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Valentini V, Bucalo A, Conti G, Celli L, Porzio V, Capalbo C, Silvestri V, Ottini L. Gender-Specific Genetic Predisposition to Breast Cancer: BRCA Genes and Beyond. Cancers (Basel) 2024; 16:579. [PMID: 38339330 PMCID: PMC10854694 DOI: 10.3390/cancers16030579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/24/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
Among neoplastic diseases, breast cancer (BC) is one of the most influenced by gender. Despite common misconceptions associating BC as a women-only disease, BC can also occur in men. Additionally, transgender individuals may also experience BC. Genetic risk factors play a relevant role in BC predisposition, with important implications in precision prevention and treatment. The genetic architecture of BC susceptibility is similar in women and men, with high-, moderate-, and low-penetrance risk variants; however, some sex-specific features have emerged. Inherited high-penetrance pathogenic variants (PVs) in BRCA1 and BRCA2 genes are the strongest BC genetic risk factor. BRCA1 and BRCA2 PVs are more commonly associated with increased risk of female and male BC, respectively. Notably, BRCA-associated BCs are characterized by sex-specific pathologic features. Recently, next-generation sequencing technologies have helped to provide more insights on the role of moderate-penetrance BC risk variants, particularly in PALB2, CHEK2, and ATM genes, while international collaborative genome-wide association studies have contributed evidence on common low-penetrance BC risk variants, on their combined effect in polygenic models, and on their role as risk modulators in BRCA1/2 PV carriers. Overall, all these studies suggested that the genetic basis of male BC, although similar, may differ from female BC. Evaluating the genetic component of male BC as a distinct entity from female BC is the first step to improve both personalized risk assessment and therapeutic choices of patients of both sexes in order to reach gender equality in BC care. In this review, we summarize the latest research in the field of BC genetic predisposition with a particular focus on similarities and differences in male and female BC, and we also discuss the implications, challenges, and open issues that surround the establishment of a gender-oriented clinical management for BC.
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Affiliation(s)
- Virginia Valentini
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy; (V.V.); (A.B.); (G.C.); (L.C.); (V.P.); (C.C.); (V.S.)
| | - Agostino Bucalo
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy; (V.V.); (A.B.); (G.C.); (L.C.); (V.P.); (C.C.); (V.S.)
| | - Giulia Conti
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy; (V.V.); (A.B.); (G.C.); (L.C.); (V.P.); (C.C.); (V.S.)
| | - Ludovica Celli
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy; (V.V.); (A.B.); (G.C.); (L.C.); (V.P.); (C.C.); (V.S.)
| | - Virginia Porzio
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy; (V.V.); (A.B.); (G.C.); (L.C.); (V.P.); (C.C.); (V.S.)
| | - Carlo Capalbo
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy; (V.V.); (A.B.); (G.C.); (L.C.); (V.P.); (C.C.); (V.S.)
- Medical Oncology Unit, Sant’Andrea University Hospital, 00189 Rome, Italy
| | - Valentina Silvestri
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy; (V.V.); (A.B.); (G.C.); (L.C.); (V.P.); (C.C.); (V.S.)
| | - Laura Ottini
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy; (V.V.); (A.B.); (G.C.); (L.C.); (V.P.); (C.C.); (V.S.)
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Kumpula TA, Vorimo S, Mattila TT, O’Gorman L, Astuti G, Tervasmäki A, Koivuluoma S, Mattila TM, Grip M, Winqvist R, Kuismin O, Moilanen J, Hoischen A, Gilissen C, Mantere T, Pylkäs K. Exome sequencing identified rare recurrent copy number variants and hereditary breast cancer susceptibility. PLoS Genet 2023; 19:e1010889. [PMID: 37578974 PMCID: PMC10449128 DOI: 10.1371/journal.pgen.1010889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 08/24/2023] [Accepted: 07/27/2023] [Indexed: 08/16/2023] Open
Abstract
Copy number variants (CNVs) are a major source of genetic variation and can disrupt genes or affect gene dosage. They are known to be causal or underlie predisposition to various diseases. However, the role of CNVs in inherited breast cancer susceptibility has not been thoroughly investigated. To address this, we performed whole-exome sequencing based analysis of rare CNVs in 98 high-risk Northern Finnish breast cancer cases. After filtering, selected candidate alleles were validated and characterized with a combination of orthogonal methods, including PCR-based approaches, optical genome mapping and long-read sequencing. This revealed three recurrent alterations: a 31 kb deletion co-occurring with a retrotransposon insertion (delins) in RAD52, a 13.4 kb deletion in HSD17B14 and a 64 kb partial duplication of RAD51C. Notably, all these genes encode proteins involved in pathways previously identified as essential for breast cancer development. Variants were genotyped in geographically matched cases and controls (altogether 278 hereditary and 1983 unselected breast cancer cases, and 1229 controls). The RAD52 delins and HSD17B14 deletion both showed significant enrichment among cases with indications of hereditary disease susceptibility. RAD52 delins was identified in 7/278 cases (2.5%, P = 0.034, OR = 2.86, 95% CI = 1.10-7.45) and HSD17B14 deletion in 8/278 cases (2.9%, P = 0.014, OR = 3.28, 95% CI = 1.31-8.23), the frequency of both variants in the controls being 11/1229 (0.9%). This suggests a role for RAD52 and HSD17B14 in hereditary breast cancer susceptibility. The RAD51C duplication was very rare, identified only in 2/278 of hereditary cases and 2/1229 controls (P = 0.157, OR = 4.45, 95% CI = 0.62-31.70). The identification of recurrent CNVs in these genes, and especially the relatively high frequency of RAD52 and HSD17B14 alterations in the Finnish population, highlights the importance of studying CNVs alongside single nucleotide variants when searching for genetic factors underlying hereditary disease predisposition.
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Affiliation(s)
- Timo A. Kumpula
- Laboratory of Cancer Genetics and Tumor Biology, Research Unit of Translational Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Sandra Vorimo
- Laboratory of Cancer Genetics and Tumor Biology, Research Unit of Translational Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Taneli T. Mattila
- Department of Pathology, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Luke O’Gorman
- Department of Human Genetics and Radboud Institute of Medical Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Galuh Astuti
- Department of Human Genetics and Radboud Institute of Medical Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Anna Tervasmäki
- Laboratory of Cancer Genetics and Tumor Biology, Research Unit of Translational Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Susanna Koivuluoma
- Laboratory of Cancer Genetics and Tumor Biology, Research Unit of Translational Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Tiina M. Mattila
- Laboratory of Cancer Genetics and Tumor Biology, Research Unit of Translational Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Mervi Grip
- Department of Surgery, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Robert Winqvist
- Laboratory of Cancer Genetics and Tumor Biology, Research Unit of Translational Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Outi Kuismin
- Department of Clinical Genetics, Medical Research Center Oulu and PEDEGO Research Unit, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Jukka Moilanen
- Department of Clinical Genetics, Medical Research Center Oulu and PEDEGO Research Unit, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Alexander Hoischen
- Department of Human Genetics and Radboud Institute of Medical Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, the Netherlands
| | - Christian Gilissen
- Department of Human Genetics and Radboud Institute of Medical Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Tuomo Mantere
- Laboratory of Cancer Genetics and Tumor Biology, Research Unit of Translational Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland
- Department of Human Genetics and Radboud Institute of Medical Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Katri Pylkäs
- Laboratory of Cancer Genetics and Tumor Biology, Research Unit of Translational Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland
- Northern Finland Laboratory Centre Nordlab, Oulu, Finland
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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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4
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DeVries AA, Dennis J, Tyrer JP, Peng PC, Coetzee SG, Reyes AL, Plummer JT, Davis BD, Chen SS, Dezem FS, Aben KKH, Anton-Culver H, Antonenkova NN, Beckmann MW, Beeghly-Fadiel A, Berchuck A, Bogdanova NV, Bogdanova-Markov N, Brenton JD, Butzow R, Campbell I, Chang-Claude J, Chenevix-Trench G, Cook LS, DeFazio A, Doherty JA, Dörk T, Eccles DM, Eliassen AH, Fasching PA, Fortner RT, Giles GG, Goode EL, Goodman MT, Gronwald J, Håkansson N, Hildebrandt MAT, Huff C, Huntsman DG, Jensen A, Kar S, Karlan BY, Khusnutdinova EK, Kiemeney LA, Kjaer SK, Kupryjanczyk J, Labrie M, Lambrechts D, Le ND, Lubiński J, May T, Menon U, Milne RL, Modugno F, Monteiro AN, Moysich KB, Odunsi K, Olsson H, Pearce CL, Pejovic T, Ramus SJ, Riboli E, Riggan MJ, Romieu I, Sandler DP, Schildkraut JM, Setiawan VW, Sieh W, Song H, Sutphen R, Terry KL, Thompson PJ, Titus L, Tworoger SS, Van Nieuwenhuysen E, Edwards DV, Webb PM, Wentzensen N, Whittemore AS, Wolk A, Wu AH, Ziogas A, Freedman ML, Lawrenson K, Pharoah PDP, Easton DF, Gayther SA, Jones MR. Copy Number Variants Are Ovarian Cancer Risk Alleles at Known and Novel Risk Loci. J Natl Cancer Inst 2022; 114:1533-1544. [PMID: 36210504 PMCID: PMC9949586 DOI: 10.1093/jnci/djac160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 04/13/2022] [Accepted: 08/18/2022] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Known risk alleles for epithelial ovarian cancer (EOC) account for approximately 40% of the heritability for EOC. Copy number variants (CNVs) have not been investigated as EOC risk alleles in a large population cohort. METHODS Single nucleotide polymorphism array data from 13 071 EOC cases and 17 306 controls of White European ancestry were used to identify CNVs associated with EOC risk using a rare admixture maximum likelihood test for gene burden and a by-probe ratio test. We performed enrichment analysis of CNVs at known EOC risk loci and functional biofeatures in ovarian cancer-related cell types. RESULTS We identified statistically significant risk associations with CNVs at known EOC risk genes; BRCA1 (PEOC = 1.60E-21; OREOC = 8.24), RAD51C (Phigh-grade serous ovarian cancer [HGSOC] = 5.5E-4; odds ratio [OR]HGSOC = 5.74 del), and BRCA2 (PHGSOC = 7.0E-4; ORHGSOC = 3.31 deletion). Four suggestive associations (P < .001) were identified for rare CNVs. Risk-associated CNVs were enriched (P < .05) at known EOC risk loci identified by genome-wide association study. Noncoding CNVs were enriched in active promoters and insulators in EOC-related cell types. CONCLUSIONS CNVs in BRCA1 have been previously reported in smaller studies, but their observed frequency in this large population-based cohort, along with the CNVs observed at BRCA2 and RAD51C gene loci in EOC cases, suggests that these CNVs are potentially pathogenic and may contribute to the spectrum of disease-causing mutations in these genes. CNVs are likely to occur in a wider set of susceptibility regions, with potential implications for clinical genetic testing and disease prevention.
