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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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52
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Scott DE, Marsh M, Blundell TL, Abell C, Hyvönen M. Structure-activity relationship of the peptide binding-motif mediating the BRCA2:RAD51 protein-protein interaction. FEBS Lett 2016; 590:1094-102. [PMID: 26992456 PMCID: PMC4855620 DOI: 10.1002/1873-3468.12139] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Revised: 02/25/2016] [Accepted: 03/14/2016] [Indexed: 12/18/2022]
Abstract
RAD51 is a recombinase involved in the homologous recombination of double‐strand breaks in DNA. RAD51 forms oligomers by binding to another molecule of RAD51 via an ‘FxxA’ motif, and the same recognition sequence is similarly utilised to bind BRCA2. We have tabulated the effects of mutation of this sequence, across a variety of experimental methods and from relevant mutations observed in the clinic. We use mutants of a tetrapeptide sequence to probe the binding interaction, using both isothermal titration calorimetry and X‐ray crystallography. Where possible, comparison between our tetrapeptide mutational study and the previously reported mutations is made, discrepancies are discussed and the importance of secondary structure in interpreting alanine scanning and mutational data of this nature is considered.
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Affiliation(s)
- Duncan E Scott
- Department of Chemistry, University of Cambridge, Cambridge, UK
| | - May Marsh
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Chris Abell
- Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Marko Hyvönen
- Department of Biochemistry, University of Cambridge, Cambridge, UK
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53
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Recurrent mutations of BRCA1, BRCA2 and PALB2 in the population of breast and ovarian cancer patients in Southern Poland. Hered Cancer Clin Pract 2016; 14:5. [PMID: 26843898 PMCID: PMC4739084 DOI: 10.1186/s13053-016-0046-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 01/28/2016] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Mutations in the BRCA1, BRCA2 and PALB2 genes are well-established risk factors for the development of breast and/or ovarian cancer. The frequency and spectrum of mutations in these genes has not yet been examined in the population of Southern Poland. METHODS We examined the entire coding sequences of the BRCA1 and BRCA2 genes and genotyped a recurrent mutation of the PALB2 gene (c.509_510delGA) in 121 women with familial and/or early-onset breast or ovarian cancer from Southern Poland. RESULTS A BRCA1 mutation was identified in 11 of 121 patients (9.1 %) and a BRCA2 mutation was identified in 10 of 121 patients (8.3 %). Two founder mutations of BRCA1 accounted for 91 % of all BRCA1 mutation carriers (c.5266dupC was identified in six patients and c.181 T > G was identified in four patients). Three of the seven different BRCA2 mutations were detected in two patients each (c.9371A > T, c.9403delC and c.1310_1313delAAGA). Three mutations have not been previously reported in the Polish population (BRCA1 c.3531delT, BRCA2 c.1310_1313delAAGA and BRCA2 c.9027delT). The recurrent PALB2 mutation c.509_510delGA was identified in two patients (1.7 %). CONCLUSIONS The standard panel of BRCA1 founder mutations is sufficiently sensitive for the identification of BRCA1 mutation carriers in Southern Poland. The BRCA2 mutations c.9371A > T and c.9403delC as well as the PALB2 mutation c.509_510delGA should be included in the testing panel for this population.
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54
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Acedo A, Hernández-Moro C, Curiel-García Á, Díez-Gómez B, Velasco EA. Functional classification of BRCA2 DNA variants by splicing assays in a large minigene with 9 exons. Hum Mutat 2015; 36:210-21. [PMID: 25382762 PMCID: PMC4371643 DOI: 10.1002/humu.22725] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 10/27/2014] [Indexed: 01/04/2023]
Abstract
Numerous pathogenic DNA variants impair the splicing mechanism in human genetic diseases. Minigenes are optimal approaches to test variants under the splicing viewpoint without the need of patient samples. We aimed to design a robust minigene construct of the breast cancer gene BRCA2 in order to investigate the impact of variants on splicing. BRCA2 exons 19-27 (MGBR2_ex19-27) were cloned in the new vector pSAD. It produced a large transcript of the expected size (2,174 nucleotides) and exon structure (V1-ex19-27-V2). Splicing assays showed that 18 (17 splice-site and 1 silencer variants) out of 40 candidate DNA variants induced aberrant patterns. Twenty-four anomalous transcripts were accurately detected by fluorescent-RT-PCR that were generated by exon-skipping, alternative site usage, and intron-retention events. Fourteen variants induced major anomalies and were predicted to disrupt protein function so they could be classified as pathogenic. Furthermore, minigene mimicked previously reported patient RNA outcomes of seven variants supporting the reproducibility of minigene assays. Therefore, a relevant fraction of variants are involved in breast cancer through splicing alterations. MGBR2_ex19-27 is the largest reported BRCA2 minigene and constitutes a valuable tool for the functional and clinical classification of sequence variations.
