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Fabi A, Cortesi L, Duranti S, Cordisco EL, Di Leone A, Terribile D, Paris I, de Belvis AG, Orlandi A, Marazzi F, Muratore M, Garganese G, Fuso P, Paoletti F, Dell'Aquila R, Minucci A, Scambia G, Franceschini G, Masetti R, Genuardi M. Multigenic panels in breast cancer: Clinical utility and management of patients with pathogenic variants other than BRCA1/2. Crit Rev Oncol Hematol 2024; 201:104431. [PMID: 38977141 DOI: 10.1016/j.critrevonc.2024.104431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 06/14/2024] [Accepted: 06/24/2024] [Indexed: 07/10/2024] Open
Abstract
Multigene panels can analyze high and moderate/intermediate penetrance genes that predispose to breast cancer (BC), providing an opportunity to identify at-risk individuals within affected families. However, considering the complexity of different pathogenic variants and correlated clinical manifestations, a multidisciplinary team is needed to effectively manage BC. A classification of pathogenic variants included in multigene panels was presented in this narrative review to evaluate their clinical utility in BC. Clinical management was discussed for each category and focused on BC, including available evidence regarding the multidisciplinary and integrated management of patients with BC. The integration of both genetic testing and counseling is required for customized decisions in therapeutic strategies and preventative initiatives, as well as for a defined multidisciplinary approach, considering the continuous evolution of guidelines and research in the field.
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Affiliation(s)
- Alessandra Fabi
- Precision Medicine Unit in Senology, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Laura Cortesi
- Department of Oncology and Haematology, Modena Hospital University, Modena Italy (Cortesi)
| | - Simona Duranti
- Scientific Directorate, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy.
| | - Emanuela Lucci Cordisco
- Section of Genomic Medicine, Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, Rome, Italy; Medical Genetics Unit, Department of Laboratory and Infectious Sciences, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Alba Di Leone
- Breast Unit, Department of Woman and Child's Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Daniela Terribile
- Breast Unit, Department of Woman and Child's Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Ida Paris
- Division of Gynecologic Oncology, Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Antonio Giulio de Belvis
- Value Lab, Faculty of Economics, Università Cattolica del Sacro Cuore, Rome, Italy; Critical Pathways and Outcomes Evaluation Unit, Fondazione Policlinico Universitario "A. Gemelli", IRCCS, Rome, Italy
| | - Armando Orlandi
- Unit of Oncology, Comprehensive Cancer Centre, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Fabio Marazzi
- UOC Oncological Radiotherapy, Department of Diagnostic Imaging, Radiation Oncology and Haematology, Fondazione Policlinico Universitario A. Gemelli, IRCCS, Roma, Italy
| | - Margherita Muratore
- Division of Gynecologic Oncology, Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy; IRCCS Istituto Romagnolo per lo Studio dei Tumori "Dino Amadori"
| | - Giorgia Garganese
- Division of Gynecologic Oncology, Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy; Section of Obstetrics and Gynecology, Department of Woman and Child Health and Public Health, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Paola Fuso
- Division of Gynecologic Oncology, Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Filippo Paoletti
- Critical Pathways and Outcomes Evaluation Unit, Fondazione Policlinico Universitario "A. Gemelli", IRCCS, Rome, Italy
| | - Rossella Dell'Aquila
- Critical Pathways and Outcomes Evaluation Unit, Fondazione Policlinico Universitario "A. Gemelli", IRCCS, Rome, Italy
| | - Angelo Minucci
- Genomics Core Facility, Gemelli Science and Technology Park (GSTeP), Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Giovanni Scambia
- Division of Gynecologic Oncology, Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy; Catholic University of the Sacred Heart, Rome, Italy
| | - Gianluca Franceschini
- Breast Unit, Department of Woman and Child's Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy; Catholic University of the Sacred Heart, Rome, Italy
| | - Riccardo Masetti
- Breast Unit, Department of Woman and Child's Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy; Catholic University of the Sacred Heart, Rome, Italy
| | - Maurizio Genuardi
- Section of Genomic Medicine, Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, Rome, Italy; Medical Genetics Unit, Department of Laboratory and Infectious Sciences, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
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2
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Khan MA, Varma AK. In silico and structure-based assessment to classify VUS identified in the α-helical domain of BRCA2. J Biomol Struct Dyn 2023; 41:9879-9889. [PMID: 36404616 DOI: 10.1080/07391102.2022.2148127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 11/10/2022] [Indexed: 11/22/2022]
Abstract
Breast cancer type 2 susceptibility (BRCA2) protein plays a crucial role in DNA double-strand breaks repair mechanism by homologous recombination. Pathogenic mutations in the BRCA2 gene confer an increased risk of hereditary breast and ovarian cancer (HBOC). Different missense mutations are identified from a larger cohort of patient populations in the BRCA2. However, most missense mutations are classified as 'Variants of Uncertain Significance' (VUS) due to a lack of data from structural, functional, and clinical assessments. Therefore, this study focused on assessing VUS identified in the α-helical domain of h-BRCA2 using different in silico tools and structure-based molecular dynamics simulation. A total of 286 identified VUS were evaluated using Align-GVGD, PROVEAN and PANTHER servers and 18 variants were predicted to be pathogenic. Further, out of 18 variants analyzed using the ConSurf server, 16 variants were found to be evolutionary conserved. These 16 conserved variants were submitted to PremPS and Dynamut server to assess the effect of the mutation at the protein structure level; 12 mutations were predicted to have a destabilizing effect on the native protein structure. Finally, molecular dynamics simulations revealed 5 variants BRCA2 Cys2646Tyr, Asp2665Val, Trp2619Arg, Trp2619Ser and Tyr2660Cys can alter the folding pattern and need further validation using in vitro, structural and in vivo studies to classify as pathogenic.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mudassar Ali Khan
- Tata Memorial Centre, Advanced Centre for Treatment, Research and Education in Cancer, Navi Mumbai, Maharashtra, India
- Homi Bhabha National Institute, Mumbai, Maharashtra, India
| | - Ashok K Varma
- Tata Memorial Centre, Advanced Centre for Treatment, Research and Education in Cancer, Navi Mumbai, Maharashtra, India
- Homi Bhabha National Institute, Mumbai, Maharashtra, India
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3
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De Paolis E, Paris I, Tilocca B, Roncada P, Foca L, Tiberi G, D’Angelo T, Pavese F, Muratore M, Carbognin L, Garganese G, Masetti R, Di Leone A, Fabi A, Scambia G, Urbani A, Generali D, Minucci A, Santonocito C. Assessing the pathogenicity of BRCA1/2 variants of unknown significance: Relevance and challenges for breast cancer precision medicine. Front Oncol 2023; 12:1053035. [PMID: 36741700 PMCID: PMC9891372 DOI: 10.3389/fonc.2022.1053035] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 12/28/2022] [Indexed: 01/19/2023] Open
Abstract
Introduction Breast cancer (BC) is the leading cause of cancer-related death in women worldwide. Pathogenic variants in BRCA1 and BRCA2 genes account for approximately 50% of all hereditary BC, with 60-80% of patients characterized by Triple Negative Breast Cancer (TNBC) at an early stage phenotype. The identification of a pathogenic BRCA1/2 variant has important and expanding roles in risk-reducing surgeries, treatment planning, and familial surveillance. Otherwise, finding unclassified Variants of Unknown Significance (VUS) limits the clinical utility of the molecular test, leading to an "imprecise medicine". Methods We reported the explanatory example of the BRCA1 c.5057A>C, p.(His1686Pro) VUS identified in a patient with TNBC. We integrated data from family history and clinic-pathological evaluations, genetic analyses, and bioinformatics in silico investigations to evaluate the VUS classification. Results Our evaluation posed evidences for the pathogenicity significance of the investigated VUS: 1) association of the BRCA1 variant to cancer-affected members of the family; 2) absence of another high-risk mutation; 3) multiple indirect evidences derived from gene and protein structural analysis. Discussion In line with the ongoing efforts to uncertain variants classification, we speculated about the relevance of an in-depth assessment of pathogenicity of BRCA1/2 VUS for a personalized management of patients with BC. We underlined that the efficient integration of clinical data with the widest number of supporting molecular evidences should be adopted for the proper management of patients, with the final aim of effectively guide the best prognostic and therapeutic paths.