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Grants
- P01 CA017054 NCI NIH HHS
- N01 CN025403 NCI NIH HHS
- UM1 CA176726 NCI NIH HHS
- R01 CA058860 NCI NIH HHS
- P50 CA105009 NCI NIH HHS
- R01-CA122443 NIH HHS
- 076113 Wellcome Trust
- G0401527 Medical Research Council
- U19-CA148112 NCI NIH HHS
- P50 CA136393 NCI NIH HHS
- C490/A10119 C490/A10124 Cancer Research UK
- 1000143 Medical Research Council
- R01-CA54419 NIH HHS
- C8221/A19170 Cancer Research UK
- R01 CA049449 NCI NIH HHS
- P50 CA159981 NCI NIH HHS
- T32 GM118288 NIGMS NIH HHS
- CA1X01HG007491-01 NIH HHS
- Z01-ES044005 NIEHS NIH HHS
- R01 CA106414 NCI NIH HHS
- R01 CA095023 NCI NIH HHS
- N01 PC067010 NCI NIH HHS
- R01 CA058598 NCI NIH HHS
- U01 CA176726 NCI NIH HHS
- S10 RR025141 NCRR NIH HHS
- M01 RR000056 NCRR NIH HHS
- Department of Health
- 5T32GM118288-03 NIH HHS
- MR/N003284/1 Medical Research Council
- P30 CA014089 NCI NIH HHS
- K07-CA080668 NCI NIH HHS
- 14136 Cancer Research UK
- Worldwide Cancer Research
- MR_UU_12023 Medical Research Council
- R01 CA067262 NCI NIH HHS
- UM1 CA186107 NCI NIH HHS
- P30 CA015083 NCI NIH HHS
- G1000143 Medical Research Council
- R01 CA076016 NCI NIH HHS
- NHGRI NIH HHS
- P01 CA087969 NCI NIH HHS
- R01- CA61107 NCI NIH HHS
- R01-CA58598 NIH HHS
- U19 CA148112 NCI NIH HHS
- ULTR000445 NCATS NIH HHS
- R03 CA115195 NCI NIH HHS
- Wellcome Trust
- Breast Cancer Now
- R01 CA160669 NCI NIH HHS
- R01-CA058860 NIH HHS
- MC_UU_00004/01 Medical Research Council
- C570/A16491 Cancer Research UK
- R01-CA76016 NIH HHS
- R01-CA106414-A2 NIH HHS
- 001 World Health Organization
- Z01 ES049033 Intramural NIH HHS
- R01 CA126841 NCI NIH HHS
- MR/M012190/1 Medical Research Council
- 209057 Wellcome Trust
- R03 CA113148 NCI NIH HHS
- R01 CA149429 NCI NIH HHS
- National Institute of General Medical Sciences
- National Institutes of Health
- CSMC Precision Health Initiative
- Tell Every Amazing Lady About Ovarian Cancer Louisa M. McGregor Ovarian Cancer Foundation
- Ovarian Cancer Research Fund thanks
- National Cancer Institute
- National Human Genome Research Institute
- Canadian Institutes of Health Research
- Ovarian Cancer Research Fund
- European Commission’s Seventh Framework Programme
- Army Medical Research and Materiel Command
- National Health & Medical Research Council of Australia
- Cancer Councils of New South Wales, Victoria, Queensland, South Australia and Tasmania and Cancer Foundation of Western Australia
- Ovarian Cancer Australia
- Peter MacCallum Foundation
- University of Erlangen-Nuremberg
- National Kankerplan
- Breast Cancer Now, Institute of Cancer Research
- National Center for Advancing Translational Sciences
- European Commission
- International Agency for Research on Cancer
- Danish Cancer Society
- Ligue Contre le Cancer, Institut Gustave Roussy, Mutuelle Générale de l’Education Nationale
- Institut National de la Santé et de la Recherche Médicale
- German Cancer Aid; German Cancer Research Center
- Federal Ministry of Education and Research
- Hellenic Health Foundation
- Associazione Italiana per la Ricerca sul Cancro-AIRC-Italy
- National Research Council
- Dutch Ministry of Public Health, Welfare and Sports
- Netherlands Cancer Registry
- LK Research Funds
- Dutch Prevention Funds
- World Cancer Research Fund
- Nordforsk, Nordic Centre of Excellence programme on Food, Nutrition and Health
- Health Research Fund
- Regional Governments of Andalucía, Asturias, Basque Country, Murcia and Navarra
- Swedish Cancer Society, Swedish Research Council and County Councils of Skåne and Västerbotten
- German Federal Ministry of Education and Research, Programme of Clinical Biomedical Research
- German Cancer Research Center
- Rudolf-Bartling Foundation
- Helsinki University Hospital Research Fund
- University of Pittsburgh School of Medicine Dean’s Faculty Advancement Award
- Department of Defense
- NCI
- Swedish Cancer Society, Swedish Research Council, Beta Kamprad Foundation
- Danish Cancer Society, Copenhagen
- Mayo Foundation
- Minnesota Ovarian Cancer Alliance
- Fred C. and Katherine B. Andersen Foundation
- VicHealth and Cancer Council Victoria, Cancer Council Victoria
- National Health and Medical Research Council of Australia
- NHMRC
- DOD Ovarian Cancer Research Program
- Moffitt Cancer Center
- Merck Pharmaceuticals
- Radboud University Medical Centre
- UK National Institute for Health Research Biomedical Research Centres at the University of Cambridge
- National Institute of Environmental Health Sciences
- The Swedish Cancer Foundation
- the Swedish Research Council
- American Cancer Society
- Celma Mastry Ovarian Cancer Foundation
- Lon V Smith Foundation
- The Eve Appeal
- National Institute for Health Research University College London Hospitals Biomedical Research Centre
- California Cancer Research Program
- National Science Centre
- NIH
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Affiliation(s)
- Amber A DeVries
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Jonathan P Tyrer
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Pei-Chen Peng
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Simon G Coetzee
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Alberto L Reyes
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jasmine T Plummer
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Applied Genomics, Computation and Translational Core, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Brian D Davis
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Applied Genomics, Computation and Translational Core, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Stephanie S Chen
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Applied Genomics, Computation and Translational Core, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Felipe Segato Dezem
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Katja K H Aben
- Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
- Netherlands Comprehensive Cancer Organisation, Utrecht, The Netherlands
| | - Hoda Anton-Culver
- Department of Medicine, Genetic Epidemiology Research Institute, University of California Irvine, Irvine, CA, USA
| | - Natalia N Antonenkova
- N.N. Alexandrov Research Institute of Oncology and Medical Radiology, Minsk, Belarus
| | - Matthias W Beckmann
- Department of Gynecology and Obstetrics, Comprehensive Cancer Center Erlangen-European Metropolitan Region of Nuremberg, Friedrich-Alexander University Erlangen-Nuremberg, University Hospital Erlangen, Erlangen, Germany
| | - Alicia Beeghly-Fadiel
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Andrew Berchuck
- Department of Gynecologic Oncology, Duke University Hospital, Durham, NC, USA
| | - Natalia V Bogdanova
- N.N. Alexandrov Research Institute of Oncology and Medical Radiology, Minsk, Belarus
- Department of Radiation Oncology, Hannover Medical School, Hannover, Germany
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | | | - James D Brenton
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Ralf Butzow
- Department of Pathology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Ian Campbell
- Cancer Genetics Laboratory, Research Division, Peter MacCallum Cancer Center, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Cancer Epidemiology Group, University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Georgia Chenevix-Trench
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Linda S Cook
- Epidemiology, School of Public Health, University of Colorado, Aurora, CO, USA
- Community Health Sciences, University of Calgary, Calgary, AB, Canada
| | - Anna DeFazio
- Centre for Cancer Research, The Westmead Institute for Medical Research, Sydney, New South Wales, Australia
- Department of Gynaecological Oncology, Westmead Hospital, Sydney, New South Wales, Australia
- The Daffodil Centre, a joint venture with Cancer Council NSW, The University of Sydney, Sydney, New South Wales, Australia
| | - Jennifer A Doherty
- Huntsman Cancer Institute, Department of Population Health Sciences, University of Utah, Salt Lake City, UT, USA
| | - Thilo Dörk
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Diana M Eccles
- Faculty of Medicine, University of Southampton, Southampton, UK
| | - A Heather Eliassen
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Peter A Fasching
- Department of Gynecology and Obstetrics, Comprehensive Cancer Center Erlangen-European Metropolitan Region of Nuremberg, Friedrich-Alexander University Erlangen-Nuremberg, University Hospital Erlangen, Erlangen, Germany
- David Geffen School of Medicine, Department of Medicine Division of Hematology and Oncology, University of California at Los Angeles, Los Angeles, CA, USA
| | - Renée T Fortner
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Graham G Giles
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Ellen L Goode
- Department of Quantitative Health Sciences, Division of Epidemiology, Mayo Clinic, Rochester, MN, USA
| | - Marc T Goodman
- Samuel Oschin Comprehensive Cancer Institute, Cancer Prevention and Genetics Program, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jacek Gronwald
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Niclas Håkansson
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | | | - Chad Huff
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - David G Huntsman
- Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, BC, Canada
- Department of Molecular Oncology, BC Cancer Research Centre, Vancouver, BC, Canada
| | - Allan Jensen
- Department of Lifestyle, Reproduction and Cancer, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Siddhartha Kar
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Section of Translational Epidemiology, Division of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Beth Y Karlan
- David Geffen School of Medicine, Department of Obstetrics and Gynecology, University of California at Los Angeles, Los Angeles, CA, USA
| | - Elza K Khusnutdinova
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa, Russia
- Saint Petersburg State University, Saint Petersburg, Russia
| | - Lambertus A Kiemeney
- Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Susanne K Kjaer
- Department of Lifestyle, Reproduction and Cancer, Danish Cancer Society Research Center, Copenhagen, Denmark
- Department of Gynaecology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Jolanta Kupryjanczyk
- Department of Pathology and Laboratory Diagnostics, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Marilyne Labrie
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Diether Lambrechts
- VIB Center for Cancer Biology, VIB, Leuven, Belgium
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Nhu D Le
- Cancer Control Research, BC Cancer, Vancouver, BC, Canada
| | - Jan Lubiński
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Taymaa May
- Division of Gynecologic Oncology, University Health Network, Princess Margaret Hospital, Toronto, Ontario, Canada
| | - Usha Menon
- MRC Clinical Trials Unit, Institute of Clinical Trials & Methodology, University College London, London, UK
| | - Roger L Milne
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Francesmary Modugno
- Women's Cancer Research Center, Magee-Womens Research Institute and Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Alvaro N Monteiro
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Kirsten B Moysich
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Kunle Odunsi
- Department of Oncology, University of Chicago Medicine Comprehensive Cancer Center, Chicago, IL, USA
- Department of Obstetrics and Gynecology, University of Chicago Medicine Comprehensive Cancer Center, Chicago, IL, USA
| | - Håkan Olsson
- Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Celeste L Pearce
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Tanja Pejovic
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
- Department of Obstetrics and Gynecology, Oregon Health & Science University, Portland, OR, USA
| | - Susan J Ramus
- School of Women's and Children's Health, Faculty of Medicine and Health, University of NSW Sydney, Sydney, New South Wales, Australia
- Adult Cancer Program, Lowy Cancer Research Centre, University of NSW Sydney, Sydney, New South Wales, Australia
| | | | - Marjorie J Riggan
- Department of Gynecologic Oncology, Duke University Hospital, Durham, NC, USA
| | - Isabelle Romieu
- Nutrition and Metabolism Section, International Agency for Research on Cancer (IARC-WHO), Lyon, France
| | - Dale P Sandler
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Joellen M Schildkraut
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - V Wendy Setiawan
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Weiva Sieh
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Honglin Song
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Rebecca Sutphen
- Epidemiology Center, College of Medicine, University of South Florida, Tampa, FL, USA
| | - Kathryn L Terry
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Obstetrics and Gynecology Epidemiology Center, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Pamela J Thompson
- Samuel Oschin Comprehensive Cancer Institute, Cancer Prevention and Genetics Program, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Linda Titus
- Muskie School of Public Policy, Public Health, Portland, ME, USA
| | - Shelley S Tworoger
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Els Van Nieuwenhuysen