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Affiliation(s)
- Alberto Acedo
- Splicing and Genetic Susceptibility to Cancer, Instituto de Biología y Genética Molecular (CSIC-UVa), Valladolid, Spain
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55
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Taylor JC, Martin HC, Lise S, Broxholme J, Cazier JB, Rimmer A, Kanapin A, Lunter G, Fiddy S, Allan C, Aricescu AR, Attar M, Babbs C, Becq J, Beeson D, Bento C, Bignell P, Blair E, Buckle VJ, Bull K, Cais O, Cario H, Chapel H, Copley RR, Cornall R, Craft J, Dahan K, Davenport EE, Dendrou C, Devuyst O, Fenwick AL, Flint J, Fugger L, Gilbert RD, Goriely A, Green A, Greger IH, Grocock R, Gruszczyk AV, Hastings R, Hatton E, Higgs D, Hill A, Holmes C, Howard M, Hughes L, Humburg P, Johnson D, Karpe F, Kingsbury Z, Kini U, Knight JC, Krohn J, Lamble S, Langman C, Lonie L, Luck J, McCarthy D, McGowan SJ, McMullin MF, Miller KA, Murray L, Németh AH, Nesbit MA, Nutt D, Ormondroyd E, Oturai AB, Pagnamenta A, Patel SY, Percy M, Petousi N, Piazza P, Piret SE, Polanco-Echeverry G, Popitsch N, Powrie F, Pugh C, Quek L, Robbins PA, Robson K, Russo A, Sahgal N, van Schouwenburg PA, Schuh A, Silverman E, Simmons A, Sørensen PS, Sweeney E, Taylor J, Thakker RV, Tomlinson I, Trebes A, Twigg SR, Uhlig HH, Vyas P, Vyse T, Wall SA, Watkins H, Whyte MP, Witty L, Wright B, Yau C, Buck D, Humphray S, Ratcliffe PJ, Bell JI, Wilkie AO, Bentley D, Donnelly P, McVean G. Factors influencing success of clinical genome sequencing across a broad spectrum of disorders. Nat Genet 2015; 47:717-726. [PMID: 25985138 PMCID: PMC4601524 DOI: 10.1038/ng.3304] [Citation(s) in RCA: 250] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 04/22/2015] [Indexed: 12/12/2022]
Abstract
To assess factors influencing the success of whole-genome sequencing for mainstream clinical diagnosis, we sequenced 217 individuals from 156 independent cases or families across a broad spectrum of disorders in whom previous screening had identified no pathogenic variants. We quantified the number of candidate variants identified using different strategies for variant calling, filtering, annotation and prioritization. We found that jointly calling variants across samples, filtering against both local and external databases, deploying multiple annotation tools and using familial transmission above biological plausibility contributed to accuracy. Overall, we identified disease-causing variants in 21% of cases, with the proportion increasing to 34% (23/68) for mendelian disorders and 57% (8/14) in family trios. We also discovered 32 potentially clinically actionable variants in 18 genes unrelated to the referral disorder, although only 4 were ultimately considered reportable. Our results demonstrate the value of genome sequencing for routine clinical diagnosis but also highlight many outstanding challenges.
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Affiliation(s)
- Jenny C Taylor
- NIHR Comprehensive Biomedical Research Centre, Oxford, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Hilary C Martin
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Stefano Lise
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - John Broxholme
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Andy Rimmer
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Alexander Kanapin
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Gerton Lunter
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Simon Fiddy
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Chris Allan
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - A Radu Aricescu
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Moustafa Attar
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Christian Babbs
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | | | - David Beeson
- Neurosciences Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Celeste Bento
- Hematology Department, Centro Hospitalar e Universitário de Coimbra, Portugal
| | - Patricia Bignell
- Molecular Haematology Department, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Edward Blair
- Department of Clinical Genetics, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Veronica J Buckle
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Katherine Bull
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Centre for Cellular and Molecular Physiology, University of Oxford, Oxford, UK
| | - Ondrej Cais
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Holger Cario
- Department of Pediatrics and Adolescent Medicine, University Medical Center, Ulm, Germany
| | - Helen Chapel
- Primary Immunodeficiency Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Richard R Copley
- NIHR Comprehensive Biomedical Research Centre, Oxford, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Richard Cornall
- Centre for Cellular and Molecular Physiology, University of Oxford, Oxford, UK
| | - Jude Craft
- NIHR Comprehensive Biomedical Research Centre, Oxford, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Karin Dahan
- Centre de Génétique Humaine, Institut de Génétique et de Pathologie, Gosselies, Belgium
- Cliniques Universitaires Saint-Luc, Université Catholique de Louvain, Brussels, Belgium
| | - Emma E Davenport
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Calliope Dendrou
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Olivier Devuyst
- Institute of Physiology, Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland
| | - Aimée L Fenwick
- Clinical Genetics Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Jonathan Flint
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Lars Fugger
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Rodney D Gilbert
- University Hospital Southampton NHS Foundation Trust, University of Southampton, Southampton, UK
| | - Anne Goriely
- Clinical Genetics Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Angie Green
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Ingo H Greger
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge, UK
| | | | - Anja V Gruszczyk
- Clinical Genetics Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Robert Hastings
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Edouard Hatton
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Doug Higgs
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Adrian Hill
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Chris Holmes
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Department of Statistics, University of Oxford, Oxford, UK
| | - Malcolm Howard
- NIHR Comprehensive Biomedical Research Centre, Oxford, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Linda Hughes
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Peter Humburg
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - David Johnson
- Craniofacial Unit, Department of Plastic and Reconstructive Surgery, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Fredrik Karpe
- Oxford Laboratory for Integrative Physiology, Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, UK
| | | | - Usha Kini
