne Muller
- Department of Cancer Biology and Genetics, CLCC François Baclesse, Normandy Centre for Genomic and Personalized Medicine, Caen, France.,Inserm U1079-IRIB, Normandy Centre for Genomic and Personalized Medicine, University of Rouen, Rouen, France
| | - Robin Fouillet
- Department of Cancer Biology and Genetics, CLCC François Baclesse, Normandy Centre for Genomic and Personalized Medicine, Caen, France
| | - Baptiste Brault
- Department of Cancer Biology and Genetics, CLCC François Baclesse, Normandy Centre for Genomic and Personalized Medicine, Caen, France.,Inserm U1079-IRIB, Normandy Centre for Genomic and Personalized Medicine, University of Rouen, Rouen, France
| | - Anna S Smirnova
- Inserm U1079-IRIB, Normandy Centre for Genomic and Personalized Medicine, University of Rouen, Rouen, France
| | - Fréderic Lemoine
- GenoSplice Technology, iPEPS-ICM, Pitié-Salpétrière Hospital, Paris, France
| | | | | | | | - Claude Houdayer
- Department of Genetics, Institut Curie, Paris, France.,Inserm U830, Paris, France.,Université Paris-Descartes, Sorbonne Paris Cité, Paris, France
| | - Françoise Bonnet
- Laboratory of Molecular Genetics, Institut Bergonié, Bordeaux, France
| | - Cécile Blanc-Fournier
- Department of Pathology, CLCC François Baclesse, Caen, France.,Tumorothèque de Caen Basse-Normandie, Caen, France
| | - Pascaline Gaildrat
- Inserm U1079-IRIB, Normandy Centre for Genomic and Personalized Medicine, University of Rouen, Rouen, France
| | - Thierry Frebourg
- Inserm U1079-IRIB, Normandy Centre for Genomic and Personalized Medicine, University of Rouen, Rouen, France.,Department of Genetics, University Hospital, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Alexandra Martins
- Inserm U1079-IRIB, Normandy Centre for Genomic and Personalized Medicine, University of Rouen, Rouen, France
| | - Dominique Vaur
- Department of Cancer Biology and Genetics, CLCC François Baclesse, Normandy Centre for Genomic and Personalized Medicine, Caen, France.,Inserm U1079-IRIB, Normandy Centre for Genomic and Personalized Medicine, University of Rouen, Rouen, France
| | - Sophie Krieger
- Department of Cancer Biology and Genetics, CLCC François Baclesse, Normandy Centre for Genomic and Personalized Medicine, Caen, France.,Inserm U1079-IRIB, Normandy Centre for Genomic and Personalized Medicine, University of Rouen, Rouen, France.,University of Caen Normandy, Caen, France
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McVeigh TP, Cody N, Carroll C, Duff M, Farrell M, Bradley L, Gallagher D, McDevitt T, Green AJ. Recurrent large genomic rearrangements in BRCA1 and BRCA2 in an Irish case series. Cancer Genet 2017; 214-215:1-8. [PMID: 28595730 DOI: 10.1016/j.cancergen.2017.02.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 02/24/2017] [Accepted: 02/25/2017] [Indexed: 12/12/2022]
Abstract
Mutations in BRCA1 and BRCA2 confer a highly increased risk of cancers, mainly of the breast and ovary. Most variants are point mutations or small insertions/deletions detectable by Sanger sequencing. Large genomic rearrangements, including deletions/duplications of multiple exons, are not routinely detectable by Sanger sequencing, but can be reliably identified by Multiplex Ligation-dependent Probe Amplification (MLPA), and account for 5-17% mutations in different populations. Comprehensive mutation testing using these two methods has been facilitated via our centre since 2005. The aim of this study was to investigate the incidence of and phenotype associated with large genomic rearrangements in BRCA1 and BRCA2 in an Irish cohort. An observational cohort study was undertaken. Patients with large genomic rearrangements in BRCA1/BRCA2 were identified from a prospectively maintained database of MLPA test results. Phenotypic and genotypic data were retrieved by chart review. Large genomic rearrangements in BRCA1 were identified in 49 families; and in BRCA2 in 7 families, representing ~11% of mutations in BRCA1/BRCA2 in Ireland. The most common large genomic rearrangement in BRCA1 was deletion of exons 1-23 (11 families, 7 from Co. Galway). Other common mutations included deletions of exon 3 (8 families) and exons 1-2 (6 families). Deletion of exons 19-20 in BRCA2 represented the familial mutation in five families, all from East Ireland (Wexford/Wicklow/Dublin). It is evident that a significant proportion of highly penetrant pathogenic variants in BRCA1 and BRCA2 will be missed if testing is limited to PCR-based Sanger sequencing alone. Screening for large genomic rearrangements in BRCA1 and BRCA2 in the routine diagnostic workflow is critical to avoid false negative results.
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Affiliation(s)
- Terri P McVeigh
- Department of Clinical Genetics, Our Lady's Children's Hospital, Crumlin, Ireland.