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Affiliation(s)
- Elisa De Paolis
- Clinical Chemistry, Biochemistry and Molecular Biology Operations (UOC), Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy,Department of Basic Biotechnological Sciences, Intensivological and Perioperative Clinics, Catholic University of Sacred Heart, Rome, Italy
| | - Ida Paris
- Division of Oncological Gynecology, Department of Women’s and Children’s Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy,*Correspondence: Ida Paris,
| | - Bruno Tilocca
- Department of Health Science, University “Magna Graecia” of Catanzaro, Catanzaro, Italy
| | - Paola Roncada
- Department of Health Science, University “Magna Graecia” of Catanzaro, Catanzaro, Italy
| | - Laura Foca
- Clinical Chemistry, Biochemistry and Molecular Biology Operations (UOC), Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Giordana Tiberi
- Division of Oncological Gynecology, Department of Women’s and Children’s Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Tatiana D’Angelo
- Division of Oncological Gynecology, Department of Women’s and Children’s Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Francesco Pavese
- Division of Oncological Gynecology, Department of Women’s and Children’s Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Margherita Muratore
- Division of Oncological Gynecology, Department of Women’s and Children’s Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Luisa Carbognin
- Division of Oncological Gynecology, Department of Women’s and Children’s Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Giorgia Garganese
- Gynaecology and Breast Care Center, Mater Olbia Hospital, Olbia, Italy,Dipartimento Universitario Scienze della Vita e Sanità Pubblica, Sezione di Ginecologia ed Ostetricia, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Riccardo Masetti
- Division of Oncological Gynecology, Department of Women’s and Children’s Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Alba Di Leone
- Division of Oncological Gynecology, Department of Women’s and Children’s Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Alessandra Fabi
- Unit of Precision Medicine in Breast Cancer, Scientific Directorate, Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli, IRCCS, Rome, Italy
| | - Giovanni Scambia
- Division of Oncological Gynecology, Department of Women’s and Children’s Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Andrea Urbani
- Clinical Chemistry, Biochemistry and Molecular Biology Operations (UOC), Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy,Department of Basic Biotechnological Sciences, Intensivological and Perioperative Clinics, Catholic University of Sacred Heart, Rome, Italy
| | - Daniele Generali
- Department of Medical, Surgery and Health Sciences, University of Trieste, Trieste, Italy
| | - Angelo Minucci
- Departmental Unit of Molecular and Genomic Diagnostics, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Concetta Santonocito
- Clinical Chemistry, Biochemistry and Molecular Biology Operations (UOC), Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy,Department of Basic Biotechnological Sciences, Intensivological and Perioperative Clinics, Catholic University of Sacred Heart, Rome, Italy
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Nepomuceno TC, Dos Santos APP, Fernandes VC, Elias ABR, Gomes TT, Suarez-Kurtz G, Iversen ES, Couch FJ, Monteiro ANA, Carvalho MA. Assessment of small in-frame indels and C-terminal nonsense variants of BRCA1 using a validated functional assay. Sci Rep 2022; 12:16203. [PMID: 36171434 PMCID: PMC9519549 DOI: 10.1038/s41598-022-20500-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 09/14/2022] [Indexed: 11/29/2022] Open
Abstract
BRCA1 (Breast Cancer 1, early onset) is linked to breast and ovarian cancer predisposition. Still, the risks conferred by a significant portion of BRCA1 variants identified in the population remains unknown. Most of these variants of uncertain significance are missense alterations. However, the functional implications of small in-frame deletions and/or insertions (indels) are also difficult to predict. Our group has previously evaluated the functional impact of 347 missense variants using an extensively validated transcriptional activity assay. Here we show a systematic assessment of 30 naturally occurring in-frame indels located at the C-terminal region of BRCA1. We identified positions sensitive and tolerant to alterations, expanding the knowledge of structural determinants of BRCA1 function. We further designed and assessed the impact of four single codon deletions in the tBRCT linker region and six nonsense variants at the C-terminus end of BRCA1. Amino acid substitutions, deletions or insertions in the disordered region do not significantly impact activity and are not likely to constitute pathogenic alleles. On the other hand, a sizeable fraction of in-frame indels at the BRCT domain significantly impact function. We then use a Bayesian integrative statistical model to derive the probability of pathogenicity for each variant. Our data highlights the importance of assessing the impact of small in-frame indels in BRCA1 to improve risk assessment and clinical decisions for carriers.
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Affiliation(s)
- Thales C Nepomuceno
- Divisão de Pesquisa Clínica, Instituto Nacional de Câncer, Rio de Janeiro, 20230-130, Brazil.,Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL, 33612, USA
| | - Ana P P Dos Santos
- Divisão de Pesquisa Clínica, Instituto Nacional de Câncer, Rio de Janeiro, 20230-130, Brazil
| | - Vanessa C Fernandes
- Divisão de Pesquisa Clínica, Instituto Nacional de Câncer, Rio de Janeiro, 20230-130, Brazil
| | - Anna B R Elias
- Divisão de Pesquisa Clínica, Instituto Nacional de Câncer, Rio de Janeiro, 20230-130, Brazil
| | - Thiago T Gomes
- Divisão de Pesquisa Clínica, Instituto Nacional de Câncer, Rio de Janeiro, 20230-130, Brazil
| | - Guilherme Suarez-Kurtz
- Divisão de Pesquisa Clínica, Instituto Nacional de Câncer, Rio de Janeiro, 20230-130, Brazil
| | - Edwin S Iversen
- Department of Statistical Science, Duke University, Durham, NC, 27708, USA
| | | | - Alvaro N A Monteiro
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL, 33612, USA.
| | - Marcelo A Carvalho
- Divisão de Pesquisa Clínica, Instituto Nacional de Câncer, Rio de Janeiro, 20230-130, Brazil. .,Laboratório de Genética Molecular, Instituto Federal Do Rio de Janeiro, Rua Senador Furtado, Campus Rio de Janeiro121, Rio de Janeiro, RJ, 20270-021, Brazil.
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5
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Khan MA, Siddiqui MQ, Kuligina E, Varma AK. Evaluation of conformational transitions of h-BRCA2 functional domain and unclassified variant Arg2502Cys using multimodal approach. Int J Biol Macromol 2022; 209:716-724. [PMID: 35413318 DOI: 10.1016/j.ijbiomac.2022.04.049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 04/02/2022] [Accepted: 04/06/2022] [Indexed: 11/26/2022]
Abstract
Breast cancer type 2 susceptibility (BRCA2) protein plays an essential role in the repair mechanism of DNA double-strand breaks and interstrand cross-links by Homologous recombination. Germline mutations identified in the BRCA2 gene confer an increased risk of hereditary breast and ovarian cancer. Missense mutations are identified all over the gene, including the DNA binding region of BRCA2 that interacts with FANCD2. However, the majority of these missense mutations are classified as 'Variants of Uncertain Significance' due to a lack of structural, functional and clinical correlations. Therefore, multi-disciplinary in-silico, in-vitro and biophysical approaches have been explored to characterize an unclassified missense mutation, BRCA2 Arg2502Cys, identified from a case-control study. Circular-dichroism and Fluorescence spectroscopy show that the Arg2502Cys mutation in hBRCA2 (residues 2350-2545) decreases the α-helical/β-sheet propensity of the wild-type protein and perturb the tertiary structure conformation. Molecular dynamics simulations revealed alteration in the intramolecular H-bonds, overall compactness and stability of the hydrophobic core were observed in the mutant protein. Principle component analysis indicated that Arg2502Cys mutant exhibited comparatively large conformational transitions and periodic fluctuation. Therefore, to our conclusion, BRCA2 Arg2502Cys mutant perturbed the structural integrity and conformational dynamics of BRCA2.
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Affiliation(s)
- Mudassar Ali Khan
- Advanced Centre for Treatment, Research and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra 410210, India; Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai 400094, India
| | - M Quadir Siddiqui
- Advanced Centre for Treatment, Research and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra 410210, India; Present address: Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada
| | - Ekaterina Kuligina
- N.N. Petrov Institute of Oncology, Laboratory of Molecular Oncology, RU-197758, Pesochny-2, St.-Petersburg, Russia
| | - Ashok K Varma
- Advanced Centre for Treatment, Research and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra 410210, India; Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai 400094, India.
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6
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Bellè F, Mercatanti A, Lodovichi S, Congregati C, Guglielmi C, Tancredi M, Caligo MA, Cervelli T, Galli A. Validation and Data-Integration of Yeast-Based Assays for Functional Classification of BRCA1 Missense Variants. Int J Mol Sci 2022; 23:ijms23074049. [PMID: 35409408 PMCID: PMC8999655 DOI: 10.3390/ijms23074049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 04/01/2022] [Accepted: 04/03/2022] [Indexed: 11/23/2022] Open
Abstract
Germline mutations in the BRCA1 gene have been reported to increase the lifetime risk of developing breast and/or ovarian cancer (BOC). By new sequencing technologies, numerous variants of uncertain significance (VUS) are identified. It is mandatory to develop new tools to evaluate their functional impact and pathogenicity. As the expression of pathogenic BRCA1 variants in Saccharomyces cerevisiae increases the frequency of intra- and inter-chromosomal homologous recombination (HR), and gene reversion (GR), we validated the two HR and the GR assays by testing 23 benign and 23 pathogenic variants and compared the results with those that were obtained in the small colony phenotype (SCP) assay, an additional yeast-based assay, that was validated previously. We demonstrated that they scored high accuracy, sensitivity, and sensibility. By using a classifier that was based on majority of voting, we have integrated data from HR, GR, and SCP assays and developed a reliable method, named yBRCA1, with high sensitivity to obtain an accurate VUS functional classification (benign or pathogenic). The classification of BRCA1 variants, important for assessing the risk of developing BOC, is often difficult to establish with genetic methods because they occur rarely in the population. This study provides a new tool to get insights on the functional impact of the BRCA1 variants.
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Affiliation(s)
- Francesca Bellè
- Yeast Genetics and Genomics, Laboratory of Functional Genetics and Genomics, Institute of Clinical Physiology, CNR via Moruzzi 1, 56125 Pisa, Italy; (F.B.); (A.M.); (S.L.); (T.C.)
| | - Alberto Mercatanti
- Yeast Genetics and Genomics, Laboratory of Functional Genetics and Genomics, Institute of Clinical Physiology, CNR via Moruzzi 1, 56125 Pisa, Italy; (F.B.); (A.M.); (S.L.); (T.C.)
| | - Samuele Lodovichi
- Yeast Genetics and Genomics, Laboratory of Functional Genetics and Genomics, Institute of Clinical Physiology, CNR via Moruzzi 1, 56125 Pisa, Italy; (F.B.); (A.M.); (S.L.); (T.C.)
| | - Caterina Congregati
- Division of Internal Medicine, University Hospital of Pisa, 56125 Pisa, Italy;
| | - Chiara Guglielmi
- Molecular Genetics Unit, Department of Laboratory Medicine, University Hospital of Pisa, 56125 Pisa, Italy; (C.G.); (M.T.)
| | - Mariella Tancredi
- Molecular Genetics Unit, Department of Laboratory Medicine, University Hospital of Pisa, 56125 Pisa, Italy; (C.G.); (M.T.)
| | - Maria Adelaide Caligo
- Molecular Genetics Unit, Department of Laboratory Medicine, University Hospital of Pisa, 56125 Pisa, Italy; (C.G.); (M.T.)
