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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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Yadav S, Couch FJ, Domchek SM. Germline Genetic Testing for Hereditary Breast and Ovarian Cancer: Current Concepts in Risk Evaluation. Cold Spring Harb Perspect Med 2024; 14:a041318. [PMID: 38151326 PMCID: PMC11293548 DOI: 10.1101/cshperspect.a041318] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
Our understanding of hereditary breast and ovarian cancer has significantly improved over the past two decades. In addition to BRCA1/2, pathogenic variants in several other DNA-repair genes have been shown to increase the risks of breast and ovarian cancer. The magnitude of cancer risk is impacted not only by the gene involved, but also by family history of cancer, polygenic risk scores, and, in certain genes, pathogenic variant type or location. While estimates of breast and ovarian cancer risk associated with pathogenic variants are available, these are predominantly based on studies of high-risk populations with young age at diagnosis of cancer, multiple primary cancers, or family history of cancer. More recently, breast cancer risk for germline pathogenic variant carriers has been estimated from population-based studies. Here, we provide a review of the field of germline genetic testing and risk evaluation for hereditary breast and ovarian cancers in high-risk and population-based settings.
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Affiliation(s)
- Siddhartha Yadav
- Department of Oncology, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Fergus J Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55901, USA
| | - Susan M Domchek
- Basser Center for BRCA, Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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Stella S, Vitale SR, Massimino M, Martorana F, Tornabene I, Tomarchio C, Drago M, Pavone G, Gorgone C, Barone C, Bianca S, Manzella L. In Silico Prediction of BRCA1 and BRCA2 Variants with Conflicting Clinical Interpretation in a Cohort of Breast Cancer Patients. Genes (Basel) 2024; 15:943. [PMID: 39062721 PMCID: PMC11276437 DOI: 10.3390/genes15070943] [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: 06/28/2024] [Revised: 07/10/2024] [Accepted: 07/11/2024] [Indexed: 07/28/2024] Open
Abstract
Germline BRCA1/2 alteration has been linked to an increased risk of hereditary breast and ovarian cancer syndromes. As a result, genetic testing, based on NGS, allows us to identify a high number of variants of uncertain significance (VUS) or conflicting interpretation of pathogenicity (CIP) variants. The identification of CIP/VUS is often considered inconclusive and clinically not actionable for the patients' and unaffected carriers' management. In this context, their assessment and classification remain a significant challenge. The aim of the study was to investigate whether the in silico prediction tools (PolyPhen-2, SIFT, Mutation Taster and PROVEAN) could predict the potential clinical impact and significance of BRCA1/2 CIP/VUS alterations, eventually impacting the clinical management of Breast Cancer subjects. In a cohort of 860 BC patients, 10.6% harbored BRCA1 or BRCA2 CIP/VUS alterations, mostly observed in BRCA2 sequences (85%). Among them, forty-two out of fifty-five alterations were predicted as damaging, with at least one in silico that used tools. Prediction agreement of the four tools was achieved in 45.5% of patients. Moreover, the highest consensus was obtained in twelve out of forty-two (28.6%) mutations by considering three out of four in silico algorithms. The use of prediction tools may help to identify variants with a potentially damaging effect. The lack of substantial agreement between the different algorithms suggests that the bioinformatic approaches should be combined with the personal and family history of the cancer patients.
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Affiliation(s)
- Stefania Stella
- Department of Clinical and Experimental Medicine, University of Catania, 95123 Catania, Italy; (F.M.); (I.T.); (C.T.); (M.D.); (G.P.); (L.M.)
- Center of Experimental Oncology and Hematology, A.O.U. Policlinico “G. Rodolico—San Marco”, 95123 Catania, Italy; (S.R.V.); (M.M.)
| | - Silvia Rita Vitale
- Center of Experimental Oncology and Hematology, A.O.U. Policlinico “G. Rodolico—San Marco”, 95123 Catania, Italy; (S.R.V.); (M.M.)
| | - Michele Massimino
- Center of Experimental Oncology and Hematology, A.O.U. Policlinico “G. Rodolico—San Marco”, 95123 Catania, Italy; (S.R.V.); (M.M.)
- Department of General Surgery and Medical-Surgical Specialties, University of Catania, 95123 Catania, Italy
| | - Federica Martorana
- Department of Clinical and Experimental Medicine, University of Catania, 95123 Catania, Italy; (F.M.); (I.T.); (C.T.); (M.D.); (G.P.); (L.M.)
| | - Irene Tornabene
- Department of Clinical and Experimental Medicine, University of Catania, 95123 Catania, Italy; (F.M.); (I.T.); (C.T.); (M.D.); (G.P.); (L.M.)
- Division of Pathology, Humanitas Istituto Clinico Catanese, 95045 Catania, Italy
| | - Cristina Tomarchio
- Department of Clinical and Experimental Medicine, University of Catania, 95123 Catania, Italy; (F.M.); (I.T.); (C.T.); (M.D.); (G.P.); (L.M.)
- Center of Experimental Oncology and Hematology, A.O.U. Policlinico “G. Rodolico—San Marco”, 95123 Catania, Italy; (S.R.V.); (M.M.)
| | - Melissa Drago
- Department of Clinical and Experimental Medicine, University of Catania, 95123 Catania, Italy; (F.M.); (I.T.); (C.T.); (M.D.); (G.P.); (L.M.)
- Center of Experimental Oncology and Hematology, A.O.U. Policlinico “G. Rodolico—San Marco”, 95123 Catania, Italy; (S.R.V.); (M.M.)
| | - Giuliana Pavone
- Department of Clinical and Experimental Medicine, University of Catania, 95123 Catania, Italy; (F.M.); (I.T.); (C.T.); (M.D.); (G.P.); (L.M.)
- Medical Oncology Unit, Humanitas Istituto Clinico Catanese, 95045 Catania, Italy
| | | | | | | | - Livia Manzella
- Department of Clinical and Experimental Medicine, University of Catania, 95123 Catania, Italy; (F.M.); (I.T.); (C.T.); (M.D.); (G.P.); (L.M.)
- Center of Experimental Oncology and Hematology, A.O.U. Policlinico “G. Rodolico—San Marco”, 95123 Catania, Italy; (S.R.V.); (M.M.)
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Afzal MZ, Vahdat LT. Evolving Management of Breast Cancer in the Era of Predictive Biomarkers and Precision Medicine. J Pers Med 2024; 14:719. [PMID: 39063972 PMCID: PMC11278458 DOI: 10.3390/jpm14070719] [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: 05/22/2024] [Revised: 06/17/2024] [Accepted: 06/30/2024] [Indexed: 07/28/2024] Open
Abstract
Breast cancer is the most common cancer among women in the world as well as in the United States. Molecular and histological differentiation have helped clinicians optimize treatments with various therapeutics, including hormonal therapy, chemotherapy, immunotherapy, and radiation therapy. Recently, immunotherapy has become the standard of care in locally advanced triple-negative breast cancer and an option across molecular subtypes for tumors with a high tumor mutation burden. Despite the advancements in personalized medicine directing the management of localized and advanced breast cancers, the emergence of resistance to these therapies is the leading cause of death among breast cancer patients. Therefore, there is a critical need to identify and validate predictive biomarkers to direct treatment selection, identify potential responders, and detect emerging resistance to standard therapies. Areas of active scientific and clinical research include novel personalized and predictive biomarkers incorporating tumor microenvironment, tumor immune profiling, molecular characterization, and histopathological differentiation to predict response and the potential emergence of resistance.
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Affiliation(s)
- Muhammad Zubair Afzal
- Medical Oncology, Comprehensive Breast Program, Dartmouth Cancer Center, Lebanon, NH 03755, USA
| | - Linda T. Vahdat
- Medical Oncology and Hematology (Interim), Dartmouth Cancer Center, Lebanon, NH 03755, USA;
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Cragun D, Dean M, Baker D, Kelley M, Hooker G, Weidner A, Hunt P, Pal T. The Development and Evaluation of Novel Patient Educational Material for a Variant of Uncertain Significance (VUS) Result in Hereditary Cancer Genes. Curr Oncol 2024; 31:3361-3378. [PMID: 38920739 PMCID: PMC11202617 DOI: 10.3390/curroncol31060256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 05/30/2024] [Accepted: 06/12/2024] [Indexed: 06/27/2024] Open
Abstract
A Variant of Uncertain Significance (VUS) is a difference in the DNA sequence with uncertain consequences for gene function. A VUS in a hereditary cancer gene should not change medical care, yet some patients undergo medical procedures based on their VUS result, highlighting the unmet educational needs among patients and healthcare providers. To address this need, we developed, evaluated, and refined novel educational materials to explain that while VUS results do not change medical care, it remains important to share any personal or family history of cancer with family members given that their personal and family medical history can guide their cancer risk management. We began by reviewing the prior literature and transcripts from interviews with six individuals with a VUS result to identify content and design considerations to incorporate into educational materials. We then gathered feedback to improve materials via a focus group of multidisciplinary experts and multiple rounds of semi-structured interviews with individuals with a VUS result. Themes for how to improve content, visuals, and usefulness were used to refine the materials. In the final round of interviews with an additional 10 individuals with a VUS result, materials were described as relatable, useful, factual, and easy to navigate, and also increased their understanding of cancer gene VUS results.
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Affiliation(s)
- Deborah Cragun
- College of Public Health, University of South Florida, Tampa, FL 33620, USA
| | - Marleah Dean
- Department of Communication, University of South Florida, Tampa, FL 33620, USA
- Outcomes & Behavior Program, Moffitt Cancer Center, Tampa, FL 33612, USA
| | - David Baker
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37212, USA
| | - Meghan Kelley
- Morsani College of Medicine, University of South Florida, Tampa, FL 33620, USA
| | - Gillian Hooker
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37212, USA
| | - Anne Weidner
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37212, USA
| | - Paige Hunt
- College of Public Health, University of South Florida, Tampa, FL 33620, USA
| | - Tuya Pal
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37212, USA
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Elshwekh H, Alhudiri IM, Elzagheid A, Enattah N, Abbassi Y, Abou Assali L, Marino I, Stuani C, Buratti E, Romano M. Assessing the Impact of Novel BRCA1 Exon 11 Variants on Pre-mRNA Splicing. Cells 2024; 13:824. [PMID: 38786046 PMCID: PMC11119505 DOI: 10.3390/cells13100824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 05/06/2024] [Accepted: 05/09/2024] [Indexed: 05/25/2024] Open
Abstract
Our study focused on assessing the effects of three newly identified BRCA1 exon 11 variants (c.1019T>C, c.2363T>G, and c.3192T>C) on breast cancer susceptibility. Using computational predictions and experimental splicing assays, we evaluated their potential as pathogenic mutations. Our in silico analyses suggested that the c.2363T>G and c.3192T>C variants could impact both splicing and protein function, resulting in the V340A and V788G mutations, respectively. We further examined their splicing effects using minigene assays in MCF7 and SKBR3 breast cancer cell lines. Interestingly, we found that the c.2363T>G variant significantly altered splicing patterns in MCF7 cells but not in SKBR3 cells. This finding suggests a potential influence of cellular context on the variant's effects. While attempts to correlate in silico predictions with RNA binding factors were inconclusive, this observation underscores the complexity of splicing regulation. Splicing is governed by various factors, including cellular contexts and protein interactions, making it challenging to predict outcomes accurately. Further research is needed to fully understand the functional consequences of the c.2363T>G variant in breast cancer pathogenesis. Integrating computational predictions with experimental data will provide valuable insights into the role of alternative splicing regulation in different breast cancer types and stages.
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Affiliation(s)
- Halla Elshwekh
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149 Trieste, Italy; (H.E.); (Y.A.); (L.A.A.); (I.M.); (C.S.)
- Department of Genetic Engineering, Libyan Biotechnology Research Center, Tripoli P.O. Box 30313, Libya; (I.M.A.); (A.E.); (N.E.)
| | - Inas M. Alhudiri
- Department of Genetic Engineering, Libyan Biotechnology Research Center, Tripoli P.O. Box 30313, Libya; (I.M.A.); (A.E.); (N.E.)
| | - Adam Elzagheid
- Department of Genetic Engineering, Libyan Biotechnology Research Center, Tripoli P.O. Box 30313, Libya; (I.M.A.); (A.E.); (N.E.)
| | - Nabil Enattah
- Department of Genetic Engineering, Libyan Biotechnology Research Center, Tripoli P.O. Box 30313, Libya; (I.M.A.); (A.E.); (N.E.)
| | - Yasmine Abbassi
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149 Trieste, Italy; (H.E.); (Y.A.); (L.A.A.); (I.M.); (C.S.)
| | - Lubna Abou Assali
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149 Trieste, Italy; (H.E.); (Y.A.); (L.A.A.); (I.M.); (C.S.)
| | - Ilenia Marino
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149 Trieste, Italy; (H.E.); (Y.A.); (L.A.A.); (I.M.); (C.S.)
- Faculty of Medicine, University of Southampton, Southampton SO17 1BJ, UK
| | - Cristiana Stuani
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149 Trieste, Italy; (H.E.); (Y.A.); (L.A.A.); (I.M.); (C.S.)
| | - Emanuele Buratti
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149 Trieste, Italy; (H.E.); (Y.A.); (L.A.A.); (I.M.); (C.S.)
| | - Maurizio Romano
- Department of Life Sciences, University of Trieste, Via A. Valerio, 28, 34127 Trieste, Italy
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Agaoglu NB, Unal B, Hayes CP, Walker M, Ng OH, Doganay L, Can ND, Rana HQ, Ghazani AA. Genomic disparity impacts variant classification of cancer susceptibility genes in Turkish breast cancer patients. Cancer Med 2024; 13:e6852. [PMID: 38308423 PMCID: PMC10905328 DOI: 10.1002/cam4.6852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 11/23/2023] [Accepted: 12/10/2023] [Indexed: 02/04/2024] Open
Abstract
OBJECTIVE Turkish genome is underrepresented in large genomic databases. This study aims to evaluate the effect of allele frequency in the Turkish population in determining the clinical utility of germline findings in breast cancer, including invasive lobular carcinoma (ILC), mixed invasive ductal and lobular carcinoma (IDC-L), and ductal carcinoma (DC). METHODS Two clinic-based cohorts from the Umraniye Research and Training Hospital (URTH) were used in this study: a cohort consisting of 132 women with breast cancer and a non-cancer cohort consisting of 492 participants. The evaluation of the germline landscape was performed by analysis of 27 cancer genes. The frequency and type of variants in the breast cancer cohort were compared to those in the non-cancer cohort to investigate the effect of population genetics. The variant allele frequencies in Turkish Variome and gnomAD were statistically evaluated. RESULTS The genetic analysis identified 121 variants in the breast cancer cohort (actionable = 32, VUS = 89) and 223 variants in the non-cancer cohort (actionable = 25, VUS = 188). The occurrence of 21 variants in both suggested a possible genetic population effect. Evaluation of allele frequency of 121 variants from the breast cancer cohort showed 22% had a significantly higher value in Turkish Variome compared to gnomAD (p < 0.0001, 95% CI) with a mean difference of 60 times (ranging from 1.37-354.4). After adjusting for variant allele frequency using the ancestry-appropriate database, 6.7% (5/75) of VUS was reclassified to likely benign. CONCLUSION To our knowledge, this is the first study of population genetic effects in breast cancer subtypes in Turkish women. Our findings underscore the need for a large genomic database representing Turkish population-specific variants. It further highlights the significance of the ancestry-appropriate population database for accurate variant assessment in clinical settings.