- Division of Gynecologic Oncology, Department of Gynecology and Obstetrics, Leuven Cancer Institute, Leuven, Belgium
| | - Digna Velez Edwards
- Division of Quantitative Sciences, Department of Obstetrics and Gynecology, Department of Biomedical Sciences, Women's Health Research, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Penelope M Webb
- Population Health Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Alice S Whittemore
- Department of Epidemiology and Population Health, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
| | - Alicja Wolk
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Anna H Wu
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Argyrios Ziogas
- Department of Medicine, Genetic Epidemiology Research Institute, University of California Irvine, Irvine, CA, USA
| | - Matthew L Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kate Lawrenson
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Women's Cancer Program at the Samuel Oschin Cancer Institute Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Paul D P Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Simon A Gayther
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Michelle R Jones
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
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5
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Kim KB, Park S, Ha JS, Ryoo N, Kim DH. Three Cases of False-positive Multiplex Ligation-dependent Probe Amplification of BRCA1. Ann Lab Med 2022; 42:497-499. [PMID: 35177575 PMCID: PMC8859565 DOI: 10.3343/alm.2022.42.4.497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/17/2021] [Accepted: 01/17/2022] [Indexed: 11/25/2022] Open
Affiliation(s)
- Kyoung Bo Kim
- Department of Laboratory Medicine, Keimyung University School of Medicine, Daegu, Korea
| | - Sunggyun Park
- Department of Laboratory Medicine, Keimyung University School of Medicine, Daegu, Korea
| | - Jung Sook Ha
- Department of Laboratory Medicine, Keimyung University School of Medicine, Daegu, Korea
| | - Namhee Ryoo
- Department of Laboratory Medicine, Keimyung University School of Medicine, Daegu, Korea
| | - Do-Hoon Kim
- Department of Laboratory Medicine, Keimyung University School of Medicine, Daegu, Korea
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6
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Agaoglu NB, Unal B, Akgun Dogan O, Zolfagharian P, Shairfli P, Karakurt A, Can Senay B, Kizilboga T, Yildiz J, Dinler Doganay G, Doganay L. Determining the Accuracy of Next Generation Sequencing Based Copy Number Variation Analysis in Hereditary Breast and Ovarian Cancer. Expert Rev Mol Diagn 2022; 22:239-246. [PMID: 35240897 DOI: 10.1080/14737159.2022.2048373] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BACKGROUND Copy number variations (CNVs) are commonly associated with malignancies, including hereditary breast and ovarian cancers. Next generation sequencing (NGS) provides solutions for CNV detection in a single run. This study aimed to compare the accuracy of CNV detection by NGS analysing tool against Multiplex Ligation Dependent Probe Amplification (MLPA). RESEARCH DESIGN AND METHODS In total, 1276 cases were studied by targeted NGS panels and 691 cases (61 calls in 58 NGS-CNV positive and 633 NGS-CNV negative cases) were validated by MLPA. RESULTS Twenty-eight (46%) NGS-CNV positive calls were consistent, whereas 33 (54%) calls showed discordance with MLPA. Two cases were detected as SNV by the NGS and CNV by the MLPA analysis. In total, 2% of the cases showed an MLPA confirmed CNV region in BRCA1/2. The results of this study showed that despite the high false positive call rate of the NGS-CNV algorithm, there were no false negative calls. The cases that were determined to be negative by the NGS and positive by the MLPA were actually carrying SNVs that were located on the MLPA probe binding sites. CONCLUSION The diagnostic performance of NGS-CNV analysis is promising; however, the need for confirmation by different methods remains.
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Affiliation(s)
- Nihat Bugra Agaoglu
- Genomic Laboratory (GLAB), Umraniye Training and Research Hospital, University of Health Sciences, Istanbul, Turkey.,Department of Medical Genetics, Umraniye Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Busra Unal
- Genomic Laboratory (GLAB), Umraniye Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Ozlem Akgun Dogan
- Genomic Laboratory (GLAB), Umraniye Training and Research Hospital, University of Health Sciences, Istanbul, Turkey.,Department of Pediatric Genetics, Umraniye Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Payam Zolfagharian
- Genomic Laboratory (GLAB), Umraniye Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Pari Shairfli
- Genomic Laboratory (GLAB), Umraniye Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Aylin Karakurt
- Genomic Laboratory (GLAB), Umraniye Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Burak Can Senay
- Genomic Laboratory (GLAB), Umraniye Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Tugba Kizilboga
- Genomic Laboratory (GLAB), Umraniye Training and Research Hospital, University of Health Sciences, Istanbul, Turkey.,Department of Molecular Biology and Genetics, Istanbul Technical University, Istanbul, Turkey
| | - Jale Yildiz
- Genomic Laboratory (GLAB), Umraniye Training and Research Hospital, University of Health Sciences, Istanbul, Turkey.,Department of Molecular Biology and Genetics, Istanbul Technical University, Istanbul, Turkey
| | - Gizem Dinler Doganay
- Department of Molecular Biology and Genetics, Istanbul Technical University, Istanbul, Turkey
| | - Levent Doganay
- Genomic Laboratory (GLAB), Umraniye Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
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7
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Kwong A, Au CH, Shin VY, Ho DN, Wong EYL, Ho CYS, Chung Y, Chan TL, Ma ESK. Rapid Breakpoint Mapping of a Novel Germline PALB2 Duplication by PCR-Free Long-Read Sequencing for Interpretation of Its Pathogenicity. JCO Precis Oncol 2022; 5:1044-1047. [PMID: 34994627 DOI: 10.1200/po.20.00454] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Affiliation(s)
- Ava Kwong
- Department of Surgery, The University of Hong Kong and The University of Hong Kong-Shenzhen Hospital, Hong Kong, China.,Department of Surgery and Cancer Genetics Centre, Hong Kong Sanatorium and Hospital, Hong Kong, China.,Hong Kong Hereditary Breast Cancer Family Registry, Hong Kong Sanatorium and Hospital, Hong Kong, China
| | - Chun Hang Au
- Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium and Hospital, Hong Kong, China
| | - Vivian Y Shin
- Department of Surgery, The University of Hong Kong and The University of Hong Kong-Shenzhen Hospital, Hong Kong, China
| | - Dona N Ho
- Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium and Hospital, Hong Kong, China
| | - Elaine Y L Wong
- Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium and Hospital, Hong Kong, China
| | - Cecilia Y S Ho
- Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium and Hospital, Hong Kong, China
| | - Yvonne Chung
- Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium and Hospital, Hong Kong, China
| | - Tsun Leung Chan
- Hong Kong Hereditary Breast Cancer Family Registry, Hong Kong Sanatorium and Hospital, Hong Kong, China.,Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium and Hospital, Hong Kong, China
| | - Edmond S K Ma
- Hong Kong Hereditary Breast Cancer Family Registry, Hong Kong Sanatorium and Hospital, Hong Kong, China.,Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium and Hospital, Hong Kong, China
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8
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Vargas E, de Deugd R, Villegas VE, Gil F, Mora L, Viaña LF, Bruges R, Gonzalez A, Galvis JC, Hamann U, Torres D. OUP accepted manuscript. Oncologist 2022; 27:e151-e157. [PMID: 35641219 PMCID: PMC8895486 DOI: 10.1093/oncolo/oyab026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 09/08/2021] [Indexed: 11/13/2022] Open
Abstract
Background Pathogenic germline mutations in the BRCA1 and BRCA2 (BRCA1/2) genes contribute to hereditary breast/ovarian cancer (OC) in White/mestizo Colombian women. As there is virtually no genetic data on breast cancer (BC) in Colombians of African descent, we conducted a comprehensive BRCA1/2 mutational analysis of 60 Afro-Colombian families affected by breast/OC. Materials and Methods Mutation screening of the complete BRCA1/2 genes for small-scale mutations and large genomic alterations was performed in these families using next-generation sequencing and multiplex ligation-dependent probe amplification analysis. Results Four pathogenic germline mutations, including one novel mutation, were identified, comprising 3 in BRCA1 and one in BRCA2. The prevalence of BRCA1/2 mutations, including one BRCA1 founder mutation (c.5123C>A) previously identified in this sample set, was 3.9% (2/51) in female BC-affected families and 33.3% (3/9) in those affected by both breast and OC. Haplotype analysis of 2 BRCA2_c.2701delC carriers (one Afro-Colombian and one previously identified White/mestizo Colombian patient with BC) suggested that the mutation arose in a common ancestor. Conclusion Our data showed that 2/5 (40%) mutations (including the one previously identified in this sample set) are shared by White/mestizo Colombian and Afro-Colombian populations. This suggests that these 2 populations are closely related. Nevertheless, variations in the BRCA1/2 mutational spectrum among Afro-Colombian subgroups from different regions of the country were observed, suggesting that specific genetic risk assessment strategies need to be developed.
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Affiliation(s)
- Elizabeth Vargas
- Institute of Human Genetics, Pontificia Universidad Javeriana, Bogota, Colombia
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Victoria E Villegas
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogota, Colombia
- Victoria E. Villegas, Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia; Tel: +57(1) 2970200;
| | - Fabian Gil
- Unit of Clinical Epidemiology and Biostatistics, Pontificia Universidad Javeriana, Bogota, Colombia
| | - Lina Mora
- Institute of Human Genetics, Pontificia Universidad Javeriana, Bogota, Colombia
| | | | - Ricardo Bruges
- Centro Javeriano de Oncología, Pontificia Universidad Javeriana, Bogota, Colombia
| | - Alejandro Gonzalez
- Centro Javeriano de Oncología, Pontificia Universidad Javeriana, Bogota, Colombia
| | - Juan Carlos Galvis
- Centro Javeriano de Oncología, Pontificia Universidad Javeriana, Bogota, Colombia
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Diana Torres
- Institute of Human Genetics, Pontificia Universidad Javeriana, Bogota, Colombia
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Corresponding author: Diana Torres, Institute of Human Genetics, Pontificia Universidad Javeriana, Bogota, Colombia; Tel: +57(1) 3208320;
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9
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Chandrasekaran D, Sobocan M, Blyuss O, Miller RE, Evans O, Crusz SM, Mills-Baldock T, Sun L, Hammond RFL, Gaba F, Jenkins LA, Ahmed M, Kumar A, Jeyarajah A, Lawrence AC, Brockbank E, Phadnis S, Quigley M, El Khouly F, Wuntakal R, Faruqi A, Trevisan G, Casey L, Burghel GJ, Schlecht H, Bulman M, Smith P, Bowers NL, Legood R, Lockley M, Wallace A, Singh N, Evans DG, Manchanda R. Implementation of Multigene Germline and Parallel Somatic Genetic Testing in Epithelial Ovarian Cancer: SIGNPOST Study. Cancers (Basel) 2021; 13:cancers13174344. [PMID: 34503154 PMCID: PMC8431198 DOI: 10.3390/cancers13174344] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 08/09/2021] [Accepted: 08/24/2021] [Indexed: 11/16/2022] Open
Abstract
We present findings of a cancer multidisciplinary-team (MDT) coordinated mainstreaming pathway of unselected 5-panel germline BRCA1/BRCA2/RAD51C/RAD51D/BRIP1 and parallel somatic BRCA1/BRCA2 testing in all women with epithelial-OC and highlight the discordance between germline and somatic testing strategies across two cancer centres. Patients were counselled and consented by a cancer MDT member. The uptake of parallel multi-gene germline and somatic testing was 97.7%. Counselling by clinical-nurse-specialist more frequently needed >1 consultation (53.6% (30/56)) compared to a medical (15.0% (21/137)) or surgical oncologist (15.3% (17/110)) (p < 0.001). The median age was 54 (IQR = 51-62) years in germline pathogenic-variant (PV) versus 61 (IQR = 51-71) in BRCA wild-type (p = 0.001). There was no significant difference in distribution of PVs by ethnicity, stage, surgery timing or resection status. A total of 15.5% germline and 7.8% somatic BRCA1/BRCA2 PVs were identified. A total of 2.3% patients had RAD51C/RAD51D/BRIP1 PVs. A total of 11% germline PVs were large-genomic-rearrangements and missed by somatic testing. A total of 20% germline PVs are missed by somatic first BRCA-testing approach and 55.6% germline PVs missed by family history ascertainment. The somatic testing failure rate is higher (23%) for patients undergoing diagnostic biopsies. Our findings favour a prospective parallel somatic and germline panel testing approach as a clinically efficient strategy to maximise variant identification. UK Genomics test-directory criteria should be expanded to include a panel of OC genes.