- Correspondence: (M.A.C.); (A.G.)
| | - Tiziana Cervelli
- Yeast Genetics and Genomics, Laboratory of Functional Genetics and Genomics, Institute of Clinical Physiology, CNR via Moruzzi 1, 56125 Pisa, Italy; (F.B.); (A.M.); (S.L.); (T.C.)
| | - Alvaro Galli
- Yeast Genetics and Genomics, Laboratory of Functional Genetics and Genomics, Institute of Clinical Physiology, CNR via Moruzzi 1, 56125 Pisa, Italy; (F.B.); (A.M.); (S.L.); (T.C.)
- Correspondence: (M.A.C.); (A.G.)
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7
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Bellcross CA. Hereditary Breast and Ovarian Cancer. Obstet Gynecol Clin North Am 2022; 49:117-147. [DOI: 10.1016/j.ogc.2021.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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8
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OUP accepted manuscript. FEMS Yeast Res 2022; 22:6574410. [DOI: 10.1093/femsyr/foac021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 03/15/2022] [Accepted: 04/11/2022] [Indexed: 11/14/2022] Open
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9
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Ozgencil M, Barwell J, Tischkowitz M, Izatt L, Kesterton I, Simpson M, Sharpe P, de Sepulveda P, Voisset E, Solomon E. Assessing BRCA1 activity in DNA damage repair using human induced pluripotent stem cells as an approach to assist classification of BRCA1 variants of uncertain significance. PLoS One 2021; 16:e0260852. [PMID: 34855882 PMCID: PMC8638976 DOI: 10.1371/journal.pone.0260852] [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: 09/01/2021] [Accepted: 11/18/2021] [Indexed: 12/24/2022] Open
Abstract
Establishing a universally applicable protocol to assess the impact of BRCA1 variants of uncertain significance (VUS) expression is a problem which has yet to be resolved despite major progresses have been made. The numerous difficulties which must be overcome include the choices of cellular models and functional assays. We hypothesised that the use of induced pluripotent stem (iPS) cells might facilitate the standardisation of protocols for classification, and could better model the disease process. We generated eight iPS cell lines from patient samples expressing either BRCA1 pathogenic variants, non-pathogenic variants, or BRCA1 VUSs. The impact of these variants on DNA damage repair was examined using a ɣH2AX foci formation assay, a Homologous Repair (HR) reporter assay, and a chromosome abnormality assay. Finally, all lines were tested for their ability to differentiate into mammary lineages in vitro. While the results obtained from the two BRCA1 pathogenic variants were consistent with published data, some other variants exhibited differences. The most striking of these was the BRCA1 variant Y856H (classified as benign), which was unexpectedly found to present a faulty HR repair pathway, a finding linked to the presence of an additional variant in the ATM gene. Finally, all lines were able to differentiate first into mammospheres, and then into more advanced mammary lineages expressing luminal- or basal-specific markers. This study stresses that BRCA1 genetic analysis alone is insufficient to establish a reliable and functional classification for assessment of clinical risk, and that it cannot be performed without considering the other genetic aberrations which may be present in patients. The study also provides promising opportunities for elucidating the physiopathology and clinical evolution of breast cancer, by using iPS cells.
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Affiliation(s)
- Meryem Ozgencil
- Department of Medical & Molecular Genetics, King’s College London, Faculty of Life Sciences & Medicine, London, United Kingdom
| | - Julian Barwell
- Department of Genetics and Genome Biology at the University of Leicester, Leicester, United Kingdom
| | - Marc Tischkowitz
- Department of Medical Genetics, National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, United Kingdom
| | - Louise Izatt
- Clinical Genetics, Guy’s and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Ian Kesterton
- Cytogenetics Laboratory, Viapath Analytics, Guy’s and St. Thomas’ NHS Foundation Trust, Guy’s Hospital, London, United Kingdom
| | - Michael Simpson
- Department of Medical & Molecular Genetics, King’s College London, Faculty of Life Sciences & Medicine, London, United Kingdom
| | - Paul Sharpe
- Department of Craniofacial Development & Stem Cell Biology, King’s College London, London, United Kingdom
| | - Paulo de Sepulveda
- Signaling Hematopoiesis and Mechanism of Oncogenesis Lab, INSERM, CNRS, Institut Paoli-Calmettes, CRCM, Aix Marseille University, Marseille, France
| | - Edwige Voisset
- Department of Medical & Molecular Genetics, King’s College London, Faculty of Life Sciences & Medicine, London, United Kingdom
- * E-mail: (EV); (ES)
| | - Ellen Solomon
- Department of Medical & Molecular Genetics, King’s College London, Faculty of Life Sciences & Medicine, London, United Kingdom
- * E-mail: (EV); (ES)
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Biancolella M, Ouédraogo NLM, Zongo N, Zohoncon TM, Testa B, Rizzacasa B, Latini A, Conte C, Compaore TR, Ouedraogo CMRN, Traore SS, Simpore J, Novelli G. Breast cancer in West Africa: molecular analysis of BRCA genes in early-onset breast cancer patients in Burkina Faso. Hum Genomics 2021; 15:65. [PMID: 34717758 PMCID: PMC8557567 DOI: 10.1186/s40246-021-00365-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 10/17/2021] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Breast cancer (BC) is the most commonly diagnosed cancer and the second leading cause of cancer-related deaths among women in Africa after cervical cancer. Even if the epidemiological data are now aligned with those relating to industrialized countries, the knowledge concerning breast cancer in Africa, particularly in Western Africa, still lack clinical data, medical treatments, and the evaluation of genetic and non-genetic factors implicated in the etiology of the disease. The early onset and the aggressiveness of diagnosed breast cancers in patients of African ancestry strongly suggest that the genetic risk factor may be a key component, but so far, very few studies on the impact of germ line mutations in breast cancer in Africa have been conducted, with negative consequences on prevention, awareness and patient management. Through Next Generation sequencing (NGS), we analyzed all of the coding regions and the exon-intron junctions of BRCA1 and BRCA2 genes-the two most important genes in hereditary breast cancer-in fifty-one women from Burkina Faso with early onset of breast cancer with or without a family history. RESULTS We identified six different pathogenic mutations (three in BRCA1, three in BRCA2), two of which were recurrent in eight unrelated women. Furthermore, we identified, in four other patients, two variants of uncertain clinical significance (VUS) and two variants never previously described in literature, although one of them is present in the dbSNP database. CONCLUSIONS This is the first study in which the entire coding sequence of BRCA genes has been analyzed through Next Generation Sequencing in Burkinabe young women with breast cancer. Our data support the importance of genetic risk factors in the etiology of breast cancer in this population and suggest the necessity to improve the genetic cancer risk assessment. Furthermore, the identification of the most frequent mutations of BRCA1 and BRCA2 in the population of Burkina Faso will allow the development of an inexpensive genetic test for the identification of subjects at high genetic cancer risk, which could be used to design personalized therapeutic protocols.
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Affiliation(s)
- Michela Biancolella
- Department of Biology, University of Rome “Tor Vergata”, 00133 Rome, Italy
- Medical Genetics Laboratory, Tor Vergata Hospital, Rome, Italy
| | - Nabonswindé Lamoussa Marie Ouédraogo
- University Saint Thomas d’Aquin of Ouagadougou, Saint Camille Hospital, 06 BP: 10212, Ouagadougou 06, Burkina Faso
- Research Centre (CERBA), P.O. Box 364, Ouagadougou 01, Burkina Faso
| | - Nayi Zongo
- Department of Visceral Surgery of Yalgado, Ouédraogo University Hospital (CHUYO), Joseph KI ZERBO University of Ouagadougou, Ouagadougou, Burkina Faso
| | - Théodora Mahoukèdè Zohoncon
- University Saint Thomas d’Aquin of Ouagadougou, Saint Camille Hospital, 06 BP: 10212, Ouagadougou 06, Burkina Faso
- Research Centre (CERBA), P.O. Box 364, Ouagadougou 01, Burkina Faso
| | - Barbara Testa
- Department of Biomedicine and Prevention, University of Rome “Tor Vergata”, 00133 Rome, Italy
| | - Barbara Rizzacasa
- Department of Biomedicine and Prevention, University of Rome “Tor Vergata”, 00133 Rome, Italy
| | - Andrea Latini
- Department of Biomedicine and Prevention, University of Rome “Tor Vergata”, 00133 Rome, Italy
| | - Chiara Conte
- Medical Genetics Laboratory, Tor Vergata Hospital, Rome, Italy
| | | | - Charlemagne Marie Rayang-Newendé Ouedraogo
- University Saint Thomas d’Aquin of Ouagadougou, Saint Camille Hospital, 06 BP: 10212, Ouagadougou 06, Burkina Faso
- Department of the Gynecology of Bogodogo University Hospital, Joseph KI ZERBO University of Ouagadougou, 04 BP 8201, Ouagadougou 04, Burkina Faso
| | - Si Simon Traore
- University Saint Thomas d’Aquin of Ouagadougou, Saint Camille Hospital, 06 BP: 10212, Ouagadougou 06, Burkina Faso
| | - Jacques Simpore
- University Saint Thomas d’Aquin of Ouagadougou, Saint Camille Hospital, 06 BP: 10212, Ouagadougou 06, Burkina Faso
- Research Centre (CERBA), P.O. Box 364, Ouagadougou 01, Burkina Faso
| | - Giuseppe Novelli
- Medical Genetics Laboratory, Tor Vergata Hospital, Rome, Italy
- Department of Biomedicine and Prevention, University of Rome “Tor Vergata”, 00133 Rome, Italy
- IRCCS Neuromed, Pozzilli, IS Italy
- Department of Pharmacology, School of Medicine, University of Nevada, Reno, NV 89557 USA
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11
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Julien M, Ghouil R, Petitalot A, Caputo SM, Carreira A, Zinn-Justin S. Intrinsic Disorder and Phosphorylation in BRCA2 Facilitate Tight Regulation of Multiple Conserved Binding Events. Biomolecules 2021; 11:1060. [PMID: 34356684 PMCID: PMC8301801 DOI: 10.3390/biom11071060] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/09/2021] [Accepted: 07/13/2021] [Indexed: 12/26/2022] Open
Abstract
The maintenance of genome integrity in the cell is an essential process for the accurate transmission of the genetic material. BRCA2 participates in this process at several levels, including DNA repair by homologous recombination, protection of stalled replication forks, and cell division. These activities are regulated and coordinated via cell-cycle dependent modifications. Pathogenic variants in BRCA2 cause genome instability and are associated with breast and/or ovarian cancers. BRCA2 is a very large protein of 3418 amino acids. Most well-characterized variants causing a strong predisposition to cancer are mutated in the C-terminal 700 residues DNA binding domain of BRCA2. The rest of the BRCA2 protein is predicted to be disordered. Interactions involving intrinsically disordered regions (IDRs) remain difficult to identify both using bioinformatics tools and performing experimental assays. However, the lack of well-structured binding sites provides unique functional opportunities for BRCA2 to bind to a large set of partners in a tightly regulated manner. We here summarize the predictive and experimental arguments that support the presence of disorder in BRCA2. We describe how BRCA2 IDRs mediate self-assembly and binding to partners during DNA double-strand break repair, mitosis, and meiosis. We highlight how phosphorylation by DNA repair and cell-cycle kinases regulate these interactions. We finally discuss the impact of cancer-associated variants on the function of BRCA2 IDRs and more generally on genome stability and cancer risk.
