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Loboda AP, Adonin LS, Zvereva SD, Guschin DY, Korneenko TV, Telegina AV, Kondratieva OK, Frolova SE, Pestov NB, Barlev NA. BRCA Mutations-The Achilles Heel of Breast, Ovarian and Other Epithelial Cancers. Int J Mol Sci 2023; 24:ijms24054982. [PMID: 36902416 PMCID: PMC10003548 DOI: 10.3390/ijms24054982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 02/27/2023] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
Two related tumor suppressor genes, BRCA1 and BRCA2, attract a lot of attention from both fundamental and clinical points of view. Oncogenic hereditary mutations in these genes are firmly linked to the early onset of breast and ovarian cancers. However, the molecular mechanisms that drive extensive mutagenesis in these genes are not known. In this review, we hypothesize that one of the potential mechanisms behind this phenomenon can be mediated by Alu mobile genomic elements. Linking mutations in the BRCA1 and BRCA2 genes to the general mechanisms of genome stability and DNA repair is critical to ensure the rationalized choice of anti-cancer therapy. Accordingly, we review the literature available on the mechanisms of DNA damage repair where these proteins are involved, and how the inactivating mutations in these genes (BRCAness) can be exploited in anti-cancer therapy. We also discuss a hypothesis explaining why breast and ovarian epithelial tissues are preferentially susceptible to mutations in BRCA genes. Finally, we discuss prospective novel therapeutic approaches for treating BRCAness cancers.
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Affiliation(s)
- Anna P. Loboda
- Laboratory of Molecular Oncology, Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
| | | | - Svetlana D. Zvereva
- Laboratory of Molecular Oncology, Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
| | - Dmitri Y. Guschin
- School of Medicine, Nazarbayev University, Astana 010000, Kazakhstan
| | - Tatyana V. Korneenko
- Group of Cross-Linking Enzymes, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia
| | | | | | | | - Nikolay B. Pestov
- Institute of Biomedical Chemistry, 119121 Moscow, Russia
- Group of Cross-Linking Enzymes, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products, 108819 Moscow, Russia
- Correspondence: (N.B.P.); (N.A.B.)
| | - Nick A. Barlev
- Institute of Biomedical Chemistry, 119121 Moscow, Russia
- School of Medicine, Nazarbayev University, Astana 010000, Kazakhstan
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products, 108819 Moscow, Russia
- Institute of Cytology, Tikhoretsky ave 4, 194064 St-Petersburg, Russia
- Correspondence: (N.B.P.); (N.A.B.)
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2
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Akin Duman T, Ozturk FN. Frequency and distribution of BRCA1/BRCA2 large genomic rearrangements in Turkish population with breast cancer. J Hum Genet 2023. [PMID: 36864289 DOI: 10.1038/s10038-023-01140-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
Germline mutations in BRCA1 and BRCA2 genes are mainly responsible for breast and/or ovarian cancer patients. Most of the mutations in these genes are single nucleotide changes or deletions/insertions of small numbers of bases, while a minority of mutations in these genes are large genomic rearrangements (LGRs). The frequency of LGRs in the Turkish population is not clearly known. Also insufficient awareness of the importance of LGRs in breast and/or ovarian cancer development can lead to some disruptions in patient management. So, we aimed to determine the frequency and distribution of the LGRs in the BRCA1/2 genes in the Turkish population. We investigated rearrangements of BRCA genes using multiplex ligation-dependent probe amplification (MLPA) analysis in 1540 patients with a personal and/or family history of breast and/or ovarian cancer or who had familial known large deletion/duplication and applied for segregation. The estimated overall frequency of LGRs in our group was 3,4% (52/1540) with 91% in BRCA1 gene and 9% in BRCA2 gene. 13 different rearrangements were detected (10 BRCA1, 3 BRCA2). To the best our knowledge, BRCA1 exon 1-16 duplication and BRCA2 exon 6 deletion have not been previously reported before. Our study results supported that the detection of rearrangements in BRCA genes is of great importance and it should be planned routinely in patients whose mutations cannot be detected by sequence analysis in screening programs.
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Affiliation(s)
- Tugba Akin Duman
- Department of Medical Genetics, Istanbul Haseki Education and Training Hospital, Istanbul, Turkey.
| | - Fatma Nihal Ozturk
- Department of Medical Genetics, Istanbul Haseki Education and Training Hospital, Istanbul, Turkey
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3
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Caputo SM, Telly D, Briaux A, Sesen J, Ceppi M, Bonnet F, Bourdon V, Coulet F, Castera L, Delnatte C, Hardouin A, Mazoyer S, Schultz I, Sevenet N, Uhrhammer N, Bonnet C, Tilkin-Mariamé AF, Houdayer C, Moncoutier V, Andrieu C, Bièche I, Stern MH, Stoppa-Lyonnet D, Lidereau R, Toulas C, Rouleau E. 5' Region Large Genomic Rearrangements in the BRCA1 Gene in French Families: Identification of a Tandem Triplication and Nine Distinct Deletions with Five Recurrent Breakpoints. Cancers (Basel) 2021; 13:cancers13133171. [PMID: 34202044 PMCID: PMC8268747 DOI: 10.3390/cancers13133171] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/11/2021] [Accepted: 06/17/2021] [Indexed: 12/28/2022] Open
Abstract
Simple Summary Large genomic rearrangements in BRCA1 consisting of deletions/duplications of one or several exons are complex events, often occurring in the 5′ region. We characterized 10 events in 20 families: one large triplication classified as benign and nine large deletions classified as pathogenic. The breakpoint localization will certainly help to further understand the chromatin structure in regions sensitive to rearrangement. Abstract Background: Large genomic rearrangements (LGR) in BRCA1 consisting of deletions/duplications of one or several exons have been found throughout the gene with a large proportion occurring in the 5′ region from the promoter to exon 2. The aim of this study was to better characterize those LGR in French high-risk breast/ovarian cancer families. Methods: DNA from 20 families with one apparent duplication and nine deletions was analyzed with a dedicated comparative genomic hybridization (CGH) array, high-resolution BRCA1 Genomic Morse Codes analysis and Sanger sequencing. Results: The apparent duplication was in fact a tandem triplication of exons 1 and 2 and part of intron 2 of BRCA1, fully characterized here for the first time. We calculated a causality score with the multifactorial model from data obtained from six families, classifying this variant as benign. Among the nine deletions detected in this region, eight have never been identified. The breakpoints fell in six recurrent regions and could confirm some specific conformation of the chromatin. Conclusions: Taken together, our results firmly establish that the BRCA1 5′ region is a frequent site of different LGRs and highlight the importance of the segmental duplication and Alu sequences, particularly the very high homologous region, in the mechanism of a recombination event. This also confirmed that those events are not systematically deleterious.
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Affiliation(s)
- Sandrine M. Caputo
- Department of Genetics, Institut Curie, F-75248 Paris, France; (S.M.C.); (A.B.); (V.M.); (C.A.); (I.B.); (M.-H.S.); (D.S.-L.); (R.L.)
- Institut Curie, PSL Research University, F-75005 Paris, France
| | - Dominique Telly
- Laboratoire d’Oncogénétique, Institut Claudius Regaud, IUCT-O, F-31059 Toulouse, France;
| | - Adrien Briaux
- Department of Genetics, Institut Curie, F-75248 Paris, France; (S.M.C.); (A.B.); (V.M.); (C.A.); (I.B.); (M.-H.S.); (D.S.-L.); (R.L.)
- Institut Curie, PSL Research University, F-75005 Paris, France
| | - Julie Sesen
- Department of Neurosurgery, Boston Children’s Hospital, Boston, MA 02115, USA;
| | - Maurizio Ceppi
- Roche Innovation Center Basel (RICB), Roche Pharma Research and Early Development, CH-4052 Basel, Switzerland;
| | - Françoise Bonnet
- Laboratoire de Génétique Constitutionnelle et INSERM U916 VINCO, Institut Bergonié, CEDEX, F-33076 Bordeaux, France; (F.B.); (N.S.)
| | - Violaine Bourdon
- Laboratoire d’Oncogénétique Moléculaire, Département de Biologie du Cancer, Institut Paoli-Calmettes, F-13273 Marseille, France;
| | - Florence Coulet
- Department of Genetics, Pitié-Salpêtriere Hospital, Assistance Publique-Hopitaux de Paris, Sorbonne University, F-75013 Paris, France;
| | - Laurent Castera
- Laboratoire de Biologie et de Génétique du Cancer, CLCC François Baclesse, INSERM 1079 Centre Normand de Génomique et de Médecine Personnalisée, F-14076 Caen, France; (L.C.); (A.H.)
| | - Capucine Delnatte
- Service de Génétique Médicale, Unité de Génétique Moléculaire, CHU Nantes, F-44093 Nantes, France;
| | - Agnès Hardouin
- Laboratoire de Biologie et de Génétique du Cancer, CLCC François Baclesse, INSERM 1079 Centre Normand de Génomique et de Médecine Personnalisée, F-14076 Caen, France; (L.C.); (A.H.)
| | - Sylvie Mazoyer
- Centre de Recherche en Neurosciences de Lyon, INSERM, U1028, CNRS, UMR5292, Université de Lyon, F-69008 Lyon, France;
| | - Inès Schultz
- Centre Paul Strauss, Laboratoire de Biologie Tumorale—Oncogénétique, F-67000 Strasbourg, France;
| | - Nicolas Sevenet
- Laboratoire de Génétique Constitutionnelle et INSERM U916 VINCO, Institut Bergonié, CEDEX, F-33076 Bordeaux, France; (F.B.); (N.S.)
| | - Nancy Uhrhammer
- Biologie Clinique et Oncologique, Biologie Moléculaire—Centre Jean Perrin, F-63000 Clermont-Ferrand, France;
| | - Céline Bonnet
- Institut de Cancérologie, 6 Avenue de Bourgogne, F-54519 Vandœuvre-lès-Nancy, France;
| | - Anne-Françoise Tilkin-Mariamé
- Cancer Research Center of Toulouse (CRCT), Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1037, F-31000 Toulouse, France;
| | - Claude Houdayer
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, F-76183 Rouen, France;
- Normandy Centre for Genomic and 41 Personalized Medicine, Department of Genetics, University Hospital, F-76183 Rouen, France
| | - Virginie Moncoutier
- Department of Genetics, Institut Curie, F-75248 Paris, France; (S.M.C.); (A.B.); (V.M.); (C.A.); (I.B.); (M.-H.S.); (D.S.-L.); (R.L.)
- Institut Curie, PSL Research University, F-75005 Paris, France
| | - Catherine Andrieu
- Department of Genetics, Institut Curie, F-75248 Paris, France; (S.M.C.); (A.B.); (V.M.); (C.A.); (I.B.); (M.-H.S.); (D.S.-L.); (R.L.)
- Institut Curie, PSL Research University, F-75005 Paris, France
| | | | - Ivan Bièche
- Department of Genetics, Institut Curie, F-75248 Paris, France; (S.M.C.); (A.B.); (V.M.); (C.A.); (I.B.); (M.-H.S.); (D.S.-L.); (R.L.)
- Faculty of Pharmaceutical and Biological Sciences, University of Paris, F-75006 Paris, France
| | - Marc-Henri Stern
- Department of Genetics, Institut Curie, F-75248 Paris, France; (S.M.C.); (A.B.); (V.M.); (C.A.); (I.B.); (M.-H.S.); (D.S.-L.); (R.L.)
- Institut Curie, INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), PSL Research University, F-75005 Paris, France
| | - Dominique Stoppa-Lyonnet
- Department of Genetics, Institut Curie, F-75248 Paris, France; (S.M.C.); (A.B.); (V.M.); (C.A.); (I.B.); (M.-H.S.); (D.S.-L.); (R.L.)
- Institut Curie, INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), PSL Research University, F-75005 Paris, France
- Faculty of Medicine, University of Paris, F-75005 Paris, France
| | - Rosette Lidereau
- Department of Genetics, Institut Curie, F-75248 Paris, France; (S.M.C.); (A.B.); (V.M.); (C.A.); (I.B.); (M.-H.S.); (D.S.-L.); (R.L.)