- Department of Clinical Genetics, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Julian C Knight
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Jonathan Krohn
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Sarah Lamble
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Craig Langman
- Kidney Diseases, Feinberg School of Medicine, Northwestern University and the Ann and Robert H Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
| | - Lorne Lonie
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Joshua Luck
- Clinical Genetics Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Davis McCarthy
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Simon J McGowan
- Clinical Genetics Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | | | - Kerry A Miller
- Clinical Genetics Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Lisa Murray
- Illumina Cambridge Limited, Saffron Walden, UK
| | - Andrea H Németh
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - M Andrew Nesbit
- Academic Endocrine Unit, Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, UK
| | - David Nutt
- Centre for Neuropsychopharmacology, Division of Brain Sciences, Imperial College, London, UK
| | - Elizabeth Ormondroyd
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Annette Bang Oturai
- Danish Multiple Sclerosis Center, Department of Neurology, Copenhagen University Hospital, Copenhagen, Denmark
| | - Alistair Pagnamenta
- NIHR Comprehensive Biomedical Research Centre, Oxford, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Smita Y Patel
- Primary Immunodeficiency Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Melanie Percy
- Department of Haematology, Belfast City Hospital, Belfast, UK
| | - Nayia Petousi
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Paolo Piazza
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Sian E Piret
- Academic Endocrine Unit, Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, UK
| | | | - Niko Popitsch
- NIHR Comprehensive Biomedical Research Centre, Oxford, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Fiona Powrie
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Chris Pugh
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Lynn Quek
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Peter A Robbins
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Kathryn Robson
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Alexandra Russo
- Department of Pediatrics, University Hospital, Mainz, Germany
| | - Natasha Sahgal
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Anna Schuh
- NIHR Comprehensive Biomedical Research Centre, Oxford, UK
- Department of Oncology, University of Oxford, Oxford, UK
| | - Earl Silverman
- Division of Rheumatology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Alison Simmons
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Per Soelberg Sørensen
- Danish Multiple Sclerosis Center, Department of Neurology, Copenhagen University Hospital, Copenhagen, Denmark
| | - Elizabeth Sweeney
- Department of Clinical Genetics, Liverpool Women's NHS Foundation Trust, Liverpool, UK
| | - John Taylor
- NIHR Comprehensive Biomedical Research Centre, Oxford, UK
- Oxford NHS Regional Molecular Genetics Laboratory, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Rajesh V Thakker
- Academic Endocrine Unit, Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, UK
| | - Ian Tomlinson
- NIHR Comprehensive Biomedical Research Centre, Oxford, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Amy Trebes
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Stephen Rf Twigg
- Clinical Genetics Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Holm H Uhlig
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Paresh Vyas
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Tim Vyse
- Division of Genetics, King's College London, Guy's Hospital, London, UK
| | - Steven A Wall
- Craniofacial Unit, Department of Plastic and Reconstructive Surgery, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Hugh Watkins
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Michael P Whyte
- Center for Metabolic Bone Disease and Molecular Research, Shriners Hospital for Children, St Louis, Missouri, USA
| | - Lorna Witty
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Ben Wright
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Chris Yau
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - David Buck
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | | | - John I Bell
- Office of the Regius Professor of Medicine, University of Oxford, Oxford, UK
| | - Andrew Om Wilkie
- Clinical Genetics Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | | | - Peter Donnelly
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Department of Statistics, University of Oxford, Oxford, UK
| | - Gilean McVean
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
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56
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Kwiatkowski F, Arbre M, Bidet Y, Laquet C, Uhrhammer N, Bignon YJ. BRCA Mutations Increase Fertility in Families at Hereditary Breast/Ovarian Cancer Risk. PLoS One 2015; 10:e0127363. [PMID: 26047126 PMCID: PMC4457526 DOI: 10.1371/journal.pone.0127363] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 04/14/2015] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Deleterious mutations in the BRCA genes are responsible for a small, but significant, proportion of breast and ovarian cancers (5 - 10 %). Proof of de novo mutations in hereditary breast/ovarian cancer (HBOC) families is rare, in contrast to founder mutations, thousands of years old, that may be carried by as much as 1 % of a population. Thus, if mutations favoring cancer survive selection pressure through time, they must provide advantages that compensate for the loss of life expectancy. METHOD This hypothesis was tested within 2,150 HBOC families encompassing 96,325 individuals. Parameters included counts of breast/ovarian cancer, age at diagnosis, male breast cancer and other cancer locations. As expected, well-known clinical parameters discriminated between BRCA-mutated families and others: young age at breast cancer, ovarian cancer, pancreatic cancer and male breast cancer. The major fertility differences concerned men in BRCA-mutated families: they had lower first and mean age at paternity, and fewer remained childless. For women in BRCA families, the miscarriage rate was lower. In a logistic regression including clinical factors, the different miscarriage rate and men's mean age at paternity remained significant. RESULTS Fertility advantages were confirmed in a subgroup of 746 BRCA mutation carriers and 483 non-carriers from BRCA mutated families. In particular, female carriers were less often nulliparous (9.1 % of carriers versus 16.0 %, p = 0.003) and had more children (1.8 ± 1.4 SD versus 1.5 ± 1.3, p = 0.002) as well as male carriers (1.7 ± 1.3 versus 1.4 ± 1.3, p = 0.024). CONCLUSION Although BRCA mutations shorten the reproductive period due to cancer mortality, they compensate by improving fertility both in male and female carriers.