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Affiliation(s)
- Manon Julien
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, 91190 Gif-sur-Yvette, France; (M.J.); (R.G.)
- L’Institut de Biologie Intégrative de la Cellule (I2BC), UMR 9198, Paris-Saclay University, 91190 Gif-sur-Yvette, France;
| | - Rania Ghouil
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, 91190 Gif-sur-Yvette, France; (M.J.); (R.G.)
- L’Institut de Biologie Intégrative de la Cellule (I2BC), UMR 9198, Paris-Saclay University, 91190 Gif-sur-Yvette, France;
| | - Ambre Petitalot
- Service de Génétique, Unité de Génétique Constitutionnelle, Institut Curie, 75005 Paris, France; (A.P.); (S.M.C.)
- Institut Curie, Paris Sciences Lettres Research University, 75005 Paris, France
| | - Sandrine M. Caputo
- Service de Génétique, Unité de Génétique Constitutionnelle, Institut Curie, 75005 Paris, France; (A.P.); (S.M.C.)
- Institut Curie, Paris Sciences Lettres Research University, 75005 Paris, France
| | - Aura Carreira
- L’Institut de Biologie Intégrative de la Cellule (I2BC), UMR 9198, Paris-Saclay University, 91190 Gif-sur-Yvette, France;
- Institut Curie, Paris Sciences Lettres Research University, 75005 Paris, France
- Unité Intégrité du Génome, ARN et Cancer, Institut Curie, CNRS UMR3348, 91405 Orsay, France
| | - Sophie Zinn-Justin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, 91190 Gif-sur-Yvette, France; (M.J.); (R.G.)
- L’Institut de Biologie Intégrative de la Cellule (I2BC), UMR 9198, Paris-Saclay University, 91190 Gif-sur-Yvette, France;
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12
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Andreassen PR, Seo J, Wiek C, Hanenberg H. Understanding BRCA2 Function as a Tumor Suppressor Based on Domain-Specific Activities in DNA Damage Responses. Genes (Basel) 2021; 12:genes12071034. [PMID: 34356050 PMCID: PMC8307705 DOI: 10.3390/genes12071034] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/23/2021] [Accepted: 06/29/2021] [Indexed: 01/14/2023] Open
Abstract
BRCA2 is an essential genome stability gene that has various functions in cells, including roles in homologous recombination, G2 checkpoint control, protection of stalled replication forks, and promotion of cellular resistance to numerous types of DNA damage. Heterozygous mutation of BRCA2 is associated with an increased risk of developing cancers of the breast, ovaries, pancreas, and other sites, thus BRCA2 acts as a classic tumor suppressor gene. However, understanding BRCA2 function as a tumor suppressor is severely limited by the fact that ~70% of the encoded protein has not been tested or assigned a function in the cellular DNA damage response. Remarkably, even the specific role(s) of many known domains in BRCA2 are not well characterized, predominantly because stable expression of the very large BRCA2 protein in cells, for experimental purposes, is challenging. Here, we review what is known about these domains and the assay systems that are available to study the cellular roles of BRCA2 domains in DNA damage responses. We also list criteria for better testing systems because, ultimately, functional assays for assessing the impact of germline and acquired mutations identified in genetic screens are important for guiding cancer prevention measures and for tailored cancer treatments.
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Affiliation(s)
- Paul R. Andreassen
- Division of Experimental Hematology and Cancer Biology, Cancer and Blood Diseases Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA;
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
- Correspondence: ; Tel.: +1-(513)-636-0499
| | - Joonbae Seo
- Division of Experimental Hematology and Cancer Biology, Cancer and Blood Diseases Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA;
| | - Constanze Wiek
- Department of Otorhinolaryngology and Head/Neck Surgery, Heinrich Heine University, 40225 Düsseldorf, Germany; (C.W.); (H.H.)
| | - Helmut Hanenberg
- Department of Otorhinolaryngology and Head/Neck Surgery, Heinrich Heine University, 40225 Düsseldorf, Germany; (C.W.); (H.H.)
- Department of Pediatrics III, Children’s Hospital, University of Duisburg-Essen, 45122 Essen, Germany
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13
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Zhang Y, Park JY, Zhang F, Olson SH, Orlow I, Li Y, Kurtz RC, Ladanyi M, Chen J, Toland AE, Zhang L, Andreassen PR. The p.Ser64Leu and p.Pro104Leu missense variants of PALB2 identified in familial pancreatic cancer patients compromise the DNA damage response. Hum Mutat 2020; 42:150-163. [PMID: 33169439 DOI: 10.1002/humu.24133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 09/17/2020] [Accepted: 11/01/2020] [Indexed: 11/12/2022]
Abstract
PALB2 has been identified as a breast and pancreatic cancer susceptibility gene. Utilizing a targeted sequencing approach, we discovered two novel germline missense PALB2 variants c.191C>T and c.311C>T, encoding p.Ser64Leu and p.Pro104Leu, respectively, in individuals in a pancreatic cancer registry. No missense PALB2 variants from familial pancreatic cancer patients, and few PALB2 variants overall, have been functionally characterized. Given the known role of PALB2, we tested the impact of p.Ser64Leu and p.Pro104Leu variants on DNA damage responses. Neither p.Ser64Leu nor p.Pro104Leu have clear effects on interactions with BRCA1 and KEAP1, which are mediated by adjacent motifs in PALB2. However, both variants are associated with defective recruitment of PALB2, and the RAD51 recombinase downstream, to DNA damage foci. Furthermore, p.Ser64Leu and p.Pro104Leu both largely compromise DNA double-strand break-initiated homologous recombination, and confer increased cellular sensitivity to ionizing radiation (IR) and the poly (ADP-ribose) polymerase (PARP) inhibitor Olaparib. Taken together, our results represent the first demonstration of functionally deleterious PALB2 missense variants associated with familial pancreatic cancer and of deleterious variants in the N-terminus outside of the coiled-coil domain. Furthermore, our results suggest the possibility of personalized treatments, using IR or PARP inhibitor, of pancreatic and other cancers that carry a deleterious PALB2 variant.
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Affiliation(s)
- Yue Zhang
- Division of Experimental Hematology and Cancer Biology, Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA.,Peking Union Medical College Hospital, Chinese Academy of Medical Sciences - Peking Union Medical College, Beijing, China
| | - Jung-Young Park
- Division of Experimental Hematology and Cancer Biology, Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Fan Zhang
- Division of Experimental Hematology and Cancer Biology, Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Sara H Olson
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Irene Orlow
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Yirong Li
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Robert C Kurtz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jie Chen
- Peking Union Medical College Hospital, Chinese Academy of Medical Sciences - Peking Union Medical College, Beijing, China
| | - Amanda E Toland
- Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA.,Division of Human Genetics, Department of Internal Medicine, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Liying Zhang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles (UCLA), Los Angeles, California, USA
| | - Paul R Andreassen
- Division of Experimental Hematology and Cancer Biology, Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
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14
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Biswas K, Lipton GB, Stauffer S, Sullivan T, Cleveland L, Southon E, Reid S, Magidson V, Iversen ES, Sharan SK. A computational model for classification of BRCA2 variants using mouse embryonic stem cell-based functional assays. NPJ Genom Med 2020; 5:52. [PMID: 33293522 PMCID: PMC7722754 DOI: 10.1038/s41525-020-00158-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 10/29/2020] [Indexed: 12/12/2022] Open
Abstract
Sequencing-based genetic tests to identify individuals at increased risk of hereditary breast and ovarian cancers have resulted in the identification of more than 40,000 sequence variants of BRCA1 and BRCA2. A majority of these variants are considered to be variants of uncertain significance (VUS) because their impact on disease risk remains unknown, largely due to lack of sufficient familial linkage and epidemiological data. Several assays have been developed to examine the effect of VUS on protein function, which can be used to assess their impact on cancer susceptibility. In this study, we report the functional characterization of 88 BRCA2 variants, including several previously uncharacterized variants, using a well-established mouse embryonic stem cell (mESC)-based assay. We have examined their ability to rescue the lethality of Brca2 null mESC as well as sensitivity to six DNA damaging agents including ionizing radiation and a PARP inhibitor. We have also examined the impact of BRCA2 variants on splicing. In addition, we have developed a computational model to determine the probability of impact on function of the variants that can be used for risk assessment. In contrast to the previous VarCall models that are based on a single functional assay, we have developed a new platform to analyze the data from multiple functional assays separately and in combination. We have validated our VarCall models using 12 known pathogenic and 10 neutral variants and demonstrated their usefulness in determining the pathogenicity of BRCA2 variants that are listed as VUS or as variants with conflicting functional interpretation.