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Affiliation(s)
- Nihat B. Agaoglu
- Department of Medical Genetics, Division of Cancer GeneticsUmraniye Training and Research HospitalIstanbulTurkey
| | - Busra Unal
- Department of Medical Genetics, Division of Cancer GeneticsUmraniye Training and Research HospitalIstanbulTurkey
- Division of GeneticsBrigham and Women's HospitalBostonMassachusettsUSA
| | - Connor P. Hayes
- Division of GeneticsBrigham and Women's HospitalBostonMassachusettsUSA
| | - McKenzie Walker
- Division of GeneticsBrigham and Women's HospitalBostonMassachusettsUSA
| | - Ozden Hatirnaz Ng
- Department of Medical Biology, School of MedicineAcibadem UniversityIstanbulTurkey
| | - Levent Doganay
- Department of Medical Genetics, Division of Cancer GeneticsUmraniye Training and Research HospitalIstanbulTurkey
| | - Nisan D. Can
- Department of Molecular Biology Genetics and BiotechnologyIstanbul Technical UniversityIstanbulTurkey
| | - Huma Q. Rana
- Division of Cancer Genetics and PreventionDana‐Farber Cancer InstituteBostonMassachusettsUSA
- Department of MedicineBrigham and Women's HospitalBostonMassachusettsUSA
- Harvard Medical SchoolBostonMassachusettsUSA
| | - Arezou A. Ghazani
- Division of GeneticsBrigham and Women's HospitalBostonMassachusettsUSA
- Department of MedicineBrigham and Women's HospitalBostonMassachusettsUSA
- Harvard Medical SchoolBostonMassachusettsUSA
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Ning Y, Zhang Y, Tian T, Chen Y, Wang J, Lei K, Cui Z. Reclassifying BRCA1 c.4358-2A > G and BRCA2 c.475 + 5G > C variants from "Uncertain Significance" to "Pathogenic" based on minigene assays and clinical evidence. J Cancer Res Clin Oncol 2024; 150:62. [PMID: 38300310 PMCID: PMC10834553 DOI: 10.1007/s00432-023-05597-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 12/25/2023] [Indexed: 02/02/2024]
Abstract
BACKGROUND Pathogenic variants in BRCA genes play a crucial role in the pathogenesis of ovarian cancer. Intronic variants of uncertain significance (VUS) may contribute to pathogenicity by affecting splicing. Currently, the significance of many intronic variants in BRCA has not been clarified, impacting patient treatment strategies and the management of familial cases. METHOD A retrospective study was conducted to analyze BRCA intronic VUS in a cohort of 707 unrelated ovarian cancer patients at a single institution from 2018 to 2023. Three splicing predictors were employed to analyze detected intronic VUS. Variants predicted to have splicing alterations were selected for further validation through minigene assays. Patient and familial investigations were conducted to comprehend cancer incidence within pedigrees and the application of poly (ADP-ribose) polymerase inhibitors (PARPi) by the patients. In accordance with the guidelines of the American College of Medical Genetics and Genomics (ACMG), the intronic VUS were reclassified based on minigene assay results and clinical evidence. RESULT Approximately 9.8% (69/707) of patients were identified as carriers of 67 different VUS in BRCA1/2, with four intronic variants accounting for 6% (4/67) of all VUS. Splicing predictors indicated potential splicing alterations in splicing for BRCA1 c.4358-2A>G and BRCA2 c.475+5G>C variants. Minigene assays utilizing the pSPL3 exon trapping vector revealed that these variants induced changes in splicing sites and frameshift, resulting in premature termination of translation (p. Ala1453Glyfs and p. Pro143Glyfs). According to ACMG guidelines, BRCA1 c.4358-2A>G and BRCA2 c.475+5G>C were reclassified as pathogenic variants. Pedigree investigations were conducted on patients with BRCA1 c.4358-2A>G variant, and the detailed utilization of PARPi provided valuable insights into research on PARPi resistance. CONCLUSION Two intronic VUS were reclassified as pathogenic variants. A precise classification of variants is crucial for the effective treatment and management of both patients and healthy carriers.
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Affiliation(s)
- Ying Ning
- Department of Clinical Medicine, Qingdao University, Qingdao, 266003, China
| | - Yu Zhang
- Department of Clinical Medicine, Qingdao University, Qingdao, 266003, China
| | - Tian Tian
- Department of Obstetrics and Gynecology, The Affiliated Hospital of Qingdao University, No. 59 Haier Road, Laoshan District, Qingdao, 266000, China
| | - Yu Chen
- Department of Clinical Medicine, Qingdao University, Qingdao, 266003, China
| | - Jia Wang
- Center of Tumor Immunology and Cytotherapy, Medical Research Center, The Affiliated Hospital of Qingdao University, No. 59 Haier Road, Laoshan District, Qingdao, 266000, China
| | - Ke Lei
- Center of Tumor Immunology and Cytotherapy, Medical Research Center, The Affiliated Hospital of Qingdao University, No. 59 Haier Road, Laoshan District, Qingdao, 266000, China.
| | - Zhumei Cui
- Department of Obstetrics and Gynecology, The Affiliated Hospital of Qingdao University, No. 59 Haier Road, Laoshan District, Qingdao, 266000, China.
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9
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Zakerinasab F, Behfar Q, Parsaee R, Zadeh RH, Foroughi E, Amirbeik A, Ahmadi G. BRCA 1/2 mutations and risk of uterine cancer: a systematic review and meta-analysis. BMC Genom Data 2024; 25:13. [PMID: 38297203 PMCID: PMC10829221 DOI: 10.1186/s12863-024-01189-y] [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: 09/26/2023] [Accepted: 01/01/2024] [Indexed: 02/02/2024] Open
Abstract
PURPOSE In this study, we aim to investigate the association between BRCA1/2 mutation and uterine cancer incidence. MATERIAL AND METHOD We systematically searched three databases including PubMed, Scopus, and Google Scholar up to August 2023; and reviewed 23 cohorts and cross-sectional studies to explore the association between BRCA1/2 mutations and uterine cancer incidence. RESULTS This systematic review comprised a total of 21 cohort studies and 2 cross-sectional studies after the screening process. According to meta-analysis the prevalence of the BRCA1/2 gene in patients with uterine cancer was 0.02 (95%CI = [0.01,0.03], P < 0.01, I2 = 94.82%) CONCLUSIONS: Our meta-analysis investigates a 2% prevalence of BRCA1/2 mutation in patients with uterine cancer. Patients with BRCA1/2 mutations might be more conscious of uterine malignancies.
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Affiliation(s)
| | - Qumars Behfar
- Department of Neurology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Reza Parsaee
- Master Student in Molecular Genetics, Transplant Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Reza Hossein Zadeh
- Student's Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Elaheh Foroughi
- School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Amirhesam Amirbeik
- Student Research Committee, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
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10
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Speiser D, Bick U. Primary Prevention and Early Detection of Hereditary Breast Cancer. Breast Care (Basel) 2023; 18:448-454. [PMID: 38125920 PMCID: PMC10730103 DOI: 10.1159/000533391] [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: 04/16/2023] [Accepted: 08/01/2023] [Indexed: 12/23/2023] Open
Abstract
Background Primary prevention and early detection of hereditary breast cancer has been one of the main topics of breast cancer research in recent decades. The knowledge of risk factors for breast cancer has been increasing continuously just like the recommendations for risk management. Pathogenic germline variants (mutations, class 4/5) of risk genes are significant susceptibility factors in healthy individuals. At the same time, germline mutations serve as biomarkers for targeted therapy in breast cancer treatment. Therefore, management of healthy mutation carriers to enable primary prevention is in the focus as much as the consideration of pathogenic germline variants for therapeutic decisions. Since 1996, the German Consortium has provided quality-assured care for counselees and patients with familial burden of breast and ovarian cancer. Summary Currently, there are 23 university centers with over 100 cooperating DKG-certified breast and gynecological cancer centers. These centers provide standardized, evidence-based, and knowledge-generating care, which includes aspects of primary as well as secondary and tertiary prevention. An important aspect of quality assurance and development was the inclusion of the HBOC centers in the certification system of the German Cancer Society (GCS). Since 2020, the centers have been regularly audited and their quality standards continuously reviewed according to quality indicators adapted to the current state of research. The standard of care at GC-HBOC' centers involves the evaluation as well as evolution of various aspects of care like inclusion criteria, identification of new risk genes, management of variants of unknown significance (class 3), evaluation of risk-reducing options, intensified surveillance, and communication of risks. Among these, the possibility of intensified surveillance in the GC-HBOC for early detection of breast cancer is an important component of individual risk management for many counselees. As has been shown in recent years, in carriers of pathogenic variants in high-risk genes, this approach enables the detection of breast cancer at very early, more favorable stages although no reduction of mortality has been demonstrated yet. The key component of the intensified surveillance is annual contrast-enhanced breast MRI, supplemented by up to biannual breast ultrasound and mammography usually starting at age 40. Key Messages Apart from early detection, the central goal of care is the prevention of cancer. By utilizing individualized risk calculation, the optimal timeframe for risk-reducing surgery can be estimated, and counselees can be supported in reaching preference-sensitive decisions.
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Affiliation(s)
- Dorothee Speiser
- HBOC-Center, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Department of Gynecology with Breast Center, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Ulrich Bick
- HBOC-Center, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Department of Radiology, Charité-Universitätsmedizin Berlin, Berlin, Germany
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11
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Zanti M, O'Mahony DG, Parsons MT, Li H, Dennis J, Aittomäkkiki K, Andrulis IL, Anton-Culver H, Aronson KJ, Augustinsson A, Becher H, Bojesen SE, Bolla MK, Brenner H, Brown MA, Buys SS, Canzian F, Caputo SM, Castelao JE, Chang-Claude J, Czene K, Daly MB, De Nicolo A, Devilee P, Dörk T, Dunning AM, Dwek M, Eccles DM, Engel C, Evans DG, Fasching PA, Gago-Dominguez M, García-Closas M, García-Sáenz JA, Gentry-Maharaj A, Geurts - Giele WR, Giles GG, Glendon G, Goldberg MS, Garcia EBG, Güendert M, Guénel P, Hahnen E, Haiman CA, Hall P, Hamann U, Harkness EF, Hogervorst FB, Hollestelle A, Hoppe R, Hopper JL, Houdayer C, Houlston RS, Howell A, Jakimovska M, Jakubowska A, Jernström H, John EM, Kaaks R, Kitahara CM, Koutros S, Kraft P, Kristensen VN, Lacey JV, Lambrechts D, Léoné M, Lindblom A, Lubiński J, Lush M, Mannermaa A, Manoochehri M, Manoukian S, Margolin S, Martinez ME, Menon U, Milne RL, Monteiro AN, Murphy RA, Neuhausen SL, Nevanlinna H, Newman WG, Offit K, Park SK, James P, Peterlongo P, Peto J, Plaseska-Karanfilska D, Punie K, Radice P, Rashid MU, Rennert G, Romero A, Rosenberg EH, Saloustros E, Sandler DP, Schmidt MK, Schmutzler RK, Shu XO, Simard J, Southey MC, Stone J, Stoppa-Lyonnet D, Tamimi RM, Tapper WJ, Taylor JA, Teo SH, Teras LR, Terry MB, Thomassen M, Troester MA, Vachon CM, Vega A, Vreeswijk MP, Wang Q, Wappenschmidt B, Weinberg CR, Wolk A, Zheng W, Feng B, Couch FJ, Spurdle AB, Easton DF, Goldgar DE, Michailidou K. A likelihood ratio approach for utilizing case-control data in the clinical classification of rare sequence variants: application to BRCA1 and BRCA2. Hum Mutat 2023; 2023:9961341. [PMID: 38725546 PMCID: PMC11080979 DOI: 10.1155/2023/9961341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2024]
Abstract
A large number of variants identified through clinical genetic testing in disease susceptibility genes, are of uncertain significance (VUS). Following the recommendations of the American College of Medical Genetics and Genomics (ACMG) and Association for Molecular Pathology (AMP), the frequency in case-control datasets (PS4 criterion), can inform their interpretation. We present a novel case-control likelihood ratio-based method that incorporates gene-specific age-related penetrance. We demonstrate the utility of this method in the analysis of simulated and real datasets. In the analyses of simulated data, the likelihood ratio method was more powerful compared to other methods. Likelihood ratios were calculated for a case-control dataset of BRCA1 and BRCA2 variants from the Breast Cancer Association Consortium (BCAC), and compared with logistic regression results. A larger number of variants reached evidence in favor of pathogenicity, and a substantial number of variants had evidence against pathogenicity - findings that would not have been reached using other case-control analysis methods. Our novel method provides greater power to classify rare variants compared to classical case-control methods. As an initiative from the ENIGMA Analytical Working Group, we provide user-friendly scripts and pre-formatted excel calculators for implementation of the method for rare variants in BRCA1, BRCA2 and other high-risk genes with known penetrance.