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Affiliation(s)
- Fabrice Kwiatkowski
- Centre Jean Perrin, Laboratoire d'Oncologie Moléculaire, 63011, Clermont-Ferrand, France
- Université Blaise Pascal—Laboratoire de Mathématiques, UMR 6620—CNRS, Campus des Cézeaux—BP, 80026–63171, Aubière cedex, France
- * E-mail:
| | - Marie Arbre
- Centre Jean Perrin, Laboratoire d'Oncologie Moléculaire, 63011, Clermont-Ferrand, France
| | - Yannick Bidet
- Université Clermont Auvergne, Université d'Auvergne, BP 10448, F-63000, Clermont-Ferrand, France
| | - Claire Laquet
- Centre Jean Perrin, Laboratoire d'Oncologie Moléculaire, 63011, Clermont-Ferrand, France
| | - Nancy Uhrhammer
- Centre Jean Perrin, Laboratoire d'Oncologie Moléculaire, 63011, Clermont-Ferrand, France
| | - Yves-Jean Bignon
- Centre Jean Perrin, Laboratoire d'Oncologie Moléculaire, 63011, Clermont-Ferrand, France
- Université Clermont Auvergne, Université d'Auvergne, BP 10448, F-63000, Clermont-Ferrand, France
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Lesueur F. Breast Cancer Risk Gene Discovery: Opportunities and Challenges. CURRENT GENETIC MEDICINE REPORTS 2015. [DOI: 10.1007/s40142-015-0066-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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58
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Breast and ovarian cancer predisposition due to de novo BRCA1 and BRCA2 mutations. Oncogene 2015; 35:1324-7. [PMID: 26028024 DOI: 10.1038/onc.2015.181] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 04/02/2015] [Accepted: 04/07/2015] [Indexed: 02/02/2023]
Abstract
BRCA1 and BRCA2 are the two major genes predisposing to breast and ovarian cancer. Whereas high de novo mutation rates have been demonstrated for several genes, only 11 cases of de novo BRCA1/2 mutations have been reported to date and the BRCA1/2 de novo mutation rate remains unknown. The present study was designed to fill this gap based on a series of 12 805 consecutive unrelated patients diagnosed with breast and/or ovarian cancer who met the inclusion criteria for BRCA1/2 gene analysis according to French guidelines. BRCA1/2 mutations were detected in 1527 (12%) patients, and three BRCA1 mutations and one BRCA2 mutation were de novo. The BRCA1/2 de novo mutation rate was estimated to be 0.3% (0.1%; 0.7%). Although rare, it may be useful to take the possibility of de novo BRCA1/2 mutation into account in genetic counseling of relatives and to improve the understanding of complex family histories of breast and ovarian cancers.
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High prevalence of BRCA1 stop mutation c.4183C>T in the Tyrolean population: implications for genetic testing. Eur J Hum Genet 2015; 24:258-62. [PMID: 26014432 DOI: 10.1038/ejhg.2015.108] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Revised: 04/12/2014] [Accepted: 04/17/2015] [Indexed: 11/09/2022] Open
Abstract
Screening for founder mutations in BRCA1 and BRCA2 has been discussed as a cost-effective testing strategy in certain populations. In this study, comprehensive BRCA1 and BRCA2 testing was performed in a routine diagnostic setting. The prevalence of the BRCA1 stop mutation c.4183C>T, p.(Gln1395Ter), was determined in unselected breast and ovarian cancer patients from different regions in the Tyrol. Cancer registry data were used to evaluate the impact of this mutation on regional cancer incidence. The mutation c.4183C>T was detected in 30.4% of hereditary BRCA1-associated breast and ovarian cancer patients in our cohort. It was also identified in 4.1% of unselected (26% of unselected triple negative) Tyrolean breast cancer patients and 6.8% of unselected ovarian cancer patients from the Lower Inn Valley (LIV) region. Cancer incidences showed a region-specific increase in age-stratified breast and ovarian cancer risk with standardized incidence ratios of 1.23 and 2.13, respectively. We, thus, report a Tyrolean BRCA1 founder mutation that correlates to a local increase in the breast and ovarian cancer risks. On the basis of its high prevalence, we suggest that targeted genetic analysis should be offered to all women with breast or ovarian cancer and ancestry from the LIV region.