- Institut Curie, PSL Research University, F-75005 Paris, France
| | - Christine Toulas
- Laboratoire d’Oncogénétique, Institut Claudius Regaud, IUCT-O, F-31059 Toulouse, France;
- Correspondence: (C.T.); (E.R.)
| | - Etienne Rouleau
- Department of Biology, Gustave Roussy, Université Paris-Saclay, F-94805 Villejuif, France
- Correspondence: (C.T.); (E.R.)
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Sahin I, Saat H. A novel BRCA1 duplication and new insights on the spectrum and frequency of germline large genomic rearrangements in BRCA1/BRCA2. Mol Biol Rep 2021; 48:5057-5062. [PMID: 34146199 DOI: 10.1007/s11033-021-06499-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 06/15/2021] [Indexed: 10/21/2022]
Abstract
Heritable breast cancers account for 5% to 10% of all breast cancers, and monogenic, highly penetrant genes cause them. Around 90% of pathogenic variants in BRCA1 and BRCA2 are observed using gene sequencing, with another 10% identified through gene duplication/deletion analysis, which differs across various communities. In this study, we performed a next-generation sequencing panel and MLPA on 1484 patients to explain the importance of recurrent germline duplications/deletions of BRCA1-2 and their clinical results and determine how often BRCA gene LGRs were seen in people suspected of hereditary breast and ovarian cancer syndrome. The large genomic rearrangements (LGRs) frequency was approximately 1% (14/1484). All 14 mutations were heterozygous and detected in patients with breast cancer. BRCA1 mutations were more predominant (n = 8, 57.1%) than BRCA2 mutations (6, 42.9%). The most common recurrent mutations were BRCA2 exon three and BRCA1 exon 24 (23) deletions. To the best of our knowledge, BRCA1 5'UTR-exon11 duplication has never been reported before. Testing with MLPA is essential to identify patients at high risk. Our data demonstrate that BRCA1-2 LGRs should be considered when ordering genetic testing for individuals with a personal or family history of cancer, particularly breast cancer. Further research could shed light on BRCA1-2 LGRs' unique carcinogenesis roles.
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Affiliation(s)
- Ibrahim Sahin
- Department of Medical Genetics, University of Health Sciences, Dışkapı Yıldırım Beyazıt Training and Research Hospital, Ankara, Turkey.
| | - Hanife Saat
- Department of Medical Genetics, University of Health Sciences, Dışkapı Yıldırım Beyazıt Training and Research Hospital, Ankara, Turkey
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5
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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] [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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De Paolis E, De Bonis M, Concolino P, Piermattei A, Fagotti A, Urbani A, Scambia G, Minucci A, Capoluongo E. Droplet digital PCR for large genomic rearrangements detection: A promising strategy in tissue BRCA1 testing. Clin Chim Acta 2020; 513:17-24. [PMID: 33301768 DOI: 10.1016/j.cca.2020.12.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 11/10/2020] [Accepted: 12/01/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND AND AIMS With the introduction of Olaparib as target therapy for High Grade Serous Ovarian Cancer (HGSOC) patients with germline and somatic BRCA1/2 mutations, the genetic test performed on tumor tissue has become important like the germline test. In somatic testing the evaluation of Large Genomic Rearrangements (LGRs) represents the main challenge. We describe a droplet digital PCR (ddPCR) assay for the evaluation of target BRCA1 LGRs on blood and formalin-fixed paraffin-embedded (FFPE)/Fresh Frozen Tissue (FFT) samples. MATERIALS AND METHODS We analyzed blood, FFPE and FFT samples in a validation setting of n = 78 HGSOC patients. We applied the ddPCR to BRCA1 exons 2, 20 and 21 as some of the most common BRCA1 exons involved in LGRs in our cohort of patients. RESULTS The ddPCR custom assays allowed the identification of LGRs in all sample types, including FFPE specimens. Moreover, we were able to clearly detect LGRs accounted as somatic event. CONCLUSION The introduction of ddPCR in a comprehensive workflow, encompassing both germline and somatic tests, represents an improvement in BRCA1/2 testing. ddPCR can overcome challenges related to BRCA testing, especially on FFPE analysis. Finally, ddPCR represents a promising alternative strategy to the established standard methods currently used in clinical setting.
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Affiliation(s)
- Elisa De Paolis
- Molecular Diagnostic and Genomic Laboratory, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy.
| | - Maria De Bonis
- Molecular Diagnostic and Genomic Laboratory, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy.
| | - Paola Concolino
- Molecular Diagnostic and Genomic Laboratory, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy.
| | - Alessia Piermattei
- Division of Oncological Gynecology, Department of Women's and Children's Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy.
| | - Anna Fagotti
- Division of Oncological Gynecology, Department of Women's and Children's Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy; Catholic University of the Sacred Heart, 00168 Rome, Italy.
| | - Andrea Urbani
- Molecular Diagnostic and Genomic Laboratory, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy; Catholic University of the Sacred Heart, 00168 Rome, Italy.
| | - Giovanni Scambia
- Division of Oncological Gynecology, Department of Women's and Children's Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy.
| | - Angelo Minucci
- Molecular Diagnostic and Genomic Laboratory, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy.
| | - Ettore Capoluongo
- Department of Molecular Medicine and Medical Biotechnology, Federico II University, 80131 Naples, Italy; Federico II University, CEINGE, Advanced Biotechnology, 80131 Naples, Italy.
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Complex Characterization of Germline Large Genomic Rearrangements of the BRCA1 and BRCA2 Genes in High-Risk Breast Cancer Patients-Novel Variants from a Large National Center. Int J Mol Sci 2020; 21:ijms21134650. [PMID: 32629901 PMCID: PMC7370166 DOI: 10.3390/ijms21134650] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 06/19/2020] [Accepted: 06/27/2020] [Indexed: 12/23/2022] Open
Abstract
Large genomic rearrangements (LGRs) affecting one or more exons of BRCA1 and BRCA2 constitute a significant part of the mutation spectrum of these genes. Since 2004, the National Institute of Oncology, Hungary, has been involved in screening for LGRs of breast or ovarian cancer families enrolled for genetic testing. LGRs were detected by multiplex ligation probe amplification method, or next-generation sequencing. Where it was possible, transcript-level characterization of LGRs was performed. Phenotype data were collected and analyzed too. Altogether 28 different types of LGRs in 51 probands were detected. Sixteen LGRs were novel. Forty-nine cases were deletions or duplications in BRCA1 and two affected BRCA2. Rearrangements accounted for 10% of the BRCA1 mutations. Three exon copy gains, two complex rearrangements, and 23 exon losses were characterized by exact breakpoint determinations. The inferred mechanisms for LGR formation were mainly end-joining repairs utilizing short direct homologies. Comparing phenotype features of the LGR-carriers to that of the non-LGR BRCA1 mutation carriers, revealed no significant differences. Our study is the largest comprehensive report of LGRs of BRCA1/2 in familial breast and ovarian cancer patients in the Middle and Eastern European region. Our data add novel insights to genetic interpretation associated to the LGRs.
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8
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van der Merwe NC, Oosthuizen J, Theron M, Chong G, Foulkes WD. The contribution of large genomic rearrangements in BRCA1 and BRCA2 to South African familial breast cancer. BMC Cancer 2020; 20:391. [PMID: 32375709 PMCID: PMC7203887 DOI: 10.1186/s12885-020-06917-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 04/30/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Pathogenic variants that occur in the familial breast cancer genes (BRCA1/2) lead to truncated ineffective proteins in the majority of cases. These variants are mostly represented by small deletions/insertions, nonsense- and splice-site variants, although some larger pathogenic rearrangements occur. Currently, their contribution to familial breast cancer (BC) and ovarian cancer (OVC) in South Africa (SA) is unknown. METHODS Seven hundred and forty-four patients affected with BC or OVC were screened for larger genomic rearrangements (LGRs) by means of multiplex ligation-dependent probe amplification or Next Generation Sequencing using the Oncomine™ BRCA research assay. RESULTS The patients represented mostly medium to high-risk families, but also included lower risk patients without a family history of the disease, diagnosed at an early age of onset (< 40 years). Eight LGRs were detected (1.1%); seven in BRCA1 with a single whole gene deletion (WGD) detected for BRCA2. These eight LGRs accounted for 8.7% of the 92 BRCA1/2 pathogenic variants identified in the 744 cases. The pathogenic LGRs ranged from WGDs to the duplication of a single exon. CONCLUSIONS Larger rearrangements in BRCA1/2 contributed to the overall mutational burden of familial BC and OVC in SA. Almost a quarter of all pathogenic variants in BRCA1 were LGRs (7/30, 23%). The spectrum observed included two WGDs, one each for BRCA1 and BRCA2.
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Affiliation(s)
- Nerina C. van der Merwe
- Division of Human Genetics, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
- Division of Human Genetics, National Health Laboratory Services, Universitas Academic Hospital, Bloemfontein, South Africa
| | - Jaco Oosthuizen
- Division of Human Genetics, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
- Division of Human Genetics, National Health Laboratory Services, Universitas Academic Hospital, Bloemfontein, South Africa
| | - Magdalena Theron
- Division of Human Genetics, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
- Division of Human Genetics, National Health Laboratory Services, Universitas Academic Hospital, Bloemfontein, South Africa
| | - George Chong
- Lady Davis Institute and Segal Cancer Centre, Jewish General Hospital, Montréal, QC Canada
| | - William D. Foulkes
- Lady Davis Institute and Segal Cancer Centre, Jewish General Hospital, Montréal, QC Canada
- Research Institute of the McGill University Health Centre, Montréal, QC Canada
- Program in Cancer Genetics, Departments of Oncology and Human Genetics, McGill University, Montréal, QC Canada
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9
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Concolino P, Capoluongo E. Detection of BRCA1/2 large genomic rearrangements in breast and ovarian cancer patients: an overview of the current methods. Expert Rev Mol Diagn 2019; 19:795-802. [PMID: 31429350 DOI: 10.1080/14737159.2019.1657011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Introduction: Currently, genetic testing of BRCA1/2 genes includes screening for single-nucleotide variants, small insertions/deletions, and copy number variations (CNVs). In fact, many studies document the involvement of BRCA1/2 gene rearrangements in genetic predisposition to breast and ovarian cancer. Large genomic rearrangements (LGRs) of BRCA1 may account for up to one-third of all disease-causing alterations in various populations, while LGRs in BRCA2 are less frequently observed. Areas covered: We aimed to present an overview of current technologies employed in molecular diagnosis of BRCA1/2 LGRs. The most relevant literature papers, showing the application of new strategies, were considered. Expert opinion: Currently, the progress of next-generation sequencing (NGS) technologies allows for the validation of new pipelines able to provide rapid and effective results, ensuring the sensitivity and specificity requested for the detection of BRCA1/2 LGRs. Multiplex ligation-dependent probe amplification remains the gold standard to confirm NGS CNVs results and to perform fast screening in families where a pathogenic rearrangement has been detected in a proband.