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Affiliation(s)
- Maria Zanti
- Biostatistics Unit, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Denise G. O'Mahony
- Biostatistics Unit, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Michael T. Parsons
- Population Health Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Hongyan Li
- Cancer Control and Population Science, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Kristiina Aittomäkkiki
- Department of Clinical Genetics, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Irene L. Andrulis
- Fred A. Litwin Center for Cancer Genetics, Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Hoda Anton-Culver
- Department of Medicine, Genetic Epidemiology Research Institute, University of California Irvine, Irvine, CA, USA
| | - Kristan J. Aronson
- Department of Public Health Sciences, and Cancer Research Institute, Queen’s University, Kingston, ON, Canada
| | - Annelie Augustinsson
- Oncology, Department of Clinical Sciences in Lund, Lund University, Lund, Sweden
| | - Heiko Becher
- Institute for Medical Biometry and Epidemiology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stig E. Bojesen
- Copenhagen General Population Study, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Manjeet K. Bolla
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Melissa A. Brown
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Saundra S. Buys
- Department of Internal Medicine and Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sandrine M. Caputo
- Service de Génétique, Institut Curie, Paris, France
- Paris Sciences Lettres Research University, Paris, France
| | - Jose E. Castelao
- Oncology and Genetics Unit, Instituto de Investigación Sanitaria Galicia Sur (IISGS), Xerencia de Xestion Integrada de Vigo-SERGAS, Vigo, Spain
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Cancer Epidemiology Group, University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - GC-HBOC study Collaborators
- Center for Familial Breast and Ovarian Cancer, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Mary B. Daly
- Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Arcangela De Nicolo
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Peter Devilee
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Thilo Dörk
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Alison M. Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Miriam Dwek
- School of Life Sciences, University of Westminster, London, UK
| | - Diana M. Eccles
- Faculty of Medicine, University of Southampton, Southampton, UK
| | - Christoph Engel
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
- LIFE - Leipzig Research Centre for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - D. Gareth Evans
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
- North West Genomics Laboratory Hub, Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Peter A. Fasching
- Department of Gynecology and Obstetrics, Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander University Erlangen-Nuremberg, University Hospital Erlangen, Erlangen, Germany
| | - Manuela Gago-Dominguez
- Genomic Medicine Group, International Cancer Genetics and Epidemiology Group, Fundación Pública Galega de Medicina Xenómica, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago, SERGAS, Santiago de Compostela, Spain
| | - Montserrat García-Closas
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, USA
| | - José A. García-Sáenz
- Medical Oncology Department, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria San Carlos (IdISSC), Centro Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Aleksandra Gentry-Maharaj
- MRC Clinical Trials Unit, Institute of Clinical Trials & Methodology, University College London, London, UK
| | | | - Graham G. Giles
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Gord Glendon
- Fred A. Litwin Center for Cancer Genetics, Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Mark S. Goldberg
- Department of Medicine, McGill University, Montréal, QC, Canada
- Division of Clinical Epidemiology, Royal Victoria Hospital, McGill University, Montréal, QC, Canada
| | - Encarna B. Gómez Garcia
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Melanie Güendert
- Molecular Epidemiology Group, C080, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Molecular Biology of Breast Cancer, University Womens Clinic Heidelberg, University of Heidelberg, Heidelberg, Germany
- Institute of Diabetes Research, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Pascal Guénel
- Team 'Exposome and Heredity', CESP, Gustave Roussy, INSERM, University Paris-Saclay, UVSQ, Villejuif, France
| | - Eric Hahnen
- Center for Familial Breast and Ovarian Cancer, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Christopher A. Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Oncology, Södersjukhuset, Stockholm, Sweden
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Elaine F. Harkness
- Division of Informatics, Imaging and Data Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
- Nightingale & Genesis Prevention Centre, Wythenshawe Hospital, Manchester University NHS Foundation Trust, Manchester, UK
- NIHR Manchester Biomedical Research Unit, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Frans B.L. Hogervorst
- Family Cancer Clinic, The Netherlands Cancer Institute - Antoni van Leeuwenhoek hospital, Amsterdam, the Netherlands
| | | | - Reiner Hoppe
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany
- University of Tübingen, Tübingen, Germany
| | - John L. Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Claude Houdayer
- Department of Genetics, F76000 and Normandy University, UNIROUEN, Inserm U1245, Normandy Centre for Genomic and Personalized Medicine, Rouen University Hospital, Rouen, France
| | - Richard S. Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Anthony Howell
- Division of Cancer Sciences, University of Manchester, Manchester, UK
| | - ABCTB Investigators
- Australian Breast Cancer Tissue Bank, Westmead Institute for Medical Research, University of Sydney, Sydney, New South Wales, Australia
| | - Milena Jakimovska
- Research Centre for Genetic Engineering and Biotechnology 'Georgi D. Efremov', MASA, Skopje, Republic of North Macedonia
| | - Anna Jakubowska
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
- Independent Laboratory of Molecular Biology and Genetic Diagnostics, Pomeranian Medical University, Szczecin, Poland
| | - Helena Jernström
- Oncology, Department of Clinical Sciences in Lund, Lund University, Lund, Sweden
| | - Esther M. John
- Department of Epidemiology and Population Health, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Division of Oncology, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Rudolf Kaaks
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Cari M. Kitahara
- Radiation Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Stella Koutros
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, USA
| | - Peter Kraft
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Vessela N. Kristensen
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - James V. Lacey
- Department of Computational and Quantitative Medicine, City of Hope, Duarte, CA, USA
- City of Hope Comprehensive Cancer Center, City of Hope, Duarte, CA, USA
| | - Diether Lambrechts
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
- VIB Center for Cancer Biology, VIB, Leuven, Belgium
| | - Melanie Léoné
- Genetic and Cancer Medical Laboratory HCL-CLB, Hospices Civils de Lyon, Bron, France
| | - Annika Lindblom
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Jan Lubiński
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Michael Lush
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Arto Mannermaa
- Translational Cancer Research Area, University of Eastern Finland, Kuopio, Finland
- Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, Kuopio, Finland
- Biobank of Eastern Finland, Kuopio University Hospital, Kuopio, Finland
| | - Mehdi Manoochehri
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Siranoush Manoukian
- Unit of Medical Genetics, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | - Sara Margolin
- Department of Oncology, Södersjukhuset, Stockholm, Sweden
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden
| | - Maria Elena Martinez
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | - Usha Menon
- MRC Clinical Trials Unit, Institute of Clinical Trials & Methodology, University College London, London, UK
| | - Roger L. Milne
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Alvaro N. Monteiro
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Rachel A. Murphy
- School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada
- Cancer Control Research, BC Cancer, Vancouver, BC, Canada
| | - Susan L. Neuhausen
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - William G. Newman
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
- North West Genomics Laboratory Hub, Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Kenneth Offit
- Clinical Genetics Research Lab, Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sue K. Park
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Korea
- Integrated Major in Innovative Medical Science, Seoul National University College of Medicine, Seoul, South Korea
- Cancer Research Institute, Seoul National University, Seoul, Korea
| | - Paul James
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Paolo Peterlongo
- Genome Diagnostics Program, IFOM - ETS the AIRC Institute of Molecular Oncology, Milan, Italy
| | - Julian Peto
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Dijana Plaseska-Karanfilska
- Research Centre for Genetic Engineering and Biotechnology 'Georgi D. Efremov', MASA, Skopje, Republic of North Macedonia
| | - Kevin Punie
- Department of General Medical Oncology and Multidisciplinary Breast Centre, Leuven Cancer Institute and University Hospitals Leuven, Leuven, Belgium
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori (INT), Milan, Italy
| | - Muhammad U. Rashid
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Basic Sciences, Shaukat Khanum Memorial Cancer Hospital and Research Centre (SKMCH & RC), Lahore, Pakistan
| | - Gad Rennert
- Clalit National Cancer Control Center, Carmel Medical Center and Technion Faculty of Medicine, Haifa, Israel
| | - Atocha Romero
- Medical Oncology Department, Hospital Universitario Puerta de Hierro, Madrid, Spain
| | - Efraim H. Rosenberg
- Department of Pathology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek hospital, Amsterdam, the Netherlands
| | | | - Dale P. Sandler
- Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Marjanka K. Schmidt
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
- Division of Psychosocial Research and Epidemiology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek hospital, Amsterdam, the Netherlands
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Rita K. Schmutzler
- Center for Familial Breast and Ovarian Cancer, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Jacques Simard
- Genomics Center, Centre Hospitalier Universitaire de Québec – Université Laval Research Center, Québec City, QC, Canada
| | - Melissa C. Southey
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
- Department of Clinical Pathology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Jennifer Stone
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Genetic Epidemiology Group, School of Population and Global Health, University of Western Australia, Perth, Western Australia, Australia
| | - Dominique Stoppa-Lyonnet
- Service de Génétique, Institut Curie, Paris, France
- Department of Tumour Biology, INSERM U830, Paris, France
- Université Paris Descartes, Paris, France
| | - Rulla M. Tamimi
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Population Health Sciences, Weill Cornell Medicine, New York, NY, USA
| | | | - Jack A. Taylor
- Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
- Epigenetic and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Soo Hwang Teo
- Breast Cancer Research Programme, Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia
- Department of Surgery, Faculty of Medicine, University of Malaya, UM Cancer Research Institute, Kuala Lumpur, Malaysia
| | - Lauren R. Teras
- Department of Population Science, American Cancer Society, Atlanta, GA, USA
| | - Mary Beth Terry
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Mads Thomassen
- Department of Clinical Genetics, Odense University Hospital, Odence C, Denmark
| | - Melissa A. Troester
- Department of Epidemiology, Gillings School of Global Public Health and UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Celine M. Vachon
- Department of Quantitative Health Sciences, Division of Epidemiology, Mayo Clinic, Rochester, MN, USA
| | - Ana Vega
- Centro de Investigación en Red de Enfermedades Raras (CIBERER), Madrid, Spain
- Fundación Pública Galega de Medicina Xenómica, Santiago de Compostela, Spain
- Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago, SERGAS, Santiago de Compostela, Spain
| | - Maaike P.G. Vreeswijk
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Qin Wang
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Barbara Wappenschmidt
- Center for Familial Breast and Ovarian Cancer, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Clarice R. Weinberg
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Alicja Wolk
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Bingjian Feng
- Department of Dermatology, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Fergus J. Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Amanda B. Spurdle
- Population Health Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Douglas F. Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - David E. Goldgar
- Department of Dermatology, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Kyriaki Michailidou
- Biostatistics Unit, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
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12
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Henkel J, Laner A, Locher M, Wohlfrom T, Neitzel B, Becker K, Neuhann T, Abicht A, Steinke-Lange V, Holinski-Feder E. Diagnostic yield and clinical relevance of expanded germline genetic testing for nearly 7000 suspected HBOC patients. Eur J Hum Genet 2023; 31:925-930. [PMID: 37188824 PMCID: PMC10400578 DOI: 10.1038/s41431-023-01380-2] [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: 10/11/2022] [Revised: 01/18/2023] [Accepted: 04/26/2023] [Indexed: 05/17/2023] Open
Abstract
Here we report the results of a retrospective germline analysis of 6941 individuals fulfilling the criteria necessary for genetic testing of hereditary breast- and ovarian cancer (HBOC) according to the German S3 or AGO Guidelines. Genetic testing was performed by next-generation sequencing using 123 cancer-associated genes based on the Illumina TruSight® Cancer Sequencing Panel. In 1431 of 6941 cases (20.6%) at least one variant was reported (ACMG/AMP classes 3-5). Of those 56.3% (n = 806) were class 4 or 5 and 43.7% (n = 625) were a class 3 (VUS). We defined a 14 gene HBOC core gene panel and compared this to a national and different internationally recommended gene panels (German Hereditary Breast and Ovarian Cancer Consortium HBOC Consortium, ClinGen expert Panel, Genomics England PanelsApp) in regard of diagnostic yield, revealing a diagnostic range of pathogenic variants (class 4/5) from 7.8 to 11.6% depending on the panel evaluated. With the 14 HBOC core gene panel having a diagnostic yield of pathogenic variants (class 4/5) of 10.8%. Additionally, 66 (1%) pathogenic variants (ACMG/AMP class 4 or 5) were found in genes outside the 14 HBOC core gene set (secondary findings) that would have been missed with the restriction to the analysis of HBOC genes. Furthermore, we evaluated a workflow for a periodic re-evaluation of variants of uncertain clinical significance (VUS) for the improvement of clinical validity of germline genetic testing.
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Affiliation(s)
- Jan Henkel
- MGZ - Medizinisch Genetisches Zentrum, München, Germany
| | - Andreas Laner
- MGZ - Medizinisch Genetisches Zentrum, München, Germany
| | | | | | | | | | | | - Angela Abicht
- MGZ - Medizinisch Genetisches Zentrum, München, Germany
- Friedrich-Baur-Institute, Department of Neurology, Klinikum der Universität, Ludwig-Maximilians-Universität, München, Germany
| | - Verena Steinke-Lange
- MGZ - Medizinisch Genetisches Zentrum, München, Germany
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität, München, Germany
| | - Elke Holinski-Feder
- MGZ - Medizinisch Genetisches Zentrum, München, Germany.
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität, München, Germany.
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13
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Gunawardena K, Sirisena ND, Anandagoda G, Neththikumara N, Dissanayake VHW. Germline variants of uncertain significance, their frequency, and clinico-pathological features in a cohort of Sri Lankan patients with hereditary breast cancer. BMC Res Notes 2023; 16:95. [PMID: 37277882 DOI: 10.1186/s13104-023-06365-4] [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: 10/21/2022] [Accepted: 05/22/2023] [Indexed: 06/07/2023] Open
Abstract
BACKGROUND Next-Generation Sequencing (NGS)-based testing in cancer patients has led to increased detection of variants of uncertain significance (VUS). VUS are genetic variants whose impact on protein function is unknown. VUS pose a challenge to clinicians and patients due to uncertainty regarding their cancer predisposition risk. Paucity of data exists on the pattern of VUS in under-represented populations. This study describes the frequency of germline VUS and clinico-pathological features in Sri Lankan hereditary breast cancer patients. METHODS Data of 72 hereditary breast cancer patients who underwent NGS-based testing between January 2015 and December 2021 were maintained prospectively in a database and analyzed retrospectively. Data were subjected to bioinformatics analysis and variants were classified according to international guidelines. RESULTS Germline variants were detected in 33/72(45.8%) patients, comprising 16(48.5%) pathogenic/likely pathogenic variants and 17(51.5%) VUS. Distribution of VUS in breast cancer predisposing genes were :APC:1(5.8%), ATM:2(11.7%), BRCA1:1(5.8%), BRCA2:5(29.4%), BRIP1:1(5.8%), CDKN2A:1(5.8%), CHEK2:2(11.7%), FANC1:1(5.8%), MET:1(5.8%), STK11:1(5.8%), NF2:1(5.8%). Mean age at cancer diagnosis in patients with VUS was 51.2 years. Most common tumour histopathology was ductal carcinoma 11(78.6%). 50% of tumours in patients having VUS in BRCA1/2 genes were hormone receptor negative. 73.3% patients had family history of breast cancer. CONCLUSIONS A significant portion of patients had a germline VUS. Highest frequency was in BRCA2 gene. Majority had family history of breast cancer. This highlights the need to undertake functional genomic studies to determine the biological effects of VUS and identify potentially clinically actionable variants that would be useful for decision-making and patient management.
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Affiliation(s)
- Kawmadi Gunawardena
- Department of Anatomy, Genetics and Biomedical Informatics, Faculty of Medicine, University of Colombo, Colombo 8, Sri Lanka
| | - Nirmala D Sirisena
- Department of Anatomy, Genetics and Biomedical Informatics, Faculty of Medicine, University of Colombo, Colombo 8, Sri Lanka.
| | - Gayani Anandagoda
- Department of Anatomy, Genetics and Biomedical Informatics, Faculty of Medicine, University of Colombo, Colombo 8, Sri Lanka
| | - Nilaksha Neththikumara
- Department of Anatomy, Genetics and Biomedical Informatics, Faculty of Medicine, University of Colombo, Colombo 8, Sri Lanka
| | - Vajira H W Dissanayake
- Department of Anatomy, Genetics and Biomedical Informatics, Faculty of Medicine, University of Colombo, Colombo 8, Sri Lanka
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14
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O'Mahony DG, Ramus SJ, Southey MC, Meagher NS, Hadjisavvas A, John EM, Hamann U, Imyanitov EN, Andrulis IL, Sharma P, Daly MB, Hake CR, Weitzel JN, Jakubowska A, Godwin AK, Arason A, Bane A, Simard J, Soucy P, Caligo MA, Mai PL, Claes KBM, Teixeira MR, Chung WK, Lazaro C, Hulick PJ, Toland AE, Pedersen IS, Neuhausen SL, Vega A, de la Hoya M, Nevanlinna H, Dhawan M, Zampiga V, Danesi R, Varesco L, Gismondi V, Vellone VG, James PA, Janavicius R, Nikitina-Zake L, Nielsen FC, van Overeem Hansen T, Pejovic T, Borg A, Rantala J, Offit K, Montagna M, Nathanson KL, Domchek SM, Osorio A, García MJ, Karlan BY, De Fazio A, Bowtell D, McGuffog L, Leslie G, Parsons MT, Dörk T, Speith LM, Dos Santos ES, da Costa AABA, Radice P, Peterlongo P, Papi L, Engel C, Hahnen E, Schmutzler RK, Wappenschmidt B, Easton DF, Tischkowitz M, Singer CF, Tan YY, Whittemore AS, Sieh W, Brenton JD, Yannoukakos D, Fostira F, Konstantopoulou I, Soukupova J, Vocka M, Chenevix-Trench G, Pharoah PDP, Antoniou AC, Goldgar DE, Spurdle AB, Michailidou K. Ovarian cancer pathology characteristics as predictors of variant pathogenicity in BRCA1 and BRCA2. Br J Cancer 2023; 128:2283-2294. [PMID: 37076566 PMCID: PMC10241792 DOI: 10.1038/s41416-023-02263-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 02/22/2023] [Accepted: 03/24/2023] [Indexed: 04/21/2023] Open
Abstract
BACKGROUND The distribution of ovarian tumour characteristics differs between germline BRCA1 and BRCA2 pathogenic variant carriers and non-carriers. In this study, we assessed the utility of ovarian tumour characteristics as predictors of BRCA1 and BRCA2 variant pathogenicity, for application using the American College of Medical Genetics and the Association for Molecular Pathology (ACMG/AMP) variant classification system. METHODS Data for 10,373 ovarian cancer cases, including carriers and non-carriers of BRCA1 or BRCA2 pathogenic variants, were collected from unpublished international cohorts and consortia and published studies. Likelihood ratios (LR) were calculated for the association of ovarian cancer histology and other characteristics, with BRCA1 and BRCA2 variant pathogenicity. Estimates were aligned to ACMG/AMP code strengths (supporting, moderate, strong). RESULTS No histological subtype provided informative ACMG/AMP evidence in favour of BRCA1 and BRCA2 variant pathogenicity. Evidence against variant pathogenicity was estimated for the mucinous and clear cell histologies (supporting) and borderline cases (moderate). Refined associations are provided according to tumour grade, invasion and age at diagnosis. CONCLUSIONS We provide detailed estimates for predicting BRCA1 and BRCA2 variant pathogenicity based on ovarian tumour characteristics. This evidence can be combined with other variant information under the ACMG/AMP classification system, to improve classification and carrier clinical management.