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60
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Meng H, Cao Y, Qin J, Song X, Zhang Q, Shi Y, Cao L. DNA methylation, its mediators and genome integrity. Int J Biol Sci 2015; 11:604-17. [PMID: 25892967 PMCID: PMC4400391 DOI: 10.7150/ijbs.11218] [Citation(s) in RCA: 173] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 03/02/2015] [Indexed: 12/18/2022] Open
Abstract
DNA methylation regulates many cellular processes, including embryonic development, transcription, chromatin structure, X-chromosome inactivation, genomic imprinting and chromosome stability. DNA methyltransferases establish and maintain the presence of 5-methylcytosine (5mC), and ten-eleven translocation cytosine dioxygenases (TETs) oxidise 5mC to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC), which can be removed by base excision repair (BER) proteins. Multiple forms of DNA methylation are recognised by methyl-CpG binding proteins (MeCPs), which play vital roles in chromatin-based transcriptional regulation, DNA repair and replication. Accordingly, defects in DNA methylation and its mediators may cause silencing of tumour suppressor genes and misregulation of multiple cell cycles, DNA repair and chromosome stability genes, and hence contribute to genome instability in various human diseases, including cancer. Thus, understanding functional genetic mutations and aberrant expression of these DNA methylation mediators is critical to deciphering the crosstalk between concurrent genetic and epigenetic alterations in specific cancer types and to the development of new therapeutic strategies.
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Affiliation(s)
- Huan Meng
- 1. Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang 110001, China; ; 2. MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing Biomedical Research Institute, Nanjing University, China
| | - Ying Cao
- 2. MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing Biomedical Research Institute, Nanjing University, China
| | - Jinzhong Qin
- 2. MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing Biomedical Research Institute, Nanjing University, China
| | - Xiaoyu Song
- 1. Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang 110001, China
| | - Qing Zhang
- 2. MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing Biomedical Research Institute, Nanjing University, China
| | - Yun Shi
- 2. MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing Biomedical Research Institute, Nanjing University, China
| | - Liu Cao
- 1. Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang 110001, China
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Screening for common mutations in BRCA1 and BRCA2 genes: interest in genetic testing of Tunisian families with breast and/or ovarian cancer. Bull Cancer 2015; 101:E36-40. [PMID: 25418591 DOI: 10.1684/bdc.2014.2049] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
BACKGROUND In the Tunisian population, as yet a limited number of BRCA1/2 germline mutations have been reported in hereditary breast and/or ovarian cancer. These mutations are located in a few exons of BRCA1/2. The aim of the present study was to search for these mutations in 66 unrelated patients with hereditary breast and/or ovarian cancer in order to assess the interest in such a targeted approach for genetic testing in Tunisia. MATERIALS AND METHODS Blood specimens from the 66 Tunisian patients, with family history of breast and/or ovarian cancer, were collected at the Salah Azaiz Cancer Institute of Tunis. The exons 5, 20 and part of exon 11 of BRCA1 as well as part of exons 10 and 11 of BRCA2 were analyzed by Sanger sequencing. RESULTS 12 patients had deleterious mutations in the BRCA1 or BRCA2 genes (18%), including a novel frame-shift mutation of BRCA1 (c.3751dup; 3780insT). Four distinct BRCA1 mutations were detected eight patients: c.5266dup (5382insC) and c.211dup (330insA) each in three patients, c.3751dup (3870insT) and c.4041_4042del (4160delAG) each in one patient. The four remaining cases all carried the same BRCA2 mutation, c.1310_1313del (1538delAAGA). Besides these deleterious mutations, eight polymorphisms and unclassified variants were detected, one of them being never reported (BRCA1c.3030T>G, p.Pro1010Pro). CONCLUSION In this study, we show that targeting relevant exons in BRCA1 and BRCA2 genes allows detection of a substantial percentage of mutations in the Tunisian population. Therefore such an approach may be of interest in genetic testing of high-risk breast and ovarian cancer families in Tunisia.