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Affiliation(s)
- Dhivya Chandrasekaran
- Wolfson Institute of Population Health, Barts CRUK Cancer Centre, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK; (D.C.); (M.S.); (O.E.); (L.S.); (F.G.)
- Department of Gynaecological Oncology, Barts Health NHS Trust, London EC1 1BB, UK; (A.J.); (A.C.L.); (E.B.); (S.P.)
| | - Monika Sobocan
- Wolfson Institute of Population Health, Barts CRUK Cancer Centre, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK; (D.C.); (M.S.); (O.E.); (L.S.); (F.G.)
- Department of Gynaecological Oncology, Barts Health NHS Trust, London EC1 1BB, UK; (A.J.); (A.C.L.); (E.B.); (S.P.)
- Divison for Gynaecology and Perinatology, University Medical Centre Maribor, 2000 Maribor, Slovenia
| | - Oleg Blyuss
- School of Physics, Engineering and Computer Science, University of Hertfordshire, Hatfield AL10 9AB, UK;
- Department of Paediatrics and Paediatric Infectious Diseases, Sechenov First Moscow State Medical University, Moscow 119991, Russia
- World-Class Research Center “Digital Biodesign and Personalized Healthcare”, Sechenov First Moscow State Medical University, Moscow 119991, Russia
| | - Rowan E. Miller
- Department of Medical Oncology, Barts Health NHS Trust, London EC1A 7BE, UK; (R.E.M.); (S.M.C.)
| | - Olivia Evans
- Wolfson Institute of Population Health, Barts CRUK Cancer Centre, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK; (D.C.); (M.S.); (O.E.); (L.S.); (F.G.)
| | - Shanthini M. Crusz
- Department of Medical Oncology, Barts Health NHS Trust, London EC1A 7BE, UK; (R.E.M.); (S.M.C.)
| | - Tina Mills-Baldock
- Department of Medical Oncology, Barking, Havering & Redbridge University Hospitals, Essex RM7 0AG, UK; (T.M.-B.); (M.Q.); (F.E.K.)
| | - Li Sun
- Wolfson Institute of Population Health, Barts CRUK Cancer Centre, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK; (D.C.); (M.S.); (O.E.); (L.S.); (F.G.)
- Department of Health Services Research, Faculty of Public Health & Policy, London School of Hygiene & Tropical Medicine, London WC1H 9SH, UK;
| | - Rory F. L. Hammond
- Department of Pathology, Barts Health NHS Trust, London E1 1FR, UK; (R.F.L.H.); (A.F.); (G.T.); (L.C.); (N.S.)
| | - Faiza Gaba
- Wolfson Institute of Population Health, Barts CRUK Cancer Centre, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK; (D.C.); (M.S.); (O.E.); (L.S.); (F.G.)
| | - Lucy A. Jenkins
- North East Thames Regional Genetics Service, Great Ormond Street Hospital, London WC1N 3JH, UK; (L.A.J.); (M.A.); (A.K.)
| | - Munaza Ahmed
- North East Thames Regional Genetics Service, Great Ormond Street Hospital, London WC1N 3JH, UK; (L.A.J.); (M.A.); (A.K.)
| | - Ajith Kumar
- North East Thames Regional Genetics Service, Great Ormond Street Hospital, London WC1N 3JH, UK; (L.A.J.); (M.A.); (A.K.)
| | - Arjun Jeyarajah
- Department of Gynaecological Oncology, Barts Health NHS Trust, London EC1 1BB, UK; (A.J.); (A.C.L.); (E.B.); (S.P.)
| | - Alexandra C. Lawrence
- Department of Gynaecological Oncology, Barts Health NHS Trust, London EC1 1BB, UK; (A.J.); (A.C.L.); (E.B.); (S.P.)
| | - Elly Brockbank
- Department of Gynaecological Oncology, Barts Health NHS Trust, London EC1 1BB, UK; (A.J.); (A.C.L.); (E.B.); (S.P.)
| | - Saurabh Phadnis
- Department of Gynaecological Oncology, Barts Health NHS Trust, London EC1 1BB, UK; (A.J.); (A.C.L.); (E.B.); (S.P.)
| | - Mary Quigley
- Department of Medical Oncology, Barking, Havering & Redbridge University Hospitals, Essex RM7 0AG, UK; (T.M.-B.); (M.Q.); (F.E.K.)
| | - Fatima El Khouly
- Department of Medical Oncology, Barking, Havering & Redbridge University Hospitals, Essex RM7 0AG, UK; (T.M.-B.); (M.Q.); (F.E.K.)
| | - Rekha Wuntakal
- Department of Gynaecology, Barking, Havering & Redbridge University Hospitals, Essex RM7 0AG, UK;
| | - Asma Faruqi
- Department of Pathology, Barts Health NHS Trust, London E1 1FR, UK; (R.F.L.H.); (A.F.); (G.T.); (L.C.); (N.S.)
| | - Giorgia Trevisan
- Department of Pathology, Barts Health NHS Trust, London E1 1FR, UK; (R.F.L.H.); (A.F.); (G.T.); (L.C.); (N.S.)
| | - Laura Casey
- Department of Pathology, Barts Health NHS Trust, London E1 1FR, UK; (R.F.L.H.); (A.F.); (G.T.); (L.C.); (N.S.)
| | - George J. Burghel
- Manchester Centre for Genomic Medicine, Saint Marys Hospital, Manchester M13 9WL, UK; (G.J.B.); (H.S.); (M.B.); (P.S.); (N.L.B.); (A.W.); (D.G.E.)
| | - Helene Schlecht
- Manchester Centre for Genomic Medicine, Saint Marys Hospital, Manchester M13 9WL, UK; (G.J.B.); (H.S.); (M.B.); (P.S.); (N.L.B.); (A.W.); (D.G.E.)
| | - Michael Bulman
- Manchester Centre for Genomic Medicine, Saint Marys Hospital, Manchester M13 9WL, UK; (G.J.B.); (H.S.); (M.B.); (P.S.); (N.L.B.); (A.W.); (D.G.E.)
| | - Philip Smith
- Manchester Centre for Genomic Medicine, Saint Marys Hospital, Manchester M13 9WL, UK; (G.J.B.); (H.S.); (M.B.); (P.S.); (N.L.B.); (A.W.); (D.G.E.)
| | - Naomi L. Bowers
- Manchester Centre for Genomic Medicine, Saint Marys Hospital, Manchester M13 9WL, UK; (G.J.B.); (H.S.); (M.B.); (P.S.); (N.L.B.); (A.W.); (D.G.E.)
| | - Rosa Legood
- Department of Health Services Research, Faculty of Public Health & Policy, London School of Hygiene & Tropical Medicine, London WC1H 9SH, UK;
| | - Michelle Lockley
- Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK;
| | - Andrew Wallace
- Manchester Centre for Genomic Medicine, Saint Marys Hospital, Manchester M13 9WL, UK; (G.J.B.); (H.S.); (M.B.); (P.S.); (N.L.B.); (A.W.); (D.G.E.)
| | - Naveena Singh
- Department of Pathology, Barts Health NHS Trust, London E1 1FR, UK; (R.F.L.H.); (A.F.); (G.T.); (L.C.); (N.S.)
| | - D. Gareth Evans
- Manchester Centre for Genomic Medicine, Saint Marys Hospital, Manchester M13 9WL, UK; (G.J.B.); (H.S.); (M.B.); (P.S.); (N.L.B.); (A.W.); (D.G.E.)
| | - Ranjit Manchanda
- Wolfson Institute of Population Health, Barts CRUK Cancer Centre, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK; (D.C.); (M.S.); (O.E.); (L.S.); (F.G.)
- Department of Gynaecological Oncology, Barts Health NHS Trust, London EC1 1BB, UK; (A.J.); (A.C.L.); (E.B.); (S.P.)
- Department of Health Services Research, Faculty of Public Health & Policy, London School of Hygiene & Tropical Medicine, London WC1H 9SH, UK;
- Correspondence:
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10
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Bhai P, Levy MA, Rooney K, Carere DA, Reilly J, Kerkhof J, Volodarsky M, Stuart A, Kadour M, Panabaker K, Schenkel LC, Lin H, Ainsworth P, Sadikovic B. Analysis of Sequence and Copy Number Variants in Canadian Patient Cohort With Familial Cancer Syndromes Using a Unique Next Generation Sequencing Based Approach. Front Genet 2021; 12:698595. [PMID: 34326862 PMCID: PMC8314385 DOI: 10.3389/fgene.2021.698595] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 06/07/2021] [Indexed: 11/13/2022] Open
Abstract
Background Hereditary cancer predisposition syndromes account for approximately 10% of cancer cases. Next generation sequencing (NGS) based multi-gene targeted panels is now a frontline approach to identify pathogenic mutations in cancer predisposition genes in high-risk families. Recent evolvement of NGS technologies have allowed simultaneous detection of sequence and copy number variants (CNVs) using a single platform. In this study, we have analyzed frequency and nature of sequence variants and CNVs, in a Canadian cohort of patients, suspected with hereditary cancer syndrome, referred for genetic testing following specific genetic testing guidelines based on patient's personal and/or family history of cancer. Methods A 2870 patients were subjected to a single NGS based multi-gene targeted hereditary cancer panel testing algorithm to identify sequence variants and CNVs in cancer predisposition genes at our reference laboratory in Southwestern Ontario. CNVs identified by NGS were confirmed by alternative techniques like Multiplex ligation-dependent probe amplification (MLPA). Results A 15% (431/2870) patients had a pathogenic variant and 36% (1032/2870) had a variant of unknown significance (VUS), in a cancer susceptibility gene. A total of 287 unique pathogenic variant were identified, out of which 23 (8%) were novel. CNVs identified by NGS based approach accounted for 9.5% (27/287) of pathogenic variants, confirmed by alternate techniques with high accuracy. Conclusion This study emphasizes the utility of NGS based targeted testing approach to identify both sequence and CNVs in patients suspected with hereditary cancer syndromes in clinical setting and expands the mutational spectrum of high and moderate penetrance cancer predisposition genes.