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Affiliation(s)
- Denise G O'Mahony
- Biostatistics Unit, The Cyprus Institute of Neurology and Genetics, Nicosia, 2371, Cyprus
- Department of Cancer Genetics, Therapeutics and Ultrastructural Pathology, The Cyprus Institute of Neurology and Genetics, Nicosia, 2371, Cyprus
| | - Susan J Ramus
- School of Clinical Medicine, University of New South Wales Medicine and Health, University of New South Wales Sydney, Sydney, NSW, 2052, Australia
- Adult Cancer Program, Lowy Cancer Research Centre, University of New South Wales Sydney, Sydney, NSW, 2052, Australia
| | - Melissa C Southey
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, 3168, Australia
- Department of Clinical Pathology, The University of Melbourne, Melbourne, VIC, 3010, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, 3004, Australia
| | - Nicola S Meagher
- School of Clinical Medicine, University of New South Wales Medicine and Health, University of New South Wales Sydney, Sydney, NSW, 2052, Australia
- Adult Cancer Program, Lowy Cancer Research Centre, University of New South Wales Sydney, Sydney, NSW, 2052, Australia
- The Daffodil Centre, The University of Sydney, a joint venture with Cancer Council NSW, Sydney, NSW, Australia
| | - Andreas Hadjisavvas
- Department of Cancer Genetics, Therapeutics and Ultrastructural Pathology, The Cyprus Institute of Neurology and Genetics, Nicosia, 2371, Cyprus
| | - Esther M John
- Department of Epidemiology and Population Health, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Medicine, Division of Oncology, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, 94304, USA
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
| | | | - Irene L Andrulis
- Fred A. Litwin Center for Cancer Genetics, Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, ON, M5G 1×5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Priyanka Sharma
- Department of Internal Medicine, Division of Medical Oncology, University of Kansas Medical Center, Westwood, KS, 66205, USA
| | - Mary B Daly
- Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | | | | | - Anna Jakubowska
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, 171-252, Poland
- Independent Laboratory of Molecular Biology and Genetic Diagnostics, Pomeranian Medical University, Szczecin, 171-252, Poland
| | - Andrew K Godwin
- Department of Pathology and Laboratory Medicine, The University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Adalgeir Arason
- Department of Pathology, Landspitali University Hospital, Reykjavik, 101, Iceland
- BMC (Biomedical Centre), Faculty of Medicine, University of Iceland, Reykjavik, 101, Iceland
| | - Anita Bane
- Department of Pathology & Molecular Medicine, Juravinski Hospital and Cancer Centre, McMaster University, Hamilton, ON, L8V 1C3, Canada
| | - Jacques Simard
- Genomics Center, Centre Hospitalier Universitaire de Québec - Université Laval Research Center, Québec City, QC, G1V 4G2, Canada
| | - Penny Soucy
- Genomics Center, Centre Hospitalier Universitaire de Québec - Université Laval Research Center, Québec City, QC, G1V 4G2, Canada
| | - Maria A Caligo
- SOD Genetica Molecolare, University Hospital, Pisa, 56126, Italy
| | - Phuong L Mai
- Magee-Womens Hospital, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
| | | | - Manuel R Teixeira
- Department of Laboratory Genetics, Portuguese Oncology Institute of Porto (IPO Porto)/Comprehensive Cancer Center, Porto, 4200-072, Portugal
- School of Medicine and Biomedical Sciences Institute (ICBAS), University of Porto, Porto, 4050-013, Portugal
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University, New York, NY, 10032, USA
| | - Conxi Lazaro
- Hereditary Cancer Program, ONCOBELL-IDIBELL-IGTP, Catalan Institute of Oncology, CIBERONC, Barcelona, 08908, Spain
| | - Peter J Hulick
- Center for Medical Genetics, NorthShore University HealthSystem, Evanston, IL, 60201, USA
- The University of Chicago Pritzker School of Medicine, Chicago, IL, 60637, USA
| | - Amanda E Toland
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, 43210, USA
| | - Inge Sokilde Pedersen
- Molecular Diagnostics, Aalborg University Hospital, Aalborg, 9000, Denmark
- Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, 9000, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, 9000, Denmark
| | - Susan L Neuhausen
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
| | - Ana Vega
- Centro de Investigación en Red de Enfermedades Raras (CIBERER), Madrid, 28029, Spain
- Fundación Pública Galega de Medicina Xenómica, Santiago de Compostela, 15706, Spain
- Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago, SERGAS, Santiago de Compostela, 15706, Spain
| | - Miguel de la Hoya
- Molecular Oncology Laboratory, CIBERONC, Hospital Clinico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Madrid, 28040, Spain
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, Helsinki University Hospital, University of Helsinki, Helsinki, 00290, Finland
| | - Mallika Dhawan
- Cancer Genetics and Prevention Program, University of California San Francisco, San Francisco, CA, 94143-1714, USA
| | - Valentina Zampiga
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Rita Danesi
- Romagna Cancer Registry, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, 47014, Italy
| | - Liliana Varesco
- Unit of Hereditary Cancer, IRCCS Ospedale Policlinico San Martino, Genoa, 16132, Italy
| | - Viviana Gismondi
- Unit of Hereditary Cancer, IRCCS Ospedale Policlinico San Martino, Genoa, 16132, Italy
| | | | - Paul A James
- Department of Gynecology and Obstetrics, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, 14049-900, Brazil
| | - Ramunas Janavicius
- Faculty of Medicine, Institute of Biomedical Sciences, Department of Human and Medical Genetics, Vilnius University, Vilnius, LT-03101, Lithuania
- State Research Institute Centre for Innovative Medicine, Vilnius, 8410, Lithuania
| | | | - Finn Cilius Nielsen
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, DK-2100, Denmark
| | - Thomas van Overeem Hansen
- Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Copenhagen, DK-2100, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, , University of Copenhagen, Copenhagen, 2200, Denmark
| | - Tanja Pejovic
- Department of Obstetrics and Gynecology, Oregon Health & Science University, Portland, OR, 97239, USA
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Ake Borg
- Department of Oncology, Lund University and Skåne University Hospital, Lund, 222 41, Sweden
| | - Johanna Rantala
- Clinical Genetics, Karolinska Institutet, Stockholm, 171 76, Sweden
| | - Kenneth Offit
- Clinical Genetics Research Lab, Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Marco Montagna
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV - IRCCS, Padua, 35128, Italy
| | - Katherine L Nathanson
- Basser Center for BRCA, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, 19066, USA
| | - Susan M Domchek
- Basser Center for BRCA, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, 19066, USA
| | - Ana Osorio
- Human Genetics Group, Spanish National Cancer Research Centre (CNIO), Madrid, 28029, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, 28029, Spain
- Genetics Service, Fundación Jiménez Díaz, Madrid, 28040, Spain
| | - María J García
- Computational Oncology Group, Structural Biology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, 28029, Spain
| | - Beth Y Karlan
- David Geffen School of Medicine, Department of Obstetrics and Gynecology, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Anna De Fazio
- The Daffodil Centre, The University of Sydney, a joint venture with Cancer Council NSW, Sydney, NSW, Australia
- Centre for Cancer Research, The Westmead Institute for Medical Research, Sydney, Australia
- Department of Gynaecological Oncology, Westmead Hospital, Sydney, NSW, 2145, Australia
- The University of Sydney, Sydney, NSW, 2145, Australia
| | - David Bowtell
- Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, 3000, Australia
| | - Lesley McGuffog
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Goska Leslie
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Michael T Parsons
- Population Health Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Thilo Dörk
- Gynaecology Research Unit, Hannover Medical School, Hannover, 30625, Germany
| | - Lisa-Marie Speith
- Gynaecology Research Unit, Hannover Medical School, Hannover, 30625, Germany
| | - Elizabeth Santana Dos Santos
- Service de Génétique, Institut Curie, Paris, 75005, France
- Oncology Center, Hospital Sirio-Libanes, São Paulo, 01308-050, Brazil
- Department of Clinical Oncology, A.C.Camargo Cancer Center, São Paulo, 1509900, Brazil
| | - Alexandre André B A da Costa
- Department of Clinical Oncology, A.C.Camargo Cancer Center, São Paulo, 1509900, Brazil
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 2215, USA
| | - Paolo Radice
- Unit of Preventive Medicine: Molecular Bases of Genetic Risk, Department of Experimental Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori (INT), Milan, 20133, Italy
| | - Paolo Peterlongo
- Genome Diagnostics Program, IFOM ETS - the AIRC Institute of Molecular Oncology, Milan, 20139, Italy
| | - Laura Papi
- Department of Experimental and Clinical Biomedical Sciences 'Mario Serio', Medical Genetics Unit, University of Florence, Florence, 27571, Italy
| | - Christoph Engel
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, 04107, Germany
- LIFE - Leipzig Research Centre for Civilization Diseases, University of Leipzig, Leipzig, 04103, Germany
| | - Eric Hahnen
- Center for Familial Breast and Ovarian Cancer, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, 50937, Germany
- Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, 50937, Germany
| | - Rita K Schmutzler
- Center for Familial Breast and Ovarian Cancer, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, 50937, Germany
- Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, 50937, Germany
- Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, 50931, Germany
| | - Barbara Wappenschmidt
- Center for Familial Breast and Ovarian Cancer, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, 50937, Germany
- Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, 50937, Germany
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Marc Tischkowitz
- Program in Cancer Genetics, Departments of Human Genetics and Oncology, McGill University, Montréal, QC, H4A 3J1, Canada
- Department of Medical Genetics, National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Christian F Singer
- Department of OB/GYN and Comprehensive Cancer Center, Medical University of Vienna, Vienna, 1090, Austria
| | - Yen Yen Tan
- Department of OB/GYN and Comprehensive Cancer Center, Medical University of Vienna, Vienna, 1090, Austria
| | - Alice S Whittemore
- Department of Epidemiology and Population Health, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Weiva Sieh
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - James D Brenton
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, CB2 0RE, UK
| | - Drakoulis Yannoukakos
- Molecular Diagnostics Laboratory, INRASTES, National Centre for Scientific Research 'Demokritos', Athens, 15310, Greece
| | - Florentia Fostira
- Molecular Diagnostics Laboratory, INRASTES, National Centre for Scientific Research 'Demokritos', Athens, 15310, Greece
| | - Irene Konstantopoulou
- Molecular Diagnostics Laboratory, INRASTES, National Centre for Scientific Research 'Demokritos', Athens, 15310, Greece
| | - Jana Soukupova
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, 12000, Czech Republic
| | - Michal Vocka
- Department of Oncology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, 12000, Czech Republic
| | - Georgia Chenevix-Trench
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Paul D P Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Antonis C Antoniou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - David E Goldgar
- Department of Dermatology, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, 84112, USA
| | - Amanda B Spurdle
- Population Health Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Kyriaki Michailidou
- Biostatistics Unit, The Cyprus Institute of Neurology and Genetics, Nicosia, 2371, Cyprus.
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK.
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15
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McLeod EV, Walsh JC, Haigney MC, Franzos MA, Hellwig LD. Exertional-Related Sudden Cardiac Death in a Young, Presumed Healthy, and Medically Screened Population: A Military Case Series. Am J Forensic Med Pathol 2023:00000433-990000000-00071. [PMID: 37093871 DOI: 10.1097/paf.0000000000000830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
ABSTRACT Sudden cardiac death (SCD) is defined as death from cardiac causes with loss of consciousness occurring within 1 hour of a change in cardiovascular status. As subset, SCD associated with physical exertion (SCD/E) can be defined as a cardiac event whose symptoms start during or within 1 hour of physical exertion. The US military represents a unique opportunity for studying SCD/E because of medical screening at recruitment, mandatory physical training, an active surveillance system, and centralized autopsy services. Because of medical screening, recruits are presumed healthy, but significant conditions can go undetected. We present 4 diverse cases of SCD/E in the military setting. Sudden cardiac death associated with physical exertion is often the first indication of a serious occult cardiac pathology. Postmortem genetic testing revealed a causative pathogenic mutation in 1 of 4 cases, enabling genetic testing of family members to prevent similar catastrophic loss of life, underscoring the importance of postmortem evaluation including genetic testing. Further investigations will help direct screening and prevention to capture those at risk for SCD. The cases presented in this series are a sample of the diverse etiologies and contexts surrounding SCD/E in the military setting that have been captured by Armed Forces Medical Examiner System.
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Affiliation(s)
- Elizabeth V McLeod
- From the National Capital Consortium, Walter Reed National Military Medical Center, Bethesda, MD
| | - John C Walsh
- Forensic Pathology Investigations, Armed Forces Medical Examiner System, Dover, DE
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16
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McKenna DB, Sanchez P, Powers J, Brower J, Wang L, Mueller R, Symecko H, Hamilton JG, Wildman T, Domchek SM, Couch FJ, Garber JE, Offit K, Robson ME, Katona BW. Summary of the experiences, knowledge, medical management, and family communication of monoallelic MUTYH carriers. J Genet Couns 2023; 32:342-350. [PMID: 36245263 PMCID: PMC10436665 DOI: 10.1002/jgc4.1641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 09/07/2022] [Accepted: 09/08/2022] [Indexed: 11/10/2022]
Abstract
Germline genetic testing for inherited cancer risk is increasingly being performed with multigene panel testing with MUTYH often included on colorectal cancer- and polyposis-focused panels, as well as on broader pan-cancer panels. With up to 1%-2% of the general population being monoallelic MUTYH carriers, pathogenic/likely pathogenic (P/LP) variants in MUTYH are one of the most common findings on multigene cancer panels. However, little is known about patient experience and understanding of monoallelic MUTYH P/LP variants, nor whether such findings influence medical management recommendations and familial communication, which this study aims to better understand. Monoallelic P/LP MUTYH carriers were recruited from the Prospective Registry of Multiplex Testing (PROMPT) and completed a cross-sectional self-report survey on sociodemographic characteristics, medical and family history, experiences with MUTYH genetic testing, genetics and MUTYH knowledge, perceived cancer risk, and familial communication. Of 115 eligible PROMPT participants, 49 (43%) completed the survey who were primarily female (94%), white (96%), had a history of cancer (61%), and a median age of 51.4 years. Most participants (61%) reported satisfaction with how their healthcare provider managed their genetic test result and care, and 65% of survey participants reported their provider recommended colonoscopy based on their genetic test results. Participants' responses also reflected variable levels of knowledge regarding cancer risks and screening recommendations for MUTYH carriers. The majority (98%) of participants shared their genetic test results with at least some of their relatives; however, only 13% of eligible relatives reportedly underwent cascade testing. Taken together, this study provides needed insight into the overall experiences of monoallelic MUTYH carriers and highlights numerous areas for improvement in clinician education, communication, and management of these individuals.