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Affiliation(s)
- Paola Concolino
- Dipartimento Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli - IRCCS , Roma , Italia
| | - Ettore Capoluongo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II , Napoli , Italia
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10
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Identification and Characterization of a New BRCA2 Rearrangement in an Italian Family with Hereditary Breast and Ovarian Cancer Syndrome. Mol Diagn Ther 2018. [PMID: 28620890 DOI: 10.1007/s40291-017-0288-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
INTRODUCTION Many studies document the involvement of BRCA1/2 gene rearrangements in genetic predisposition to breast and ovarian cancer. Large genomic rearrangements (LGRs) of BRCA1 account for 0-27% of all disease-causing mutations in various populations, while LGRs in BRCA2 are rarer. Here, we describe a novel BRCA2 LGR, involving the duplication of exons 4-26, in an Italian family with hereditary breast and ovarian cancer (HBOC) syndrome. OBJECTIVE Our purpose was to provide an effective characterization of this variant using a combination of different methods able to establish the exact breakpoints of the duplication. METHODS A multiplex amplicon quantification (MAQ) assay was used as the primary screening method in the detection of LGRs. Array comparative genomic hybridization (CGH), reverse transcriptase polymerase chain reaction (RT-PCR) and long-range PCR were used for the careful characterization of the rearrangement and breakpoint regions. The Repeat Masker program was employed to identify Alu sequences at breakpoint junctions. RESULTS Array CGH and long-range PCR strategies revealed that the BRCA2 exons 4-26 duplication (g.12016_87170dup) involved exactly 75,154 bp nucleotides between intron 3 and intron 26 of the gene. Given that no Alu repeats were found at the junction sites, we support the hypothesis that the new duplication could be the result of a microhomology-mediated event (MH) involving very short homologous sequences at an upstream breakpoint. DISCUSSION LGR investigation is mandatory in BRCA1/2 routine testing in order to provide a complete result for a targeted therapeutic decision. Nevertheless, the characterization and classification of novel BRCA1/2 variants represents a crucial step in the support of genetic counselling. Our results, including a comprehensive co-segregation analysis, indicate that the novel duplication identifed has a pathogenic role and would be considered a causing-disease variant in genetic and oncologic counselling.
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11
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Concolino P, Rizza R, Mignone F, Costella A, Guarino D, Carboni I, Capoluongo E, Santonocito C, Urbani A, Minucci A. A comprehensive BRCA1/2 NGS pipeline for an immediate Copy Number Variation (CNV) detection in breast and ovarian cancer molecular diagnosis. Clin Chim Acta 2018; 480:173-179. [PMID: 29458049 DOI: 10.1016/j.cca.2018.02.012] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 02/10/2018] [Accepted: 02/13/2018] [Indexed: 02/07/2023]
Affiliation(s)
- Paola Concolino
- Laboratory of Molecular Biology, Institute of Biochemistry and Clinical Biochemistry, Catholic University of Sacred Heart, Largo A. Gemelli 8, 00168 Rome, Italy.
| | - Roberta Rizza
- Laboratory of Molecular Biology, Institute of Biochemistry and Clinical Biochemistry, Catholic University of Sacred Heart, Largo A. Gemelli 8, 00168 Rome, Italy
| | - Flavio Mignone
- Department of Science and Innovation Technology (DISIT), University of Piemonte Orientale, Alessandria, Italy
| | - Alessandra Costella
- Laboratory of Molecular Biology, Institute of Biochemistry and Clinical Biochemistry, Catholic University of Sacred Heart, Largo A. Gemelli 8, 00168 Rome, Italy
| | - Donatella Guarino
- Laboratory of Molecular Biology, Institute of Biochemistry and Clinical Biochemistry, Catholic University of Sacred Heart, Largo A. Gemelli 8, 00168 Rome, Italy
| | - Ilaria Carboni
- Institute of Legal Medicine, Catholic University of Sacred Heart, Largo A. Gemelli 8, 00168 Rome, Italy
| | - Ettore Capoluongo
- Laboratory of Molecular Biology, Institute of Biochemistry and Clinical Biochemistry, Catholic University of Sacred Heart, Largo A. Gemelli 8, 00168 Rome, Italy; Laboratory of Advanced Molecular Diagnostics (DIMA), Istituto Dermopatico dell'Immacolata, Fondazione Luigi Maria Monti, IRCCS, Rome, Italy
| | - Concetta Santonocito
- Laboratory of Molecular Biology, Institute of Biochemistry and Clinical Biochemistry, Catholic University of Sacred Heart, Largo A. Gemelli 8, 00168 Rome, Italy
| | - Andrea Urbani
- Laboratory of Molecular Biology, Institute of Biochemistry and Clinical Biochemistry, Catholic University of Sacred Heart, Largo A. Gemelli 8, 00168 Rome, Italy
| | - Angelo Minucci
- Laboratory of Molecular Biology, Institute of Biochemistry and Clinical Biochemistry, Catholic University of Sacred Heart, Largo A. Gemelli 8, 00168 Rome, Italy
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12
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Musani V, Sušac I, Ozretić P, Eljuga D, Levanat S. The first case report of a large deletion of the BRCA1 gene in Croatia: A case report. Medicine (Baltimore) 2017; 96:e8667. [PMID: 29310340 PMCID: PMC5728741 DOI: 10.1097/md.0000000000008667] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
RATIONALE Breast cancer is one of the most common cancers in women, and it is the leading cause of cancer related deaths in Croatia. BRCA1 and BRCA2 gene mutations are the most common cause of hereditary breast cancer. PATIENT CONCERNS In this report we describe a Croatian patient with no apparent family history of cancer, who developed breast cancer first at 29, and again at 33. DIAGNOSIS Due to the early development of first breast cancer and triple negative status of the second, the attending physician suspected a hereditary aspect. INTERVENTIONS Patient was sent to BRCA1 genetic testing. Subsequently, her mother and sister were sent to check for the mutation found in the patient. OUTCOMES BRCA1 exons 4-6 deletion was determined and sequencing confirmed the deletion as NG_005905.2:g.107648_117905del10257. Mother and sister were not affected, but since there were no available family members on the fathers' side, it was not possible to determine if this was a case of de novo mutation. Until now, only in three reports with the similar mutation the exact mutation borders were determined. The mutation in this case was not the same as previously reported and was more than twice in size. LESSONS All large deletions should be described at the nucleotide level, so that in cases with missing family data it would be possible to deduce if the mutation is already known. If the mutation is already known, it is probably not a de novo event, since it is unlikely that the breakpoints would be exactly the same more than once.
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Affiliation(s)
| | | | | | - Domagoj Eljuga
- Eljuga Polyclinic
- Department for Oncoplastic and Reconstructive Surgery, University Hospital for Tumors, University Clinical Hospital Centre Sisters of Mercy, Zagreb, Croatia
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13
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Schmidt AY, Hansen TVO, Ahlborn LB, Jønson L, Yde CW, Nielsen FC. Next-Generation Sequencing-Based Detection of Germline Copy Number Variations in BRCA1/BRCA2: Validation of a One-Step Diagnostic Workflow. J Mol Diagn 2017; 19:809-816. [PMID: 28822785 DOI: 10.1016/j.jmoldx.2017.07.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 06/23/2017] [Accepted: 07/12/2017] [Indexed: 12/19/2022] Open
Abstract
Genetic testing of BRCA1/2 includes screening for single nucleotide variants and small insertions/deletions and for larger copy number variations (CNVs), primarily by Sanger sequencing and multiplex ligation-dependent probe amplification (MLPA). With the advent of next-generation sequencing (NGS), it has become feasible to provide CNV information and sequence data using a single platform. We report the use of NGS gene panel sequencing on the Illumina MiSeq platform and JSI SeqPilot SeqNext software to call germline CNVs in BRCA1 and BRCA2. For validation 18 different BRCA1/BRCA2 CNVs previously identified by MLPA in 48 Danish breast and/or ovarian cancer families were analyzed. Moreover, 120 patient samples previously determined as negative for BRCA1/BRCA2 CNVs by MLPA were included in the analysis. Comparison of the NGS data with the data from MLPA revealed that the sensitivity was 100%, whereas the specificity was 95%. Taken together, this study validates a one-step bioinformatics work-flow to call germline BRCA1/2 CNVs using data obtained by NGS of a breast cancer gene panel. The work-flow represents a robust and easy-to-use method for full BRCA1/2 screening, which can be easily implemented in routine diagnostic testing and adapted to genes other than BRCA1/2.
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Affiliation(s)
- Ane Y Schmidt
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Thomas V O Hansen
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Lise B Ahlborn
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Lars Jønson
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Christina W Yde
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Finn C Nielsen
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark.
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14
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Buleje J, Guevara-Fujita M, Acosta O, Huaman FDP, Danos P, Murillo A, Pinto JA, Araujo JM, Aguilar A, Ponce J, Vigil C, Castaneda C, Calderon G, Gomez HL, Fujita R. Mutational analysis of BRCA1 and BRCA2 genes in Peruvian families with hereditary breast and ovarian cancer. Mol Genet Genomic Med 2017; 5:481-494. [PMID: 28944232 PMCID: PMC5606899 DOI: 10.1002/mgg3.301] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 05/05/2017] [Accepted: 05/09/2017] [Indexed: 12/21/2022] Open
Abstract
Background Breast cancer is one of the most prevalent malignancies in the world. In Peru, breast cancer is the second cause of death among women. Five to ten percent of patients present a high genetic predisposition due to BRCA1 and BRCA2 germline mutations. Methods We performed a comprehensive analysis of BRCA1 and BRCA2 genes by Sanger sequencing and multiplex ligation‐dependent probe amplification (MLPA) to detect large rearrangements in patients from 18 families, which met the criteria for hereditary breast cancer. Results In this series, we found four pathogenic mutations, three previously reported (BRCA1: c.302‐1G>C and c.815_824dup10; BRCA2: c.5946delT) and a duplication of adenines in exon 15 in BRCA1 gene (c.4647_4648dupAA, ClinVar SCV000256598.1). We also found two exonic and four intronic variants of unknown significance and 28 polymorphic variants. Conclusion This is the first report to determine the spectrum of mutations in the BRCA1/BRCA2 genes in Peruvian families selected by clinical and genetic criteria. The alteration rate in BRCA1/BRCA2 with proven pathogenic mutation was 22.2% (4 out 18) and this finding could be influenced by the reduced sample size or clinical criteria. In addition, we found three known BRCA1/BRCA2 mutations and a BRCA1 c.4647_4648dupAA as a novel pathogenic mutation.
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Affiliation(s)
- Jose Buleje
- Centro de Genética y Biología MolecularFacultad de Medicina HumanaUniversidad de San Martín de PorresLimaPerú
| | - Maria Guevara-Fujita
- Centro de Genética y Biología MolecularFacultad de Medicina HumanaUniversidad de San Martín de PorresLimaPerú
| | - Oscar Acosta
- Centro de Genética y Biología MolecularFacultad de Medicina HumanaUniversidad de San Martín de PorresLimaPerú
| | - Francia D P Huaman
- Centro de Genética y Biología MolecularFacultad de Medicina HumanaUniversidad de San Martín de PorresLimaPerú
| | - Pierina Danos
- Centro de Genética y Biología MolecularFacultad de Medicina HumanaUniversidad de San Martín de PorresLimaPerú
| | - Alexis Murillo
- Centro de Genética y Biología MolecularFacultad de Medicina HumanaUniversidad de San Martín de PorresLimaPerú
| | - Joseph A Pinto
- Unidad de Investigación Básica y TraslacionalOncosalud-AUNALimaPerú
| | | | - Alfredo Aguilar
- Unidad de Investigación Básica y TraslacionalOncosalud-AUNALimaPerú
| | | | | | | | | | | | - Ricardo Fujita
- Centro de Genética y Biología MolecularFacultad de Medicina HumanaUniversidad de San Martín de PorresLimaPerú
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15
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Concolino P, Rizza R, Hackmann K, Paris I, Minucci A, De Paolis E, Scambia G, Zuppi C, Schrock E, Capoluongo E. Characterization of a new BRCA1 rearrangement in an Italian woman with hereditary breast and ovarian cancer syndrome. Breast Cancer Res Treat 2017; 164:497-503. [PMID: 28488140 DOI: 10.1007/s10549-017-4275-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 05/03/2017] [Indexed: 11/24/2022]
Abstract
BACKGROUND We report a novel BRCA1 LGR, involving the complete duplication of exon 3, in an Italian patient with a strong family history of breast and ovarian cancer. Our purpose is to provide an effective characterization of this LGR using a combination of different methods able to establish the exact breakpoints of the duplication. METHODS MAQ assay was used as primary screening method in LGRs detection. Array CGH, RT-PCR, and Long-PCR were used for a careful characterization of rearrangement and breakpoint regions. The Repeat Masker program was employed to identify Alu sequences at breakpoint junctions. RESULTS RNA analysis showed that this in tandem duplication of exon 3 causes an in frame insertion of 18 amino acids within the protein. Array CGH and Long-PCR strategies revealed that the duplication (g.100411_102863dup) involves exactly 2.452 nucleotides between intron 2 and intron 3 of the gene. In addition, while an Alu Sx sequence was identified at upstream breakpoint, no Alu repeats were found at downstream junction. This supports the hypothesis that the new duplication was the result of a non-homologous recombination event between Alu and Non-Alu sequences. CONCLUSION Our strategy, which combines a comprehensive set of methodologies, has been able to characterize the new BRCA1 duplication confirming, as previously reported, that MAQ assay represents a reliable and effective method for a primary screening of BRCA rearrangements. We underline the relevance of incorporating quantitative methods for BRCA genes dosage testing into routine diagnostic practice.