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Affiliation(s)
- Pratibha Bhai
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada
| | - Michael A Levy
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada
| | - Kathleen Rooney
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada
| | - Deanna Alexis Carere
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada
| | - Jack Reilly
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Jennifer Kerkhof
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada
| | - Michael Volodarsky
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada
| | - Alan Stuart
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada
| | - Mike Kadour
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada.,Department of Pathology and Laboratory Medicine, London Health Sciences Centre, London, ON, Canada
| | - Karen Panabaker
- Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre, London, ON, Canada
| | - Laila C Schenkel
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Hanxin Lin
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Peter Ainsworth
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada.,Department of Pathology and Laboratory Medicine, London Health Sciences Centre, London, ON, Canada
| | - Bekim Sadikovic
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
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11
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Genetic testing results in Slovenian male breast cancer cohort indicate the BRCA2 7806-2A > G founder variant could be associated with higher male breast cancer risk. Breast Cancer Res Treat 2021; 188:811-820. [PMID: 33891299 PMCID: PMC8272709 DOI: 10.1007/s10549-021-06224-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 04/08/2021] [Indexed: 10/26/2022]
Abstract
PURPOSE To analyze the prevalence of pathogenic/likely pathogenic variants (P/LPVs) in BRCA1 and BRCA2 genes in the largest cohort of Slovenian male breast cancer (MBC) patients to date and to explore a possible correlation between the Slovenian founder variant BRCA2:c.7806-2A > G and predisposition to MBC. METHODS We performed a retrospective analysis of 81 MBC cases who underwent genetic counseling and/or testing between January 1999 and May 2020. To explore a possible genotype-phenotype correlation, we performed additional analyses of 203 unrelated families with P/LPVs in BRCA2 and 177 cases of female breast cancer (FBC) in carriers of P/LPVs in BRCA2. RESULTS Detection rate of P/LPVs in the BRCA1 and BRCA2 genes was 24.7% (20/81) with 95% of them in BRCA2 gene. The only two recurrent P/LPVs were BRCA2:c.7806-2A > G and BRCA2:c.3975_3978dupTGCT (9 and 5 MBC cases, respectively). In families with BRCA2:c.7806-2A > G, the incidence of MBC cases was higher compared to families with other P/LPVs in BRCA2; however, the difference did not reach statistical significance (17.8% vs. 8.9%, p = 0.105). BRCA2:c.7806-2A > G was detected in both families with multiple cases of MBC. This splice-site variant represented a significantly higher proportion of all BRCA2 P/LPVs detected in MBC carriers compared to FBC carriers (47.4% vs. 26%, p = 0.049). CONCLUSION We observed a high mutation detection rate and conclude this may be due to the prevalent BRCA2:c.7806-2A > G variant in Slovenia. Our results indicate a possible association between this variant and higher risk of breast cancer in males compared to other identified P/LPVs in BRCA2.
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12
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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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13
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BRCA1/2 Mutation Detection in the Tumor Tissue from Selected Polish Patients with Breast Cancer Using Next Generation Sequencing. Genes (Basel) 2021; 12:genes12040519. [PMID: 33918338 PMCID: PMC8065856 DOI: 10.3390/genes12040519] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 03/30/2021] [Accepted: 03/30/2021] [Indexed: 12/24/2022] Open
Abstract
(1) Background: Although, in the mutated BRCA detected in the Polish population of patients with breast cancer, there is a large percentage of recurrent pathogenic variants, an increasing need for the assessment of rare BRCA1/2 variants using NGS can be observed. (2) Methods: We studied 75 selected patients with breast cancer (negative for the presence of 5 mutations tested in the Polish population in the prophylactic National Cancer Control Program). DNA extracted from the cancer tissue of these patients was used to prepare a library and to sequence all coding regions of the BRCA1/2 genes. (3) Results: We detected nine pathogenic variants in 8 out of 75 selected patients (10.7%). We identified one somatic and eight germline variants. We also used different bioinformatic NGS software programs to analyze NGS FASTQ files and established that tertiary analysis performed with different tools was more likely to give the same outcome if we analyzed files received from secondary analysis using the same method. (4) Conclusions: Our study emphasizes (i) the importance of an NGS validation process with a bioinformatic procedure included; (ii) the importance of screening both somatic and germline pathogenic variants; (iii) the urgent need to identify additional susceptible genes in order to explain the high percentage of non-BRCA-related hereditary cases of breast cancer.
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14
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K3326X and Other C-Terminal BRCA2 Variants Implicated in Hereditary Cancer Syndromes: A Review. Cancers (Basel) 2021; 13:cancers13030447. [PMID: 33503928 PMCID: PMC7865497 DOI: 10.3390/cancers13030447] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 01/11/2021] [Accepted: 01/21/2021] [Indexed: 02/06/2023] Open
Abstract
Simple Summary The cancer associated protein BRCA2 is the subject of intense continual study. Because of this, new insights into the relation of specific variants of this gene and cancer are regularly generated. These discoveries shed light on cancer risk and management for patients carrying these mutations. Additionally, new techniques for variant discovery and investigation are developed and tested, further enhancing scientific and clinical understanding of this key protein. In this review we will investigate the recent literature associated with variants in the C-terminus of BRCA2 and their effect on health and cancer predisposition. Abstract Whole genome analysis and the search for mutations in germline and tumor DNAs is becoming a major tool in the evaluation of risk as well as the management of hereditary cancer syndromes. Because of the identification of cancer predisposition gene panels, thousands of such variants have been catalogued yet many remain unclassified, presenting a clinical challenge for the management of hereditary cancer syndromes. Although algorithms exist to estimate the likelihood of a variant being deleterious, these tools are rarely used for clinical decision-making. Here, we review the progress in classifying K3326X, a rare truncating variant on the C-terminus of BRCA2 and review recent literature on other novel single nucleotide polymorphisms, SNPs, on the C-terminus of the protein, defined in this review as the portion after the final BRC repeat (amino acids 2058–3418).
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15
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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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16
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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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17
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Kim DH, Cho CH, Kwon SY, Ryoo NH, Jeon DS, Lee W, Ha JS. BRCA1/2 mutations, including large genomic rearrangements, among unselected ovarian cancer patients in Korea. J Gynecol Oncol 2019; 29:e90. [PMID: 30207098 PMCID: PMC6189434 DOI: 10.3802/jgo.2018.29.e90] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 06/19/2018] [Accepted: 07/18/2018] [Indexed: 12/18/2022] Open
Abstract
Objective We performed small-scale mutation and large genomic rearrangement (LGR) analysis of BRCA1/2 in ovarian cancer patients to determine the prevalence and the characteristics of the mutations. Methods All ovarian cancer patients who visited a single institution between September 2015 and April 2017 were included. Sanger sequencing, multiplex ligation-dependent probe amplification (MLPA), and long-range polymerase chain reaction (PCR) were performed to comprehensively study BRCA1/2. The genetic risk models BRCAPRO, Myriad, and BOADICEA were used to evaluate the mutation analysis. Results In total, 131 patients were enrolled. Of the 131 patients, Sanger sequencing identified 16 different BRCA1/2 small-scale mutations in 20 patients (15.3%). Two novel nonsense mutations were detected in 2 patients with a serous borderline tumor and a large-cell neuroendocrine carcinoma. MLPA analysis of BRCA1/2 in Sanger-negative patients revealed 2 LGRs. The LGRs accounted for 14.3% of all identified BRCA1 mutations, and the prevalence of LGRs identified in this study was 1.8% in 111 Sanger-negative patients. The genetic risk models showed statistically significant differences between mutation carriers and non-carriers. The 2 patients with LGRs had at least one blood relative with breast or ovarian cancer. Conclusion Twenty-two (16.8%) of the unselected ovarian cancer patients had BRCA1/2 mutations that were detected through comprehensive BRCA1/2 genetic testing. Ovarian cancer patients with Sanger-negative results should be considered for LGR detection if they have one blood relative with breast or ovarian cancer. The detection of more BRCA1/2 mutations in patients is important for efforts to provide targeted therapy to ovarian cancer patients.
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Affiliation(s)
- Do Hoon Kim
- Department of Laboratory Medicine, Keimyung University School of Medicine, Daegu, Korea
| | - Chi Heum Cho
- Department of Obstetrics and Gynecology, Keimyung University School of Medicine, Daegu, Korea
| | - Sun Young Kwon
- Department of Pathology, Keimyung University School of Medicine, Daegu, Korea
| | - Nam Hee Ryoo
- Department of Laboratory Medicine, Keimyung University School of Medicine, Daegu, Korea
| | - Dong Seok Jeon
- Department of Laboratory Medicine, Keimyung University School of Medicine, Daegu, Korea
| | - Wonmok Lee
- Department of Laboratory Medicine, Keimyung University School of Medicine, Daegu, Korea
| | - Jung Sook Ha
- Department of Laboratory Medicine, Keimyung University School of Medicine, Daegu, Korea.
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18
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Rapid detection of copy number variations and point mutations in BRCA1/2 genes using a single workflow by ion semiconductor sequencing pipeline. Oncotarget 2018; 9:33648-33655. [PMID: 30263092 PMCID: PMC6154752 DOI: 10.18632/oncotarget.26000] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 08/04/2018] [Indexed: 01/29/2023] Open
Abstract
Molecular analysis of BRCA1 (MIM# 604370) and BRCA2 (MIM #600185) genes is essential for familial breast and ovarian cancer prevention and treatment. An efficient, rapid, cost-effective accurate strategy for the detection of pathogenic variants is crucial. Mutations detection of BRCA1/2 genes includes screening for single nucleotide variants (SNVs), small insertions or deletions (indels), and Copy Number Variations (CNVs). Sanger sequencing is unable to identify CNVs and therefore Multiplex Ligation Probe amplification (MLPA) or Multiplex Amplicon Quantification (MAQ) is used to complete the BRCA1/2 genes analysis. The rapid evolution of Next Generation Sequencing (NGS) technologies allows the search for point mutations and CNVs with a single platform and workflow. In this study we test the possibilities of NGS technology to simultaneously detect point mutations and CNVs in BRCA1/2 genes, using the OncomineTM BRCA Research Assay on Personal Genome Machine (PGM) Platform with Ion Reporter Software for sequencing data analysis (Thermo Fisher Scientific). Comparison between the NGS-CNVs, MLPA and MAQ results shows how the NGS approach is the most complete and fast method for the simultaneous detection of all BRCA mutations, avoiding the usual time consuming multistep approach in the routine diagnostic testing of hereditary breast and ovarian cancers.
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19
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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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20
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Borghei YS, Hosseini M, Ganjali MR, Hosseinkhani S. A novel BRCA1 gene deletion detection in human breast carcinoma MCF-7 cells through FRET between quantum dots and silver nanoclusters. J Pharm Biomed Anal 2018; 152:81-88. [DOI: 10.1016/j.jpba.2018.01.014] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 12/31/2017] [Accepted: 01/08/2018] [Indexed: 02/01/2023]
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21
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Borghei YS, Hosseini M, Ganjali MR. Detection of large deletion in human BRCA1 gene in human breast carcinoma MCF-7 cells by using DNA-Silver Nanoclusters. Methods Appl Fluoresc 2017; 6:015001. [PMID: 28858858 DOI: 10.1088/2050-6120/aa8988] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Here we describe a label-free detection strategy for large deletion mutation in breast cancer (BC) related gene BRCA1 based on a DNA-silver nanocluster (NC) fluorescence upon recognition-induced hybridization. The specific hybridization of DNA templated silver NCs fluorescent probe to target DNAs can act as effective templates for enhancement of AgNCs fluorescence, which can be used to distinguish the deletion of BRCA1 due to different fluorescence intensities. Under the optimal conditions, the fluorescence intensity of the DNA-AgNCs at emission peaks around 440 nm (upon excitation at 350 nm) increased with the increasing deletion type within a dynamic range from 1.0 × 10-10 to 2.4 × 10-6 M with a detection limit (LOD) of 6.4 × 10-11 M. In this sensing system, the normal type shows no significant fluorescence; on the other hand, the deletion type emits higher fluorescence than normal type. Using this nanobiosensor, we successfully determined mutation using the non-amplified genomic DNAs that were isolated from the BC cell line.