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Affiliation(s)
- Danielle B. McKenna
- Basser Center for BRCA, Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Pauleen Sanchez
- Basser Center for BRCA, Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jacquelyn Powers
- Basser Center for BRCA, Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jamie Brower
- Basser Center for BRCA, Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Louise Wang
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Rebecca Mueller
- Basser Center for BRCA, Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Heather Symecko
- Basser Center for BRCA, Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jada G. Hamilton
- Department of Psychiatry & Behavioral Sciences, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Weill Cornell Medical College, New York, New York, USA
| | - Temima Wildman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Susan M. Domchek
- Basser Center for BRCA, Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Fergus J. Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Judy E. Garber
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Kenneth Offit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Weill Cornell Medical College, New York, New York, USA
| | - Mark E. Robson
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Weill Cornell Medical College, New York, New York, USA
| | - Bryson W. Katona
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
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17
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Lux MP, Fasching PA. Breast Cancer and Genetic BRCA1/2 Testing in Routine Clinical Practice: Why, When and For Whom? Geburtshilfe Frauenheilkd 2023; 83:310-320. [PMID: 36908286 PMCID: PMC9998182 DOI: 10.1055/a-1929-2629] [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: 12/02/2022] [Accepted: 12/06/2022] [Indexed: 03/12/2023] Open
Abstract
Pathogenic variants of the tumor suppressor genes BRCA1 and BRCA2 are responsible for the majority of hereditary breast cancers; they are also becoming increasingly important to identify whether patients are suitable for targeted therapy with poly ADP-ribose polymerase inhibitors (PARPi). Patients with HER2-negative breast cancer and BRCA1/2 germline mutations can benefit significantly from PARPi therapy, and the findings of the OlympiAD and the EMBRACA phase III clinical trials for regulatory approval were recently expanded by the addition of the most recent OlympiA data on the treatment of patients with early disease and a high risk of recurrence. This means that BRCA1/2 germline testing to plan patient therapy is now also relevant for patients with early breast cancer and therefore has a direct impact on survival. Healthcare research data shows, however, that BRCA1/2 testing rates are strongly affected by familial history, cancer subtype (particularly triple-negative subtypes), and patient age at onset of disease (especially with regards to younger patients with breast cancer), despite the existing clear recommendations for BRCA1/2 germline testing to identify whether PARPi therapy is indicated. This article presents the clinical implications of identifying BRCA1/2 germline mutations in patients with breast cancer, the current recommendations on molecular diagnostics, and their implementation in practice. The treatment of patients with breast cancer has progressed greatly in recent years and now offers individual treatment concepts which can only be implemented after the targeted identification of individual parameters. As detection of a BRCA1/2 germline mutation is essential for planning individual therapy, where indicated, testing should be arranged as early as possible. It is the only way of identifying patients suitable for PARPi therapy and ensuring they receive the best possible treatment. This also applies to patients with a negative familial history, HR-positive disease, or who are older at onset of disease.
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Affiliation(s)
- Michael P. Lux
- Klinik für Gynäkologie und Geburtshilfe, Frauenklinik St. Louise, Paderborn, St. Josefs-Krankenhaus, Salzkotten, St. Vincenz Kliniken, Paderborn, Paderborn, Germany
| | - Peter A. Fasching
- Frauenklinik, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
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18
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Caleca L, Radice P. Refinement of the assignment to the ACMG/AMP BS3 and PS3 criteria of eight BRCA1 variants of uncertain significance by integrating available functional data with protein interaction assays. Front Oncol 2023; 13:1146604. [PMID: 37168384 PMCID: PMC10164951 DOI: 10.3389/fonc.2023.1146604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 04/06/2023] [Indexed: 05/13/2023] Open
Abstract
The clinical screening of cancer predisposition genes has led to the identification of a large number of variants of uncertain significance (VUS). Multifactorial likelihood models that predict the odds ratio for VUS in favor or against cancer causality, have been developed, but their use is limited by the amount of necessary data, which are difficult to obtain for rare variants. The guidelines for variant interpretation of the American College of Medical Genetics and Genomics along with the Association for Molecular Pathology (ACMG/AMP) state that "well-established" functional studies provide strong support of a pathogenic or benign impact (criteria PS3 and BS3, respectively) and can be used as evidence type to reach a final classification. Moreover, the Clinical Genome Resource Sequence Variant Interpretation Working Group developed rule specifications to refine the PS3/BS3 criteria. Recently, Lira PC et al. developed the "Hi Set" approach that generated PS3/BS3 codes for over two-thousands BRCA1 VUS. While highly successful, this approach did not discriminate a group of variants with conflicting evidences. Here, we aimed to implement the outcomes of the "Hi-set" approach applying Green Fluorescent Protein (GFP)-reassembly assays, assessing the effect of variants in the RING and BRCT domains of BRCA1 on the binding of these domains with the UbcH5a or ABRAXAS proteins, respectively. The analyses of 26 clinically classified variants, including 13 tested in our previous study, showed 100% sensitivity and specificity in identifying pathogenic and benign variants for both the RING/UbcH5a and the BRCTs/ABRAXAS interactions. We derived the strength of evidences generated by the GFP-reassembly assays corresponding to moderate for both PS3 and BS3 criteria assessment. The GFP-reassembly assays were applied to the functional characterization of 8 discordant variants from the study by Lyra et al. The outcomes of these analyses, combined with those reported in the "Hi Set" study, allowed the assignment of ACMG/AMP criteria in favor or against pathogenicity for all 8 examined variants. The above findings were validated with a semi-quantitative Mammalian Two-Hybrid approach, and totally concordant results were observed. Our data contributes in shedding light on the functional significance of BRCA1 VUS and on their clinical interpretation within the ACMG/AMP framework.
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19
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Muacevic A, Adler JR, Torres-Lopez D, Olaya L, Gutierrez-Vargas M, Olaya G, Olaya JD. Sociodemographic, Clinical, and Variation Outcomes for Breast Cancer and Breast Cancer-Related Mutations in a Ten-Year Cohort From Neiva, Huila, Colombia. Cureus 2022; 14:e32257. [PMID: 36620844 PMCID: PMC9815492 DOI: 10.7759/cureus.32257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/06/2022] [Indexed: 12/12/2022] Open
Abstract
Background Some breast cancer cases are related to inherited mutations, and this is the reason why early mutation screening is emerging as an area of focus for cost-effective care. However, breast cancer-related mutations vary according to race, ethnicity, geographic origin, and healthcare access. Surveillance for familial breast cancer is not performed routinely in Colombia. Our main aim in this study was to describe a cohort of breast cancer patients, carrying founder breast cancer gene (BRCA) mutations, which were followed up for up to 10 years (2010-2019) in Neiva, Colombia. Methods We performed a retrospective description from an outpatient care center in Huila, Colombia, a region with high breast cancer rates. This study included patients with both a breast cancer diagnosis and an incident genetic mutation for breast cancer (detected during a breast cancer consultation). We captured information from patient medical records. Descriptive analyses were performed. Results A total of 105 patients met the study's inclusion criteria and were included patients with the BRCA1 mutation and three with BRCA2 mutations. They had a median age of 45 years (IQR, 36 to 51 years). Relatives with a breast cancer history were found in 74 carriers (70.5%). Most patients had a report of Breast Imaging-Reporting and Data System (BIRADS) ≥ 4. A TNM (tumor, node, metastasis) changed reclassification was observed in anatomical vs. prognostic classification. Median follow-up was of 74 months (IQR, 44 to 130), overall observed mortality was 22.9%, and specific mortality was 19.1%. Conclusion Women with breast cancer who carry a mutation related to breast cancer are usually younger than age 50 at diagnosis. Developing strategies and specific policies for this population is needed, and a prevalent BRCA1 c.3331_3334delCAAG mutation could be used as a cost-effective first approach. Among these patients, a risk-increased reclassification was observed.
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20
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Khandakji MN, Mifsud B. Gene-specific machine learning model to predict the pathogenicity of BRCA2 variants. Front Genet 2022; 13:982930. [PMID: 36246618 PMCID: PMC9561395 DOI: 10.3389/fgene.2022.982930] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/12/2022] [Indexed: 11/18/2022] Open
Abstract
Background: Existing BRCA2-specific variant pathogenicity prediction algorithms focus on the prediction of the functional impact of a subtype of variants alone. General variant effect predictors are applicable to all subtypes, but are trained on putative benign and pathogenic variants and do not account for gene-specific information, such as hotspots of pathogenic variants. Local, gene-specific information have been shown to aid variant pathogenicity prediction; therefore, our aim was to develop a BRCA2-specific machine learning model to predict pathogenicity of all types of BRCA2 variants. Methods: We developed an XGBoost-based machine learning model to predict pathogenicity of BRCA2 variants. The model utilizes general variant information such as position, frequency, and consequence for the canonical BRCA2 transcript, as well as deleteriousness prediction scores from several tools. We trained the model on 80% of the expert reviewed variants by the Evidence-Based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) consortium and tested its performance on the remaining 20%, as well as on an independent set of variants of uncertain significance with experimentally determined functional scores. Results: The novel gene-specific model predicted the pathogenicity of ENIGMA BRCA2 variants with an accuracy of 99.9%. The model also performed excellently on predicting the functional consequence of the independent set of variants (accuracy was up to 91.3%). Conclusion: This new, gene-specific model is an accurate method for interpreting the pathogenicity of variants in the BRCA2 gene. It is a valuable addition for variant classification and can prioritize unreviewed variants for functional analysis or expert review.
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Affiliation(s)
- Mohannad N. Khandakji
- College of Health and Life Sciences, Hamad Bin Khalifa University, Ar-Rayyan, Qatar
- Hamad Medical Corporation, Doha, Qatar
| | - Borbala Mifsud
- College of Health and Life Sciences, Hamad Bin Khalifa University, Ar-Rayyan, Qatar
- William Harvey Research Institute, Queen Mary University of London, London, United Kingdom
- *Correspondence: Borbala Mifsud,
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21
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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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22
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Valenzuela-Palomo A, Sanoguera-Miralles L, Bueno-Martínez E, Esteban-Sánchez A, Llinares-Burguet I, García-Álvarez A, Pérez-Segura P, Gómez-Barrero S, de la Hoya M, Velasco-Sampedro EA. Splicing Analysis of 16 PALB2 ClinVar Variants by Minigene Assays: Identification of Six Likely Pathogenic Variants. Cancers (Basel) 2022; 14:cancers14184541. [PMID: 36139699 PMCID: PMC9496955 DOI: 10.3390/cancers14184541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/12/2022] [Accepted: 09/15/2022] [Indexed: 11/29/2022] Open
Abstract
PALB2 loss-of-function variants are associated with significant increased risk of breast cancer as well as other types of tumors. Likewise, splicing disruptions are a common mechanism of disease susceptibility. Indeed, we previously showed, by minigene assays, that 35 out of 42 PALB2 variants impaired splicing. Taking advantage of one of these constructs (mgPALB2_ex1-3), we proceeded to analyze other variants at exons 1 to 3 reported at the ClinVar database. Thirty-one variants were bioinformatically analyzed with MaxEntScan and SpliceAI. Then, 16 variants were selected for subsequent RNA assays. We identified a total of 12 spliceogenic variants, 11 of which did not produce any trace of the expected minigene full-length transcript. Interestingly, variant c.49-1G > A mimicked previous outcomes in patient RNA (transcript ∆(E2p6)), supporting the reproducibility of the minigene approach. A total of eight variant-induced transcripts were characterized, three of which (∆(E1q17), ∆(E3p11), and ∆(E3)) were predicted to introduce a premature termination codon and to undergo nonsense-mediated decay, and five (▼(E1q9), ∆(E2p6), ∆(E2), ▼(E3q48)-a, and ▼(E3q48)-b) maintained the reading frame. According to an ACMG/AMP (American College of Medical Genetics and Genomics/Association for Molecular Pathology)-based classification scheme, which integrates mgPALB2 data, six PALB2 variants were classified as pathogenic/likely pathogenic, five as VUS, and five as likely benign. Furthermore, five ±1,2 variants were catalogued as VUS because they produced significant proportions of in-frame transcripts of unknown impact on protein function.
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Affiliation(s)
- Alberto Valenzuela-Palomo
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC-UVa), 47003 Valladolid, Spain
| | - Lara Sanoguera-Miralles
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC-UVa), 47003 Valladolid, Spain
| | - Elena Bueno-Martínez
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC-UVa), 47003 Valladolid, Spain
| | - Ada Esteban-Sánchez
- Molecular Oncology Laboratory, Hospital Clínico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), 28040 Madrid, Spain
| | - Inés Llinares-Burguet
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC-UVa), 47003 Valladolid, Spain
| | - Alicia García-Álvarez
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC-UVa), 47003 Valladolid, Spain
| | - Pedro Pérez-Segura
- Molecular Oncology Laboratory, Hospital Clínico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), 28040 Madrid, Spain
| | - Susana Gómez-Barrero
- Facultad de Ciencias de la Salud, Universidad Alfonso X “El Sabio”, Avda. de la Universidad 1, Villanueva de la Cañada, 28691 Madrid, Spain
| | - Miguel de la Hoya
- Molecular Oncology Laboratory, Hospital Clínico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), 28040 Madrid, Spain
| | - Eladio A. Velasco-Sampedro
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC-UVa), 47003 Valladolid, Spain
- Correspondence:
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23
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Ceyhan-Birsoy O, Jayakumaran G, Kemel Y, Misyura M, Aypar U, Jairam S, Yang C, Li Y, Mehta N, Maio A, Arnold A, Salo-Mullen E, Sheehan M, Syed A, Walsh M, Carlo M, Robson M, Offit K, Ladanyi M, Reis-Filho JS, Stadler ZK, Zhang L, Latham A, Zehir A, Mandelker D. Diagnostic yield and clinical relevance of expanded genetic testing for cancer patients. Genome Med 2022; 14:92. [PMID: 35971132 PMCID: PMC9377129 DOI: 10.1186/s13073-022-01101-2] [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: 04/08/2022] [Accepted: 08/03/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genetic testing (GT) for hereditary cancer predisposition is traditionally performed on selected genes based on established guidelines for each cancer type. Recently, expanded GT (eGT) using large hereditary cancer gene panels uncovered hereditary predisposition in a greater proportion of patients than previously anticipated. We sought to define the diagnostic yield of eGT and its clinical relevance in a broad cancer patient population over a 5-year period. METHODS A total of 17,523 cancer patients with a broad range of solid tumors, who received eGT at Memorial Sloan Kettering Cancer Center between July 2015 to April 2020, were included in the study. The patients were unselected for current GT criteria such as cancer type, age of onset, and/or family history of disease. The diagnostic yield of eGT was determined for each cancer type. For 9187 patients with five common cancer types frequently interrogated for hereditary predisposition (breast, colorectal, ovarian, pancreatic, and prostate cancer), the rate of pathogenic/likely pathogenic (P/LP) variants in genes that have been associated with each cancer type was analyzed. The clinical implications of additional findings in genes not known to be associated with a patients' cancer type were investigated. RESULTS 16.7% of patients in a broad cancer cohort had P/LP variants in hereditary cancer predisposition genes identified by eGT. The diagnostic yield of eGT in patients with breast, colorectal, ovarian, pancreatic, and prostate cancer was 17.5%, 15.3%, 24.2%, 19.4%, and 15.9%, respectively. Additionally, 8% of the patients with five common cancers had P/LP variants in genes not known to be associated with the patient's current cancer type, with 0.8% of them having such a variant that confers a high risk for another cancer type. Analysis of clinical and family histories revealed that 74% of patients with variants in genes not associated with their current cancer type but which conferred a high risk for another cancer did not meet the current GT criteria for the genes harboring these variants. One or more variants of uncertain significance were identified in 57% of the patients. CONCLUSIONS Compared to targeted testing approaches, eGT can increase the yield of detection of hereditary cancer predisposition in patients with a range of tumors, allowing opportunities for enhanced surveillance and intervention. The benefits of performing eGT should be weighed against the added number of VUSs identified with this approach.