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Affiliation(s)
- Paola Concolino
- Laboratory of Molecular Biology, Institute of Biochemistry and Clinical Biochemistry, Catholic University of Sacred Heart, Largo A. Gemelli 8, 00168, Rome, Italy.
| | - Roberta Rizza
- Laboratory of Molecular Biology, Institute of Biochemistry and Clinical Biochemistry, Catholic University of Sacred Heart, Largo A. Gemelli 8, 00168, Rome, Italy
| | - Karl Hackmann
- Institut fuer Klinische Genetik, Medizinische Fakultaet Carl Gustav Carus, Technische Universitaet Dresden, Fetscherstr. 74, 01307, Dresden, Germany.,German Cancer Consortium (DKTK), Dresden, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,National Center for Tumor Diseases (NCT), Dresden, Germany
| | - Ida Paris
- Department of Obstetrics and Gynecology, Catholic University, Rome, Italy
| | - Angelo Minucci
- Laboratory of Molecular Biology, Institute of Biochemistry and Clinical Biochemistry, Catholic University of Sacred Heart, Largo A. Gemelli 8, 00168, Rome, Italy
| | - Elisa De Paolis
- Laboratory of Molecular Biology, Institute of Biochemistry and Clinical Biochemistry, Catholic University of Sacred Heart, Largo A. Gemelli 8, 00168, Rome, Italy
| | - Giovanni Scambia
- Department of Obstetrics and Gynecology, Catholic University, Rome, Italy
| | - Cecilia Zuppi
- Laboratory of Molecular Biology, Institute of Biochemistry and Clinical Biochemistry, Catholic University of Sacred Heart, Largo A. Gemelli 8, 00168, Rome, Italy
| | - Evelin Schrock
- Institut fuer Klinische Genetik, Medizinische Fakultaet Carl Gustav Carus, Technische Universitaet Dresden, Fetscherstr. 74, 01307, Dresden, Germany.,German Cancer Consortium (DKTK), Dresden, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,National Center for Tumor Diseases (NCT), Dresden, Germany
| | - Ettore Capoluongo
- Laboratory of Molecular Biology, Institute of Biochemistry and Clinical Biochemistry, Catholic University of Sacred Heart, Largo A. Gemelli 8, 00168, Rome, Italy
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16
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Germline mutations in BRCA1 and BRCA2 in epithelial ovarian cancer patients in Brazil. BMC Cancer 2016; 16:934. [PMID: 27914478 PMCID: PMC5135756 DOI: 10.1186/s12885-016-2966-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 11/23/2016] [Indexed: 12/20/2022] Open
Abstract
Background Approximately 8–15% epithelial ovarian cancer patients are BRCA1 or BRCA2 germline mutation carriers. Brazilian inhabitants may have peculiar genetic characteristics associated with ethnic diversity, and studies focusing on the entire BRCA1/BRCA2 gene sequencing in Brazilian ovarian cancer patients are still lacking. The aim of this study was to evaluate BRCA1/2 mutations, through entire gene sequencing, in a Brazilian population of women with epithelial ovarian cancer. Methods In a cross sectional study performed in one reference centre for cancer treatment in São Paulo, Brazil, 100 patients diagnosed with epithelial ovarian cancer unselected for family history of breast and/or ovarian cancer were included. The complete coding sequence of BRCA1/2 genes was evaluated through Next-Generation or capillary sequencing. Large deletions were investigated through Multiplex Ligation-dependent Probe Amplification (MLPA). Results Nineteen pathogenic mutations (BRCA1: n = 17 and BRCA2: n = 2) featuring 14 different mutations, including two large deletions in BRCA1 (exon 1–2 deleted and exon 5–7 deleted) were identified. Three mutations were detected more than once (c.3331_3334delCAAG, c.5266dupC and c.4484G > T). Two novel frameshift mutations were identified, one in BRCA1 (c.961_962delTG) and one in BRCA2 (c.1963_1963delC). BRCA1/2 mutations were seen in 35.5% of the patients with first and/or second-degree relatives with breast and/or ovarian cancer. Nineteen variants of uncertain significance (VUS) were detected (BRCA1: n = 2 and BRCA2: n = 17), including five distinct missense variants (BRCA1: c.5348 T > C; BRCA2: c.2350A > G, c.3515C > T, c.7534C > T, and c.8351G > A). Conclusions Among epithelial ovarian cancer patients unselected for family history of cancer, 19% were BRCA1/2 germline mutation carriers. Almost ¾ of the BRCA mutations, including two large deletions, were detected only once. Our work emphasizes the need of entire gene sequencing and MLPA screening in Brazil. Electronic supplementary material The online version of this article (doi:10.1186/s12885-016-2966-x) contains supplementary material, which is available to authorized users.
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17
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Riahi A, Chabouni-Bouhamed H, Kharrat M. Prevalence of BRCA1 and BRCA2 large genomic rearrangements in Tunisian high risk breast/ovarian cancer families: Implications for genetic testing. Cancer Genet 2016; 210:22-27. [PMID: 28212807 DOI: 10.1016/j.cancergen.2016.11.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 08/23/2016] [Accepted: 11/14/2016] [Indexed: 12/11/2022]
Abstract
Germline mutations in the BRCA tumor suppressor genes account for a substantial proportion of hereditary breast/ovarian cancer. However, this contribution is lower than expected. This underestimation can partly be explained by the BRCA alterations missed by using Sanger sequencing methods. Thus, large genomic rearrangements (LGRs) in BRCA1 and BRCA2 are responsible for 4-28% of all inherited BRCA mutations. In this study, Multiplex ligation-dependent probe amplification (MLPA) assay was used for detection of large rearrangements of BRCA1 and BRCA2 genes in 36 unrelated high-risk breast/ovarian cancer patients negative for BRCA1/2 point mutations. MLPA assay for all exons of both genes and for 1100delC variant of CHEK2 gene were performed. Positive MLPA results were confirmed by real-time quantitative PCR (qPCR). Two different rearrangements in the BRCA1 gene were identified consisting of exon 5 deletion and exon 20 duplication. MLPA analysis did not reveal any large genomic rearrangements in BRCA2 gene. Overall BRCA1/2 LGRs prevalence among high-risk Tunisian patients was 5.5%. Quantitative real-time PCR confirmed MPLA findings. Our results suggest the usefulness of screening for LGRs in BRCA genes in the Tunisian population. To avoid false-negative results, we suggest that MLPA should be used in genetic testing programs. These results are important for guidance counseling and clinical management of Tunisian high-risk patients.
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Affiliation(s)
- Aouatef Riahi
- Faculté de Médecine de Tunis, Laboratoire Génétique Humaine, University Tunis El manar, Tunis, Tunisia.
| | - Habiba Chabouni-Bouhamed
- Faculté de Médecine de Tunis, Laboratoire Génétique Humaine, University Tunis El manar, Tunis, Tunisia
| | - Maher Kharrat
- Faculté de Médecine de Tunis, Laboratoire Génétique Humaine, University Tunis El manar, Tunis, Tunisia
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18
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Contribution of BRCA1 large genomic rearrangements to early-onset and familial breast/ovarian cancer in Pakistan. Breast Cancer Res Treat 2016; 161:191-201. [PMID: 27826754 DOI: 10.1007/s10549-016-4044-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 11/01/2016] [Indexed: 10/20/2022]
Abstract
BACKGROUND Germline mutations in BRCA1 and BRCA2 (BRCA1/2) account for the majority of hereditary breast and/or ovarian cancers. Pakistan has one of the highest rates of breast cancer incidence in Asia, where BRCA1/2 small-range mutations account for 17% of early-onset and familial breast/ovarian cancer patients. We report the first study from Pakistan evaluating the prevalence of BRCA1/2 large genomic rearrangements (LGRs) in breast and/or ovarian cancer patients who do not harbor small-range BRCA1/2 mutations. MATERIALS AND METHODS Both BRCA1/2 genes were comprehensively screened for LGRs using multiplex ligation-dependent probe amplification in 120 BRCA1/2 small-range mutations negative early-onset or familial breast/ovarian cancer patients from Pakistan (Group 1). The breakpoints were characterized by long-range PCR- and DNA-sequencing analyses. An additional cohort of 445 BRCA1/2 negative high-risk patients (Group 2) was analyzed for the presence of LGRs identified in Group 1. RESULTS Three different BRCA1 LGRs were identified in Group 1 (4/120; 3.3%), two of these were novel. Exon 1-2 deletion was observed in two unrelated patients: an early-onset breast cancer patient and another bilateral breast cancer patient from a hereditary breast cancer (HBC) family. Novel exon 20-21 deletion was detected in a 29-year-old breast cancer patient from a HBC family. Another novel exon 21-24 deletion was identified in a breast-ovarian cancer patient from a hereditary breast and ovarian cancer family. The breakpoints of all deletions were characterized. Screening of the 445 patients in Group 2 for the three LGRs revealed ten additional patients harboring exon 1-2 deletion or exon 21-24 deletion (10/445; 2.2%). No BRCA2 LGRs were identified. CONCLUSIONS LGRs in BRCA1 are found with a considerable frequency in Pakistani breast/ovarian cancer cases. Our findings suggest that BRCA1 exons 1-2 deletion and exons 21-24 deletion should be included in the recurrent BRCA1/2 mutations panel for genetic testing of high-risk Pakistani breast/ovarian cancer patients.
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Apostolou P, Pertesi M, Aleporou-Marinou V, Dimitrakakis C, Papadimitriou C, Razis E, Christodoulou C, Fountzilas G, Yannoukakos D, Konstantopoulou I, Fostira F. Haplotype analysis reveals that the recurrent BRCA1 deletion of exons 23 and 24 is a Greek founder mutation. Clin Genet 2016; 91:482-487. [PMID: 27357818 DOI: 10.1111/cge.12824] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 06/07/2016] [Accepted: 06/24/2016] [Indexed: 11/28/2022]
Abstract
A recurrent large genomic rearrangement (LGR) encompassing exons 23 and 24 of the BRCA1 gene has been identified in breast-ovarian cancer families of Greek origin. Its breakpoints have been determined as c.5406 + 664_*8273del11052 (RefSeq: NM_007294.3) and a diagnostic polymerase chain reaction (PCR) has been set up for rapid screening. In a series of 2,092 high-risk families completely screened for BRCA1 and BRCA2 germline mutations, we have found the deletion in 35 families (1.68%), representing 7.83% of the mutations identified in both genes and 10.3% of the total BRCA1 mutations. In order to characterize this deletion as a founder mutation, haplotype analysis was conducted in 60 carriers from 35 families, using three BRCA1 intragenic microsatellite markers and four markers surrounding the BRCA1 locus. Our results demonstrate a common shared core disease-associated haplotype of 2.89Mb. Our calculations estimate that the deletion has originated from a common ancestor 1450 years ago, which most probably inhabited the Asia Minor area. The particular (LGR) is the third mutation of such type that is proven to have a Greek founder effect in the Greek population, illustrating the necessity for LGRs testing in individuals of Greek descent.