| | - Nuala Cody
- Department of Clinical Genetics, Our Lady's Children's Hospital, Crumlin, Ireland
| | - Cliona Carroll
- Department of Clinical Genetics, Our Lady's Children's Hospital, Crumlin, Ireland
| | - Marie Duff
- Department of Clinical Genetics, Our Lady's Children's Hospital, Crumlin, Ireland
| | - Michael Farrell
- Cancer Genetics Service, Mater Misericordiae University Hospital, Ireland
| | - Lisa Bradley
- Department of Clinical Genetics, Our Lady's Children's Hospital, Crumlin, Ireland
| | - David Gallagher
- Cancer Genetics Service, Mater Misericordiae University Hospital, Ireland; Cancer Genetics Service, St James' University Hospital, UK
| | - Trudi McDevitt
- Department of Clinical Genetics, Our Lady's Children's Hospital, Crumlin, Ireland
| | - Andrew J Green
- Department of Clinical Genetics, Our Lady's Children's Hospital, Crumlin, Ireland
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Chavarri-Guerra Y, Blazer KR, Weitzel JN. Genetic Cancer Risk Assessment for Breast Cancer in Latin America. Rev Invest Clin 2017; 69:94-102. [PMID: 28453507 PMCID: PMC5658001 DOI: 10.24875/ric.17002195] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Accepted: 03/14/2017] [Indexed: 12/14/2022]
Abstract
In Latin America, breast cancer is the most common malignancy in women, and limited available data suggest that up to 15% of all breast cancer cases in the region are hereditary. Genetic cancer risk assessment and counseling is a critical component of the appropriate clinical care of patients with hereditary breast cancer and their families. Unfortunately, genetic services are underdeveloped across Latin America, and access to genetic testing and counseling is very scarce in the region. Barriers contributing to the access to genetic care are high cost and lack of insurance coverage for genetic tests, insufficient oncogenetics training or expertise, nonexistence of genetic counseling as a clinical discipline, and lack of supportive healthcare policies. In this review, we highlight relevant initiatives undertaken in several Latin American countries aimed at creating genetic cancer risk assessment programs. Additionally, we present a review of the scientific literature on the current status of breast cancer genomics in Latin America, with specific emphasis on demographic indicators, access to cancer genetic care, training and strategies to improve outcomes, and international collaborations.
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Affiliation(s)
- Yanin Chavarri-Guerra
- Department of Hemato-Oncology, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubiran, Mexico City, Mexico
- Division of Clinical Cancer Genomics, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Kathleen Reilly Blazer
- Division of Clinical Cancer Genomics, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Jeffrey Nelson Weitzel
- Division of Clinical Cancer Genomics, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
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Pinto P, Peixoto A, Santos C, Rocha P, Pinto C, Pinheiro M, Leça L, Martins AT, Ferreira V, Bartosch C, Teixeira MR. Analysis of Founder Mutations in Rare Tumors Associated With Hereditary Breast/Ovarian Cancer Reveals a Novel Association of BRCA2 Mutations with Ampulla of Vater Carcinomas. PLoS One 2016; 11:e0161438. [PMID: 27532258 PMCID: PMC4988637 DOI: 10.1371/journal.pone.0161438] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 08/07/2016] [Indexed: 01/07/2023] Open
Abstract
BRCA1 and BRCA2 mutations are responsible for hereditary breast and ovarian cancer, but they also confer an increased risk for the development of rarer cancers associated with this syndrome, namely, cancer of the pancreas, male breast, peritoneum, and fallopian tube. The objective of this work was to quantify the contribution of the founder mutations BRCA2 c.156_157insAlu and BRCA1 c.3331_3334del for cancer etiology in unselected hospital-based cohorts of Portuguese patients diagnosed with these rarer cancers, by using a strategy that included testing of archival tumor tissue. A total of 102 male breast, 68 pancreatic and 33 peritoneal/fallopian tube carcinoma cases were included in the study. The BRCA2 c.156_157insAlu mutation was observed with a frequency of 7.8% in male breast cancers, 3.0% in peritoneal/fallopian tube cancers, and 1.6% in pancreatic cancers, with estimated total contributions of germline BRCA2 mutations of 14.3%, 5.5%, and 2.8%, respectively. No carriers of the BRCA1 c.3331_3334del mutation were identified. During our study, a patient with an ampulla of Vater carcinoma was incidentally found to carry the BRCA2 c.156_157insAlu mutation, so we decided to test a consecutive series of additional 15 ampullary carcinomas for BRCA1/BRCA2 mutations using a combination of direct founder mutation testing and full gene analysis with next generation sequencing. BRCA2 mutations were observed with a frequency of 14.3% in ampulla of Vater carcinomas. In conclusion, taking into account the implications for both the individuals and their family members, we recommend that patients with these neoplasias should be offered BRCA1/BRCA2 genetic testing and we here show that it is feasible to test for founder mutations in archival tumor tissue. Furthermore, we identified for the first time a high frequency of germline BRCA2 mutations in ampullary cancers.
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Affiliation(s)
- Pedro Pinto
- Department of Genetics, Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal
| | - Ana Peixoto
- Department of Genetics, Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal
| | - Catarina Santos
- Department of Genetics, Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal
| | - Patrícia Rocha
- Department of Genetics, Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal
| | - Carla Pinto
- Department of Genetics, Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal
| | - Manuela Pinheiro
- Department of Genetics, Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal
| | - Luís Leça
- Department of Pathology, Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal
| | - Ana Teresa Martins
- Department of Pathology, Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal
| | - Verónica Ferreira
- Department of Pathology, Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal
| | - Carla Bartosch
- Department of Pathology, Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal
| | - Manuel R. Teixeira
- Department of Genetics, Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
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36
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Alemar B, Herzog J, Brinckmann Oliveira Netto C, Artigalás O, Schwartz IVD, Matzenbacher Bittar C, Ashton-Prolla P, Weitzel JN. Prevalence of Hispanic BRCA1 and BRCA2 mutations among hereditary breast and ovarian cancer patients from Brazil reveals differences among Latin American populations. Cancer Genet 2016; 209:417-422. [PMID: 27425403 DOI: 10.1016/j.cancergen.2016.06.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 06/07/2016] [Accepted: 06/09/2016] [Indexed: 12/12/2022]
Abstract
Germline mutations in BRCA1 or BRCA2 (BRCA) are responsible for 5-15% of breast (BC) and ovarian cancers (OC), predisposing to the development of early onset and often multiple primary tumors. Since mutation carriers can benefit from risk-reducing interventions, the identification of individuals with hereditary breast and ovarian cancer (HBOC) syndrome has a significant clinical impact. We assessed whether a panel assay for recurrent Hispanic BRCA mutations (HISPANEL) has an adequate breadth of coverage to be suitable as a cost effective screening tool for HBOC in a cohort of patients from Southern Brazil. A multiplex, PCR-based panel was used to genotype 232 unrelated patients for 114 germline BRCA mutations, finding deleterious mutations in 3.5% of them. This mutation prevalence is within the range detected by the HISPANEL among BC patients unselected for family history in other Latin American settings. The HISPANEL would have accounted for 27% of the BRCA mutations detected by complete sequencing in a comparison cohort (n = 193). This prevalence may be region-specific since significant differences in population structure exist in Brazil. Comprehensive analysis of BRCA in a larger set of HBOC patients from different Brazilian regions is warranted, and the results could inform customization of the HISPANEL as an affordable mutation screening tool.