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Affiliation(s)
- Ozge Ceyhan-Birsoy
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Gowtham Jayakumaran
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yelena Kemel
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maksym Misyura
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Umut Aypar
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sowmya Jairam
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ciyu Yang
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yirong Li
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nikita Mehta
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anna Maio
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Angela Arnold
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Erin Salo-Mullen
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Margaret Sheehan
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Aijazuddin Syed
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael Walsh
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maria Carlo
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mark Robson
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kenneth Offit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marc Ladanyi
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jorge S Reis-Filho
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Zsofia K Stadler
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Liying Zhang
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Present Address: Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles (UCLA), Los Angeles, CA, USA
| | - Alicia Latham
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ahmet Zehir
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Present Address: Precision Medicine and Biosamples, Oncology R&D, AstraZeneca, New York, NY, USA.
| | - Diana Mandelker
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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24
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Beinse G, Just PA, Le Frere Belda MA, Laurent-Puig P, Jacques S, Koual M, Garinet S, Leroy K, Delanoy N, Blons H, Gervais C, Durdux C, Chapron C, Goldwasser F, Terris B, Badoual C, Taly V, Bats AS, Borghese B, Alexandre J. Discovery and validation of a transcriptional signature identifying homologous recombination-deficient breast, endometrial and ovarian cancers. Br J Cancer 2022; 127:1123-1132. [PMID: 35752712 DOI: 10.1038/s41416-022-01900-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 06/03/2022] [Accepted: 06/15/2022] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Molecular alterations leading to homologous recombination deficiency (HRD) are heterogeneous. We aimed to identify a transcriptional profile shared by endometrial (UCEC), breast (BRCA) and ovarian (OV) cancers with HRD. METHODS Genes differentially expressed with HRD genomic score (continuous gHRD score) in UCEC/BRCA/OV were identified using edgeR, and used to train a RNAseq score (ridge-regression model) predictive of the gHRD score (PanCanAtlas, N = 1684 samples). The RNAseq score was applied in independent gynaecological datasets (CARPEM/CPTAC/SCAN/TCGA, N = 4038 samples). Validations used ROC curves, linear regressions and Pearson correlations. Overall survival (OS) analyses used Kaplan-Meier curves and Cox models. RESULTS In total, 656 genes were commonly up/downregulated with gHRD score in UCEC/BRCA/OV. Upregulated genes were enriched for nuclear/chromatin/DNA-repair processes, while downregulated genes for cytoskeleton (gene ontologies). The RNAseq score correlated with gHRD score in independent gynaecological cancers (R² = 0.4-0.7, Pearson correlation = 0.64-0.86, all P < 10-11), and was predictive of gHRD score >42 (RNAseq HRD profile; AUC = 0.95/0.92/0.78 in UCEC/BRCA/OV). RNAseq HRD profile was associated (i) with better OS in platinum-treated advanced TP53-mutated-UCEC (P < 0.001) and OV (P = 0.013), and (ii) with poorer OS (P < 0.001) and higher benefit of adjuvant chemotherapy in Stage I-III BRCA (interaction test, P < 0.001). CONCLUSIONS UCEC/BRCA/OV with HRD-associated genomic scars share a common transcriptional profile. RNAseq signatures might be relevant for identifying HRD-gynaecological cancers, for prognostication and for therapeutic decision.
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Affiliation(s)
- Guillaume Beinse
- Centre de Recherche des Cordeliers, « Equipe labélisée Ligue Contre le Cancer », CNRS SNC 5096, Sorbonne Université, Université de Paris Cité, INSERM, Paris, France.,Institut du Cancer Paris CARPEM, AP-HP, APHP.Centre, Department of Medical Oncology, Hopital Cochin, Paris, France
| | - Pierre-Alexandre Just
- Institut du Cancer Paris CARPEM, AP-HP, APHP.Centre, Department of Pathology, Hopital Cochin, Paris, France.,Université de Paris Cité, Paris, France
| | - Marie-Aude Le Frere Belda
- Institut du Cancer Paris CARPEM, AP-HP, APHP.Centre, Department of Pathology, Hopital Européen Georges Pompidou, Paris, France
| | - Pierre Laurent-Puig
- Centre de Recherche des Cordeliers, « Equipe labélisée Ligue Contre le Cancer », CNRS SNC 5096, Sorbonne Université, Université de Paris Cité, INSERM, Paris, France.,Université de Paris Cité, Paris, France.,Institut du Cancer Paris CARPEM, AP-HP, APHP.Centre, Department of Biology, Hopital Européen Georges Pompidou, Paris, France.,Institut du Cancer Paris CARPEM, AP-HP, APHP.Centre, Paris, France
| | | | - Meriem Koual
- Université de Paris Cité, Paris, France.,Institut du Cancer Paris CARPEM, AP-HP, APHP.Centre, Department of Gynecological Surgery, Hopital Européen Georges Pompidou, Paris, France
| | - Simon Garinet
- Centre de Recherche des Cordeliers, « Equipe labélisée Ligue Contre le Cancer », CNRS SNC 5096, Sorbonne Université, Université de Paris Cité, INSERM, Paris, France.,Université de Paris Cité, Paris, France.,Institut du Cancer Paris CARPEM, AP-HP, APHP.Centre, Department of Biology, Hopital Européen Georges Pompidou, Paris, France
| | - Karen Leroy
- Université de Paris Cité, Paris, France.,Institut du Cancer Paris CARPEM, AP-HP, APHP.Centre, Department of Biology, Hopital Européen Georges Pompidou, Paris, France
| | - Nicolas Delanoy
- Institut du Cancer Paris CARPEM, AP-HP, APHP.Centre, Department of Medical Oncology, Hopital Européen Georges Pompidou, Paris, France
| | - Helene Blons
- Université de Paris Cité, Paris, France.,Institut du Cancer Paris CARPEM, AP-HP, APHP.Centre, Department of Biology, Hopital Européen Georges Pompidou, Paris, France
| | - Claire Gervais
- Université de Paris Cité, Paris, France.,Institut du Cancer Paris CARPEM, AP-HP, APHP.Centre, Department of Medical Oncology, Hopital Européen Georges Pompidou, Paris, France
| | - Catherine Durdux
- Université de Paris Cité, Paris, France.,Institut du Cancer Paris CARPEM, AP-HP, APHP.Centre, Department of Radiotherapy, Hopital Européen Georges Pompidou, Paris, France
| | - Charles Chapron
- Université de Paris Cité, Paris, France.,Institut du Cancer Paris CARPEM, AP-HP, APHP.Centre, Department of Gynecological Surgery, Hopital Cochin, Paris, France
| | - François Goldwasser
- Institut du Cancer Paris CARPEM, AP-HP, APHP.Centre, Department of Medical Oncology, Hopital Cochin, Paris, France.,Université de Paris Cité, Paris, France
| | - Benoit Terris
- Institut du Cancer Paris CARPEM, AP-HP, APHP.Centre, Department of Pathology, Hopital Cochin, Paris, France.,Université de Paris Cité, Paris, France
| | - Cecile Badoual
- Université de Paris Cité, Paris, France.,Institut du Cancer Paris CARPEM, AP-HP, APHP.Centre, Department of Pathology, Hopital Européen Georges Pompidou, Paris, France
| | - Valerie Taly
- Centre de Recherche des Cordeliers, « Equipe labélisée Ligue Contre le Cancer », CNRS SNC 5096, Sorbonne Université, Université de Paris Cité, INSERM, Paris, France
| | - Anne-Sophie Bats
- Centre de Recherche des Cordeliers, « Equipe labélisée Ligue Contre le Cancer », CNRS SNC 5096, Sorbonne Université, Université de Paris Cité, INSERM, Paris, France.,Université de Paris Cité, Paris, France.,Institut du Cancer Paris CARPEM, AP-HP, APHP.Centre, Department of Gynecological Surgery, Hopital Européen Georges Pompidou, Paris, France
| | - Bruno Borghese
- Centre de Recherche des Cordeliers, « Equipe labélisée Ligue Contre le Cancer », CNRS SNC 5096, Sorbonne Université, Université de Paris Cité, INSERM, Paris, France.,Université de Paris Cité, Paris, France.,Institut du Cancer Paris CARPEM, AP-HP, APHP.Centre, Department of Gynecological Surgery, Hopital Cochin, Paris, France
| | - Jérôme Alexandre
- Centre de Recherche des Cordeliers, « Equipe labélisée Ligue Contre le Cancer », CNRS SNC 5096, Sorbonne Université, Université de Paris Cité, INSERM, Paris, France. .,Institut du Cancer Paris CARPEM, AP-HP, APHP.Centre, Department of Medical Oncology, Hopital Cochin, Paris, France. .,Université de Paris Cité, Paris, France.
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25
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Aljarf R, Shen M, Pires DEV, Ascher DB. Understanding and predicting the functional consequences of missense mutations in BRCA1 and BRCA2. Sci Rep 2022; 12:10458. [PMID: 35729312 PMCID: PMC9213547 DOI: 10.1038/s41598-022-13508-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 05/25/2022] [Indexed: 11/21/2022] Open
Abstract
BRCA1 and BRCA2 are tumour suppressor genes that play a critical role in maintaining genomic stability via the DNA repair mechanism. DNA repair defects caused by BRCA1 and BRCA2 missense variants increase the risk of developing breast and ovarian cancers. Accurate identification of these variants becomes clinically relevant, as means to guide personalized patient management and early detection. Next-generation sequencing efforts have significantly increased data availability but also the discovery of variants of uncertain significance that need interpretation. Experimental approaches used to measure the molecular consequences of these variants, however, are usually costly and time-consuming. Therefore, computational tools have emerged as faster alternatives for assisting in the interpretation of the clinical significance of newly discovered variants. To better understand and predict variant pathogenicity in BRCA1 and BRCA2, various machine learning algorithms have been proposed, however presented limited performance. Here we present BRCA1 and BRCA2 gene-specific models and a generic model for quantifying the functional impacts of single-point missense variants in these genes. Across tenfold cross-validation, our final models achieved a Matthew's Correlation Coefficient (MCC) of up to 0.98 and comparable performance of up to 0.89 across independent, non-redundant blind tests, outperforming alternative approaches. We believe our predictive tool will be a valuable resource for providing insights into understanding and interpreting the functional consequences of missense variants in these genes and as a tool for guiding the interpretation of newly discovered variants and prioritizing mutations for experimental validation.
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Affiliation(s)
- Raghad Aljarf
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC, 3004, Australia.,Department of Biochemistry and Pharmacology, University of Melbourne, Melbourne, VIC, 3010, Australia.,Systems and Computational Biology, Bio21 Institute, University of Melbourne, 30 Flemington Rd, Parkville, VIC, 3052, Australia
| | - Mengyuan Shen
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC, 3004, Australia.,Department of Biochemistry and Pharmacology, University of Melbourne, Melbourne, VIC, 3010, Australia.,Systems and Computational Biology, Bio21 Institute, University of Melbourne, 30 Flemington Rd, Parkville, VIC, 3052, Australia.,School of Computing and Information Systems, University of Melbourne, Melbourne, VIC, 3053, Australia
| | - Douglas E V Pires
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC, 3004, Australia. .,Department of Biochemistry and Pharmacology, University of Melbourne, Melbourne, VIC, 3010, Australia. .,Systems and Computational Biology, Bio21 Institute, University of Melbourne, 30 Flemington Rd, Parkville, VIC, 3052, Australia. .,School of Computing and Information Systems, University of Melbourne, Melbourne, VIC, 3053, Australia.
| | - David B Ascher
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC, 3004, Australia. .,Department of Biochemistry and Pharmacology, University of Melbourne, Melbourne, VIC, 3010, Australia. .,Systems and Computational Biology, Bio21 Institute, University of Melbourne, 30 Flemington Rd, Parkville, VIC, 3052, Australia. .,Department of Biochemistry, University of Cambridge, 80 Tennis Ct Rd, Cambridge, CB2 1GA, UK.
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26
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Iversen ES, Lipton G, Hart SN, Lee KY, Hu C, Polley EC, Pesaran T, Yussuf A, LaDuca H, Chao E, Karam R, Goldgar DE, Couch FJ, Monteiro ANA. An integrative model for the comprehensive classification of BRCA1 and BRCA2 variants of uncertain clinical significance. NPJ Genom Med 2022; 7:35. [PMID: 35665744 PMCID: PMC9166814 DOI: 10.1038/s41525-022-00302-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 05/04/2022] [Indexed: 12/14/2022] Open
Abstract
Loss-of-function variants in the BRCA1 and BRCA2 susceptibility genes predispose carriers to breast and/or ovarian cancer. The use of germline testing panels containing these genes has grown dramatically, but the interpretation of the results has been complicated by the identification of many sequence variants of undefined cancer relevance, termed "Variants of Uncertain Significance (VUS)." We have developed functional assays and a statistical model called VarCall for classifying BRCA1 and BRCA2 VUS. Here we describe a multifactorial extension of VarCall, called VarCall XT, that allows for co-analysis of multiple forms of genetic evidence. We evaluated the accuracy of models defined by the combinations of functional, in silico protein predictors, and family data for VUS classification. VarCall XT classified variants of known pathogenicity status with high sensitivity and specificity, with the functional assays contributing the greatest predictive power. This approach could be used to identify more patients that would benefit from personalized cancer risk assessment and management.