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Affiliation(s)
- P Apostolou
- Molecular Diagnostics Laboratory, INRaSTES, National Center for Scientific Research "Demokritos", Athens, Greece.,Department of Genetics & Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - M Pertesi
- Molecular Diagnostics Laboratory, INRaSTES, National Center for Scientific Research "Demokritos", Athens, Greece.,Division of Hematology and Transfusion Medicine, Faculty of Medicine, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - V Aleporou-Marinou
- Department of Genetics & Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - C Dimitrakakis
- Breast Unit of the 1st Department of Obstetrics and Gynecology, Athens University Medical School, Athens, Greece
| | - C Papadimitriou
- Department of Clinical Therapeutics, "Alexandra" Hospital, School of Medicine, University of Athens, Athens, Greece
| | - E Razis
- Third Medical Oncology Department, Hygeia Hospital, Athens, Greece
| | - C Christodoulou
- Second Department of Medical Oncology, Metropolitan Hospital, Piraeus, Greece
| | - G Fountzilas
- School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - D Yannoukakos
- Molecular Diagnostics Laboratory, INRaSTES, National Center for Scientific Research "Demokritos", Athens, Greece
| | - I Konstantopoulou
- Molecular Diagnostics Laboratory, INRaSTES, National Center for Scientific Research "Demokritos", Athens, Greece
| | - F Fostira
- Molecular Diagnostics Laboratory, INRaSTES, National Center for Scientific Research "Demokritos", Athens, Greece
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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: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [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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21
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Palmero EI, Alemar B, Schüler-Faccini L, Hainaut P, Moreira-Filho CA, Ewald IP, dos Santos PK, Ribeiro PLI, de Oliveira CB, Kelm FLC, Tavtigian S, Cossio SL, Giugliani R, Caleffi M, Ashton-Prolla P. Screening for germline BRCA1, BRCA2, TP53 and CHEK2 mutations in families at-risk for hereditary breast cancer identified in a population-based study from Southern Brazil. Genet Mol Biol 2016; 39:210-22. [PMID: 27223485 PMCID: PMC4910552 DOI: 10.1590/1678-4685-gmb-2014-0363] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 11/24/2015] [Indexed: 01/22/2023] Open
Abstract
In Brazil, breast cancer is a public health care problem due to its high incidence and mortality rates. In this study, we investigated the prevalence of hereditary breast cancer syndromes (HBCS) in a population-based cohort in Brazils southernmost capital, Porto Alegre. All participants answered a questionnaire about family history (FH) of breast, ovarian and colorectal cancer and those with a positive FH were invited for genetic cancer risk assessment (GCRA). If pedigree analysis was suggestive of HBCS, genetic testing of the BRCA1, BRCA2, TP53, and CHEK2 genes was offered. Of 902 women submitted to GCRA, 214 had pedigrees suggestive of HBCS. Fifty of them underwent genetic testing: 18 and 40 for BRCA1/BRCA2 and TP53 mutation screening, respectively, and 7 for CHEK2 1100delC testing. A deleterious BRCA2 mutation was identified in one of the HBOC probands and the CHEK2 1100delC mutation occurred in one of the HBCC families. No deleterious germline alterations were identified in BRCA1 or TP53. Although strict inclusion criteria and a comprehensive testing approach were used, the suspected genetic risk in these families remains unexplained. Further studies in a larger cohort are necessary to better understand the genetic component of hereditary breast cancer in Southern Brazil.
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Affiliation(s)
- Edenir Inêz Palmero
- Programa de Pós Graduação em Genética e Biologia Molecular,
Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
- Laboratório de Medicina Genômica, Hospital de Clinicas de Porto
Alegre, Porto Alegre, RS, Brazil
- Cluster of Molecular Carcinogenesis, International Agency for
Research on Cancer, Lyon, France
- Centro de Pesquisa em Oncologia Molecular, Hospital de Câncer de
Barretos, Barretos, SP, Brazil
- Faculdade de Ciências da Saúde Dr. Paulo Prata, São Paulo, SP,
Brazil
| | - Bárbara Alemar
- Programa de Pós Graduação em Genética e Biologia Molecular,
Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
- Laboratório de Medicina Genômica, Hospital de Clinicas de Porto
Alegre, Porto Alegre, RS, Brazil
| | - Lavínia Schüler-Faccini
- Programa de Pós Graduação em Genética e Biologia Molecular,
Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
- Serviço de Genética Médica, Hospital de Clinicas de Porto Alegre,
Porto Alegre, RS, Brazil
- Departmento de Genética, Universidade Federal do Rio Grande do Sul,
Porto Alegre, RS, Brazil
| | - Pierre Hainaut
- Cluster of Molecular Carcinogenesis, International Agency for
Research on Cancer, Lyon, France
| | - Carlos Alberto Moreira-Filho
- Centro de Pesquisa Experimental, Instituto de Educação e Pesquisa
Albert Einstein, São Paulo, SP, Brazil
- Departmento de Imunologia, Instituto de Ciências Biomédicas,
Universidade de São Paulo, São Paulo, SP, Brazil
| | - Ingrid Petroni Ewald
- Laboratório de Medicina Genômica, Hospital de Clinicas de Porto
Alegre, Porto Alegre, RS, Brazil
| | - Patricia Koehler dos Santos
- Programa de Pós Graduação em Genética e Biologia Molecular,
Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
- Laboratório de Medicina Genômica, Hospital de Clinicas de Porto
Alegre, Porto Alegre, RS, Brazil
| | | | | | - Florence Le Calvez Kelm
- Cluster of Molecular Carcinogenesis, International Agency for
Research on Cancer, Lyon, France
| | - Sean Tavtigian
- Cluster of Molecular Carcinogenesis, International Agency for
Research on Cancer, Lyon, France
| | - Silvia Liliana Cossio
- Laboratório de Medicina Genômica, Hospital de Clinicas de Porto
Alegre, Porto Alegre, RS, Brazil
- Programa de Pós Graduação em Gastroenterologia, Universidade Federal
do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Roberto Giugliani
- Programa de Pós Graduação em Genética e Biologia Molecular,
Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
- Serviço de Genética Médica, Hospital de Clinicas de Porto Alegre,
Porto Alegre, RS, Brazil
- Departmento de Genética, Universidade Federal do Rio Grande do Sul,
Porto Alegre, RS, Brazil
| | - Maira Caleffi
- Nucleo Mama Porto Alegre e Associação Hospitalar Moinhos de Vento,
Porto Alegre, RS, Brazil
| | - Patricia Ashton-Prolla
- Programa de Pós Graduação em Genética e Biologia Molecular,
Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
- Laboratório de Medicina Genômica, Hospital de Clinicas de Porto
Alegre, Porto Alegre, RS, Brazil
- Serviço de Genética Médica, Hospital de Clinicas de Porto Alegre,
Porto Alegre, RS, Brazil
- Departmento de Genética, Universidade Federal do Rio Grande do Sul,
Porto Alegre, RS, Brazil
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22
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Tessereau C, Léoné M, Buisson M, Duret L, Sinilnikova OM, Mazoyer S. Occurrence of a non deleterious gene conversion event in the BRCA1 gene. Genes Chromosomes Cancer 2015; 54:646-52. [PMID: 26171949 DOI: 10.1002/gcc.22278] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 06/04/2015] [Accepted: 06/05/2015] [Indexed: 12/12/2022] Open
Abstract
The duplication in the primate lineage of a portion of the breast and ovarian cancer susceptibility gene BRCA1 has created a BRCA1 pseudogene 45 kb away. Non-allelic homologous recombination (NAHR) between BRCA1 and BRCA1P1 has generated recurrent deleterious germ-line 37-kb deletions encompassing the first two exons of BRCA1, accounting for several breast and ovarian cancer families in various populations. In principle, NAHR intermediates resolution could also lead through a non-crossover configuration to interlocus gene conversion (IGC), but none had been described as yet. Here, we report for the first time an IGC event identified in a breast and ovarian cancer family involving exactly the same segment as that involved in the 37-kb deletions. Close examination of the consequences of this IGC event showed that it does not impact BRCA1 expression. Detailed analysis of the regions of homology between BRCA1 and its pseudogene revealed the specificity of the segment where recombination systematically occurs.
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Affiliation(s)
- Chloé Tessereau
- "Genetics of Breast Cancer" Team, Cancer Research Centre of Lyon, CNRS UMR5286/Inserm U1052/Université Lyon 1, Centre Léon Bérard, Lyon, France
| | - Mélanie Léoné
- Unité Mixte de Génétique Constitutionnelle des Cancers Fréquents, Hospices Civils de Lyon/Centre Léon Bérard, Lyon, France
| | - Monique Buisson
- "Genetics of Breast Cancer" Team, Cancer Research Centre of Lyon, CNRS UMR5286/Inserm U1052/Université Lyon 1, Centre Léon Bérard, Lyon, France
| | - Laurent Duret
- Laboratoire de Biométrie et Biologie Evolutive, CNRS UMR5558, Université Lyon 1, Lyon, France
| | - Olga M Sinilnikova
- "Genetics of Breast Cancer" Team, Cancer Research Centre of Lyon, CNRS UMR5286/Inserm U1052/Université Lyon 1, Centre Léon Bérard, Lyon, France.,Unité Mixte de Génétique Constitutionnelle des Cancers Fréquents, Hospices Civils de Lyon/Centre Léon Bérard, Lyon, France
| | - Sylvie Mazoyer
- "Genetics of Breast Cancer" Team, Cancer Research Centre of Lyon, CNRS UMR5286/Inserm U1052/Université Lyon 1, Centre Léon Bérard, Lyon, France
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23
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Aygun N. Correlations between long inverted repeat (LIR) features, deletion size and distance from breakpoint in human gross gene deletions. Sci Rep 2015; 5:8300. [PMID: 25657065 PMCID: PMC4319165 DOI: 10.1038/srep08300] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 01/14/2015] [Indexed: 11/09/2022] Open
Abstract
Long inverted repeats (LIRs) have been shown to induce genomic deletions in yeast. In this study, LIRs were investigated within ±10 kb spanning each breakpoint from 109 human gross deletions, using Inverted Repeat Finder (IRF) software. LIR number was significantly higher at the breakpoint regions, than in control segments (P < 0.001). In addition, it was found that strong correlation between 5' and 3' LIR numbers, suggesting contribution to DNA sequence evolution (r = 0.85, P < 0.001). 138 LIR features at ±3 kb breakpoints in 89 (81%) of 109 gross deletions were evaluated. Significant correlations were found between distance from breakpoint and loop length (r = -0.18, P < 0.05) and stem length (r = -0.18, P < 0.05), suggesting DNA strands are potentially broken in locations closer to bigger LIRs. In addition, bigger loops cause larger deletions (r = 0.19, P < 0.05). Moreover, loop length (r = 0.29, P < 0.02) and identity between stem copies (r = 0.30, P < 0.05) of 3' LIRs were more important in larger deletions. Consequently, DNA breaks may form via LIR-induced cruciform structure during replication. DNA ends may be later repaired by non-homologous end-joining (NHEJ), with following deletion.
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Affiliation(s)
- Nevim Aygun
- Department of Medical Biology, Faculty of Medicine, Dokuz Eylul University, Inciralti, Izmir, Turkey
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24
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Cheeseman K, Rouleau E, Vannier A, Thomas A, Briaux A, Lefol C, Walrafen P, Bensimon A, Lidereau R, Conseiller E, Ceppi M. A diagnostic genetic test for the physical mapping of germline rearrangements in the susceptibility breast cancer genes BRCA1 and BRCA2. Hum Mutat 2012; 33:998-1009. [PMID: 22473970 DOI: 10.1002/humu.22060] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Accepted: 02/03/2012] [Indexed: 12/12/2022]
Abstract
The BRCA1 and BRCA2 genes are involved in breast and ovarian cancer susceptibility. About 2 to 4% of breast cancer patients with positive family history, negative for point mutations, can be expected to carry large rearrangements in one of these two genes. We developed a novel diagnostic genetic test for the physical mapping of large rearrangements, based on molecular combing (MC), a FISH-based technique for direct visualization of single DNA molecules at high resolution. We designed specific Genomic Morse Codes (GMCs), covering the exons, the noncoding regions, and large genomic portions flanking both genes. We validated our approach by testing 10 index cases with positive family history of breast cancer and 50 negative controls. Large rearrangements, corresponding to deletions and duplications with sizes ranging from 3 to 40 kb, were detected and characterized on both genes, including four novel mutations. The nature of all the identified mutations was confirmed by high-resolution array comparative genomic hybridization (aCGH) and breakpoints characterized by sequencing. The developed GMCs allowed to localize several tandem repeat duplications on both genes. We propose the developed genetic test as a valuable tool to screen large rearrangements in BRCA1 and BRCA2 to be combined in clinical settings with an assay capable of detecting small mutations.