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Affiliation(s)
- Kajal Biswas
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Gary B Lipton
- Department of Statistical Science, Duke University, Durham, NC, 27708, USA
| | - Stacey Stauffer
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Teresa Sullivan
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Linda Cleveland
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Eileen Southon
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Susan Reid
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Valentin Magidson
- Optical Microscopy and Analysis Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Edwin S Iversen
- Department of Statistical Science, Duke University, Durham, NC, 27708, USA.
| | - Shyam K Sharan
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA.
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15
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Waisertreiger I, Barlow J. Fragile site instability: measuring more than breaks. Oncoscience 2020; 7:60-67. [PMID: 33195735 PMCID: PMC7640903 DOI: 10.18632/oncoscience.513] [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: 05/13/2020] [Accepted: 05/17/2020] [Indexed: 12/23/2022] Open
Abstract
Genome instability is not only a hallmark of cancer, it is necessary for its initiation and evolution, and naturally accumulates as cells age. Replication stress is a potent source of genome instability found in many tumor types [1]. Chromosomal fragile sites are genomic loci highly prone to DNA damage specifically from replication stress and are frequently mutated in cancer [2-4]2-4]. While tracking the origin of individual mutations has proved challenging, measuring DNA damage and repair at endogenous sites can offer key insights into understanding the etiology of cancer. In the past 15 years, the causal link between replication stress, oncogene activation, and tumor initiation and evolution has become increasingly clear [1, 5-9]. Replication-associated damage accumulates at early stages of tumorigenesis and may promote further transformation. Studying the causes and consequences of fragile site instability can offer a window into the earliest stages of carcinogenesis [10-13]. In particular, fragile site studies will help us understand the molecular underpinnings influencing the frequency of DNA breakage, successful repair processes suppressing genome instability, and unsuccessful repair leading to mutations and chromosome rearrangements. Of these, measuring successful repair is the most challenging as it leaves little evidence behind.
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Affiliation(s)
- Irina Waisertreiger
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA, USA
| | - Jacqueline Barlow
- Department of Microbiology and Molecular Genetics & Genome Center, University of California, Davis, CA, USA
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16
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Nepomuceno TC, Carvalho MA, Rodrigue A, Simard J, Masson JY, Monteiro ANA. PALB2 Variants: Protein Domains and Cancer Susceptibility. Trends Cancer 2020; 7:188-197. [PMID: 33139182 DOI: 10.1016/j.trecan.2020.10.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 10/05/2020] [Accepted: 10/06/2020] [Indexed: 01/09/2023]
Abstract
Since its discovery, partner and localizer of breast cancer 2 (BRCA2) (PALB2) has emerged as a major tumor suppressor gene linked to breast cancer (BC), pancreatic cancer (PC), and ovarian cancer (OC) susceptibility. Its protein product plays a pivotal role in the maintenance of genome integrity. Here we discuss the first functional evaluation of a large set of PALB2 missense variants of uncertain significance (VUSs). Assessment of 136 VUSs interrogating a range of PALB2 biological functions resulted in the identification of 15 variants with consistent loss of function across different assays. All loss-of-function variants are located at the PALB2 coiled coil (CC) or at the WD40 domain, highlighting the importance of modular domains mechanistically involved in the DNA damage response (DDR) and pinpointing their roles in tumor suppression.
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Affiliation(s)
- Thales C Nepomuceno
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA; Divisão de Pesquisa Clínica, Instituto Nacional de Câncer, Rio de Janeiro 20230-130, Brazil
| | - Marcelo A Carvalho
- Divisão de Pesquisa Clínica, Instituto Nacional de Câncer, Rio de Janeiro 20230-130, Brazil; Instituto Federal do Rio de Janeiro (IFRJ), Rio de Janeiro 20270-021, Brazil
| | - Amélie Rodrigue
- Genome Stability Laboratory, CHU de Québec Research Center, HDQ Pavilion, Oncology Division, 9 McMahon, Quebec City, QC G1R 3S3, Canada
| | - Jacques Simard
- Genomics Center, CHU de Quebec-Université Laval Research Center, Quebec City, QC, Canada
| | - Jean-Yves Masson
- Genome Stability Laboratory, CHU de Québec Research Center, HDQ Pavilion, Oncology Division, 9 McMahon, Quebec City, QC G1R 3S3, Canada; Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Quebec City, QC G1V 0A6, Canada
| | - Alvaro N A Monteiro
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA.
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17
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Lyra PCM, Nepomuceno TC, de Souza MLM, Machado GF, Veloso MF, Henriques TB, Dos Santos DZ, Ribeiro IG, Ribeiro RS, Rangel LBA, Richardson M, Iversen ES, Goldgar D, Couch FJ, Carvalho MA, Monteiro ANA. Integration of functional assay data results provides strong evidence for classification of hundreds of BRCA1 variants of uncertain significance. Genet Med 2020; 23:306-315. [PMID: 33087888 PMCID: PMC7862071 DOI: 10.1038/s41436-020-00991-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 09/21/2020] [Accepted: 09/22/2020] [Indexed: 12/13/2022] Open
Abstract
Purpose BRCA1 pathogenic variant heterozygotes are at a substantially increased risk for breast and ovarian cancer. The widespread uptake of testing has led to a significant increase in the detection of missense variants in BRCA1, the vast majority of which are variants of uncertain clinical significance (VUS), posing a challenge to genetic counseling. Here, we harness a wealth of functional data for thousands of variants to aid in variant classification. Methods We have collected, curated, and harmonized functional data for 2701 missense variants representing 24.5% of possible missense variants in BRCA1. Results were harmonized across studies by converting data into binary categorical variables (functional impact versus no functional impact). Using a panel of reference variants we identified a subset of assays with high sensitivity and specificity (≥80%) and apply the American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) variant interpretation guidelines to assign evidence criteria for classification. Results Integration of data from validated assays provided ACMG/AMP evidence criteria in favor of pathogenicity for 297 variants or against pathogenicity for 2058 representing 96.2% of current VUS functionally assessed. We also explore discordant results and identify limitations in the approach. Conclusion High quality functional data are available for BRCA1 missense variants and provide evidence for classification of 2355 VUS according to their pathogenicity.
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Affiliation(s)
- Paulo C M Lyra
- Biotechnology/RENORBIO Program, Federal University of Espírito Santo, Vitória, ES, Brazil
| | - Thales C Nepomuceno
- Instituto Nacional de Câncer, Programa de Pesquisa Clínica, Rio de Janeiro, Brazil.,Divisão de Pesquisa Clínica, Instituto Nacional de Câncer, Rio de Janeiro, Brazil.,Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Marcele L M de Souza
- Biotechnology/RENORBIO Program, Federal University of Espírito Santo, Vitória, ES, Brazil
| | - Géssica F Machado
- Biotechnology/RENORBIO Program, Federal University of Espírito Santo, Vitória, ES, Brazil
| | - Mariana F Veloso
- Biotechnology/RENORBIO Program, Federal University of Espírito Santo, Vitória, ES, Brazil
| | - Taciane B Henriques
- Biotechnology/RENORBIO Program, Federal University of Espírito Santo, Vitória, ES, Brazil
| | - Diandra Z Dos Santos
- Biotechnology/RENORBIO Program, Federal University of Espírito Santo, Vitória, ES, Brazil
| | - Iuly G Ribeiro
- Biotechnology/RENORBIO Program, Federal University of Espírito Santo, Vitória, ES, Brazil
| | - Roberto S Ribeiro
- Biotechnology/RENORBIO Program, Federal University of Espírito Santo, Vitória, ES, Brazil
| | - Leticia B A Rangel
- Biotechnology/RENORBIO Program, Federal University of Espírito Santo, Vitória, ES, Brazil
| | | | - Edwin S Iversen
- Department of Statistical Science, Duke University, Durham, NC, USA
| | - David Goldgar
- Department of Dermatology, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | | | - Marcelo A Carvalho
- Instituto Nacional de Câncer, Programa de Pesquisa Clínica, Rio de Janeiro, Brazil.,Instituto Federal do Rio de Janeiro-IFRJ, Rio de Janeiro, Brazil
| | - Alvaro N A Monteiro
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA.