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Affiliation(s)
- Yasaman-Sadat Borghei
- Department of Life Science Engineering, Faculty of New Sciences & Technologies, University of Tehran, Tehran, Iran
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22
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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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23
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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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Spectrum of genetic variants of BRCA1 and BRCA2 in a German single center study. Arch Gynecol Obstet 2017; 295:1227-1238. [PMID: 28324225 DOI: 10.1007/s00404-017-4330-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 02/10/2017] [Indexed: 12/11/2022]
Abstract
BACKGROUND Determination of mutation status of BRCA1 and BRCA2 has become part of the clinical routine. However, the spectrum of genetic variants differs between populations. The aim of this study was to deliver a comprehensive description of all detected variants. METHODS In families fulfilling one of the German Consortium for Hereditary Breast and Ovarian Cancer (GC-HBOC) criteria for genetic testing, one affected was chosen for analysis. DNA of blood lymphocytes was amplified by PCR and prescreened by DHPLC. Aberrant fragments were sequenced. All coding exons and splice sites of BRCA1 and BRCA2 were analyzed. Screening for large rearrangements in both genes was performed by MLPA. RESULTS Of 523 index patients, 121 (23.1%) were found to carry a pathogenic or likely pathogenic (class 4/5) mutation. A variant of unknown significance (VUS) was detected in 73/523 patients (13.9%). Two mutations p.Gln1756Profs*74 and p.Cys61Gly comprised 42.3% (n = 33/78) of all detected pathogenic mutations in BRCA1. Most of the other mutations were unique mutations. The most frequently detected mutation in BRCA2 was p.Val1283Lys (13.9%; n = 6/43). Altogether, 101 different neutral genetic variants were counted in BRCA1 (n = 35) and in BRCA2 (n = 66). CONCLUSION The two most frequently detected mutations are founder mutations in Poland and Czech Republic. More similarities seem to be shared with our direct neighbor countries compared to other European countries. For comparison of the extended genotype, a shared database is needed.
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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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Sedghi M, Esfandiari E, Fazel-Najafabadi E, Salehi M, Salavaty A, Fattahpour S, Dehghani L, Nouri N, Mokarian F. Genomic rearrangement screening of the BRCA1 from seventy Iranian high-risk breast cancer families. JOURNAL OF RESEARCH IN MEDICAL SCIENCES 2016; 21:95. [PMID: 28163741 PMCID: PMC5244654 DOI: 10.4103/1735-1995.193167] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 06/01/2016] [Accepted: 07/01/2016] [Indexed: 01/23/2023]
Abstract
Background: The second leading cause of cancer deaths in women is breast cancer. Germline mutations in susceptibility breast cancer gene BRCA1 increase the lifetime risk of breast cancer. Eighty-one large genomic rearrangements (LGRs) have been reported up to date in BRCA1 gene, and evaluation of these rearrangements helps with precise risk assessment in high-risk individuals. In this study, we have investigated LGRs in BRCA1 among Iranian high-risk breast cancer families. Materials and Methods: Seventy patients with breast cancer who were identified negative for point mutations or small deletions/insertions of BRCA1 gene were selected. Deletions and duplications of BRCA1 gene were evaluated using multiplex ligation-dependent probe amplification (MLPA). Results: Two deletions, deletion of exons 1A/1B-2 and exon 24, were detected in two patients with breast cancer. The former alteration was found in a woman with a strong family history of breast cancer while the latter one was detected in a woman with early onset of breast cancer. Conclusion: Although our data confirm that LGRs in BRCA1 comprise a relatively small proportion of mutations in hereditary breast cancer in the Iranian population, MLPA analysis might be considered for screening of LGRs in high-risk individuals. It is worth to note that our results are consistent with previous studies in various Asian and European countries.
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Affiliation(s)
- Maryam Sedghi
- Medical Genetics Laboratory, Alzahra University Hospital, Isfahan University of Medical Sciences, Isfahan, Iran; Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Non-communicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Elham Esfandiari
- Medical Genetics Laboratory, Alzahra University Hospital, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Esmat Fazel-Najafabadi
- Medical Genetics Laboratory, Alzahra University Hospital, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mansoor Salehi
- Medical Genetics Laboratory, Alzahra University Hospital, Isfahan University of Medical Sciences, Isfahan, Iran; Division of Genetics and Molecular Biology, Medical School, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Abbas Salavaty
- Medical Genetics Laboratory, Alzahra University Hospital, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Shirin Fattahpour
- Medical Genetics Laboratory, Alzahra University Hospital, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Leila Dehghani
- Department of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Isfahan Neurosciences Research Center, Alzahra University Hospital, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Nayerossadat Nouri
- Medical Genetics Laboratory, Alzahra University Hospital, Isfahan University of Medical Sciences, Isfahan, Iran; Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Non-communicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Fariborz Mokarian
- Department of Oncology, Isfahan University of Medical Sciences, Isfahan, Iran
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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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James PA, Sawyer S, Boyle S, Young MA, Kovalenko S, Doherty R, McKinley J, Alsop K, Beshay V, Harris M, Fox S, Lindeman GJ, Mitchell G. Large genomic rearrangements in the familial breast and ovarian cancer gene BRCA1 are associated with an increased frequency of high risk features. Fam Cancer 2016; 14:287-95. [PMID: 25678442 DOI: 10.1007/s10689-015-9785-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Large genomic rearrangements (LGRs) account for at least 10% of the mutations in BRCA1 and 5% of BRCA2 mutations in outbred hereditary breast and ovarian cancer (HBOC) families. Data from some series suggest LGRs represent particularly penetrant mutations. 1,034 index cases from HBOC families underwent comprehensive BRCA1 and BRCA2 mutation testing, including screening for LGRs. The personal and family history of 254 identified mutation carriers were compared based on mutation type. Thirty-six LGRs were detected; 32/122 (26%) BRCA1 and 4/132 (3%) BRCA2 mutations. High risk features (bilateral breast cancer, diagnosis <40 years, ovarian cancer, male breast cancer) were more commonly associated with an LGR than a non-LGR mutation (p = 0.008), In families with a BRCA1 LGR the mean age of breast cancer diagnosis was younger than in families with a non-LGR BRCA1 mutation (42.5 vs. 46.1 years, p = 0.007). Across the entire group of mutation positive families the number of relatives affected by breast or ovarian cancer was increased [LGR 3.7 vs. non- LGR 2.8 per family, p value (adjusted for genotype) = 0.047]. Excluding index cases, the odds ratio for breast cancer in BRCA1 families with an LGR was 1.42 (95% CI 1.24-1.63) and for ovarian cancer 1.66 (95% CI 1.10-2.49). The increased cancer risk was reflected in significantly higher risk assessments by mutation prediction tools. LGRs are associated with higher cancer risks. If validated, LGRs could be included in cancer risk prediction tools to improve personalised cancer risk prediction estimates and may guide cost-minimising mutation screening strategies in some healthcare settings.
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Affiliation(s)
- Paul A James
- Familial Cancer Centre, Peter MacCallum Cancer Centre, St Andrews Place, East Melbourne, VIC, 3002, Australia
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29
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BRCA1/BRCA2 founder mutations and cancer risks: impact in the western Danish population. Fam Cancer 2016; 15:507-12. [DOI: 10.1007/s10689-016-9875-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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30
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Jønson L, Ahlborn LB, Steffensen AY, Djursby M, Ejlertsen B, Timshel S, Nielsen FC, Gerdes AM, Hansen TVO. Identification of six pathogenic RAD51C mutations via mutational screening of 1228 Danish individuals with increased risk of hereditary breast and/or ovarian cancer. Breast Cancer Res Treat 2016; 155:215-22. [PMID: 26740214 DOI: 10.1007/s10549-015-3674-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2015] [Accepted: 12/29/2015] [Indexed: 11/26/2022]
Abstract
Germ-line mutations in the RAD51C gene have recently been identified in families with breast and ovarian cancer and have been associated with an increased risk of ovarian cancer. In this study, we describe the frequency of pathogenic RAD51C mutations identified in Danish breast and/or ovarian cancer families. We screened the RAD51C gene in 1228 Danish hereditary breast and/or ovarian cancer families by next-generation sequencing analysis. The frequency of the identified variants was examined in the exome sequencing project database and in data from 2000 Danish exomes and the presumed significance of missense and intronic variants was predicted by in silico analysis. We identified six families with a pathogenic mutation in RAD51C, including three frameshift mutations, one nonsense mutation, and 2 missense mutations. Overall, pathogenic RAD51C mutations were identified in 0.5 % of Danish families with increased risk of hereditary breast and/or ovarian cancer. Moreover, we identified 24 additional RAD51C variants of which 14 have not been previously reported in the literature. In this study, we determine the prevalence of RAD51C mutations in Danish breast and/or ovarian cancer families. We identified six pathogenic RAD51C mutations as well as 23 variants of uncertain clinical significance and one benign variant. Together, the study extends our knowledge of the RAD51C mutation spectrum and supports that RAD51C should be included in gene panel testing of individuals with high risk of breast and ovarian cancer.
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Affiliation(s)
- Lars Jønson
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Blegdamsvej 9, 2100, Copenhagen, Denmark
| | - Lise B Ahlborn
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Blegdamsvej 9, 2100, Copenhagen, Denmark
| | - Ane Y Steffensen
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Blegdamsvej 9, 2100, Copenhagen, Denmark
| | - Malene Djursby
- Department of Clinical Genetics, Rigshospitalet, University of Copenhagen, Blegdamsvej 9, 2100, Copenhagen, Denmark
| | - Bent Ejlertsen
- Department of Oncology, Rigshospitalet, University of Copenhagen, Blegdamsvej 9, 2100, Copenhagen, Denmark
| | - Susanne Timshel
- Kennedy Center, Rigshospitalet, University of Copenhagen, Blegdamsvej 9, 2100, Copenhagen, Denmark
| | - Finn C Nielsen
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Blegdamsvej 9, 2100, Copenhagen, Denmark
| | - Anne-Marie Gerdes
- Department of Clinical Genetics, Rigshospitalet, University of Copenhagen, Blegdamsvej 9, 2100, Copenhagen, Denmark
| | - Thomas V O Hansen
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Blegdamsvej 9, 2100, Copenhagen, Denmark.