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62
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Silva FC, Lisboa BCG, Figueiredo MCP, Torrezan GT, Santos ÉMM, Krepischi AC, Rossi BM, Achatz MI, Carraro DM. Hereditary breast and ovarian cancer: assessment of point mutations and copy number variations in Brazilian patients. BMC MEDICAL GENETICS 2014; 15:55. [PMID: 24884479 PMCID: PMC4038072 DOI: 10.1186/1471-2350-15-55] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Accepted: 04/29/2014] [Indexed: 11/10/2022]
Abstract
BACKGROUND Germ line mutations in BRCA1 and BRCA2 (BRCA1/2) and other susceptibility genes have been identified as genetic causes of hereditary breast and ovarian cancer (HBOC). To identify the disease-causing mutations in a cohort of 120 Brazilian women fulfilling criteria for HBOC, we carried out a comprehensive screening of BRCA1/2, TP53 R337H, CHEK2 1100delC, followed by an analysis of copy number variations in 14 additional breast cancer susceptibility genes (PTEN, ATM, NBN, RAD50, RAD51, BRIP1, PALB2, MLH1, MSH2, MSH6, TP53, CDKN2A, CDH1 and CTNNB1). METHODS Capillary sequencing and multiplex ligation-dependent probe amplification (MLPA) were used for detecting point mutations and copy number variations (CNVs), respectively, for the BRCA1 and BRCA2 genes; capillary sequencing was used for point mutation for both variants TP53 R337H and CHEK2 1100delC, and finally array comparative genomic hybridization (array-CGH) was used for identifying CNVs in the 14 additional genes. RESULTS The positive detection rate in our series was 26%. BRCA1 pathogenic mutations were found in 20 cases, including two cases with CNVs, whereas BRCA2 mutations were found in 7 cases. We also found three patients with the TP53 R337H mutation and one patient with the CHEK2 1100delC mutation. Seven (25%) pathogenic mutations in BRCA1/2 were firstly described, including a splice-site BRCA1 mutation for which pathogenicity was confirmed by the presence of an aberrant transcript showing the loss of the last 62 bp of exon 7. Microdeletions of exon 4 in ATM and exon 2 in PTEN were identified in BRCA2-mutated and BRCA1/2-negative patients, respectively. CONCLUSIONS In summary, our results showed a high frequency of BRCA1/2 mutations and a higher prevalence of BRCA1 (64.5%) gene. Moreover, the detection of the TP53 R337H variant in our series and the fact that this variant has a founder effect in our population prompted us to suggest that all female breast cancer patients with clinical criteria for HBOC and negative for BRCA1/2 genes should be tested for the TP53 R337H variant. Furthermore, the presence of genomic structural rearrangement resulting in CNVs in other genes that predispose breast cancer in conjunction with BRCA2 point mutations demonstrated a highly complex genetic etiology in Brazilian breast cancer families.
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Affiliation(s)
- Felipe C Silva
- Laboratory of Genomics and Molecular Biology, CIPE - A. C. Camargo Cancer Center, São Paulo, Brazil
| | - Bianca CG Lisboa
- Laboratory of Genomics and Molecular Biology, CIPE - A. C. Camargo Cancer Center, São Paulo, Brazil
| | - Marcia CP Figueiredo
- Laboratory of Genomics and Molecular Biology, CIPE - A. C. Camargo Cancer Center, São Paulo, Brazil
| | - Giovana T Torrezan
- Laboratory of Genomics and Molecular Biology, CIPE - A. C. Camargo Cancer Center, São Paulo, Brazil
| | - Érika MM Santos
- Department of Colorectal Tumors, A. C. Camargo Cancer Center, São Paulo, Brazil
| | - Ana C Krepischi
- Laboratory of Genomics and Molecular Biology, CIPE - A. C. Camargo Cancer Center, São Paulo, Brazil
- National Institute of Science and Technology in Oncogenomics (INCITO), São Paulo, Brazil
| | - Benedito M Rossi
- Department of Colorectal Tumors, A. C. Camargo Cancer Center, São Paulo, Brazil
| | - Maria I Achatz
- National Institute of Science and Technology in Oncogenomics (INCITO), São Paulo, Brazil
- Department of Oncogenetics, A. C. Camargo Cancer Center, São Paulo, Brazil
| | - Dirce M Carraro
- Laboratory of Genomics and Molecular Biology, CIPE - A. C. Camargo Cancer Center, São Paulo, Brazil
- National Institute of Science and Technology in Oncogenomics (INCITO), São Paulo, Brazil
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63
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Next-generation sequencing for the diagnosis of hereditary breast and ovarian cancer using genomic capture targeting multiple candidate genes. Eur J Hum Genet 2014; 22:1305-13. [PMID: 24549055 DOI: 10.1038/ejhg.2014.16] [Citation(s) in RCA: 184] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 01/15/2014] [Accepted: 01/16/2014] [Indexed: 02/08/2023] Open
Abstract
To optimize the molecular diagnosis of hereditary breast and ovarian cancer (HBOC), we developed a next-generation sequencing (NGS)-based screening based on the capture of a panel of genes involved, or suspected to be involved in HBOC, on pooling of indexed DNA and on paired-end sequencing in an Illumina GAIIx platform, followed by confirmation by Sanger sequencing or MLPA/QMPSF. The bioinformatic pipeline included CASAVA, NextGENe, CNVseq and Alamut-HT. We validated this procedure by the analysis of 59 patients' DNAs harbouring SNVs, indels or large genomic rearrangements of BRCA1 or BRCA2. We also conducted a blind study in 168 patients comparing NGS versus Sanger sequencing or MLPA analyses of BRCA1 and BRCA2. All mutations detected by conventional procedures were detected by NGS. We then screened, using three different versions of the capture set, a large series of 708 consecutive patients. We detected in these patients 69 germline deleterious alterations within BRCA1 and BRCA2, and 4 TP53 mutations in 468 patients also tested for this gene. We also found 36 variations inducing either a premature codon stop or a splicing defect among other genes: 5/708 in CHEK2, 3/708 in RAD51C, 1/708 in RAD50, 7/708 in PALB2, 3/708 in MRE11A, 5/708 in ATM, 3/708 in NBS1, 1/708 in CDH1, 3/468 in MSH2, 2/468 in PMS2, 1/708 in BARD1, 1/468 in PMS1 and 1/468 in MLH3. These results demonstrate the efficiency of NGS in performing molecular diagnosis of HBOC. Detection of mutations within other genes than BRCA1 and BRCA2 highlights the genetic heterogeneity of HBOC.