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18
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High-throughput functional evaluation of BRCA2 variants of unknown significance. Nat Commun 2020; 11:2573. [PMID: 32444794 PMCID: PMC7244490 DOI: 10.1038/s41467-020-16141-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 04/17/2020] [Indexed: 12/14/2022] Open
Abstract
Numerous nontruncating missense variants of the BRCA2 gene have been identified, but there is a lack of convincing evidence, such as familial data, demonstrating their clinical relevance and they thus remain unactionable. To assess the pathogenicity of variants of unknown significance (VUSs) within BRCA2, here we develop a method, the MANO-B method, for high-throughput functional evaluation utilizing BRCA2-deficient cells and poly (ADP-ribose) polymerase (PARP) inhibitors. The estimated sensitivity and specificity of this assay compared to those of the International Agency for Research on Cancer classification system is 95% and 95% (95% confidence intervals: 77–100% and 82–99%), respectively. We classify the functional impact of 186 BRCA2 VUSs with our computational pipeline, resulting in the classification of 126 variants as normal/likely normal, 23 as intermediate, and 37 as abnormal/likely abnormal. We further describe a simplified, on-demand annotation system that could be used as a companion diagnostic for PARP inhibitors in patients with unknown BRCA2 VUSs. Many germline variants are found in the BRCA2 gene, some of which pre-dispose women to breast and ovarian cancer. Here, the authors develop a method to determine the functional significance of BRCA2 variants and show that it is comparable to the IARC system of classifying variants.
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19
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Bypass of premature stop codons and generation of functional BRCA2 by exon skipping. J Hum Genet 2020; 65:805-809. [PMID: 32393813 DOI: 10.1038/s10038-020-0768-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 04/08/2020] [Accepted: 04/21/2020] [Indexed: 11/08/2022]
Abstract
A pathogenic mutation in BRCA2 significantly increases the risk of breast and ovarian cancers making it imperative to examine the functional consequences of variants of uncertain clinical significance. Variants that are predicted to result in a truncated protein are unambiguously classified as pathogenic. We have previously shown how a pathogenic splice site variant known to generate a premature termination codon (PTC) in exon 9 and a nonsense mutation at exon 7, can generate functional BRCA2 by skipping exons 4-7 and restoring the reading frame. Using a well-established mouse embryonic stem cell-based assay, we functionally characterize here one splice site mutation and 11 pathogenic BRCA2 variants that are either nonsense mutation or generate PTC in different exons ranging from exons 4 to 7. Our study shows that five variants can restore the open reading frame by exon skipping and generate a functional protein. This suggests further need to exercise prudence when classifying clearly pathogenic variants.
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20
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Variants of uncertain significance in the era of high-throughput genome sequencing: a lesson from breast and ovary cancers. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2020; 39:46. [PMID: 32127026 PMCID: PMC7055088 DOI: 10.1186/s13046-020-01554-6] [Citation(s) in RCA: 101] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 02/26/2020] [Indexed: 02/06/2023]
Abstract
The promising expectations about personalized medicine have opened the path to routine large-scale sequencing and increased the importance of genetic counseling for hereditary cancers, among which hereditary breast and ovary cancers (HBOC) have a major impact. High-throughput sequencing, or Next-Generation Sequencing (NGS), has improved cancer patient management, ameliorating diagnosis and treatment decisions. In addition to its undeniable clinical utility, NGS is also unveiling a large number of variants that we are still not able to clearly define and classify, the variants of uncertain significance (VUS), which account for about 40% of total variants. At present, VUS use in the clinical context is challenging. Medical reports may omit this kind of data and, even when included, they limit the clinical utility of genetic information. This has prompted the scientific community to seek easily applicable tests to accurately classify VUS and increase the amount of usable information from NGS data. In this review, we will focus on NGS and classification systems for VUS investigation, with particular attention on HBOC-related genes and in vitro functional tests developed for ameliorating and accelerating variant classification in cancer.
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Systematic misclassification of missense variants in BRCA1 and BRCA2 "coldspots". Genet Med 2020; 22:825-830. [PMID: 31911673 PMCID: PMC7200594 DOI: 10.1038/s41436-019-0740-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 12/19/2019] [Indexed: 12/15/2022] Open
Abstract
Purpose Guidelines for variant interpretation incorporate variant hotspots in critical functional domains as evidence for pathogenicity (e.g., PM1 and PP2), but do not use “coldspots,” that is, regions without essential functions that tolerate variation, as evidence a variant is benign. To improve variant classification we evaluated BRCA1 and BRCA2 missense variants reported in ClinVar to identify regions where pathogenic missenses are extremely infrequent, defined as coldspots. Methods We used Bayesian approaches to model variant classification in these regions. Results BRCA1 exon 11 (~60% of the coding sequence), and BRCA2 exons 10 and 11 (~65% of the coding sequence), are coldspots. Of 89 pathogenic (P) or likely pathogenic (LP) missense variants in BRCA1, none are in exon 11 (odds <0.01, 95% confidence interval [CI] 0.0–0.01). Of 34 P or LP missense variants in BRCA2, none are in exons 10–11 (odds <0.01, 95% CI 0.0–0.01). More than half of reported missense variants of uncertain significance (VUS) in BRCA1 and BRCA2 are in coldspots (3115/5301 = 58.8%). Reclassifying these 3115 VUS as likely benign would substantially improve variant classification. Conclusion In BRCA1 and BRCA2 coldspots, missense variants are very unlikely to be pathogenic. Classification schemes that incorporate coldspots can reduce the number of VUS and mitigate risks from reporting benign variation as VUS.
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Impact of proactive high-throughput functional assay data on BRCA1 variant interpretation in 3684 patients with breast or ovarian cancer. J Hum Genet 2020; 65:209-220. [PMID: 31907386 DOI: 10.1038/s10038-019-0713-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 12/12/2019] [Accepted: 12/16/2019] [Indexed: 11/08/2022]
Abstract
The clinical utility of BRCA1/2 genotyping was recently extended from the selection of subjects at high risk for hereditary breast and ovary cancer to the identification of candidates for poly (ADP-ribose) polymerase (PARP) inhibitor treatment. This underscores the importance of accurate interpretation of BRCA1/2 genetic variants and of reducing the number of variants of uncertain significance (VUSs). Two recent studies by Findlay et al. and Starita et al. introduced high-throughput functional assays, and proactively analyzed variants in specific regions regardless of whether they had been previously observed. We retrospectively reviewed all BRCA1 and BRCA2 germline genetic test reports from patients with breast or ovarian cancer examined at Asan Medical Center (Seoul, Korea) between September 2011 and December 2018. Variants were assigned pathogenic or benign strong evidence codes according to the functional classification and were reclassified according to the ACMG/AMP 2015 guidelines. Among 3684 patients with available BRCA1 and BRCA2 germline genetic test reports, 429 unique variants (181 from BRCA1) were identified. Of 34 BRCA1 variants intersecting with the data reported by Findlay et al., three missense single-nucleotide variants from four patients (0.11%, 4/3684) were reclassified from VUSs to likely pathogenic variants. Four variants scored as functional were reclassified into benign or likely benign variants. Three variants that overlapped with the data reported by Starita et al. could not be reclassified. In conclusion, proactive high-throughput functional study data are useful for the reclassification of clinically observed VUSs. Integrating additional evidence, including functional assay results, may help reduce the number of VUSs.
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23
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Esposito MV, Minopoli G, Esposito L, D'Argenio V, Di Maggio F, Sasso E, D'Aiuto M, Zambrano N, Salvatore F. A Functional Analysis of the Unclassified Pro2767Ser BRCA2 Variant Reveals Its Potential Pathogenicity that Acts by Hampering DNA Binding and Homology-Mediated DNA Repair. Cancers (Basel) 2019; 11:E1454. [PMID: 31569370 PMCID: PMC6826418 DOI: 10.3390/cancers11101454] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 09/16/2019] [Accepted: 09/25/2019] [Indexed: 12/12/2022] Open
Abstract
BRCA1 and BRCA2 are the genes most frequently associated with hereditary breast and ovarian cancer (HBOC). They are crucial for the maintenance of genome stability, particularly in the homologous recombination-mediated repair pathway of DNA double-strand breaks (HR-DSBR). Widespread BRCA1/2 next-generation sequencing (NGS) screening has revealed numerous variants of uncertain significance. Assessing the clinical significance of these variants is challenging, particularly regarding the clinical management of patients. Here, we report the functional characterization of the unclassified BRCA2 c.8299C > T variant, identified in a young breast cancer patient during BRCA1/2 NGS screening. This variant causes the change of Proline 2767 to Serine in the DNA binding domain (DBD) of the BRCA2 protein, necessary for the loading of RAD51 on ssDNA during the HR-DSBR. Our in silico analysis and 3D-structure modeling predicted that the p.Pro2767Ser substitution is likely to alter the BRCA2 DBD structure and function. Therefore, to evaluate the functional impact of the p.Pro2767Ser variant, we used a minigene encoding a truncated protein that contains the BRCA2 DBD and the nearby nuclear localization sequence. We found that the ectopically expressed truncated protein carrying the normal DBD, which retains the DNA binding function and lacks the central RAD51 binding domain, interferes with endogenous wild-type BRCA2 mediator functions in the HR-DSBR. We also demonstrated that the BRCA2 Pro2767Ser DBD is unable to compete with endogenous BRCA2 DNA binding, thereby suggesting that the p.Pro2767Ser substitution in the full-length protein causes the functional loss of BRCA2. Consequently, our data suggest that the p.Pro2767Ser variant should be considered pathogenic, thus supporting a revision of the ClinVar interpretation. Moreover, our experimental strategy could be a valid method with which to preliminarily evaluate the pathogenicity of the unclassified BRCA2 germline variants in the DBD and their risk of predisposing to HBOC.
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Affiliation(s)
- Maria Valeria Esposito
- CEINGE-Biotecnologie Avanzate, 8014 Naples, Italy.