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31
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Rudnicka H, Masojc B, van de Wetering T, Debniak T, Cybulski C, Gronwald J, Scott R, Lubinski J, Gorski B. First recurrent large genomic rearrangement in the BRCA1 gene found in Poland. Cancer Epidemiol 2014; 38:382-5. [DOI: 10.1016/j.canep.2014.05.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Revised: 05/05/2014] [Accepted: 05/08/2014] [Indexed: 11/28/2022]
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32
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Rizzolo P, Silvestri V, Tommasi S, Pinto R, Danza K, Falchetti M, Gulino M, Frati P, Ottini L. Male breast cancer: genetics, epigenetics, and ethical aspects. Ann Oncol 2014; 24 Suppl 8:viii75-viii82. [PMID: 24131976 DOI: 10.1093/annonc/mdt316] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND AND STUDY DESIGN Male breast cancer (MBC) is a rare disease compared with female BC and our current understanding regarding breast carcinogenesis in men has been largely extrapolated from the female counterpart. We focus on differences between the ethical issues related to male and female BC patients. A systematic literature search by using PubMed (http://www.ncbi.nlm.nih.gov/pubmed/), was carried out to provide a synopsis of the current research in the field of MBC genetics, epigenetics and ethics. Original articles and reviews published up to September 2012 were selected by using the following search key words to query the PubMed website: 'male breast cancer', 'male breast cancer and genetic susceptibility', 'male breast cancer and epigenetics', 'male breast cancer and methylation', 'male breast cancer and miRNA', 'male breast cancer and ethics'. RESULTS AND CONCLUSIONS As in women, three classes of breast cancer genetic susceptibility (high, moderate, and low penetrance) are recognized in men. However, genes involved and their impact do not exactly overlap in female and male BC. Epigenetic alterations are currently scarcely investigated in MBC, however, the different methylation and miRNA expression profiles identified to date in female and male BCs suggest a potential role for epigenetic alterations as diagnostic biomarkers. Overall, much still needs to be learned about MBC and, because of its rarity, the main effort is to develop large consortia for moving forward in understanding MBC and improving the management of MBC patients on a perspective of gender medicine.
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Affiliation(s)
- P Rizzolo
- Department of Molecular Medicine, 'Sapienza' University of Rome, Rome
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Functional characterization of BRCA1 gene variants by mini-gene splicing assay. Eur J Hum Genet 2014; 22:1362-8. [PMID: 24667779 PMCID: PMC4231409 DOI: 10.1038/ejhg.2014.40] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Revised: 02/12/2014] [Accepted: 02/19/2014] [Indexed: 02/06/2023] Open
Abstract
Mutational screening of the breast cancer susceptibility gene BRCA1 leads to the identification of numerous pathogenic variants such as frameshift and nonsense variants, as well as large genomic rearrangements. The screening moreover identifies a large number of variants, for example, missense, silent, and intron variants, which are classified as variants of unknown clinical significance owing to the lack of causal evidence. Variants of unknown clinical significance can potentially have an impact on splicing and therefore functional examinations are warranted to classify whether these variants are pathogenic or benign. Here we validate a mini-gene splicing assay by comparing the results of 24 variants with previously published data from RT-PCR analysis on RNA from blood samples/lymphoblastoid cell lines. The analysis showed an overall concordance of 100%. In addition, we investigated 13 BRCA1 variants of unknown clinical significance or putative variants affecting splicing by in silico analysis and mini-gene splicing assay. Both the in silico analysis and mini-gene splicing assay classified six BRCA1 variants as pathogenic (c.80+1G>A, c.132C>T (p.=), c.213-1G>A, c.670+1delG, c.4185+1G>A, and c.5075-1G>C), whereas six BRCA1 variants were classified as neutral (c.-19-22_-19-21dupAT, c.302-15C>G, c.547+14delG, c.4676-20A>G, c.4987-21G>T, and c.5278-14C>G) and one BRCA1 variant remained unclassified (c.670+16G>A). In conclusion, our study emphasizes that in silico analysis and mini-gene splicing assays are important for the classification of variants, especially if no RNA is available from the patient. This knowledge is crucial for proper genetic counseling of patients and their family members.
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Mahon SM. Large genomic rearrangements in BRCA1 and BRCA2: implications for patient care. Oncol Nurs Forum 2013; 40:220-2. [PMID: 23615136 DOI: 10.1188/13.onf.220-222] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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35
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Expression of human BRCA1Δ17-19 alternative splicing variant with a truncated BRCT domain in MCF-7 cells results in impaired assembly of DNA repair complexes and aberrant DNA damage response. Cell Signal 2013; 25:1186-93. [PMID: 23416467 DOI: 10.1016/j.cellsig.2013.02.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Accepted: 02/08/2013] [Indexed: 11/23/2022]
Abstract
Alternative pre-mRNA splicing is a fundamental post-transcriptional regulatory mechanism. Cancer-specific misregulation of the splicing process may lead to formation of irregular alternative splicing variants (ASVs) with a potentially negative impact on cellular homeostasis. Alternative splicing of BRCA1 pre-mRNA can give rise to BRCA1 protein isoforms that possess dramatically altered biological activities compared with full-length wild-type BRCA1. During the screening of high-risk breast cancer (BC) families we ascertained numerous BRCA1 ASVs, however, their clinical significance for BC development is largely unknown. In this study, we examined the influence of the BRCA1Δ17-19 ASV, which lacks a portion of the BRCT domain, on DNA repair capacity using human MCF-7 BC cell clones with stably modified BRCA1 expression. Our results show that overexpression of BRCA1Δ17-19 impairs homologous recombination repair (sensitizes cells to mitomycin C), delays repair of ionizing radiation-induced DNA damage and dynamics of the ionizing radiation-induced foci (IRIF) formation, and undermines also the non-homologous end joining repair (NHEJ) activity. Mechanistically, BRCA1Δ17-19 cannot interact with the partner proteins Abraxas and CtIP, thus preventing interactions known to be critical for processing of DNA lesions. We propose that the observed inability of BRCA1Δ17-19 to functionally replace wtBRCA1 in repair of DNA double-strand breaks (DDSB) reflects impaired capacity to form the BRCA1-A and -C repair complexes. Our findings indicate that expression of BRCA1Δ17-19 may negatively influence genome stability by reducing the DDSB repair velocity, thereby contributing to enhanced probability of cancer development in the affected families.
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36
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Characteristics and spectrum of BRCA1 and BRCA2 mutations in 3,922 Korean patients with breast and ovarian cancer. Breast Cancer Res Treat 2012; 134:1315-26. [PMID: 22798144 DOI: 10.1007/s10549-012-2159-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Accepted: 06/27/2012] [Indexed: 01/01/2023]
Abstract
This investigation is aimed at evaluating the epidemiologic characteristics of BRCA1/2 germline mutations in Korean patients with breast and ovarian cancer (BOC). We analyzed the entire mutational data of BRCA1/2 genes in BOC patients who were tested in Korea since the first Korean report of BRCA1 mutation in 1995 with the exception of the data covered in the Korean Hereditary Breast Cancer (KOHBRA) study, the project launched in 2007 for establishing BRCA1/2 carrier cohorts in Korea. In total, BRCA1/2 gene mutations of 3,922 Korean BOC patients were evaluated, including the unpublished data of 2,139 breast cancer patients examined by four Korean institutions and the data of 1,783 BOC patients covered in ten previous reports. Overall, 420 (150 distinct) pathogenic mutations were identified, 211 (73 distinct) in BRCA1 and 209 (77 distinct) in BRCA2. The majority (134 of 150) of the distinct mutations resulted in premature termination codon of the BRCA1/2 translation. BRCA1 c.4186-1593_4676-1465del was the only large genomic rearrangements mutation. Out of 150 distinct BRCA1/2 mutations, 84 (56 %) mutations were considered specific to Korean BOC. Eighty-five BRCA1/2 mutations were detected in at least two unrelated patients. These recurrent mutations account for 84.5 % (355 of 420) of mutations detected in the Korean population. In the pooled mutational data of BRCA1/2 genes, this study discovered the prevalence of BRCA1/2 mutations in the Korean BOC patients is similar to those found in other ethnic groups. Large genomic rearrangements in BRCA1/2 genes were infrequently detected among the Korean patients with BOC. There were several BRCA1/2 mutation candidates for founder mutations. To further establish a Korean cohort for BRCA1/2 mutations, the nationwide KOHBRA study is in progress.
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Silva AG, Ewald IP, Sapienza M, Pinheiro M, Peixoto A, de Nóbrega AF, Carraro DM, Teixeira MR, Ashton-Prolla P, Achatz MIW, Rosenberg C, Krepischi ACV. Li-Fraumeni-like syndrome associated with a large BRCA1 intragenic deletion. BMC Cancer 2012; 12:237. [PMID: 22691290 PMCID: PMC3502571 DOI: 10.1186/1471-2407-12-237] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Accepted: 05/24/2012] [Indexed: 01/08/2023] Open
Abstract
Background Li-Fraumeni (LFS) and Li-Fraumeni-like (LFL) syndromes are associated to germline TP53 mutations, and are characterized by the development of central nervous system tumors, sarcomas, adrenocortical carcinomas, and other early-onset tumors. Due to the high frequency of breast cancer in LFS/LFL families, these syndromes clinically overlap with hereditary breast cancer (HBC). Germline point mutations in BRCA1, BRCA2, and TP53 genes are associated with high risk of breast cancer. Large rearrangements involving these genes are also implicated in the HBC phenotype. Methods We have screened DNA copy number changes by MLPA on BRCA1, BRCA2, and TP53 genes in 23 breast cancer patients with a clinical diagnosis consistent with LFS/LFL; most of these families also met the clinical criteria for other HBC syndromes. Results We found no DNA copy number alterations in the BRCA2 and TP53 genes, but we detected in one patient a 36.4 Kb BRCA1 microdeletion, confirmed and further mapped by array-CGH, encompassing exons 9–19. Breakpoints sequencing analysis suggests that this rearrangement was mediated by flanking Alu sequences. Conclusion This is the first description of a germline intragenic BRCA1 deletion in a breast cancer patient with a family history consistent with both LFL and HBC syndromes. Our results show that large rearrangements in these known cancer predisposition genes occur, but are not a frequent cause of cancer susceptibility.
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Affiliation(s)
- Amanda Gonçalves Silva
- International Center for Research and Training, A. C. Camargo Cancer Hospital, São Paulo, Brazil
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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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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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Shannon KM, Rodgers LH, Chan-Smutko G, Patel D, Gabree M, Ryan PD. Which individuals undergoing BRACAnalysis need BART testing? Cancer Genet 2011; 204:416-22. [PMID: 21962891 DOI: 10.1016/j.cancergen.2011.07.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Revised: 07/07/2011] [Accepted: 07/11/2011] [Indexed: 12/11/2022]
Abstract
Deleterious mutations in BRCA1 and BRCA2 include those identified by sequencing technology as well as large genomic rearrangements (LGR). The main testing laboratory in the United States, Myriad Genetics Laboratory (MGL), has defined criteria for inclusion of LGR testing (i.e., BRACAnalysis Rearrangement Test, or BART™) when BRCA1 and BRCA2 testing is ordered. We were interested in determining how many of our patients with LGR mutations in BRCA1 and BRCA2 fulfilled these MGL criteria. A retrospective chart review was performed on all individuals who underwent genetic testing at our institution since August 2006. Individuals who underwent LGR testing were classified as either having or not having a LGR in BRCA1 or BRCA2. Each individual's history was classified as meeting MGL defined LGR criteria, meeting criteria using third-degree relatives, or not meeting criteria. A total of 257 BART tests were ordered at our institution from August 2006 to August 2009. Five individuals (1.9%) had an LGR mutation. Two LGR were identified in patients who met MGL defined LGR criteria. One LGR was identified in a patient that met MGL defined LGR criteria only when using third-degree relatives. Two LGR were identified in individuals who did not meet MGL defined criteria. LGR are present in individuals who do not have a high pretest probability of carrying a mutation in BRCA1 or BRCA2. These data suggest that when BRCA1 and BRCA2 genetic testing is performed, testing should always include LGR testing so that the results are the most comprehensive and reliable.