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Guidugli L, Carreira A, Caputo SM, Ehlen A, Galli A, Monteiro ANA, Neuhausen SL, Hansen TVO, Couch FJ, Vreeswijk MPG. Functional assays for analysis of variants of uncertain significance in BRCA2. Hum Mutat 2013; 35:151-64. [PMID: 24323938 DOI: 10.1002/humu.22478] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Accepted: 10/28/2013] [Indexed: 01/11/2023]
Abstract
Missense variants in the BRCA2 gene are routinely detected during clinical screening for pathogenic mutations in patients with a family history of breast and ovarian cancer. These subtle changes frequently remain of unknown clinical significance because of the lack of genetic information that may help establish a direct correlation with cancer predisposition. Therefore, alternative ways of predicting the pathogenicity of these variants are urgently needed. Since BRCA2 is a protein involved in important cellular mechanisms such as DNA repair, replication, and cell cycle control, functional assays have been developed that exploit these cellular activities to explore the impact of the variants on protein function. In this review, we summarize assays developed and currently utilized for studying missense variants in BRCA2. We specifically depict details of each assay, including variants of uncertain significance analyzed, and describe a validation set of (genetically) proven pathogenic and neutral missense variants to serve as a golden standard for the validation of each assay. Guidelines are proposed to enable implementation of laboratory-based methods to assess the impact of the variant on cancer risk.
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Affiliation(s)
- Lucia Guidugli
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
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65
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Di Giacomo D, Gaildrat P, Abuli A, Abdat J, Frébourg T, Tosi M, Martins A. Functional analysis of a large set of BRCA2 exon 7 variants highlights the predictive value of hexamer scores in detecting alterations of exonic splicing regulatory elements. Hum Mutat 2013; 34:1547-57. [PMID: 23983145 DOI: 10.1002/humu.22428] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 08/14/2013] [Indexed: 11/06/2022]
Abstract
Exonic variants can alter pre-mRNA splicing either by changing splice sites or by modifying splicing regulatory elements. Often these effects are difficult to predict and are only detected by performing RNA analyses. Here, we analyzed, in a minigene assay, 26 variants identified in the exon 7 of BRCA2, a cancer predisposition gene. Our results revealed eight new exon skipping mutations in this exon: one directly altering the 5' splice site and seven affecting potential regulatory elements. This brings the number of splicing regulatory mutations detected in BRCA2 exon 7 to a total of 11, a remarkably high number considering the total number of variants reported in this exon (n = 36), all tested in our minigene assay. We then exploited this large set of splicing data to test the predictive value of splicing regulator hexamers' scores recently established by Ke et al. (). Comparisons of hexamer-based predictions with our experimental data revealed high sensitivity in detecting variants that increased exon skipping, an important feature for prescreening variants before RNA analysis. In conclusion, hexamer scores represent a promising tool for predicting the biological consequences of exonic variants and may have important applications for the interpretation of variants detected by high-throughput sequencing.