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Affiliation(s)
- Bárbara Alemar
- Programa de Pós-graduação em Genética e Biologia Molecular (PPGBM), Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves, 9500-Prédio 43323M, Porto Alegre, Rio Grande do Sul 91501-970, Brazil; Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre (HCPA), Rua Ramiro Barcelos, 2350, Porto Alegre, Rio Grande do Sul 90035-903, Brazil
| | - Josef Herzog
- Department of Population Sciences, Division of Clinical Cancer Genetics, City of Hope, 1500 East Duarte Road, Duarte, CA 91010, USA
| | - Cristina Brinckmann Oliveira Netto
- Serviço de Genética Médica, Hospital de Clínicas de Porto Alegre (HCPA), Rua Ramiro Barcelos, 2350, Porto Alegre, Rio Grande do Sul 90035-903, Brazil
| | - Osvaldo Artigalás
- Hospital Moinhos de Vento (HMV), Rua Ramiro Barcelos, 910, Porto Alegre, Rio Grande do Sul 91790-560, Brazil
| | - Ida Vanessa D Schwartz
- Programa de Pós-graduação em Genética e Biologia Molecular (PPGBM), Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves, 9500-Prédio 43323M, Porto Alegre, Rio Grande do Sul 91501-970, Brazil; Serviço de Genética Médica, Hospital de Clínicas de Porto Alegre (HCPA), Rua Ramiro Barcelos, 2350, Porto Alegre, Rio Grande do Sul 90035-903, Brazil; Departamento de Genética, UFRGS, Av. Bento Gonçalves, 9500-Prédio 43323M, Porto Alegre, Rio Grande do Sul 91501-970, Brazil
| | - Camila Matzenbacher Bittar
- Programa de Pós-graduação em Genética e Biologia Molecular (PPGBM), Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves, 9500-Prédio 43323M, Porto Alegre, Rio Grande do Sul 91501-970, Brazil
| | - Patricia Ashton-Prolla
- Programa de Pós-graduação em Genética e Biologia Molecular (PPGBM), Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves, 9500-Prédio 43323M, Porto Alegre, Rio Grande do Sul 91501-970, Brazil; Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre (HCPA), Rua Ramiro Barcelos, 2350, Porto Alegre, Rio Grande do Sul 90035-903, Brazil; Serviço de Genética Médica, Hospital de Clínicas de Porto Alegre (HCPA), Rua Ramiro Barcelos, 2350, Porto Alegre, Rio Grande do Sul 90035-903, Brazil; Departamento de Genética, UFRGS, Av. Bento Gonçalves, 9500-Prédio 43323M, Porto Alegre, Rio Grande do Sul 91501-970, Brazil.
| | - Jeffrey N Weitzel
- Department of Population Sciences, Division of Clinical Cancer Genetics, City of Hope, 1500 East Duarte Road, Duarte, CA 91010, USA
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Ewald IP, Cossio SL, Palmero EI, Pinheiro M, Nascimento ILDO, Machado TMB, Sandes KA, Toralles B, Garicochea B, Izetti P, Pereira MLS, Bock H, Vargas FR, Moreira MÂM, Peixoto A, Teixeira MR, Ashton-Prolla P. BRCA1 and BRCA2 rearrangements in Brazilian individuals with Hereditary Breast and Ovarian Cancer Syndrome. Genet Mol Biol 2016; 39:223-31. [PMID: 27303907 PMCID: PMC4910561 DOI: 10.1590/1678-4685-gmb-2014-0350] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2014] [Accepted: 03/16/2015] [Indexed: 01/09/2023] Open
Abstract
Approximately 5-10% of breast cancers are caused by germline mutations in high
penetrance predisposition genes. Among these, BRCA1 and
BRCA2, which are associated with the Hereditary Breast and
Ovarian Cancer (HBOC) syndrome, are the most frequently affected genes. Recent
studies confirm that gene rearrangements, especially in BRCA1, are
responsible for a significant proportion of mutations in certain populations. In this
study we determined the prevalence of BRCA rearrangements in 145
unrelated Brazilian individuals at risk for HBOC syndrome who had not been previously
tested for BRCA mutations. Using Multiplex Ligation-dependent Probe
Amplification (MLPA) and a specific PCR-based protocol to identify a Portuguese
founder BRCA2 mutation, we identified two (1,4%) individuals with
germline BRCA1 rearrangements (c.547+240_5193+178del and
c.4675+467_5075-990del) and three probands with the c.156_157insAlu founder
BRCA2 rearrangement. Furthermore, two families with false
positive MLPA results were shown to carry a deleterious point mutation at the probe
binding site. This study comprises the largest Brazilian series of HBOC families
tested for BRCA1 and BRCA2 rearrangements to date
and includes patients from three regions of the country. The overall observed
rearrangement frequency of 3.44% indicates that rearrangements are relatively
uncommon in the admixed population of Brazil.