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Affiliation(s)
- Kristen M Shannon
- Massachusetts General Hospital, Center for Cancer Risk Assessment, Boston, MA, USA.
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Rizzolo P, Silvestri V, Falchetti M, Ottini L. Inherited and acquired alterations in development of breast cancer. APPLICATION OF CLINICAL GENETICS 2011; 4:145-58. [PMID: 23776375 PMCID: PMC3681186 DOI: 10.2147/tacg.s13226] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Breast cancer is the most common cancer among women, accounting for about 30% of all cancers. In contrast, breast cancer is a rare disease in men, accounting for less than 1% of all cancers. Up to 10% of all breast cancers are hereditary forms, caused by inherited germ-line mutations in "high-penetrance," "moderate-penetrance," and "low-penetrance" breast cancer susceptibility genes. The remaining 90% of breast cancers are due to acquired somatic genetic and epigenetic alterations. A heterogeneous set of somatic alterations, including mutations and gene amplification, are reported to be involved in the etiology of breast cancer. Promoter hypermethylation of genes involved in DNA repair and hormone-mediated cell signaling, as well as altered expression of micro RNAs predicted to regulate key breast cancer genes, play an equally important role as genetic factors in development of breast cancer. Elucidation of the inherited and acquired genetic and epigenetic alterations involved in breast cancer may not only clarify molecular pathways involved in the development and progression of breast cancer itself, but may also have an important clinical and therapeutic impact on improving the management of patients with the disease.
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Affiliation(s)
- Piera Rizzolo
- Department of Molecular Medicine, "La Sapienza" University of Rome, Rome, Italy
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Hansen TVO, Jønson L, Steffensen AY, Andersen MK, Kjaergaard S, Gerdes AM, Ejlertsen B, Nielsen FC. Screening of 1331 Danish breast and/or ovarian cancer families identified 40 novel BRCA1 and BRCA2 mutations. Fam Cancer 2011; 10:207-12. [PMID: 21318380 DOI: 10.1007/s10689-011-9422-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Germ-line mutations in the tumour suppressor genes BRCA1 and BRCA2 predispose to breast and ovarian cancer. Since 1999 we have performed mutational screening of breast and/or ovarian cancer patients in East Denmark. During this period we have identified 40 novel sequence variations in BRCA1 and BRCA2 in high risk breast and/or ovarian cancer families. The mutations were detected via pre-screening using dHPLC or high-resolution melting and direct sequencing. We identified 16 variants in BRCA1, including 9 deleterious frame-shift mutations, 2 intronic variants, 4 missense mutations, and 1 synonymous variant. The remaining 24 variants were identified in BRCA2, including 10 deleterious mutants (6 frame-shift and 4 nonsense), 2 intronic variants, 10 missense mutations and 2 synonymous variants. The frequency of the variants of unknown significance was examined in control individuals. Moreover, the presumed significance of the missense mutations was predicted in silico using the align GVGD algorithm. In conclusion, the mutation screening identified 40 novel variants in the BRCA1 and BRCA2 genes and thereby extends the knowledge of the BRCA1/BRCA2 mutation spectrum. Nineteen of the mutations were interpreted as pathogenic, 3 missense mutations were suggested to be pathogenic based on in silico analysis, 6 mutations were suggested to be benign since they were identified in patients together with a well-known disease-causing BRCA1/BRCA2 mutation, while 12 were variants of unknown significance.
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Affiliation(s)
- Thomas V O Hansen
- Genomic Medicine, Department of Clinical Biochemistry, Rigshospitalet, Copenhagen University Hospital, Blegdamsvej 9, 2100 Copenhagen, Denmark.
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Steffensen AY, Jønson L, Ejlertsen B, Gerdes AM, Nielsen FC, Hansen TVO. Identification of a Danish breast/ovarian cancer family double heterozygote for BRCA1 and BRCA2 mutations. Fam Cancer 2010; 9:283-7. [PMID: 20455026 PMCID: PMC2921502 DOI: 10.1007/s10689-010-9345-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mutations in the two breast cancer susceptibility genes BRCA1 and BRCA2 are associated with increased risk of breast and ovarian cancer. Patients with mutations in both genes are rarely reported and often involve Ashkenazi founder mutations. Here we report the first identification of a Danish breast and ovarian cancer family heterozygote for mutations in the BRCA1 and BRCA2 genes. The BRCA1 nucleotide 5215G > A/c.5096G > A mutation results in the missense mutation Arg1699Gln, while the BRCA2 nucleotide 859 + 4A > G/c.631 + 4A > G is novel. Exon trapping experiments and reverse transcriptase (RT)–PCR analysis revealed that the BRCA2 mutation results in skipping of exon 7, thereby introducing a frameshift and a premature stop codon. We therefore classify the mutation as disease causing. Since the BRCA1 Arg1699Gln mutation is also suggested to be disease-causing, we consider this family double heterozygote for BRCA1 and BRCA2 mutations.
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Affiliation(s)
- Ane Y Steffensen
- Department of Clinical Biochemistry 4111, Rigshospitalet, Blegdamsvej 9, 2100, Copenhagen, Denmark
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Aktas D, Gultekin M, Kabacam S, Alikasifoglu M, Turan A, Tulunay G, Kose M, Ortac F, Yüce K, Tunçbilek E, Ayhan A. Identification of point mutations and large rearrangements in the BRCA1 gene in 667 Turkish unselected ovarian cancer patients. Gynecol Oncol 2010; 119:131-5. [DOI: 10.1016/j.ygyno.2010.05.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2010] [Revised: 05/10/2010] [Accepted: 05/17/2010] [Indexed: 11/26/2022]
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Spectrum of BRCA1/2 point mutations and genomic rearrangements in high-risk breast/ovarian cancer Chilean families. Breast Cancer Res Treat 2010; 126:705-16. [PMID: 20859677 DOI: 10.1007/s10549-010-1170-y] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2010] [Accepted: 09/06/2010] [Indexed: 11/27/2022]
Abstract
The distribution of BRCA1/2 germline mutations in breast/ovarian cancer (BC/OC) families varies among different populations. In the Chilean population, there are only two reports of mutation analysis of BRCA1/2, and these included a low number of BC and/or OC patients. Moreover, the prevalence of BRCA1/2 genomic rearrangements in Chilean and in other South American populations is unknown. In this article, we present the mutation-detection data corresponding to a set of 326 high-risk families analyzed by conformation-sensitive gel electrophoresis and heteroduplex analysis. To determine the contribution of BRCA1/2 LGRs in Chilean BC patients, we analyzed 56 high-risk subjects with no pathogenic BRCA1/2 point mutations. Germline BRCA1/2 point mutations were found in 23 (7.1%) of the 326 Chilean families. Families which had at least three BC and/or OC cases showed the highest frequency of mutations (15.9%). We identified 14 point pathogenic mutations. Three recurrent mutations in BRCA1 (c.187_188delAG, c.2605_2606delTT, and c.3450_3453delCAAG) and three in BRCA2 (c.4969_4970insTG, c.5374_5377delTATG, and c.6503_6504delTT) contributed to 63.6 and 66.7% of all the deleterious mutations of each gene, which may reflect the presence of region-specific founder effects. Taken together BRCA1/2 recurrent point mutations account for 65.2% (15/23) of the BRCA1/2 (+) families. No large deletions or duplications involving BRCA1/2 were identified in a subgroup of 56 index cases negative for BRCA1/2 point mutations. Our study, which is the largest conducted to date in a South American population, provides a comprehensive analysis on the type and distribution of BRCA1/2 mutations and allelic variants.
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Pertesi M, Konstantopoulou I, Yannoukakos D. Haplotype analysis of two recurrent genomic rearrangements in the BRCA1 gene suggests they are founder mutations for the Greek population. Clin Genet 2010; 80:375-82. [DOI: 10.1111/j.1399-0004.2010.01532.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Kang P, Mariapun S, Phuah SY, Lim LS, Liu J, Yoon SY, Thong MK, Mohd Taib NA, Yip CH, Teo SH. Large BRCA1 and BRCA2 genomic rearrangements in Malaysian high risk breast-ovarian cancer families. Breast Cancer Res Treat 2010; 124:579-84. [PMID: 20617377 DOI: 10.1007/s10549-010-1018-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2010] [Accepted: 06/23/2010] [Indexed: 12/11/2022]
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Abstract
Detection of mutations in hereditary breast and ovarian cancer-related BRCA1 and BRCA2 genes is an effective method of cancer prevention and early detection. Different ethnic and geographical regions have different BRCA1 and BRCA2 mutation spectrum and prevalence. Along with the emerging targeted therapy, demand and uptake for rapid BRCA1/2 mutations testing will increase in a near future. However, current patients selection and genetic testing strategies in most countries impose significant lag in this practice. The knowledge of the genetic structure of particular populations is important for the developing of effective screening protocol and may provide more efficient approach for the individualization of genetic testing. Elucidating of founder effect in BRCA1/2 genes can have an impact on the management of hereditary cancer families on a national and international healthcare system level, making genetic testing more affordable and cost-effective. The purpose of this review is to summarize current evidence about the BRCA1/2 founder mutations diversity in European populations.
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Hansen TVO, Jønson L, Albrechtsen A, Steffensen AY, Bergsten E, Myrhøj T, Ejlertsen B, Nielsen FC. Identification of a novel BRCA1 nucleotide 4803delCC/c.4684delCC mutation and a nucleotide 249T>A/c.130T>A (p.Cys44Ser) mutation in two Greenlandic Inuit families: implications for genetic screening of Greenlandic Inuit families with high risk for breast and/or ovarian cancer. Breast Cancer Res Treat 2010; 124:259-64. [PMID: 20437199 DOI: 10.1007/s10549-010-0909-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2010] [Accepted: 04/19/2010] [Indexed: 11/26/2022]
Abstract
Germ-line mutations in the tumour suppressor proteins BRCA1 and BRCA2 predispose to breast and ovarian cancer. We have recently identified a Greenlandic Inuit BRCA1 nucleotide 234T>G/c.115T>G (p.Cys39Gly) founder mutation, which at that time was the only disease-causing BRCA1/BRCA2 mutation identified in this population. Here, we describe the identification of a novel disease-causing BRCA1 nucleotide 4803delCC/c.4684delCC mutation in a Greenlandic Inuit with ovarian cancer. The mutation introduces a frameshift and a premature stop at codon 1572. We have also identified a BRCA1 nucleotide 249T>A/c.130T>A (p.Cys44Ser) mutation in another Greenlandic individual with ovarian cancer. This patient share a 1-2 Mb genomic fragment, containing the BRCA1 gene, with four Danish families harbouring the same mutation, suggesting that the 249T>A/c.130T>A (p.Cys44Ser) mutation originates from a Danish ancestor. We conclude that screening of Greenlandic Inuits with high risk of breast or ovarian cancer should include sequencing of the entire BRCA1 gene.
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Affiliation(s)
- Thomas V O Hansen
- Department of Clinical Biochemistry, Rigshospitalet, Blegdamsvej 9, 2100 Copenhagen, Denmark.
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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: 98] [Impact Index Per Article: 7.0] [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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