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Affiliation(s)
- Kevin Cheeseman
- Genomic Vision, 80–84 rue des Meuniers,Bagneux, Paris, France
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25
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Ruiz de Garibay G, Gutiérrez-Enríquez S, Garre P, Bonache S, Romero A, Palomo L, Sánchez de Abajo A, Benítez J, Balmaña J, Pérez-Segura P, Díaz-Rubio E, Díez O, Caldés T, de la Hoya M. Characterization of four novel BRCA2 large genomic rearrangements in Spanish breast/ovarian cancer families: review of the literature, and reevaluation of the genetic mechanisms involved in their origin. Breast Cancer Res Treat 2012; 133:273-83. [PMID: 22434521 DOI: 10.1007/s10549-011-1909-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2011] [Accepted: 11/30/2011] [Indexed: 11/30/2022]
Abstract
Large genomic rearrangements (LGRs) at the BRCA2 locus explain a non-negligible proportion of hereditary breast and ovarian cancer (HBOC) syndromes. The multiplex ligation and probe amplification (MLPA) assay has permitted in recent years to identify several families carrying LGRs at this locus, but very few such alterations have been fully characterized at the molecular level. Yet, molecular characterization is essential to identify recurrent alterations, to analyze the genetic mechanisms underlying such alterations, or to investigate potential genotype/phenotype relationships. We have used MLPA to identify BRCA2 LGRs in 7 out of 813 Spanish HBOC families previously tested negative for BRCA1 and BRCA2 small genomic alterations (substitutions and indels) and BRCA1 LGRs. We used a combination of long-range PCR, restriction mapping, and cDNA analysis to characterize the alterations at the molecular level. We found that Del Exon1-Exon2, Del Exon12-Exon16 and Del Exon22-Exon24 explain one family each, while Del Exon2 appears to be a Spanish founder mutation explaining four independent families. Finally, we have combined our data with a comprehensive review of the literature to reevaluate the genetic mechanisms underlying LGRs at the BRCA2 locus. Our study substantially increases the spectrum of BRCA2 LGRs fully characterized at the molecular level. Further on, we provide data to suggest that non-allelic homologous recombination has been overestimated as a mechanism underlying these alterations, while the opposite might be true for microhomology-mediated events.
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Affiliation(s)
- Gorka Ruiz de Garibay
- Laboratorio de Oncología Molecular, Instituto de Investigación Sanitaria San Carlos, Hospital Clínico San Carlos, C/Martín Lagos s/n, 28040 Madrid, Spain
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26
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Garcia-Casado Z, Romero I, Fernandez-Serra A, Rubio L, Llopis F, Garcia A, Llombart P, Lopez-Guerrero JA. A de novo complete BRCA1 gene deletion identified in a Spanish woman with early bilateral breast cancer. BMC MEDICAL GENETICS 2011; 12:134. [PMID: 21989022 PMCID: PMC3207938 DOI: 10.1186/1471-2350-12-134] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2011] [Accepted: 10/11/2011] [Indexed: 11/10/2022]
Abstract
BACKGROUND Germline mutations in either of the two tumor-suppressor genes, BRCA1 and BRCA2, account for a significant proportion of hereditary breast and ovarian cancer cases. Most of these mutations consist of deletions, insertions, nonsense mutations, and splice variants, however an increasing number of large genomic rearrangements have been identified in these genes. METHODS We analysed BRCA1 and BRCA2 genes by direct sequencing and MLPA. We confirmed the results by an alternative MLPA kit and characterized the BRCA1 deletion by Array CGH. RESULTS We describe the first case of a patient with no strong family history of the disease who developed early-onset bilateral breast cancer with a de novo complete BRCA1 gene deletion in the germinal line. The detected deletion started from the region surrounding the VAT1 locus to the beginning of NBR1 gene, including the RND2, ΨBRCA1, BRCA1 and NBR2 complete genes. CONCLUSION This finding supports the large genomic rearrangement screening of BRCA genes in young breast cancer patients without family history, as well as in hereditary breast and ovarian cancer families previously tested negative for other variations.
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Affiliation(s)
- Zaida Garcia-Casado
- Laboratory of Molecular Biology, Fundación Instituto Valenciano de Oncología, Valencia, Spain
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27
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Large genomic rearrangements of the BRCA1 and BRCA2 genes: review of the literature and report of a novel BRCA1 mutation. Breast Cancer Res Treat 2010; 125:325-49. [PMID: 20232141 DOI: 10.1007/s10549-010-0817-z] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2010] [Accepted: 02/22/2010] [Indexed: 10/19/2022]
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28
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Ticha I, Kleibl Z, Stribrna J, Kotlas J, Zimovjanova M, Mateju M, Zikan M, Pohlreich P. Screening for genomic rearrangements in BRCA1 and BRCA2 genes in Czech high-risk breast/ovarian cancer patients: high proportion of population specific alterations in BRCA1 gene. Breast Cancer Res Treat 2010; 124:337-47. [PMID: 20135348 DOI: 10.1007/s10549-010-0745-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2009] [Accepted: 01/12/2010] [Indexed: 01/18/2023]
Abstract
Large genomic rearrangements (LGR) represent substantial proportion of pathogenic mutations in the BRCA1 gene, whereas the frequency of rearrangements in the BRCA2 gene is low in many populations. We screened for LGRs in BRCA1 and BRCA2 genes by multiplex ligation-dependent probe amplification (MLPA) in 521 unrelated patients negative for BRCA1/2 point mutations selected from 655 Czech high-risk breast and/or ovarian cancer patients. Besides long range PCR, a chromosome 17-specific oligonucleotide-based array comparative genomic hybridization (aCGH) was used for accurate location of deletions. We identified 14 patients carrying 8 different LGRs in BRCA1 that accounted for 12.3% of all pathogenic BRCA1 mutations. No LGRs were detected in the BRCA2 gene. In a subgroup of 239 patients from high-risk families, we found 12 LGRs (5.0%), whereas two LGRs were revealed in a subgroup of 282 non-familial cancer cases (0.7%). Five LGRs (deletion of exons 1-17, 5-10, 13-19, 18-22 and 21-24) were novel; two LGRs (deletion of exons 5-14 and 21-22) belong to the already described Czech-specific mutations; one LGR (deletion of exons 1-2) was reported from several countries. The deletions of exons 1-17 and 5-14, identified each in four families, represented Czech founder mutations. The present study indicates that screening for LGRs in BRCA1 should include patients from breast or ovarian cancer families as well as high-risk patients with non-familial cancer, in particular cases with early-onset breast or ovarian cancer. On the contrary, our analyses do not support the need to screen for LGRs in the BRCA2 gene. Implementation of chromosome-specific aCGH could markedly facilitate the design of primers for amplification and sequence analysis of junction fragments, especially in deletions overlapping gene boundaries.
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Affiliation(s)
- Ivana Ticha
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University in Prague, U Nemocnice 5, 128 53, Prague 2, Czech Republic
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29
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del Valle J, Feliubadaló L, Nadal M, Teulé A, Miró R, Cuesta R, Tornero E, Menéndez M, Darder E, Brunet J, Capellà G, Blanco I, Lázaro C. Identification and comprehensive characterization of large genomic rearrangements in the BRCA1 and BRCA2 genes. Breast Cancer Res Treat 2009; 122:733-43. [DOI: 10.1007/s10549-009-0613-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2009] [Accepted: 10/20/2009] [Indexed: 11/25/2022]
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30
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Ewald IP, Ribeiro PLI, Palmero EI, Cossio SL, Giugliani R, Ashton-Prolla P. Genomic rearrangements in BRCA1 and BRCA2: A literature review. Genet Mol Biol 2009; 32:437-46. [PMID: 21637503 PMCID: PMC3036053 DOI: 10.1590/s1415-47572009005000049] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2008] [Accepted: 12/08/2008] [Indexed: 12/17/2022] Open
Abstract
Women with mutations in the breast cancer genes BRCA1 or BRCA2 have an increased lifetime risk of developing breast, ovarian and other BRCA-associated cancers. However, the number of detected germline mutations in families with hereditary breast and ovarian cancer (HBOC) syndrome is lower than expected based upon genetic linkage data. Undetected deleterious mutations in the BRCA genes in some high-risk families are due to the presence of intragenic rearrangements such as deletions, duplications or insertions that span whole exons. This article reviews the molecular aspects of BRCA1 and BRCA2 rearrangements and their frequency among different populations. An overview of the techniques used to screen for large rearrangements in BRCA1 and BRCA2 is also presented. The detection of rearrangements in BRCA genes, especially BRCA1, offers a promising outlook for mutation screening in clinical practice, particularly in HBOC families that test negative for a germline mutation assessed by traditional methods.
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Affiliation(s)
- Ingrid Petroni Ewald
- Laboratório de Medicina Genômica, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS Brazil
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31
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van den Ouweland AMW, Dinjens WNM, Dorssers LCJ, van Veghel-Plandsoen MM, Brüggenwirth HT, Withagen-Hermans CJ, Collée JM, Joosse SA, Terlouw-Kromosoeto JNR, Nederlof PM. Deletion of exons 1a-2 of BRCA1: a rather frequent pathogenic abnormality. Genet Test Mol Biomarkers 2009; 13:399-406. [PMID: 19405878 DOI: 10.1089/gtmb.2008.0155] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Women carrying a pathogenic mutation in either BRCA1 or BRCA2 have a major risk of developing breast and/or ovarian cancer. The majority of mutations in these genes are small point mutations. Since the development of multiplex ligation-dependent probe amplification, an increasing number of large genomic rearrangements have been detected. Here, we describe the characterization of pathogenic deletions of exons 1a-2 of BRCA1 in six families using loss of heterozygosity, array comparative genomic hybridization, and sequence analyses. Two families harbor a 37 kb deletion starting in intron 2 of psi BRCA1, encompassing NBR2, and exons 1a-2 of BRCA1, while the other four families have an 8 kb deletion with breakpoints in intron 2 of NBR2 and intron 2 of BRCA1. This observation, together with the previously described families with exon 1a-2 deletions of BRCA1, demonstrates that this type of deletions is relatively frequent in breast/ovarian cancer families.
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Affiliation(s)
- Ans M W van den Ouweland
- Department of Clinical Genetics, Josephine Nefkens Institute, Erasmus Medical Center, Rotterdam, The Netherlands.
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32
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Palma MD, Domchek SM, Stopfer J, Erlichman J, Siegfried JD, Tigges-Cardwell J, Mason BA, Rebbeck TR, Nathanson KL. The relative contribution of point mutations and genomic rearrangements in BRCA1 and BRCA2 in high-risk breast cancer families. Cancer Res 2008; 68:7006-14. [PMID: 18703817 PMCID: PMC2752710 DOI: 10.1158/0008-5472.can-08-0599] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The demand for BRCA1 and BRCA2 mutation screening is increasing as their identification will affect medical management. However, both the contribution of different mutation types in BRCA1 and BRCA2 and whom should be offered testing for large genomic rearrangements have not been well established in the U.S. high-risk population. We define the prevalence and spectrum of point mutations and genomic rearrangements in BRCA genes in a large U.S. high-risk clinic population of both non-Ashkenazi and Ashkenazi Jewish descent, using a sample set representative of the U.S. genetic testing population. Two hundred fifty-one probands ascertained through the University of Pennsylvania high-risk clinic, all with commercial testing for BRCA1 and BRCA2, with an estimated prevalence of BRCA mutation >or=10% using the Myriad II model and a DNA sample available, were studied. Individuals without deleterious point mutations were screened for genomic rearrangements in BRCA1 and BRCA2. In the 136 non-Ashkenazi Jewish probands, 36 (26%) BRCA point mutations and 8 (6%) genomic rearrangements (7 in BRCA1 and 1 in BRCA2) were identified. Forty-seven of the 115 (40%) Ashkenazi Jewish probands had point mutations; no genomic rearrangements were identified in the group without mutations. In the non-Ashkenazi Jewish probands, genomic rearrangements constituted 18% of all identified BRCA mutations; estimated mutation prevalence (Myriad II model) was not predictive of their presence. Whereas these findings should be confirmed in larger sample sets, our data suggest that genomic rearrangement testing be considered in all non-Ashkenazi Jewish women with an estimated mutation prevalence >or=10%.