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Affiliation(s)
- Ingrid Petroni Ewald
- Laboratório de Medicina Genômica, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, RS, Brazil.,Programa de Pós-Graduação em Medicina: Ciências Médicas, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Silvia Liliana Cossio
- Laboratório de Medicina Genômica, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, RS, Brazil
| | - Edenir Inez Palmero
- Centro de Pesquisa em Oncologia Molecular - Hospital do Câncer de Barretos, Barretos, SP, Brazil
| | - Manuela Pinheiro
- Departamento de Genética, Instituto Português de Oncologia do Porto, Porto, Portugal
| | - Ivana Lucia de Oliveira Nascimento
- Laboratório de Imunologia e Biologia Molecular, Instituto de Ciências da Saúde (ICS), Universidade Federal da Bahia (UFBA), Salvador, BA, Brazil
| | - Taisa Manuela Bonfim Machado
- Laboratório de Imunologia e Biologia Molecular, Instituto de Ciências da Saúde (ICS), Universidade Federal da Bahia (UFBA), Salvador, BA, Brazil
| | - Kiyoko Abe Sandes
- Laboratório de Imunologia e Biologia Molecular, Instituto de Ciências da Saúde (ICS), Universidade Federal da Bahia (UFBA), Salvador, BA, Brazil
| | - Betânia Toralles
- Departamento de Pediatria, Universidade Federal da Bahia (UFBA), Salvador, BA, Brazil
| | | | - Patricia Izetti
- Laboratório de Medicina Genômica, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, RS, Brazil.,Programa de Pós Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Maria Luiza Saraiva Pereira
- Programa de Pós Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.,Laboratório de Identificação Genética, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, RS, Brazil
| | - Hugo Bock
- Serviço de Genética Médica, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, RS, Brazil
| | - Fernando Regla Vargas
- Departamento de Bioquímica, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.,Divisão de Genética, Instituto Nacional de Câncer (INCA), Rio de Janeiro, RJ, Brazil
| | - Miguel Ângelo Martins Moreira
- Departamento de Bioquímica, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.,Instituto Nacional de Genética Médica Populacional (INAGEMP), Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, RS, Brazil.,Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz (IOC-FIOCRUZ), Rio de Janeiro, RJ, Brazil
| | - Ana Peixoto
- Departamento de Genética, Instituto Português de Oncologia do Porto, Porto, Portugal
| | - Manuel R Teixeira
- Departamento de Genética, Instituto Português de Oncologia do Porto, Porto, Portugal.,Departamento de Genética e Biologia Molecular, Centro de Ciências Biológicas e da Saúde, Universidade Federal do Estado do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Patricia Ashton-Prolla
- Laboratório de Medicina Genômica, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, RS, Brazil.,Programa de Pós-Graduação em Medicina: Ciências Médicas, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.,Programa de Pós Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.,Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Porto, Portugal.,Divisão de Genética, Instituto Nacional de Câncer (INCA), Rio de Janeiro, RJ, Brazil
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Ossa CA, Torres D. Founder and Recurrent Mutations in BRCA1 and BRCA2 Genes in Latin American Countries: State of the Art and Literature Review. Oncologist 2016; 21:832-9. [PMID: 27286788 DOI: 10.1634/theoncologist.2015-0416] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2015] [Accepted: 03/07/2016] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Numerous epidemiological factors affect the probability of developing breast or ovarian cancer, but no predictor is as determinant as inheriting a mutation in BRCA1 or BRCA2. The concept of the founder effect explains the reduced genetic variability in some populations, according to the theory that new populations can be formed from a reduced number of individuals, so the new population would carry only a small fraction of the genetic variability of the original population. The main purpose of this review is to provide an update on the state of the art in founder mutations and some recurrent mutations that have recently been described in Latin America. METHODS A literature search was performed in the electronic databases of PUBMED, EMBASE, LILACS, and BIREME using the terms BRCA1, BRCA2, founder mutation, Latin American population, and Hispanic. Sixty-two papers were identified, of which 38 were considered relevant for this review. Each result is shown per country. RESULTS In Latin America, clear founder effects have been reported in Mexico (BRCA1 del exons 9-12), Brazil (BRCA1 5382insC and BRCA2 c.156_157insAlu), and Colombia (BRCA1 3450del4, A1708E, and BRCA2 3034del4) and in Latinas residing in Southern California (BRCA1 185delAG, IVS5+1G>A, S955x, and R1443x). Of these, mutation BRCA1 3450del4 has also been reported in Brazil and Chile, whereas mutation BRCA2 3034del4 has been reported in Argentina and Peru. These data support the idea that although most Hispanic populations are the result of a mixture between Europeans, Africans, and Amerindians, the relative proportion of each genetic component varies throughout the Hispanic populations, making it necessary to identify the mutations characteristic of each population to generate mutation profiles adjusted to each one of them. CONCLUSION In Latin American countries, and even among regions of the same country, there is great heterogeneity of ancestors. Therefore, Latinas should not be analyzed like other population groups without taking into account their genetic ancestry. The presence of founder mutations in specific population groups represents a cost-effective analysis. The importance of determining the founder mutations lies mainly in the decrease in costs. If we manage to decrease costs, screenings could be offered more widely and cover a larger number of women. IMPLICATIONS FOR PRACTICE Hispanic and African-American populations are four to five times less likely than other populations worldwide to receive screening for BRCA mutations, a main reason being the high costs of these tools. The present study seeks to identify the prevalent mutations and the founder effect in the BRCA gene in the Hispanic population to address specific panels for this population group in the future and develop strategies for population screening.