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, 80131 Naples, Italy.
| | - Giuseppina Minopoli
- CEINGE-Biotecnologie Avanzate, 8014 Naples, Italy.
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, 80131 Naples, Italy.
| | - Luciana Esposito
- Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16, I-80134 Naples, Italy.
| | - Valeria D'Argenio
- CEINGE-Biotecnologie Avanzate, 8014 Naples, Italy.
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, 80131 Naples, Italy.
| | - Federica Di Maggio
- CEINGE-Biotecnologie Avanzate, 8014 Naples, Italy.
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, 80131 Naples, Italy.
| | - Emanuele Sasso
- CEINGE-Biotecnologie Avanzate, 8014 Naples, Italy.
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, 80131 Naples, Italy.
| | - Massimiliano D'Aiuto
- Department of Senology, Istituto Nazionale Tumori-IRCCS Fondazione Pascale, 80131 Naples, Italy.
| | - Nicola Zambrano
- CEINGE-Biotecnologie Avanzate, 8014 Naples, Italy.
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, 80131 Naples, Italy.
| | - Francesco Salvatore
- CEINGE-Biotecnologie Avanzate, 8014 Naples, Italy.
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, 80131 Naples, Italy.
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25
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Identifying a BRCA2 c.5722_5723del mutation in a Han-Chinese family with breast cancer. Biosci Rep 2019; 39:BSR20182471. [PMID: 30940775 PMCID: PMC6488854 DOI: 10.1042/bsr20182471] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 03/19/2019] [Accepted: 04/01/2019] [Indexed: 12/17/2022] Open
Abstract
Breast cancer (BC) is the most common female cancer found worldwide. It is responsible for 25% of all cancer patients in females. Hereditary BC accounts for about 5–10% of all BC cases. The breast cancer 1 gene (BRCA1) and the breast cancer 2 gene (BRCA2) are the two most-studied BC susceptibility genes. Genetic testing for disease-causing mutations in BRCA1, BRCA2, and other BC susceptibility genes is strongly recommended for members of families having a BC family history. The present study found a heterozygous c.5722_5723del mutation in the BRCA2 exon 11 of a large Han-Chinese BC family using whole exome sequencing and Sanger sequencing. It may cause DNA double-strand breaks repair dysfunction by disturbing homologous recombination, further resulting in BC. The study findings may help supplement and further improve genetic testing strategies and BC risk estimation methodologies in China.
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26
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Macedo GS, Alemar B, Ashton-Prolla P. Reviewing the characteristics of BRCA and PALB2-related cancers in the precision medicine era. Genet Mol Biol 2019; 42:215-231. [PMID: 31067289 PMCID: PMC6687356 DOI: 10.1590/1678-4685-gmb-2018-0104] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 10/24/2018] [Indexed: 12/24/2022] Open
Abstract
Germline mutations in BRCA1 and BRCA2 (BRCA) genes confer high risk of developing cancer, especially breast and ovarian tumors. Since the cloning of these tumor suppressor genes over two decades ago, a significant amount of research has been done. Most recently, monoallelic loss-of-function mutations in PALB2 have also been shown to increase the risk of breast cancer. The identification of BRCA1, BRCA2 and PALB2 as proteins involved in DNA double-strand break repair by homologous recombination and of the impact of complete loss of BRCA1 or BRCA2 within tumors have allowed the development of novel therapeutic approaches for patients with germline or somatic mutations in said genes. Despite the advances, especially in the clinical use of PARP inhibitors, key gaps remain. Now, new roles for BRCA1 and BRCA2 are emerging and old concepts, such as the classical two-hit hypothesis for tumor suppression, have been questioned, at least for some BRCA functions. Here aspects regarding cancer predisposition, cellular functions, histological and genomic findings in BRCA and PALB2-related tumors will be presented, in addition to an up-to-date review of the evolution and challenges in the development and clinical use of PARP inhibitors.
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Affiliation(s)
- Gabriel S Macedo
- Post-Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.,Precision Medicine Program, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
| | - Barbara Alemar
- Post-Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Patricia Ashton-Prolla
- Post-Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.,Precision Medicine Program, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
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27
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Genetic Testing to Guide Risk-Stratified Screens for Breast Cancer. J Pers Med 2019; 9:jpm9010015. [PMID: 30832243 PMCID: PMC6462925 DOI: 10.3390/jpm9010015] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 02/18/2019] [Accepted: 02/22/2019] [Indexed: 12/14/2022] Open
Abstract
Breast cancer screening modalities and guidelines continue to evolve and are increasingly based on risk factors, including genetic risk and a personal or family history of cancer. Here, we review genetic testing of high-penetrance hereditary breast and ovarian cancer genes, including BRCA1 and BRCA2, for the purpose of identifying high-risk individuals who would benefit from earlier screening and more sensitive methods such as magnetic resonance imaging. We also consider risk-based screening in the general population, including whether every woman should be genetically tested for high-risk genes and the potential use of polygenic risk scores. In addition to enabling early detection, the results of genetic screens of breast cancer susceptibility genes can be utilized to guide decision-making about when to elect prophylactic surgeries that reduce cancer risk and the choice of therapeutic options. Variants of uncertain significance, especially missense variants, are being identified during panel testing for hereditary breast and ovarian cancer. A finding of a variant of uncertain significance does not provide a basis for increased cancer surveillance or prophylactic procedures. Given that variant classification is often challenging, we also consider the role of multifactorial statistical analyses by large consortia and functional tests for this purpose.
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28
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Fernandes VC, Golubeva VA, Di Pietro G, Shields C, Amankwah K, Nepomuceno TC, de Gregoriis G, Abreu RBV, Harro C, Gomes TT, Silva RF, Suarez-Kurtz G, Couch FJ, Iversen ES, Monteiro ANA, Carvalho MA. Impact of amino acid substitutions at secondary structures in the BRCT domains of the tumor suppressor BRCA1: Implications for clinical annotation. J Biol Chem 2019; 294:5980-5992. [PMID: 30765603 DOI: 10.1074/jbc.ra118.005274] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 02/06/2019] [Indexed: 01/07/2023] Open
Abstract
Genetic testing for BRCA1, a DNA repair protein, can identify carriers of pathogenic variants associated with a substantially increased risk for breast and ovarian cancers. However, an association with increased risk is unclear for a large fraction of BRCA1 variants present in the human population. Most of these variants of uncertain clinical significance lead to amino acid changes in the BRCA1 protein. Functional assays are valuable tools to assess the potential pathogenicity of these variants. Here, we systematically probed the effects of substitutions in the C terminus of BRCA1: the N- and C-terminal borders of its tandem BRCT domain, the BRCT-[N-C] linker region, and the α1 and α'1 helices in BRCT-[N] and -[C]. Using a validated transcriptional assay based on a fusion of the GAL4 DNA-binding domain to the BRCA1 C terminus (amino acids 1396-1863), we assessed the functional impact of 99 missense variants of BRCA1. We include the data obtained for these 99 missense variants in a joint analysis to generate the likelihood of pathogenicity for 347 missense variants in BRCA1 using VarCall, a Bayesian integrative statistical model. The results from this analysis increase our understanding of BRCA1 regions less tolerant to changes, identify functional borders of structural domains, and predict the likelihood of pathogenicity for 98% of all BRCA1 missense variants in this region recorded in the population. This knowledge will be critical for improving risk assessment and clinical treatment of carriers of BRCA1 variants.
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Affiliation(s)
- Vanessa C Fernandes
- From the Instituto Nacional de Câncer, Programa de Pesquisa Clínica, Rio de Janeiro, Brazil 20231-050
| | - Volha A Golubeva
- the Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612
| | - Giuliano Di Pietro
- the Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612; the Universidade Federal de Sergipe, Campus São Cristóvão, Brazil 49100-000
| | - Cara Shields
- the Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612
| | - Kwabena Amankwah
- the Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612
| | - Thales C Nepomuceno
- From the Instituto Nacional de Câncer, Programa de Pesquisa Clínica, Rio de Janeiro, Brazil 20231-050; the Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612
| | - Giuliana de Gregoriis
- From the Instituto Nacional de Câncer, Programa de Pesquisa Clínica, Rio de Janeiro, Brazil 20231-050
| | - Renata B V Abreu
- From the Instituto Nacional de Câncer, Programa de Pesquisa Clínica, Rio de Janeiro, Brazil 20231-050
| | - Carly Harro
- the Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612; the Department of Cell Biology, Microbiology, College of Arts and Sciences, University of South Florida Cancer Biology Ph.D. Program, Tampa, Florida 33612
| | - Thiago T Gomes
- the Instituto Federal do Rio de Janeiro, Rio de Janeiro 20270-021, Brazil
| | - Ricceli F Silva
- the Instituto Federal do Rio de Janeiro, Rio de Janeiro 20270-021, Brazil
| | - Guilherme Suarez-Kurtz
- From the Instituto Nacional de Câncer, Programa de Pesquisa Clínica, Rio de Janeiro, Brazil 20231-050
| | - Fergus J Couch
- the Department of Laboratory Medicine, Mayo Clinic, Rochester, Minnesota 55905
| | - Edwin S Iversen
- the Department of Statistics, Duke University, Durham, North Carolina 27710
| | - Alvaro N A Monteiro
- the Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612.
| | - Marcelo A Carvalho
- From the Instituto Nacional de Câncer, Programa de Pesquisa Clínica, Rio de Janeiro, Brazil 20231-050.