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Affiliation(s)
- Edwin S. Iversen
- grid.26009.3d0000 0004 1936 7961Department of Statistical Science, Duke University, Durham, NC 27708 USA
| | - Gary Lipton
- grid.26009.3d0000 0004 1936 7961Department of Statistical Science, Duke University, Durham, NC 27708 USA
| | - Steven N. Hart
- grid.66875.3a0000 0004 0459 167XDepartment of Health Sciences Research, Mayo Clinic, Rochester, MN 55901 USA
| | - Kun Y. Lee
- grid.66875.3a0000 0004 0459 167XDepartment of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55902 USA
| | - Chunling Hu
- grid.66875.3a0000 0004 0459 167XDepartment of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55902 USA
| | - Eric C. Polley
- grid.66875.3a0000 0004 0459 167XDepartment of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55902 USA
| | - Tina Pesaran
- grid.465138.d0000 0004 0455 211XAmbry Genetics Corporation, Aliso Viejo, CA 92656 USA
| | - Amal Yussuf
- grid.465138.d0000 0004 0455 211XAmbry Genetics Corporation, Aliso Viejo, CA 92656 USA
| | - Holly LaDuca
- grid.465138.d0000 0004 0455 211XAmbry Genetics Corporation, Aliso Viejo, CA 92656 USA
| | - Elizabeth Chao
- grid.465138.d0000 0004 0455 211XAmbry Genetics Corporation, Aliso Viejo, CA 92656 USA
| | - Rachid Karam
- grid.465138.d0000 0004 0455 211XAmbry Genetics Corporation, Aliso Viejo, CA 92656 USA
| | - David E. Goldgar
- grid.223827.e0000 0001 2193 0096Department of Dermatology, University of Utah School of Medicine, Salt Lake City, UT 84132 USA
| | - Fergus J. Couch
- grid.66875.3a0000 0004 0459 167XDepartment of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55902 USA
| | - Alvaro N. A. Monteiro
- grid.468198.a0000 0000 9891 5233Cancer Epidemiology Program, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612 USA
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27
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Gervas P, Molokov A, Babyshkina N, Kiselev A, Zarubin A, Yumov E, Pisareva L, Choynzonov E, Cherdyntseva N. Pathogenicity Reclassification of Genetic Variants Related to Early-Onset Breast Cancer among Women of Mongoloid Origin. Asian Pac J Cancer Prev 2022; 23:2027-2033. [PMID: 35763645 PMCID: PMC9587833 DOI: 10.31557/apjcp.2022.23.6.2027] [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: 02/04/2022] [Accepted: 06/24/2022] [Indexed: 06/15/2023] Open
Abstract
BACKGROUND Germline alterations in BRCA1, BRCA2, and other genes are responsible for early-onset breast cancer. However, up to 20% of molecular tests report genetic variant of unknown significance (VUS) or novel variants that have never been previously described and their clinical significance are unknown. This study aimed to reclassify variant of unknown significance (VUS) or novel variants by using the ActiveDriveDB database that annotates variants through the lens of sites of post-translational modifications (PTM). METHODS Our study included thirty-eighth young Buryat BC patients, belonging to the Mongoloid race and anthropologically to the Central Asia. Genomic DNA was extracted from the peripheral blood lymphocytes using the phenol/chloroform method. DNA library were prepared using the Hereditary Cancer SolutionTM kit (Sophia GENETICS, Switzerland) to cover 27 genes, such as ATM, APC, BARD1, BRCA1, BRCA2, BRIP1, CDH1, CHEK2, EPCAM, FAM175A, MLH1, MRE11A, MSH2, MSH6, MUTYH, NBN, PALB2, PIK3CA, PMS2, PMS2CL, PTEN, RAD50, RAD51C, RAD51D, STK11, TP53, and XRCC2. Paired-end sequencing (2 x 150 bp) was conducted using NextSeq 500 system (Illumina, USA). RESULTS We re-examined 135 rare variants (41 VUS, 25 conflicting, 64 benign and 5 new variants). We identified 10 out of 135 (7.4%) mutations that affected the sites of post-translational modification in proteins. Of 135 rare mutations, 1 benign variant was reclassified as network-rewiring - motif loss mutation, 3 VUS and 1 new variant were reclassified as distal PTM- mutations, 2 new and 1 benign variant were classified as proximal PTM- mutations and 1 benign and 1 conflicting variant were classified as direct PTM- mutations. CONCLUSIONS For the first time, 7.4% (10 out of 135) of mutations that affected the sites of post-translational modification in proteins were identified among early-onset breast cancer women of Mongoloid origin.
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Affiliation(s)
- Polina Gervas
- Department of Molecular oncology and Immunology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Science, Tomsk, Russia.
| | - Aleksey Molokov
- Department of Molecular oncology and Immunology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Science, Tomsk, Russia.
| | - Nataliya Babyshkina
- Department of Molecular oncology and Immunology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Science, Tomsk, Russia.
| | - Artem Kiselev
- Almazov National Medical Research Centre, St. Petersburg, Russia.
| | - Aleksei Zarubin
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russia.
| | - Evgeny Yumov
- Department of Surgery, GBUZ “Buryat Republican clinical oncology dispensary”, Republic of Buryatia, Ulan-Ude, Russia.
| | - Lubov Pisareva
- Department of Molecular oncology and Immunology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Science, Tomsk, Russia.
| | - Evgeny Choynzonov
- Department of Molecular oncology and Immunology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Science, Tomsk, Russia.
| | - Nadezda Cherdyntseva
- Department of Molecular oncology and Immunology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Science, Tomsk, Russia.
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28
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Kwong A, Ho CYS, Shin VY, Au CH, Chan TL, Ma ESK. How does re-classification of variants of unknown significance (VUS) impact the management of patients at risk for hereditary breast cancer? BMC Med Genomics 2022; 15:122. [PMID: 35641994 PMCID: PMC9158111 DOI: 10.1186/s12920-022-01270-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 03/30/2022] [Indexed: 11/23/2022] Open
Abstract
Background The popularity of multigene testing increases the probability of identifying variants of uncertain significance (VUS). While accurate variant interpretation enables clinicians to be better informed of the genetic risk of their patients, currently, there is a lack of consensus management guidelines for clinicians on VUS. Methods Among the BRCA1 and BRCA2 mutations screening in 3,544 subjects, 236 unique variants (BRCA1: 86; BRCA2: 150) identified in 459 patients were being reviewed. These variants consist of 231 VUS and 5 likely benign variants at the initial classification. Results The variants in 31.8% (146/459) patients were reclassified during the review, which involved 26 unique variants (11.0%). Also, 31 probands (6.8%) and their family members were offered high-risk surveillance and related management after these variants were reclassified to pathogenic or likely pathogenic. At the same time, 69 probands (15%) had their VUS downgraded to cancer risk equivalent to the general population level. Conclusion A review of archival variants from BRCA1 and BRCA2 genetic testing changed the management for 31.8% of the families due to increased or reduced risk. We encourage regular updates of variant databases, reference to normal population and collaboration between research laboratories on functional studies to define the clinical significances of VUS better. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-022-01270-4.
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Affiliation(s)
- Ava Kwong
- Chief of Breast Surgery Division, Department of Surgery, The University of Hong Kong and University of Hong Kong-Shenzhen Hospital, Pokfulam, Hong Kong SAR. .,Department of Surgery, Hong Kong Sanatorium & Hospital, Happy Valley, Hong Kong SAR. .,Hong Kong Hereditary Breast Cancer Family Registry, Shau Kei Wan, Hong Kong SAR.
| | - Cecilia Yuen Sze Ho
- Department of Molecular Pathology, Hong Kong Sanatorium & Hospital, Happy Valley, Hong Kong SAR
| | - Vivian Yvonne Shin
- Chief of Breast Surgery Division, Department of Surgery, The University of Hong Kong and University of Hong Kong-Shenzhen Hospital, Pokfulam, Hong Kong SAR
| | - Chun Hang Au
- Department of Molecular Pathology, Hong Kong Sanatorium & Hospital, Happy Valley, Hong Kong SAR
| | - Tsun-Leung Chan
- Hong Kong Hereditary Breast Cancer Family Registry, Shau Kei Wan, Hong Kong SAR.,Department of Molecular Pathology, Hong Kong Sanatorium & Hospital, Happy Valley, Hong Kong SAR
| | - Edmond Shiu Kwan Ma
- Hong Kong Hereditary Breast Cancer Family Registry, Shau Kei Wan, Hong Kong SAR.,Department of Molecular Pathology, Hong Kong Sanatorium & Hospital, Happy Valley, Hong Kong SAR
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29
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Menko FH, Monkhorst K, Hogervorst FB, Rosenberg EH, Adank M, Ruijs MW, Bleiker EM, Sonke GS, Russell NS, Oldenburg HS, van der Kolk LE. Challenges in breast cancer genetic testing. A call for novel forms of multidisciplinary care and long-term evaluation. Crit Rev Oncol Hematol 2022; 176:103642. [DOI: 10.1016/j.critrevonc.2022.103642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 02/04/2022] [Accepted: 02/16/2022] [Indexed: 11/25/2022] Open
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30
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Sánchez-Lorenzo L, Salas-Benito D, Villamayor J, Patiño-García A, González-Martín A. The BRCA Gene in Epithelial Ovarian Cancer. Cancers (Basel) 2022; 14:1235. [PMID: 35267543 PMCID: PMC8909050 DOI: 10.3390/cancers14051235] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 02/20/2022] [Accepted: 02/21/2022] [Indexed: 01/27/2023] Open
Abstract
Epithelial ovarian cancer (EOC) is still the most lethal gynecological cancer. Germline alterations in breast cancer 1 (gBRCA1) and breast cancer 2 (gBRCA2) genes have been identified in up to 18% of women diagnosed with EOC, and somatic mutations are found in an additional 7%. Testing of BRCA at the primary diagnosis of patients with EOC is recommended due to the implications in the genomic counseling of the patients and their families, as well as for the therapeutic implications. Indeed, the introduction of poly-(ADP ribose) polymerase inhibitors (PARPis) has changed the natural history of patients harboring a mutation in BRCA, and has resulted in a new era in the treatment of patients with ovarian cancer harboring a BRCA mutation.
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Affiliation(s)
- Luisa Sánchez-Lorenzo
- Department of Medical Oncology, Clínica Universidad de Navarra, 28027 Madrid, Spain; (L.S.-L.); (D.S.-B.); (J.V.); (A.P.-G.)
| | - Diego Salas-Benito
- Department of Medical Oncology, Clínica Universidad de Navarra, 28027 Madrid, Spain; (L.S.-L.); (D.S.-B.); (J.V.); (A.P.-G.)
| | - Julia Villamayor
- Department of Medical Oncology, Clínica Universidad de Navarra, 28027 Madrid, Spain; (L.S.-L.); (D.S.-B.); (J.V.); (A.P.-G.)
| | - Ana Patiño-García
- Department of Medical Oncology, Clínica Universidad de Navarra, 28027 Madrid, Spain; (L.S.-L.); (D.S.-B.); (J.V.); (A.P.-G.)
- Solid Tumor Program (CIMA), Clínica Universidad de Navarra, 31008 Pamplona, Spain
| | - Antonio González-Martín
- Department of Medical Oncology, Clínica Universidad de Navarra, 28027 Madrid, Spain; (L.S.-L.); (D.S.-B.); (J.V.); (A.P.-G.)
- Solid Tumor Program (CIMA), Clínica Universidad de Navarra, 31008 Pamplona, Spain
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31
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Liu J, Zhao H, Zheng Y, Dong L, Zhao S, Huang Y, Huang S, Qian T, Zou J, Liu S, Li J, Yan Z, Li Y, Zhang S, Huang X, Wang W, Li Y, Wang J, Ming Y, Li X, Xing Z, Qin L, Zhao Z, Jia Z, Li J, Liu G, Zhang M, Feng K, Wu J, Zhang J, Yang Y, Wu Z, Liu Z, Ying J, Wang X, Su J, Wang X, Wu N. DrABC: deep learning accurately predicts germline pathogenic mutation status in breast cancer patients based on phenotype data. Genome Med 2022; 14:21. [PMID: 35209950 PMCID: PMC8876403 DOI: 10.1186/s13073-022-01027-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 02/10/2022] [Indexed: 11/10/2022] Open
Abstract
Background Identifying breast cancer patients with DNA repair pathway-related germline pathogenic variants (GPVs) is important for effectively employing systemic treatment strategies and risk-reducing interventions. However, current criteria and risk prediction models for prioritizing genetic testing among breast cancer patients do not meet the demands of clinical practice due to insufficient accuracy. Methods The study population comprised 3041 breast cancer patients enrolled from seven hospitals between October 2017 and 11 August 2019, who underwent germline genetic testing of 50 cancer predisposition genes (CPGs). Associations among GPVs in different CPGs and endophenotypes were evaluated using a case-control analysis. A phenotype-based GPV risk prediction model named DNA-repair Associated Breast Cancer (DrABC) was developed based on hierarchical neural network architecture and validated in an independent multicenter cohort. The predictive performance of DrABC was compared with currently used models including BRCAPRO, BOADICEA, Myriad, PENN II, and the NCCN criteria. Results In total, 332 (11.3%) patients harbored GPVs in CPGs, including 134 (4.6%) in BRCA2, 131 (4.5%) in BRCA1, 33 (1.1%) in PALB2, and 37 (1.3%) in other CPGs. GPVs in CPGs were associated with distinct endophenotypes including the age at diagnosis, cancer history, family cancer history, and pathological characteristics. We developed a DrABC model to predict the risk of GPV carrier status in BRCA1/2 and other important CPGs. In predicting GPVs in BRCA1/2, the performance of DrABC (AUC = 0.79 [95% CI, 0.74–0.85], sensitivity = 82.1%, specificity = 63.1% in the independent validation cohort) was better than that of previous models (AUC range = 0.57–0.70). In predicting GPVs in any CPG, DrABC (AUC = 0.74 [95% CI, 0.69–0.79], sensitivity = 83.8%, specificity = 51.3% in the independent validation cohort) was also superior to previous models in their current versions (AUC range = 0.55–0.65). After training these previous models with the Chinese-specific dataset, DrABC still outperformed all other methods except for BOADICEA, which was the only previous model with the inclusion of pathological features. The DrABC model also showed higher sensitivity and specificity than the NCCN criteria in the multi-center validation cohort (83.8% and 51.3% vs. 78.8% and 31.2%, respectively, in predicting GPVs in any CPG). The DrABC model implementation is available online at http://gifts.bio-data.cn/. Conclusions By considering the distinct endophenotypes associated with different CPGs in breast cancer patients, a phenotype-driven prediction model based on hierarchical neural network architecture was created for identification of hereditary breast cancer. The model achieved superior performance in identifying GPV carriers among Chinese breast cancer patients. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-022-01027-9.