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Affiliation(s)
- Carlos Andrés Ossa
- Instituto Cancerología Las Americas, Medellín, Colombia Centro de Excelencia en Mama de Antioquia, Medellín, Colombia
| | - Diana Torres
- Institute of Human Genetics, Pontificia Universidad Javeriana, Bogotá, Colombia
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39
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Fackenthal JD, Yoshimatsu T, Zhang B, de Garibay GR, Colombo M, De Vecchi G, Ayoub SC, Lal K, Olopade OI, Vega A, Santamariña M, Blanco A, Wappenschmidt B, Becker A, Houdayer C, Walker LC, López-Perolio I, Thomassen M, Parsons M, Whiley P, Blok MJ, Brandão RD, Tserpelis D, Baralle D, Montalban G, Gutiérrez-Enríquez S, Díez O, Lazaro C, Spurdle AB, Radice P, de la Hoya M. Naturally occurring BRCA2 alternative mRNA splicing events in clinically relevant samples. J Med Genet 2016; 53:548-58. [PMID: 27060066 DOI: 10.1136/jmedgenet-2015-103570] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 03/10/2016] [Indexed: 12/21/2022]
Abstract
BACKGROUND BRCA1 and BRCA2 are the two principal tumour suppressor genes associated with inherited high risk of breast and ovarian cancer. Genetic testing of BRCA1/2 will often reveal one or more sequence variants of uncertain clinical significance, some of which may affect normal splicing patterns and thereby disrupt gene function. mRNA analyses are therefore among the tests used to interpret the clinical significance of some genetic variants. However, these could be confounded by the appearance of naturally occurring alternative transcripts unrelated to germline sequence variation or defects in gene function. To understand which novel splicing events are associated with splicing mutations and which are part of the normal BRCA2 splicing repertoire, a study was undertaken by members of the Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) consortium to characterise the spectrum of naturally occurring BRCA2 mRNA alternate-splicing events. METHODS mRNA was prepared from several blood and breast tissue-derived cells and cell lines by contributing ENIGMA laboratories. cDNA representing BRCA2 alternate splice sites was amplified and visualised using capillary or agarose gel electrophoresis, followed by sequencing. RESULTS We demonstrate the existence of 24 different BRCA2 mRNA alternate-splicing events in lymphoblastoid cell lines and both breast cancer and non-cancerous breast cell lines. CONCLUSIONS These naturally occurring alternate-splicing events contribute to the array of cDNA fragments that may be seen in assays for mutation-associated splicing defects. Caution must be observed in assigning alternate-splicing events to potential splicing mutations.
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Affiliation(s)
| | - Toshio Yoshimatsu
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | - Bifeng Zhang
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | | | - Mara Colombo
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori (INT), Milano, Italy
| | - Giovanna De Vecchi
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori (INT), Milano, Italy
| | - Samantha C Ayoub
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | - Kumar Lal
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | | | - Ana Vega
- Fundación Pública Galega de Medicina Xenómica-SERGAS, Grupo de Medicina Xenómica-USC, CIBERER, IDIS, Santiago de Compostela, Spain
| | - Marta Santamariña
- Fundación Pública Galega de Medicina Xenómica-SERGAS, Grupo de Medicina Xenómica-USC, CIBERER, IDIS, Santiago de Compostela, Spain
| | - Ana Blanco
- Fundación Pública Galega de Medicina Xenómica-SERGAS, Grupo de Medicina Xenómica-USC, CIBERER, IDIS, Santiago de Compostela, Spain
| | - Barbara Wappenschmidt
- Medical Faculty, Center for Hereditary Breast and Ovarian Cancer, Center for Integrated Oncology (CIO) and Center for Molecular Medicine Cologne (CMMC), University of Cologne and University Hospital Cologne, Germany
| | - Alexandra Becker
- Medical Faculty, Center for Hereditary Breast and Ovarian Cancer, Center for Integrated Oncology (CIO) and Center for Molecular Medicine Cologne (CMMC), University of Cologne and University Hospital Cologne, Germany
| | - Claude Houdayer
- Service de Génétique and INSERM U830, Institut Curie and Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Logan C Walker
- Department of Pathology, University of Otago, Christchurch, New Zealand
| | - Irene López-Perolio
- Laboratorio de Oncología Molecular, Instituto de Investigación Sanitaria San Carlos (IdISSC), Hospital Clínico San Carlos, Madrid, Spain
| | - Mads Thomassen
- Department of Clinical Genetics, Odense University Hospital, Odense C, Denmark
| | - Michael Parsons
- Genetics and Computational Biology Division, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Phillip Whiley
- Genetics and Computational Biology Division, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Marinus J Blok
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Rita D Brandão
- Maastricht Science Programme, Faculty of Humanities and Sciences, Maastricht University, Maastricht, The Netherlands
| | - Demis Tserpelis
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Diana Baralle
- Human Development and Health Academic Unit, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, UK
| | - Gemma Montalban
- Oncogenetics Group, Vall d'Hebron Institute of Oncology (VHIO) and Universitat Autonoma de Barcelona, Barcelona, Spain
| | - Sara Gutiérrez-Enríquez
- Oncogenetics Group, Vall d'Hebron Institute of Oncology (VHIO) and Universitat Autonoma de Barcelona, Barcelona, Spain
| | - Orland Díez
- Oncogenetics Group, Vall d'Hebron Institute of Oncology (VHIO) and Universitat Autonoma de Barcelona, Barcelona, Spain Clinical and Molecular Genetics Area, University Hospital Vall d'Hebron, Barcelona, Spain
| | - Conxi Lazaro
- Molecular Diagnostic Unit, Hereditary Cancer Program, IDIBELL-Catalan Institute of Oncology, Barcelona, Spain
| | | | - Amanda B Spurdle
- Genetics and Computational Biology Division, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori (INT), Milano, Italy
| | - Miguel de la Hoya
- Laboratorio de Oncología Molecular, Instituto de Investigación Sanitaria San Carlos (IdISSC), Hospital Clínico San Carlos, Madrid, Spain
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Quiles F, Teulé À, Martinussen Tandstad N, Feliubadaló L, Tornero E, Del Valle J, Menéndez M, Salinas M, Wethe Rognlien V, Velasco A, Izquierdo A, Capellá G, Brunet J, Lázaro C. Identification of a founder BRCA1 mutation in the Moroccan population. Clin Genet 2016; 90:361-5. [PMID: 26864382 DOI: 10.1111/cge.12747] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 01/26/2016] [Accepted: 01/26/2016] [Indexed: 11/30/2022]
Abstract
Breast cancer (BC) is the most frequent cancer among women in Morocco. However, the role of the most prevalent BC-predisposing genes, BRCA1 and BRCA2, has been largely unexplored. To help define the role of BRCA1 in BC in Morocco, we characterized the first potential BRCA1 founder mutation in this population. Genetic testing of BRCA1 and BRCA2 in BC high-risk families identified mutation BRCA1 c.5309G>T, p.(Gly1770Val) or G1770V in five independent families from Morocco, suggesting a founder effect. To confirm this hypothesis, haplotype construction was performed using seven intragenic and flanking BRCA1 microsatellite markers. Clinical data were also compiled. Clinical data from carriers of mutation G1770V correspond to data from carriers of BRCA1 pathogenic mutations. Microsatellite analysis showed a common haplotype for the five families in a region comprising 1.54 Mb, confirming G1770V as the first specific founder BRCA1 mutation in the Moroccan population. Our findings contribute to a better understanding of BC genetics in the Moroccan population. Nevertheless, comprehensive studies of mutation G1770V in large series of BC patients from Morocco are needed to assess the real prevalence of this mutation and to improve genetic testing and risk assessment in this population.