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29
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Zemanek T, Melichar B, Lovecek M, Soucek P, Mohelnikova-Duchonova B. Biomarkers and pathways of chemoresistance and chemosensitivity for personalized treatment of pancreatic adenocarcinoma. Pharmacogenomics 2018; 20:113-127. [PMID: 30539680 DOI: 10.2217/pgs-2018-0073] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Pancreatic carcinoma is usually diagnosed late when treatment options are limited and is considered a chemo-resistant malignancy. However, early stage, good performance status and specific patient subgroup are thought to have a more favorable prognosis. Search for novel molecular biomarkers, which could predict treatment resistance, represents a major opportunity, but also a challenge in further research. This review summarizes most aspects of individualized therapy of pancreatic cancer including promising biomarkers, BRCA-deficient pancreatic cancer and its etiology. It may be estimated that nearly a third of metastatic pancreatic ductal adenocarcinoma patients could benefit from treatment other than gold standard chemotherapy. Thus, other aspects of an individualized approach concerning the main factors for the choice of the best therapy for individual pancreatic cancer patient (surgery and chemotherapy), as well as the future directions (target therapy and immunotherapy), are also addressed.
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Affiliation(s)
- Tomas Zemanek
- Department of Oncology, Faculty of Medicine & Dentistry, Palacky University Olomouc, University Hospital Olomouc, Czech Republic
| | - Bohuslav Melichar
- Department of Oncology, Faculty of Medicine & Dentistry, Palacky University Olomouc, University Hospital Olomouc, Czech Republic.,Institute of Molecular & Translational Medicine, Faculty of Medicine & Dentistry, Palacky University, Olomouc, Czech Republic
| | - Martin Lovecek
- Department of Surgery I, Faculty of Medicine & Dentistry, Palacky University, Olomouc, University Hospital Olomouc, Czech Republic
| | - Pavel Soucek
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Beatrice Mohelnikova-Duchonova
- Department of Oncology, Faculty of Medicine & Dentistry, Palacky University Olomouc, University Hospital Olomouc, Czech Republic.,Institute of Molecular & Translational Medicine, Faculty of Medicine & Dentistry, Palacky University, Olomouc, Czech Republic
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30
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Rashed WM, Saad A, Al-Husseini M, Galal AM, Ismael AM, Al-Tayep AM, El Shafie A, Ali MA, Alfaar AS. Incidence of adrenal gland tumor as a second primary malignancy: SEER-based study. Endocr Connect 2018; 7:EC-18-0304. [PMID: 30139816 PMCID: PMC6198183 DOI: 10.1530/ec-18-0304] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 08/02/2018] [Accepted: 08/20/2018] [Indexed: 11/10/2022]
Abstract
PURPOSE Advances in cancer treatment achieved during the past decades have resulted in increased survival of most pediatric and adult patients that suffered from different adrenal tumor types. This article reviews the incidence and survival of adrenal gland tumors as second primary tumors, according to data from the Surveillance, Epidemiology, and End Results (SEER) database. METHOD The SEER 13 Registries Database from 1992 to 2013 was used. All primary cancer sites were selected using the Multiple Primary Standardized Incidence Ratios (MP-SIR) session. RESULTS Data for a total of 2,887,468 persons with cancer were reviewed. 117 of whom had suffered second primary adrenal tumors. The overall standardized incidence ratio (SIR) of adrenal gland tumor as a second primary was 1.49. A high incidence ratio of the event was also detected in specific primary tumor sites: hypopharynx (Observed/Expected(O/E) = 44.59); other endocrine tissue (including the thymus) (O/E=38.27); chronic myeloid leukemia (O/E=11.15); small intestine (O/E=8.86); liver (O/E=8.74); stomach (O/E=4.95); nodal NHL (O/E=3.79); kidney and renal pelvis (O/E=3.19); and breast (O/E=1.78). CONCLUSION The underlying shared mechanisms should be investigated between adrenal tumors and hypopharyngeal, endocrine and other tumors. Racial disparity is an important challenge in cancer treatment at US and should be taken into consideration in the design of cancer prevention programs. This could be achieved through follow-up programs at specialized national cancer networks, especially for rare tumors like adrenal gland.
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Affiliation(s)
- Wafaa M Rashed
- Research DepartmentChildren’s Cancer Hospital Egypt (CCHE-57357), Cairo, Egypt
- Armed Forces College of MedicineCairo, Egypt
| | - Anas Saad
- Faculty of MedicineDamascus University, Damascus, Syria
| | | | | | | | | | | | | | - Ahmad Samir Alfaar
- Charité – Universitätsmedizin Berlin, Campus Virchow Klinikum, Ophthalmology DepartmentBerlin, Germany
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Cusin I, Teixeira D, Zahn-Zabal M, Rech de Laval V, Gleizes A, Viassolo V, Chappuis PO, Hutter P, Bairoch A, Gaudet P. A new bioinformatics tool to help assess the significance of BRCA1 variants. Hum Genomics 2018; 12:36. [PMID: 29996917 PMCID: PMC6042458 DOI: 10.1186/s40246-018-0168-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 06/25/2018] [Indexed: 12/23/2022] Open
Abstract
Background Germline pathogenic variants in the breast cancer type 1 susceptibility gene BRCA1 are associated with a 60% lifetime risk for breast and ovarian cancer. This overall risk estimate is for all BRCA1 variants; obviously, not all variants confer the same risk of developing a disease. In cancer patients, loss of BRCA1 function in tumor tissue has been associated with an increased sensitivity to platinum agents and to poly-(ADP-ribose) polymerase (PARP) inhibitors. For clinical management of both at-risk individuals and cancer patients, it would be important that each identified genetic variant be associated with clinical significance. Unfortunately for the vast majority of variants, the clinical impact is unknown. The availability of results from studies assessing the impact of variants on protein function may provide insight of crucial importance. Results and conclusion We have collected, curated, and structured the molecular and cellular phenotypic impact of 3654 distinct BRCA1 variants. The data was modeled in triple format, using the variant as a subject, the studied function as the object, and a predicate describing the relation between the two. Each annotation is supported by a fully traceable evidence. The data was captured using standard ontologies to ensure consistency, and enhance searchability and interoperability. We have assessed the extent to which functional defects at the molecular and cellular levels correlate with the clinical interpretation of variants by ClinVar submitters. Approximately 30% of the ClinVar BRCA1 missense variants have some molecular or cellular assay available in the literature. Pathogenic variants (as assigned by ClinVar) have at least some significant functional defect in 94% of testable cases. For benign variants, 77% of ClinVar benign variants, for which neXtProt Cancer variant portal has data, shows either no or mild experimental functional defects. While this does not provide evidence for clinical interpretation of variants, it may provide some guidance for variants of unknown significance, in the absence of more reliable data. The neXtProt Cancer variant portal (https://www.nextprot.org/portals/breast-cancer) contains over 6300 observations at the molecular and/or cellular level for BRCA1 variants.
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Affiliation(s)
- Isabelle Cusin
- CALIPHO group, SIB Swiss Institute of Bioinformatics, 1211, Geneva 4, Switzerland
| | - Daniel Teixeira
- CALIPHO group, SIB Swiss Institute of Bioinformatics, 1211, Geneva 4, Switzerland
| | - Monique Zahn-Zabal
- CALIPHO group, SIB Swiss Institute of Bioinformatics, 1211, Geneva 4, Switzerland
| | - Valentine Rech de Laval
- CALIPHO group, SIB Swiss Institute of Bioinformatics, 1211, Geneva 4, Switzerland.,Department of Human Protein Sciences, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Anne Gleizes
- CALIPHO group, SIB Swiss Institute of Bioinformatics, 1211, Geneva 4, Switzerland
| | - Valeria Viassolo
- Oncogenetics and Cancer Prevention Unit, Division of Oncology, University Hospitals of Geneva, 1205, Geneva, Switzerland
| | - Pierre O Chappuis
- Oncogenetics and Cancer Prevention Unit, Division of Oncology, University Hospitals of Geneva, 1205, Geneva, Switzerland.,Division of Genetic Medicine, University Hospitals of Geneva, 1205, Geneva, Switzerland
| | - Pierre Hutter
- Sophia Genetics, Rue du Centre 172, 1025, Saint Sulpice, Switzerland
| | - Amos Bairoch
- CALIPHO group, SIB Swiss Institute of Bioinformatics, 1211, Geneva 4, Switzerland.,Department of Human Protein Sciences, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Pascale Gaudet
- CALIPHO group, SIB Swiss Institute of Bioinformatics, 1211, Geneva 4, Switzerland. .,Department of Human Protein Sciences, Faculty of Medicine, University of Geneva, Geneva, Switzerland.
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Strande NT, Brnich SE, Roman TS, Berg JS. Navigating the nuances of clinical sequence variant interpretation in Mendelian disease. Genet Med 2018; 20:918-926. [PMID: 29988079 PMCID: PMC6679919 DOI: 10.1038/s41436-018-0100-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 06/12/2018] [Indexed: 12/24/2022] Open
Abstract
Understanding clinical genetic test results in the era of next-generation sequencing has become increasingly complex, necessitating clear and thorough guidelines for sequence variant interpretation. To meet this need the American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP) published guidelines for a systematic approach for sequence variant interpretation in 2015. This framework is intended to be adaptable to any Mendelian condition, promoting transparency and consistency in variant interpretation, yet its comprehensive nature yields important challenges and caveats that end users must understand. In this review, we address some of these nuances and discuss the evolving efforts to refine and adapt this framework. We also consider the added complexity of distinguishing between variant-level interpretations and case-level conclusions, particularly in the context of the large gene panel approach to clinical diagnostics.
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Affiliation(s)
- Natasha T Strande
- Department of Pathology and Laboratory Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Sarah E Brnich
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Tamara S Roman
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jonathan S Berg
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
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