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Affiliation(s)
- Daniela Di Giacomo
- Inserm U1079, University of Rouen, Institute for Research and Innovation in Biomedicine, Rouen, France; Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, Italy
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66
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Novaković S, Milatović M, Cerkovnik P, Stegel V, Krajc M, Hočevar M, Zgajnar J, Vakselj A. Novel BRCA1 and BRCA2 pathogenic mutations in Slovene hereditary breast and ovarian cancer families. Int J Oncol 2012; 41:1619-27. [PMID: 22923021 PMCID: PMC3583621 DOI: 10.3892/ijo.2012.1595] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Accepted: 07/27/2012] [Indexed: 12/19/2022] Open
Abstract
The estimated proportion of hereditary breast and ovarian cancers among all breast and ovarian cancer cases is 5–10%. According to the literature, inherited mutations in the BRCA1 and BRCA2 tumour-suppressor genes, account for the majority of hereditary breast and ovarian cancer cases. The aim of this report is to present novel mutations that have not yet been described in the literature and pathogenic BRCA1 and BRCA2 mutations which have been detected in HBOC families for the first time in the last three years. In the period between January 2009 and December 2011, 559 individuals from 379 families affected with breast and/or ovarian cancer were screened for mutations in the BRCA1 and BRCA2 genes. Three novel mutations were detected: one in BRCA1 - c.1193C>A (p.Ser398*) and two in BRCA2 - c.5101C>T (p.Gln1701*) and c.5433_5436delGGAA (p.Glu1811Aspfs*3). These novel mutations are located in the exons 11 of BRCA1 or BRCA2 and encode truncated proteins. Two of them are nonsense while one is a frameshift mutation. Also, 11 previously known pathogenic mutations were detected for the first time in the HBOC families studied here (three in BRCA1 and eight in BRCA2). All, except one cause premature formation of stop codons leading to truncation of the respective BRCA1 or BRCA2 proteins.
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Affiliation(s)
- Srdjan Novaković
- Department of Molecular Diagnostics, Institute of Oncology Ljubljana, Ljubljana, Slovenia.
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67
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Millot GA, Carvalho MA, Caputo SM, Vreeswijk MPG, Brown MA, Webb M, Rouleau E, Neuhausen SL, Hansen TVO, Galli A, Brandão RD, Blok MJ, Velkova A, Couch FJ, Monteiro ANA. A guide for functional analysis of BRCA1 variants of uncertain significance. Hum Mutat 2012; 33:1526-37. [PMID: 22753008 DOI: 10.1002/humu.22150] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Accepted: 05/29/2012] [Indexed: 12/12/2022]
Abstract
Germline mutations in the tumor suppressor gene BRCA1 confer an estimated lifetime risk of 56-80% for breast cancer and 15-60% for ovarian cancer. Since the mid 1990s when BRCA1 was identified, genetic testing has revealed over 1,500 unique germline variants. However, for a significant number of these variants, the effect on protein function is unknown making it difficult to infer the consequences on risks of breast and ovarian cancers. Thus, many individuals undergoing genetic testing for BRCA1 mutations receive test results reporting a variant of uncertain clinical significance (VUS), leading to issues in risk assessment, counseling, and preventive care. Here, we describe functional assays for BRCA1 to directly or indirectly assess the impact of a variant on protein conformation or function and how these results can be used to complement genetic data to classify a VUS as to its clinical significance. Importantly, these methods may provide a framework for genome-wide pathogenicity assignment.
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Affiliation(s)
- Gaël A Millot
- Institut Curie, CNRS, UMR 3244 Université Pierre et Marie Curie, Paris, France
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68
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Jalkh N, Nassar-Slaba J, Chouery E, Salem N, Uhrchammer N, Golmard L, Stoppa-Lyonnet D, Bignon YJ, Mégarbané A. Prevalance of BRCA1 and BRCA2 mutations in familial breast cancer patients in Lebanon. Hered Cancer Clin Pract 2012; 10:7. [PMID: 22713736 PMCID: PMC3441239 DOI: 10.1186/1897-4287-10-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Accepted: 06/19/2012] [Indexed: 12/27/2022] Open
Abstract
Breast cancer is the most prevalent malignancy in women in Western countries, currently accounting for one third of all female cancers. Familial aggregation is thought to account for 5–10 % of all BC cases, and germline mutations in BRCA1 and BRCA2 account for less of the half of these inherited cases. In Lebanon, breast cancer represents the principal death-causing malignancy among women, with 50 % of the cases diagnosed before the age of 50 years. In order to study BRCA1/2 mutation spectra in the Lebanese population, 72 unrelated patients with a reported family history of breast and/or ovarian cancers or with an early onset breast cancer were tested. Fluorescent direct sequencing of the entire coding region and intronic sequences flanking each exon was performed. A total of 38 BRCA1 and 40 BRCA2 sequence variants were found. Seventeen of them were novel. Seven confirmed deleterious mutations were identified in 9 subjects providing a frequency of mutations of 12.5 %. Fifteen variants were considered of unknown clinical significance according to BIC and UMD-BRCA1/BRCA2 databases. In conclusion, this study represents the first evaluation of the deleterious and unclassified genetic variants in the BRCA1/2 genes found in a Lebanese population with a relatively high risk of breast cancer.
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Affiliation(s)
- Nadine Jalkh
- Unité de Génétique Médicale et laboratoire associé INSERM à l'Unité UMR_S910, Université Saint-Joseph, Beirut, Lebanon.
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69
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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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