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Affiliation(s)
- F Quiles
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO-IDIBELL, ICO-IdIBGi, ICO-IGTP), L'Hospitalet de Llobregat, Barcelona, Spain
| | - À Teulé
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO-IDIBELL, ICO-IdIBGi, ICO-IGTP), L'Hospitalet de Llobregat, Barcelona, Spain
| | | | - L Feliubadaló
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO-IDIBELL, ICO-IdIBGi, ICO-IGTP), L'Hospitalet de Llobregat, Barcelona, Spain
| | - E Tornero
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO-IDIBELL, ICO-IdIBGi, ICO-IGTP), L'Hospitalet de Llobregat, Barcelona, Spain
| | - J Del Valle
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO-IDIBELL, ICO-IdIBGi, ICO-IGTP), L'Hospitalet de Llobregat, Barcelona, Spain
| | - M Menéndez
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO-IDIBELL, ICO-IdIBGi, ICO-IGTP), L'Hospitalet de Llobregat, Barcelona, Spain
| | - M Salinas
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO-IDIBELL, ICO-IdIBGi, ICO-IGTP), L'Hospitalet de Llobregat, Barcelona, Spain
| | - V Wethe Rognlien
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - A Velasco
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO-IDIBELL, ICO-IdIBGi, ICO-IGTP), L'Hospitalet de Llobregat, Barcelona, Spain
| | - A Izquierdo
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO-IDIBELL, ICO-IdIBGi, ICO-IGTP), L'Hospitalet de Llobregat, Barcelona, Spain
| | - G Capellá
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO-IDIBELL, ICO-IdIBGi, ICO-IGTP), L'Hospitalet de Llobregat, Barcelona, Spain
| | - J Brunet
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO-IDIBELL, ICO-IdIBGi, ICO-IGTP), L'Hospitalet de Llobregat, Barcelona, Spain
| | - C Lázaro
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO-IDIBELL, ICO-IdIBGi, ICO-IGTP), L'Hospitalet de Llobregat, Barcelona, Spain.
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41
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Warner WA, Morrison RL, Lee TY, Williams TM, Ramnarine S, Roach V, Slovacek S, Maharaj R, Bascombe N, Bondy ML, Ellis MJ, Toriola AT, Roach A, Llanos AAM. Associations among ancestry, geography and breast cancer incidence, mortality, and survival in Trinidad and Tobago. Cancer Med 2015; 4:1742-53. [PMID: 26338451 PMCID: PMC4674001 DOI: 10.1002/cam4.503] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 07/06/2015] [Accepted: 07/07/2015] [Indexed: 12/19/2022] Open
Abstract
UNLABELLED Breast cancer (BC) is the most common newly diagnosed cancer among women in Trinidad and Tobago (TT) and BC mortality rates are among the highest in the world. Globally, racial/ethnic trends in BC incidence, mortality and survival have been reported. However, such investigations have not been conducted in TT, which has been noted for its rich diversity. In this study, we investigated associations among ancestry, geography and BC incidence, mortality and survival in TT. Data on 3767 incident BC cases, reported to the National Cancer Registry of TT, from 1995 to 2007, were analyzed in this study. Women of African ancestry had significantly higher BC incidence and mortality rates ( INCIDENCE 66.96; MORTALITY 30.82 per 100,000) compared to women of East Indian ( INCIDENCE 41.04, MORTALITY: 14.19 per 100,000) or mixed ancestry ( INCIDENCE 36.72, MORTALITY: 13.80 per 100,000). Geographically, women residing in the North West Regional Health Authority (RHA) catchment area followed by the North Central RHA exhibited the highest incidence and mortality rates. Notable ancestral differences in survival were also observed. Women of East Indian and mixed ancestry experienced significantly longer survival than those of African ancestry. Differences in survival by geography were not observed. In TT, ancestry and geographical residence seem to be strong predictors of BC incidence and mortality rates. Additionally, disparities in survival by ancestry were found. These data should be considered in the design and implementation of strategies to reduce BC incidence and mortality rates in TT.