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Affiliation(s)
- Maurizia Dalla Palma
- Division of Medical Genetics, University of Pennsylvania School of Medicine, Philadelphia, PA
| | - Susan M. Domchek
- Division of Hematology-Oncology, Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA
- Abramson Cancer Center, Department of Biostatistics and Epidemiology, University of Pennsylvania School of Medicine, Philadelphia, PA
| | - Jill Stopfer
- Abramson Cancer Center, Department of Biostatistics and Epidemiology, University of Pennsylvania School of Medicine, Philadelphia, PA
| | - Julie Erlichman
- Abramson Cancer Center, Department of Biostatistics and Epidemiology, University of Pennsylvania School of Medicine, Philadelphia, PA
| | - Jill D. Siegfried
- Joan Karnell Cancer Center at Pennsylvania Hospital, University of Pennsylvania School of Medicine, Philadelphia, PA
| | - Jessica Tigges-Cardwell
- Abramson Cancer Center, Department of Biostatistics and Epidemiology, University of Pennsylvania School of Medicine, Philadelphia, PA
| | - Bernard A. Mason
- Division of Medical Genetics, University of Pennsylvania School of Medicine, Philadelphia, PA
- Joan Karnell Cancer Center at Pennsylvania Hospital, University of Pennsylvania School of Medicine, Philadelphia, PA
| | - Timothy R. Rebbeck
- Division of Hematology-Oncology, Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA
- Abramson Cancer Center, Department of Biostatistics and Epidemiology, University of Pennsylvania School of Medicine, Philadelphia, PA
| | - Katherine L. Nathanson
- Division of Medical Genetics, University of Pennsylvania School of Medicine, Philadelphia, PA
- Abramson Cancer Center, Department of Biostatistics and Epidemiology, University of Pennsylvania School of Medicine, Philadelphia, PA
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Engert S, Wappenschmidt B, Betz B, Kast K, Kutsche M, Hellebrand H, Goecke TO, Kiechle M, Niederacher D, Schmutzler RK, Meindl A. MLPA screening in the BRCA1 gene from 1,506 German hereditary breast cancer cases: novel deletions, frequent involvement of exon 17, and occurrence in single early-onset cases. Hum Mutat 2008; 29:948-58. [PMID: 18431737 DOI: 10.1002/humu.20723] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We present a comprehensive analysis of 1,506 German families for large genomic rearrangements (LGRs) in the BRCA1 gene and of 450 families in the BRCA2 gene by the multiplex ligation-dependent probe amplification (MLPA) technique. A total of 32 pathogenic rearrangements in the BRCA1 gene were found, accounting for 1.6% of all mutations, but for 9.6% of all BRCA1 mutations identified in a total of 1,996 families, including 490 with small pathogenic BRCA1/2 mutations. Considering only high risk groups for hereditary breast/ovarian cancer, the prevalence of rearrangements is 2.1%. Interestingly, deletions involving exon 17 of the BRCA1 gene seem to be most frequent in Germany. Apart from recurrent aberrations like del ex17, dupl ex13, and del ex22, accounting for more than 50% of all BRCA1 LGRs, we could fully characterize 11 novel deletions. Moreover, one novel deletion involving exons 1-7 and one deletion affecting the entire BRCA1 gene were identified. All rearrangements were detected in families with: 1) at least two breast cancer cases prior to the age of 51 years; 2) breast and ovarian cancer cases; 3) ovarian cancer only families with at least two ovarian cancer cases; or 4) a single breast cancer case prior to the age of 36 years, while no mutations were detected in breast cancer only families with no or only one breast cancer case prior to the age of 51 years. Analysis for gross rearrangements in 412 high-risk individuals, revealed no event in the BRCA2 gene and only two known CHEK2 mutations. However, in an additional 38 high-risk families with cooccurrence of female breast/ovarian and male breast cancer, one rearrangement in the BRCA2 gene was found. In summary, we advise restricting BRCA1 MLPA screening to those subgroups that revealed LGRs and recommend BRCA2 MLPA screening only for families presenting with cooccurrence of female and male breast cancer.
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Affiliation(s)
- Stefanie Engert
- Department of Obstetrics and Gynecology, Division of Tumor Genetics, Technical University, Munich, Germany
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Hansen TVO, Jønson L, Albrechtsen A, Andersen MK, Ejlertsen B, Nielsen FC. Large BRCA1 and BRCA2 genomic rearrangements in Danish high risk breast-ovarian cancer families. Breast Cancer Res Treat 2008; 115:315-23. [PMID: 18546071 DOI: 10.1007/s10549-008-0088-0] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2008] [Accepted: 05/30/2008] [Indexed: 10/22/2022]
Abstract
BRCA1 and BRCA2 germ-line mutations predispose to breast and ovarian cancer. Large genomic rearrangements of BRCA1 account for 0-36% of all disease causing mutations in various populations, while large genomic rearrangements in BRCA2 are more rare. We examined 642 East Danish breast and/or ovarian cancer patients in whom a deleterious mutation in BRCA1 and BRCA2 was not detected by sequencing using the multiplex ligation-dependent probe amplification (MLPA) assay. We identified 15 patients with 7 different genomic rearrangements, including a BRCA1 exon 5-7 deletion with a novel breakpoint, a BRCA1 exon 13 duplication, a BRCA1 exon 17-19 deletion, a BRCA1 exon 3-16 deletion, and a BRCA2 exon 20 deletion with a novel breakpoint as well as two novel BRCA1 exon 17-18 and BRCA1 exon 19 deletions. The large rearrangements in BRCA1 and BRCA2 accounted for 9.2% (15/163) of all BRCA1 and BRCA2 mutations in East Denmark. Nine patients had the exon 3-16 deletion in BRCA1. By SNP analysis we find that the patients share a 5 Mb fragment of chromosome 17, including BRCA1, indicating that the exon 3-16 deletion represents a Danish founder mutation.
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Affiliation(s)
- Thomas v O Hansen
- Department of Clinical Biochemistry 4111, Rigshospitalet, Blegdamsvej 9, Copenhagen 2100, Denmark.
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35
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Identification of a novel BRCA1 large genomic rearrangement in a Spanish breast/ovarian cancer family. Breast Cancer Res Treat 2007; 112:63-7. [DOI: 10.1007/s10549-007-9839-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2007] [Accepted: 11/21/2007] [Indexed: 10/22/2022]
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Falchetti M, Lupi R, Rizzolo P, Ceccarelli K, Zanna I, Calò V, Tommasi S, Masala G, Paradiso A, Gulino A, Giannini G, Russo A, Palli D, Ottini L. BRCA1/BRCA2 rearrangements and CHEK2 common mutations are infrequent in Italian male breast cancer cases. Breast Cancer Res Treat 2007; 110:161-7. [PMID: 17661168 DOI: 10.1007/s10549-007-9689-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2007] [Accepted: 07/10/2007] [Indexed: 10/23/2022]
Abstract
Male breast cancer (MBC) is a rare and poorly known disease. Germ-line mutations of BRCA2 and, to lesser extent, BRCA1 genes are the highest risk factors associated with MBC. Interestingly, BRCA2 germ-line rearrangements have been described in high-risk breast/ovarian cancer families which included at least one MBC case. Germ-line mutations of CHEK2 gene have been also implicated in inherited MBC predisposition. The CHEK2 1100delC mutation has been shown to increase the risk of breast cancer in men lacking BRCA1/BRCA2 mutations. Intriguingly, two other CHEK2 mutations (IVS2+1G>A and I157T) and a CHEK2 large genomic deletion (del9-10) have been associated with an elevated risk for prostate cancer. Here, we investigated the contribution of BRCA1, BRCA2 and CHEK2 alterations to MBC predisposition in Italy by analysing a large series of MBC cases, unselected for breast cancer family history and all negative for BRCA1/BRCA2 germ-line mutations. A total of 102 unrelated Italian MBC cases were screened for deletions/duplications of BRCA1, BRCA2 and CHEK2 by multiplex ligation-dependent probe amplification. No BRCA1, BRCA2 and CHEK2 genomic rearrangements, including the CHEK2 del9-10, were found in the series analysed. Furthermore, none of the MBC cases and 263 male population controls, also included in this study, carried the CHEK2 1100delC, IVS2+1G>A and I157T common mutations. Overall, our data suggest that screening of BRCA1/2 rearrangements is not advantageous in MBC cases not belonging to high-risk breast cancer families and that common CHEK2 mutations play an irrelevant role in MBC predisposition in Italy.
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Affiliation(s)
- Mario Falchetti
- Department of Experimental Medicine, University of Rome La Sapienza, Viale Regina Elena, 324, Rome, 00161, Italy
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Weitzel JN, Lagos VI, Herzog JS, Judkins T, Hendrickson B, Ho JS, Ricker CN, Lowstuter KJ, Blazer KR, Tomlinson G, Scholl T. Evidence for common ancestral origin of a recurring BRCA1 genomic rearrangement identified in high-risk Hispanic families. Cancer Epidemiol Biomarkers Prev 2007; 16:1615-20. [PMID: 17646271 DOI: 10.1158/1055-9965.epi-07-0198] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Large rearrangements account for 8% to 15% of deleterious BRCA mutations, although none have been characterized previously in individuals of Mexican ancestry. METHODS DNA from 106 Hispanic patients without an identifiable BRCA mutation by exonic sequence analysis was subjected to multiplexed quantitative differential PCR. One case of Native American and African American ancestry was identified via multiplex ligation-dependent probe amplification. Long-range PCR was used to confirm deletion events and to clone and sequence genomic breakpoints. Splicing patterns were derived by sequencing cDNA from reverse transcription-PCR of lymphoblastoid cell line RNA. Haplotype analysis was conducted for recurrent mutations. RESULTS The same deletion of BRCA1 exons 9 through 12 was identified in five unrelated families. Long-range PCR and sequencing indicated a deletion event of 14.7 kb. A 3-primer PCR assay was designed based on the deletion breakpoints, identified within an AluSp element in intron 8 and an AluSx element in intron 12. Haplotype analysis confirmed common ancestry. Analysis of cDNA showed direct splicing of exons 8 to 13, resulting in a frameshift mutation and predicted truncation of the BRCA1 protein. CONCLUSIONS We identified and characterized a novel large BRCA1 deletion in five unrelated families-four of Mexican ancestry and one of African and Native American ancestry, suggesting the possibility of founder effect of Amerindian or Mestizo origin. This BRCA1 rearrangement was detected in 3.8% (4 of 106) of BRCA sequence-negative Hispanic families. An assay for this mutation should be considered for sequence-negative high-risk Hispanic patients.
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Affiliation(s)
- Jeffrey N Weitzel
- Department of Clinical Cancer Genetics, City of Hope, 1500 East Duarte Road, Duarte, CA 91010, USA.
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Lim YK, Lau PTC, Ali AB, Lee SC, Wong JEL, Putti TC, Sng JH. Identification of novel BRCA large genomic rearrangements in Singapore Asian breast and ovarian patients with cancer. Clin Genet 2007; 71:331-42. [PMID: 17470134 DOI: 10.1111/j.1399-0004.2007.00773.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Large genomic rearrangements have been reported to account for about 10-15% of BRCA1 gene mutations. Approximately, 90 BRCA rearrangements have been described to date, all of which but one have been reported in Caucasian populations of predominantly Western European descent. Knowledge of BRCA genomic rearrangements in Asian populations is still largely unknown. In this study, we have investigated for the presence of BRCA rearrangements among Asian patients with early onset or familial history of breast or ovarian cancer. Using multiplex ligation-dependent probe amplification (MLPA), we have analyzed 100 Singapore patients who previously tested negative for deleterious BRCA mutations by the conventional polymerase chain reaction-based mutation detection methods. Three novel BRCA rearrangements were detected, two of which were characterized. The patients with the rearrangements, a BRCA1 exon 13 duplication, a BRCA1 exon 13-15 deletion and a BRCA2 exon 4-11 duplication, comprise 3% of those previously tested negative for BRCA mutations. Of the BRCA1 and BRCA2 pathogenic mutations identified in our studies on Asian high-risk breast and ovarian patients with cancer to date, these rearrangements constitute 2/19 and 1/2 of the BRCA1 and BRCA2 pathogenic mutations, respectively. Given the increasing number of rearrangements reported in recent years and their contribution to the BRCA mutation spectrum, the presence of BRCA large exon rearrangements in Asian populations should be investigated where clinical, diagnostic service is recommended.