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Affiliation(s)
- Wayne A Warner
- Oncology Division, Washington University School of Medicine, St. Louis, Missouri.,Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri
| | - Robert L Morrison
- Oncology Division, Washington University School of Medicine, St. Louis, Missouri
| | - Tammy Y Lee
- California State University, Los Angeles, California
| | | | - Shelina Ramnarine
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri
| | - Veronica Roach
- Dr. Elizabeth Quamina Cancer Registry, Eric Williams Medical Sciences Complex, Mt. Hope, Trinidad and Tobago
| | | | - Ravi Maharaj
- Department of Clinical Surgical Sciences, Faculty of Medical Sciences, University of the West Indies, Trinidad and Tobago
| | - Nigel Bascombe
- Department of Clinical Surgical Sciences, Faculty of Medical Sciences, University of the West Indies, Trinidad and Tobago
| | - Melissa L Bondy
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
| | - Matthew J Ellis
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
| | - Adetunji T Toriola
- Department of Surgery, Washington University School of Medicine, St. Louis, Missouri
| | - Allana Roach
- Public Health and Primary Care Unit, Department of Paraclinical Sciences, Faculty of Medical Sciences, University of the West Indies, Trinidad and Tobago
| | - Adana A M Llanos
- Rutgers School of Public Health and Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, New Jersey
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Maia S, Cardoso M, Paulo P, Pinheiro M, Pinto P, Santos C, Pinto C, Peixoto A, Henrique R, Teixeira MR. The role of germline mutations in the BRCA1/2 and mismatch repair genes in men ascertained for early-onset and/or familial prostate cancer. Fam Cancer 2015; 15:111-21. [DOI: 10.1007/s10689-015-9832-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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43
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Cho JY, Cho DY, Ahn SH, Choi SY, Shin I, Park HG, Lee JW, Kim HJ, Yu JH, Ko BS, Ku BK, Son BH. Large genomic rearrangement of BRCA1 and BRCA2 genes in familial breast cancer patients in Korea. Fam Cancer 2015; 13:205-11. [PMID: 24566764 DOI: 10.1007/s10689-014-9704-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
We screened large genomic rearrangements of the BRCA1 and BRCA2 genes in Korean, familial breast cancer patients. Multiplex ligation-dependent probe amplification assay was used to identify BRCA1 and BRCA2 genomic rearrangements in 226 Korean familial breast cancer patients with risk factors for BRCA1 and BRCA2 mutations, who previously tested negative for point mutations in the two genes. We identified only one large deletion (c.4186-1593_4676-1465del) in BRCA1. No large rearrangements were found in BRCA2. Our result indicates that large genomic rearrangement in the BRCA1 and BRCA2 genes does not seem like a major determinant of breast cancer susceptibility in the Korean population. A large-scale study needs to validate our result in Korea.
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Affiliation(s)
- Ja Young Cho
- Division of Breast and Endocrine Surgery, Department of Surgery College of Medicine, University of Ulsan, Asan Medical Center, 388-1 Pungnap-dong, Songpa-gu, Seoul, 138-736, Korea
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44
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Felix GE, Abe-Sandes C, Machado-Lopes TM, Bomfim TF, Guindalini RS, Santos VC, Meyer L, Oliveira PC, Cláudio Neiva J, Meyer R, Romeo M, Betânia Toralles M, Nascimento I, Abe-Sandes K. Germline mutations in BRCA1, BRCA2, CHEK2 and TP53 in patients at high-risk for HBOC: characterizing a Northeast Brazilian Population. Hum Genome Var 2014; 1:14012. [PMID: 27081505 DOI: 10.1038/hgv.2014.12] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 07/11/2014] [Accepted: 07/31/2014] [Indexed: 11/08/2022] Open
Abstract
Considering the importance of BRCA1, BRCA2, CHEK2 and TP53 in the development of hereditary early-onset breast and ovarian cancer and that the genetic susceptibility profile of the Northeast population from Brazil has never been analyzed, this study aimed to verify the frequency of mutations of clinical significance in these genes in high-risk hereditary breast and ovarian cancer (HBOC) syndrome patients from that region. DNA samples from 106 high-risk unrelated patients mostly from Bahia, the biggest state in the Northeast region, were analyzed. These patients underwent full BRCA1 gene sequencing, screening for common founder mutations in the BRCA2, CHEK2 and TP53 genes and genetic ancestry analysis with nine ancestry informative markers. The positive results were confirmed by two sequencing reactions. Three mutations of clinical significance were found: BRCA1 p.R71G (4.71%), 3450del4 (3.77%) and TP53 p.R337H (0.94%). The genetic ancestry analysis showed a high European ancestry contribution (62.2%) as well as considerable African (31.2%) and Amerindian (6.6%) ancestry contributions (r2=0.991); this degree of heterogeneity was also significant in the population structure analysis (r=0.604). This population is highly admixed with a different spectrum of genetic susceptibility, with the Galician founder mutation BRCA1 p.R71G accounting for 50% of all identified mutations in high-risk HBOC patients. TP53 p.R337H was also significantly frequent; thus, the combined screening of BRCA1/2 and TP53 should be offered to high-risk HBOC patients from Northeast Brazil.
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Abstract
Approximately 10% of all cancers are considered hereditary and are primarily caused by germline, high penetrance mutations in cancer predisposition genes. Although most cancer predisposition genes are considered molecularly heterogeneous, displaying hundreds of different disease-causing sequence alterations, founder mutations have been identified in certain populations. In some Latin American countries, founder mutations associated with increased risk of breast and other cancers have been described. This is particularly interesting considering that in most of these countries, populations are highly admixed with genetic contributions from native populations and from the in-flux of several distinct populations of immigrants. In this article, we present a review of the scientific literature on the subject and describe current data available on founder mutations described in the most common breast cancer predisposition genes: BRCA1, BRCA2 and TP53.
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Affiliation(s)
- Patricia Ashton-Prolla
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil . ; Serviço de Genética Médica e Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brasil
| | - Fernando Regla Vargas
- Departamento de Genética e Biologia Molecular, Universidade Federal do Estado do Rio de Janeiro, Rio de Janeiro, RJ, Brasil ; Laboratório de Epidemiologia de Malformações Congênitas, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil
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46
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Milting H, Klauke B, Christensen AH, Musebeck J, Walhorn V, Grannemann S, Munnich T, ari T, Rasmussen TB, Jensen HK, Mogensen J, Baecker C, Romaker E, Laser KT, zu Knyphausen E, Kassner A, Gummert J, Judge DP, Connors S, Hodgkinson K, Young TL, van der Zwaag PA, van Tintelen JP, Anselmetti D. The TMEM43 Newfoundland mutation p.S358L causing ARVC-5 was imported from Europe and increases the stiffness of the cell nucleus. Eur Heart J 2014; 36:872-81. [DOI: 10.1093/eurheartj/ehu077] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 02/03/2014] [Indexed: 02/03/2023] Open
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47
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Castéra L, Krieger S, Rousselin A, Legros A, Baumann JJ, Bruet O, Brault B, Fouillet R, Goardon N, Letac O. Next-generation sequencing for the diagnosis of hereditary breast and ovarian cancer using genomic capture targeting multiple candidate genes. Eur J Hum Genet. 2014;22:1305-1313. [PMID: 24549055 DOI: 10.1038/ejhg.2014.16] [Citation(s) in RCA: 184] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 01/15/2014] [Accepted: 01/16/2014] [Indexed: 02/08/2023] Open
Abstract
To optimize the molecular diagnosis of hereditary breast and ovarian cancer (HBOC), we developed a next-generation sequencing (NGS)-based screening based on the capture of a panel of genes involved, or suspected to be involved in HBOC, on pooling of indexed DNA and on paired-end sequencing in an Illumina GAIIx platform, followed by confirmation by Sanger sequencing or MLPA/QMPSF. The bioinformatic pipeline included CASAVA, NextGENe, CNVseq and Alamut-HT. We validated this procedure by the analysis of 59 patients' DNAs harbouring SNVs, indels or large genomic rearrangements of BRCA1 or BRCA2. We also conducted a blind study in 168 patients comparing NGS versus Sanger sequencing or MLPA analyses of BRCA1 and BRCA2. All mutations detected by conventional procedures were detected by NGS. We then screened, using three different versions of the capture set, a large series of 708 consecutive patients. We detected in these patients 69 germline deleterious alterations within BRCA1 and BRCA2, and 4 TP53 mutations in 468 patients also tested for this gene. We also found 36 variations inducing either a premature codon stop or a splicing defect among other genes: 5/708 in CHEK2, 3/708 in RAD51C, 1/708 in RAD50, 7/708 in PALB2, 3/708 in MRE11A, 5/708 in ATM, 3/708 in NBS1, 1/708 in CDH1, 3/468 in MSH2, 2/468 in PMS2, 1/708 in BARD1, 1/468 in PMS1 and 1/468 in MLH3. These results demonstrate the efficiency of NGS in performing molecular diagnosis of HBOC. Detection of mutations within other genes than BRCA1 and BRCA2 highlights the genetic heterogeneity of HBOC.
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Abstract
Alu elements are ∼300bp sequences that have amplified via an RNA intermediate leading to the accumulation of over 1 million copies in the human genome. Although a few of the copies are active, Alu germline activity is the highest of all human retrotransposons and does significantly contribute to genetic disease and population diversity. There are two basic mechanisms by which Alu elements contribute to disease: through insertional mutagenesis and as a large source of repetitive sequences that contribute to nonallelic homologous recombination (NAHR) that cause genetic deletions and duplications.
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Affiliation(s)
- Catherine Ade
- Tulane University, Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane Cancer Center, Consortium Of Mobile Elements at Tulane)
| | - Astrid M. Roy-Engel
- Tulane University, Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane Cancer Center, Consortium Of Mobile Elements at Tulane)
| | - Prescott L. Deininger
- Tulane University, Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane Cancer Center, Consortium Of Mobile Elements at Tulane)
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49
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Rudnicka H, Debniak T, Cybulski C, Huzarski T, Gronwald J, Lubinski J, Gorski B. Large BRCA1 and BRCA2 genomic rearrangements in Polish high-risk breast and ovarian cancer families. Mol Biol Rep 2013; 40:6619-23. [DOI: 10.1007/s11033-013-2775-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 09/14/2013] [Indexed: 12/20/2022]
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50
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Tarabeux J, Zeitouni B, Moncoutier V, Tenreiro H, Abidallah K, Lair S, Legoix-Né P, Leroy Q, Rouleau E, Golmard L, Barillot E, Stern MH, Rio-Frio T, Stoppa-Lyonnet D, Houdayer C. Streamlined ion torrent PGM-based diagnostics: BRCA1 and BRCA2 genes as a model. Eur J Hum Genet 2014; 22:535-41. [PMID: 23942203 DOI: 10.1038/ejhg.2013.181] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Revised: 07/11/2013] [Accepted: 07/16/2013] [Indexed: 11/08/2022] Open
Abstract
To meet challenges in terms of throughput and turnaround time, many diagnostic laboratories are shifting from Sanger sequencing to higher throughput next-generation sequencing (NGS) platforms. Bearing in mind that the performance and quality criteria expected from NGS in diagnostic or research settings are strikingly different, we have developed an Ion Torrent's PGM-based routine diagnostic procedure for BRCA1/2 sequencing. The procedure was first tested on a training set of 62 control samples, and then blindly validated on 77 samples in parallel with our routine technique. The training set was composed of difficult cases, for example, insertions and/or deletions of various sizes, large-scale rearrangements and, obviously, mutations occurring in homopolymer regions. We also compared two bioinformatic solutions in this diagnostic context, an in-house academic pipeline and the commercially available NextGene software (Softgenetics). NextGene analysis provided higher sensitivity, as four previously undetected single-nucleotide variations were found. Regarding specificity, an average of 1.5 confirmatory Sanger sequencings per patient was needed for complete BRCA1/2 screening. Large-scale rearrangements were identified by two distinct analyses, that is, bioinformatics and fragment analysis with electrophoresis profile comparison. Turnaround time was enhanced, as a series of 30 patients were sequenced by one technician, making the results available for the clinician in 10 working days following blood sampling. BRCA1/2 genes are a good model, representative of the difficulties commonly encountered in diagnostic settings, which is why we believe our findings are of interest for the whole community, and the pipeline described can be adapted by any user of PGM for diagnostic purposes.
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