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Affiliation(s)
- Y K Lim
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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39
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Vasickova P, Machackova E, Lukesova M, Damborsky J, Horky O, Pavlu H, Kuklova J, Kosinova V, Navratilova M, Foretova L. High occurrence of BRCA1 intragenic rearrangements in hereditary breast and ovarian cancer syndrome in the Czech Republic. BMC MEDICAL GENETICS 2007; 8:32. [PMID: 17561994 PMCID: PMC1904436 DOI: 10.1186/1471-2350-8-32] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2006] [Accepted: 06/11/2007] [Indexed: 01/07/2023]
Abstract
Background Alterations in the highly penetrant cancer susceptibility gene BRCA1 are responsible for the majority of hereditary breast and/or ovarian cancers. However, the number of detected germline mutations has been lower than expected based upon genetic linkage data. Undetected deleterious mutations in the BRCA1 gene in some high-risk families could be due to the presence of intragenic rearrangements as deletions, duplications or insertions spanning whole exons. Standard PCR-based screening methods are mainly focused on detecting point mutations and small insertions/deletions, but large rearrangements might escape detection. The purpose of this study was to determine the type and frequency of large genomic rearrangements in the BRCA1 gene in hereditary breast and ovarian cancer cases in the Czech Republic. Methods Multiplex ligation-dependent probe amplification (MLPA) was used to examine BRCA1 rearrangements in 172 unrelated patients with hereditary breast and/or ovarian cancer syndrome without finding deleterious mutation after complete screening of whole coding regions of BRCA1/2 genes. Positive MLPA results were confirmed and located by long-range PCR. The breakpoints of detected rearrangements were characterized by sequencing. Results Six different large deletions in the BRCA1 gene were identified in 10 out of 172 unrelated high-risk patients: exons 1A/1B and 2 deletion; partial deletion of exon 11 and exon 12; exons 18 and 19 deletion; exon 20 deletion; exons 21 and 22 deletion; and deletion of exons 5 to 14. The breakpoint junctions were localized and further characterized. Destabilization and global unfolding of the mutated BRCT domains explain the molecular and genetic defects associated with the exon 20 in-frame deletion and the exon 21 and 22 in-frame deletion, respectively. Conclusion Using MLPA, mutations were detected in 6% of high-risk patients previously designated as BRCA1/2 mutation-negative. The breakpoints of five out of six large deletions detected in Czech patients are novel. Screening for large genomic rearrangements in the BRCA1 gene in the Czech high-risk patients is highly supported by this study.
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Affiliation(s)
| | | | | | - Jiri Damborsky
- Loschmidt Laboratories, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Ondrej Horky
- Center of Molecular Biology and Gene Therapy, University Hospital, Brno, Czech Republic
| | - Hana Pavlu
- Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Jitka Kuklova
- Masaryk Memorial Cancer Institute, Brno, Czech Republic
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Veschi S, Aceto G, Scioletti AP, Gatta V, Palka G, Cama A, Mariani-Costantini R, Battista P, Calò V, Barbera F, Bazan V, Russo A, Stuppia L. High prevalence of BRCA1 deletions in BRCAPRO-positive patients with high carrier probability. Ann Oncol 2007; 18 Suppl 6:vi86-92. [PMID: 17591842 DOI: 10.1093/annonc/mdm233] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Mutation screening of the BRCA1 and BRCA2 genes in probands with familial breast/ovarian cancer has been greatly improved by the multiplex ligation-dependent probe amplification (MLPA) assay able to evidence gene rearrangements not detectable by standard screening methods. However, no criteria for selection of cases to be submitted to the MLPA test have been reported yet. We used the BRCAPro software for the selection of familial breast/ovarian cancer probands investigated with the MLPA approach after negative BRCA1/2 conventional mutation screening. One hundred and seventy-seven probands were investigated for germline BRCA1/2 mutations after assessment of genetic risk using BRCAPro. Probands were classified as BRCAPro positive (n = 67) when the carrier probability (CP) was >10% and as BRCAPro negative (n = 110), when the CP was <10%. Conventional mutational analyses of the BRCA1/2 genes and, in one case, of p53 identified 22 pathogenetic germline mutations, 12 in BRCA1, 9 in BRCA2 and 1 in p53, in 22/177 (12.4%) probands. All the mutations except one were detected in BRCAPro-positive patients. In the 46 BRCAPro-positive cases that resulted negative by BRCA1/2 mutation, screening analysis of rearrangements within BRCA1/2 by MLPA was carried out. Three patients with a very high CP showed BRCA1 deletions, consisting of deletions of exons 1-2 in two probands and of exon 24 in the third proband. In one case, the exons 1-2 deletion was shown to cosegregate with disease in the family. No BRCA2 rearrangements were detected, but one patient showed the 1100delC of the CHEK2 gene, whose probe is present in the BRCA2 kit. In our series, the highest carrier detection rate of mutation screening plus MLPA analysis (52.3%) was in patients with a BRCAPro CP >50%.
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Affiliation(s)
- S Veschi
- Center of Excellence on Aging, University G. d'Annunzio University Foundation, Chieti, Pescara
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Buffone A, Capalbo C, Ricevuto E, Sidoni T, Ottini L, Falchetti M, Cortesi E, Marchetti P, Scambia G, Tomao S, Rinaldi C, Zani M, Ferraro S, Frati L, Screpanti I, Gulino A, Giannini G. Prevalence of BRCA1 and BRCA2 genomic rearrangements in a cohort of consecutive Italian breast and/or ovarian cancer families. Breast Cancer Res Treat 2007; 106:289-96. [PMID: 17333342 DOI: 10.1007/s10549-007-9499-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2006] [Accepted: 01/01/2007] [Indexed: 10/23/2022]
Abstract
Germline point mutations in BRCA1 and BRCA2 genes account for about 30% of the inherited breast and ovarian cancers. Germline genomic rearrangements have been found in both BRCA1 and BRCA2 genes, but the extent to which these alterations might contribute to increasing the actual mutation detection rate is still debated. Here we screened a cohort of 112 consecutive Italian families at moderate-to-high risk for breast and/or ovarian cancer for BRCA1 and BRCA2 point mutations and genomic rearrangements. Of the 83 point mutation negative probands, two (2.4%) showed BRCA1 rearrangements, accounting for 10.5% of the BRCA1 mutations. BRCA1 del18-19 has been previously described in another Italian family, while the molecular characterization of the BRCA1 del23-24 is given here for the first time. Conversely, we failed to identify any BRCA2 rearrangements even in the hereditary breast cancer families, where we detected an higher prevalence of BRCA2 compared to BRCA1 point mutations. Our results support the idea that search for BRCA1 rearrangements should be included in the genetic screening of even moderate risk breast/ovarian cancer families. In contrast, they suggest BRCA2 rearrangements might be very rare out of the high risk families including a male breast cancer.
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Affiliation(s)
- Amelia Buffone
- Department of Experimental Medicine, University La Sapienza, Policlinico Umberto I, Viale Regina Elena, 324, Rome 00161, Italy
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Armaou S, Konstantopoulou I, Anagnostopoulos T, Razis E, Boukovinas I, Xenidis N, Fountzilas G, Yannoukakos D. Novel genomic rearrangements in the BRCA1 gene detected in Greek breast/ovarian cancer patients. Eur J Cancer 2006; 43:443-53. [PMID: 17174087 DOI: 10.1016/j.ejca.2006.09.021] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2006] [Revised: 09/12/2006] [Accepted: 09/16/2006] [Indexed: 11/30/2022]
Abstract
The identification of genomic rearrangements in breast/ovarian cancer families has widened the mutational spectrum of the BRCA1 gene, increasing the number of patients who can benefit from molecular screening. More than 60 different BRCA1 genomic rearrangements with mapped breakpoints have been reported up to date, in all exons of the gene. The proportion of BRCA1 mutations due to genomic rearrangements varies from 8 to 27% in different populations, probably due to both ethnic diversity and the technical approach employed. In order to estimate the contribution of BRCA1 genomic rearrangements to hereditary breast/ovarian cancer (HBOC) predisposition in Greek families, probands from 95 families with breast/ovarian history but negative for point mutations or small insertions/deletions in BRCA1 and BRCA2 genes, were screened using Quantitative Multiplex PCR of Short Fluorescent Fragments (QMPSF). Two large deletions of 4.2 and 4.4 kb were identified in exons 20 and 24 respectively. Additional screening, using diagnostic primers for the above deletions in exons 20 and 24, performed on another 86 probands from families with breast/ovarian cancer history and 210 cases of sporadic breast/ovarian cancer resulted in the identification of two more large genomic rearrangements. One, identified in a familial case, identical to the previous exon 24 deletion and a second, identified in a case reported as sporadic, 3.2 kb deletion involving exon 20 and reported elsewhere in another Greek patient. Three out of four genomic rearrangements described in this study were detected in patients who had developed both breast and ovarian cancer; thus suggesting a correlation between the specific phenotype and the high probability of detecting inherited rearrangements in BRCA1.
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Affiliation(s)
- Sophia Armaou
- Molecular Diagnostics Laboratory, I/R-RP, National Centre for Scientific Research Demokritos, Athens, Greece
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Gutiérrez-Enríquez S, de la Hoya M, Martínez-Bouzas C, Sanchez de Abajo A, Ramón y Cajal T, Llort G, Blanco I, Beristain E, Díaz-Rubio E, Alonso C, Tejada MI, Caldés T, Diez O. Screening for large rearrangements of the BRCA2 gene in Spanish families with breast/ovarian cancer. Breast Cancer Res Treat 2006; 103:103-7. [PMID: 17063271 DOI: 10.1007/s10549-006-9376-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2006] [Accepted: 08/11/2006] [Indexed: 10/24/2022]
Abstract
Germ-line mutations in BRCA1 and BRCA2 are responsible for about 30-60% of the hereditary breast and ovarian cancer (HBOC). A large number of point mutations have been described in both genes. However, large deletions and duplications that disrupt one or more exons are overlooked by point mutation detection approaches. Over the past years several rearrangements have been identified in BRCA1, while few studies have been designed to screen this type of mutations in BRCA2. Our aim was to estimate the prevalence of large genomic rearrangements in the BRCA2 gene in Spanish breast/ovarian cancer families. The multiplex ligation-dependent probe amplification (MLPA) was employed to search gross deletions or duplications of BRCA2 in 335 Spanish moderate to high-risk breast/ovarian cancer families previously screened negative for point mutations by conventional methods. Four different and novel large genomic alterations were consistently identified by MLPA in five families, respectively: deletions of exon 2, exons 10-12 and exons 15-16 and duplication of exon 20 (in two families). RT-PCR experiments confirmed the deletion of exons 15-16. All patients harbouring a genomic rearrangement were members of high-risk families, with three or more breast/ovarian cancer cases or the presence of breast cancer in males. We provide evidence that the BRCA2 rearrangements seem to account for a relatively small proportion of familial breast cancer cases in Spanish population. The screening for these alterations as part of the comprehensive genetic testing can be recommended, especially in multiple case breast/ovarian families and families with male breast cancer cases.
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Affiliation(s)
- Sara Gutiérrez-Enríquez
- Servei de Genètica, Hospital de la Santa Creu i Sant Pau, Pare Claret 167, Barcelona 08025, Spain.
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