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Affiliation(s)
- Jiaqi Liu
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.,Institute of Biomedical Big Data, Wenzhou Medical University, Wenzhou, 325027, China
| | - Hengqiang Zhao
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Yu Zheng
- Fintech Innovation Center, Southwestern University of Finance and Economics, Chengdu, 611130, China
| | - Lin Dong
- Department of Pathology, National Cancer Center /National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Sen Zhao
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Yukuan Huang
- Institute of Biomedical Big Data, Wenzhou Medical University, Wenzhou, 325027, China.,School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Shengkai Huang
- Department of Laboratory Medicine, National Cancer Center /National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Tianyi Qian
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Jiali Zou
- Department of Breast Surgery, Guiyang Maternal and Child Healthcare Hospital, Guiyang, 550001, China
| | - Shu Liu
- Department of Breast Surgery, the Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China
| | - Jun Li
- Department of Molecular Pathology, the Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, 450000, China
| | - Zihui Yan
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Yalun Li
- Department of Breast Surgery, the Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, 264000, China
| | - Shuo Zhang
- Department of Breast Surgery, the Fourth Hospital of Hebei Medical University, Shijiazhuang, 050019, Hebei, China
| | - Xin Huang
- Department of Breast Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Wenyan Wang
- Department of Breast Surgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
| | - Yiqun Li
- Department of Oncology, National Cancer Center /National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Jie Wang
- Department of Ultrasound, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Yue Ming
- PET-CT Center, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Xiaoxin Li
- Medical Research Center, Beijing Key Laboratory for Genetic Research of Skeletal Deformity & Key Laboratory of Big Data for Spinal Deformities, All at Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Zeyu Xing
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Ling Qin
- Department of Breast Surgical Oncology, Cancer Hospital of HuanXing, Beijing, 100021, China
| | - Zhengye Zhao
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Ziqi Jia
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Jiaxin Li
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Gang Liu
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Menglu Zhang
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Kexin Feng
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Jiang Wu
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Jianguo Zhang
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China.,Key Laboratory of Big Data for Spinal Deformities, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China.,State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Yongxin Yang
- Machine Intelligence Group, University of Edinburgh, Edinburgh, EH8 9YL, UK
| | - Zhihong Wu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China.,Medical Research Center, Beijing Key Laboratory for Genetic Research of Skeletal Deformity & Key Laboratory of Big Data for Spinal Deformities, All at Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China.,Key Laboratory of Big Data for Spinal Deformities, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China.,State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Zhihua Liu
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Jianming Ying
- Department of Pathology, National Cancer Center /National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Xin Wang
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Jianzhong Su
- Institute of Biomedical Big Data, Wenzhou Medical University, Wenzhou, 325027, China. .,School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China. .,Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, 325011, China.
| | - Xiang Wang
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
| | - Nan Wu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China. .,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China. .,Key Laboratory of Big Data for Spinal Deformities, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China. .,State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China.
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Fanale D, Pivetti A, Cancelliere D, Spera A, Bono M, Fiorino A, Pedone E, Barraco N, Brando C, Perez A, Guarneri MF, Russo TDB, Vieni S, Guarneri G, Russo A, Bazan V. BRCA1/2 variants of unknown significance in hereditary breast and ovarian cancer (HBOC) syndrome: looking for the hidden meaning. Crit Rev Oncol Hematol 2022; 172:103626. [PMID: 35150867 DOI: 10.1016/j.critrevonc.2022.103626] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/28/2022] [Accepted: 02/07/2022] [Indexed: 01/04/2023] Open
Abstract
Hereditary breast and ovarian cancer syndrome is caused by germline mutations in BRCA1/2 genes. These genes are very large and their mutations are heterogeneous and scattered throughout the coding sequence. In addition to the above-mentioned mutations, variants of uncertain/unknown significance (VUSs) have been identified in BRCA genes, which make more difficult the clinical management of the patient and risk assessment. In the last decades, several laboratories have developed different databases that contain more than 2000 variants for the two genes and integrated strategies which include multifactorial prediction models based on direct and indirect genetic evidence, to classify the VUS and attribute them a clinical significance associated with a deleterious, high-low or neutral risk. This review provides a comprehensive overview of literature studies concerning the VUSs, in order to assess their impact on the population and provide new insight for the appropriate patient management in clinical practice.
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Affiliation(s)
- Daniele Fanale
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Alessia Pivetti
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Daniela Cancelliere
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Antonio Spera
- Department of Radiotherapy, San Giovanni di Dio Hospital, ASP of Agrigento, Agrigento, Italy
| | - Marco Bono
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Alessia Fiorino
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Erika Pedone
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Nadia Barraco
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Chiara Brando
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Alessandro Perez
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | | | - Tancredi Didier Bazan Russo
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Salvatore Vieni
- Division of General and Oncological Surgery, Department of Surgical, Oncological and Oral Sciences, University of Palermo, Italy
| | - Girolamo Guarneri
- Gynecology Section, Mother - Child Department, University of Palermo, 90127 Palermo, Italy
| | - Antonio Russo
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy.
| | - Viviana Bazan
- Department of Biomedicine, Neuroscience and Advanced Diagnostics, University of Palermo, 90127 Palermo, Italy
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Liu H, Zhang Z, Chen L, Pang J, Wu H, Liang Z. Next-Generation Sequencing Reveals a Very Low Prevalence of Deleterious Mutations of Homologous Recombination Repair Genes and Homologous Recombination Deficiency in Ovarian Clear Cell Carcinoma. Front Oncol 2022; 11:798173. [PMID: 35096598 PMCID: PMC8791260 DOI: 10.3389/fonc.2021.798173] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 12/14/2021] [Indexed: 12/31/2022] Open
Abstract
Ovarian clear cell carcinoma (OCCC) is aggressive and drug-resistant. The prevalence of homologous recombination repair (HRR) gene mutations and homologous recombination deficiency (HRD) remains largely unknown. It is also not clear whether the commonly used molecular-based classification for endometrial carcinoma (EC) is potentially applicable in OCCC. In this study, surgically resected samples were collected from 44 patients with OCCC. Genomic alterations were determined using next-generation sequencing. HRD was estimated by genomic instability. Of 44 patients with OCCC, two (4.5%) harbored likely pathogenic mutations in HRR genes. Notably, no pathogenic or likely pathogenic mutations were found in BRCA1/2. A total of 24 variants of uncertain significance (VUS) in HRR-related genes occurred in 18 (40.9%) patients. HRD was observed in only one case (2.3%). In addition, TP53 mutation and microsatellite instability-high (MSI-H) were identified in three patients (6.8%) and in one patient (2.3%), respectively. TP53 mutation was significantly associated with disease-free survival and overall survival. No POLE mutations were found. In conclusion, our results revealed a very low prevalence of HRR gene mutations and HRD in OCCC. Moreover, TP53 mutations and MSI-H are uncommon, while POLE mutations are extremely rare in OCCC. Our findings indicate that the evaluation of HRR gene mutations, HRD status, POLE mutations, and MSI-H may have limited clinical significance for OCCC treatment and prognostic stratification.
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Affiliation(s)
- Hangqi Liu
- Department of Pathology, State Key Laboratory of Complex Severe and Rare Disease, Molecular Pathology Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhiwen Zhang
- Department of Pathology, State Key Laboratory of Complex Severe and Rare Disease, Molecular Pathology Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Longyun Chen
- Department of Pathology, State Key Laboratory of Complex Severe and Rare Disease, Molecular Pathology Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Junyi Pang
- Department of Pathology, State Key Laboratory of Complex Severe and Rare Disease, Molecular Pathology Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Huanwen Wu
- Department of Pathology, State Key Laboratory of Complex Severe and Rare Disease, Molecular Pathology Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhiyong Liang
- Department of Pathology, State Key Laboratory of Complex Severe and Rare Disease, Molecular Pathology Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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Opinions and experiences of recontacting patients: a survey of Australasian genetic health professionals. J Community Genet 2022; 13:193-199. [PMID: 35013911 DOI: 10.1007/s12687-021-00570-z] [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: 07/23/2021] [Accepted: 12/03/2021] [Indexed: 10/19/2022] Open
Abstract
The issue of recontacting past genetics patients is increasingly relevant, particularly with the introduction of next-generation sequencing. Improved testing can provide additional information on the pathogenicity and prevalence of genetic variants, often leading to a need to recontact patients. Some international genetics societies have position statements and recommendations to guide genetic health professionals (GHPs) navigating the legal, ethical and practical issues of recontacting. In the absence of a standardised Australasian protocol, we explored the experiences and opinions of Australasian GHPs regarding patient follow-up and recontacting practices. Forty-five respondents completed an online survey. Most respondents indicated that recontacting occurred on an ad hoc basis, but most genetic services relied on patients (or family) initiating recontact. Implementation of a routine recontacting system was widely dismissed by 73% of respondents, citing lack of resources, limited information on legal responsibility and setting unrealistic expectations as common barriers. If recontact was contemplated, e-communication was an acceptable first step. This study identified the need for integrated familial cancer registries to assist under-resourced genetic services to maintain up-to-date patient records. Developing a standard recontacting protocol with flexibility to account for patient individuality and circumstances might enable provision of equitable service within Australasia.
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Wu H, Xu B, Gao Q, Zhou X, Shao J, Liang Z, Ma D. Discrepancies in Genetic Testing Procedures of BRCA1/2 Mutations: A National Survey Across China. Mol Diagn Ther 2021; 24:715-721. [PMID: 32970304 DOI: 10.1007/s40291-020-00489-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
International guidelines recommend BRCA testing for patients with breast and ovarian cancer. Little is known about the genetic testing practices of BRCA1/2 mutations in laboratories across China. This study was designed to assess the discrepancies in genetic testing procedures of BRCA1/2 mutations across China. An online survey was developed for depicting the BRCA1/2 testing landscape in China. Our results show that there were several variations among the laboratories in technologies adopted, large genomic rearrangement detection, probe design, quality control, variant of uncertain significance interpretation, and disposition of variants in public databases. The discrepancies observed in our study would affect the authenticity of results, thus necessitating the formulation of proper national and international guidelines for optimal BRCA1/2 testing clinical practice for efficient management and patient care of this population.
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Affiliation(s)
- Huanwen Wu
- Department of Pathology, Molecular Pathology Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Binghe Xu
- National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qinglei Gao
- Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoyan Zhou
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College; Institute of Pathology, Fudan University, Shanghai, China
| | - Jianyong Shao
- Department of Molecular Diagnostics, Sun Yat-Sen University Cancer Center, Guangzhou, China
- Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Zhiyong Liang
- Department of Pathology, Molecular Pathology Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China.
| | - Ding Ma
- Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
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Lee YC, Lee YL, Li CY. BRCA Genes and Related Cancers: A Meta-Analysis from Epidemiological Cohort Studies. MEDICINA (KAUNAS, LITHUANIA) 2021; 57:905. [PMID: 34577828 PMCID: PMC8464901 DOI: 10.3390/medicina57090905] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/10/2021] [Accepted: 08/27/2021] [Indexed: 12/24/2022]
Abstract
Background and Objectives:BRCA1 and BRCA2 are genes located in different chromosomes that are disproportionately associated with hereditary breast and ovarian cancer syndrome. Their association with other cancers remains to be explored. Materials and Methods: We systematically reviewed cohort studies to explore the association of BRCA 1 and BRCA2 with various cancers except lung cancer. We searched PubMed, Medline (EBSCOhost) and relevant articles published up to 10 May 2021. The odds ratio, standardised morbidity rate and cancer-specific standardised incidence ratio were pooled together as relative risk (RR) estimates. Results: Twelve studies were included for analysis. BRCA mutation increased pancreatic and uterine cancers by around 3-5- and 1.5-fold, respectively. BRCA mutation did not increase brain cancer; colorectal cancer; prostate, bladder and kidney cancer; cervical cancer; or malignant melanoma. BRCA2 increased gastric cancer with RR = 2.15 (1.98-2.33). Conclusion: The meta-analysis results can provide clinicians and relevant families with information regarding increased specific cancer risk in BRCA1 and BRCA2 mutation carriers.
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Affiliation(s)
- Yen-Chien Lee
- Department of Oncology, Tainan Hospital, Ministry of Health and Welfare, Executive Yuan, Tainan 700, Taiwan;
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, Tainan 700, Taiwan
| | - Yen-Ling Lee
- Department of Oncology, Tainan Hospital, Ministry of Health and Welfare, Executive Yuan, Tainan 700, Taiwan;
| | - Chung-Yi Li
- Department of Public Health, College of Medicine, National Cheng Kung University, Tainan 700, Taiwan;
- Department of Public Health, College of Health, China Medical University, Taichung 406, Taiwan
- Department of Healthcare Administration, College of Medical and Health Science, Asia University, Taichung 413, Taiwan
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37
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Chandrasekaran D, Sobocan M, Blyuss O, Miller RE, Evans O, Crusz SM, Mills-Baldock T, Sun L, Hammond RFL, Gaba F, Jenkins LA, Ahmed M, Kumar A, Jeyarajah A, Lawrence AC, Brockbank E, Phadnis S, Quigley M, El Khouly F, Wuntakal R, Faruqi A, Trevisan G, Casey L, Burghel GJ, Schlecht H, Bulman M, Smith P, Bowers NL, Legood R, Lockley M, Wallace A, Singh N, Evans DG, Manchanda R. Implementation of Multigene Germline and Parallel Somatic Genetic Testing in Epithelial Ovarian Cancer: SIGNPOST Study. Cancers (Basel) 2021; 13:cancers13174344. [PMID: 34503154 PMCID: PMC8431198 DOI: 10.3390/cancers13174344] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 08/09/2021] [Accepted: 08/24/2021] [Indexed: 11/16/2022] Open
Abstract
We present findings of a cancer multidisciplinary-team (MDT) coordinated mainstreaming pathway of unselected 5-panel germline BRCA1/BRCA2/RAD51C/RAD51D/BRIP1 and parallel somatic BRCA1/BRCA2 testing in all women with epithelial-OC and highlight the discordance between germline and somatic testing strategies across two cancer centres. Patients were counselled and consented by a cancer MDT member. The uptake of parallel multi-gene germline and somatic testing was 97.7%. Counselling by clinical-nurse-specialist more frequently needed >1 consultation (53.6% (30/56)) compared to a medical (15.0% (21/137)) or surgical oncologist (15.3% (17/110)) (p < 0.001). The median age was 54 (IQR = 51-62) years in germline pathogenic-variant (PV) versus 61 (IQR = 51-71) in BRCA wild-type (p = 0.001). There was no significant difference in distribution of PVs by ethnicity, stage, surgery timing or resection status. A total of 15.5% germline and 7.8% somatic BRCA1/BRCA2 PVs were identified. A total of 2.3% patients had RAD51C/RAD51D/BRIP1 PVs. A total of 11% germline PVs were large-genomic-rearrangements and missed by somatic testing. A total of 20% germline PVs are missed by somatic first BRCA-testing approach and 55.6% germline PVs missed by family history ascertainment. The somatic testing failure rate is higher (23%) for patients undergoing diagnostic biopsies. Our findings favour a prospective parallel somatic and germline panel testing approach as a clinically efficient strategy to maximise variant identification. UK Genomics test-directory criteria should be expanded to include a panel of OC genes.
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Affiliation(s)
- Dhivya Chandrasekaran
- Wolfson Institute of Population Health, Barts CRUK Cancer Centre, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK; (D.C.); (M.S.); (O.E.); (L.S.); (F.G.)
- Department of Gynaecological Oncology, Barts Health NHS Trust, London EC1 1BB, UK; (A.J.); (A.C.L.); (E.B.); (S.P.)
| | - Monika Sobocan
- Wolfson Institute of Population Health, Barts CRUK Cancer Centre, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK; (D.C.); (M.S.); (O.E.); (L.S.); (F.G.)
- Department of Gynaecological Oncology, Barts Health NHS Trust, London EC1 1BB, UK; (A.J.); (A.C.L.); (E.B.); (S.P.)
- Divison for Gynaecology and Perinatology, University Medical Centre Maribor, 2000 Maribor, Slovenia
| | - Oleg Blyuss
- School of Physics, Engineering and Computer Science, University of Hertfordshire, Hatfield AL10 9AB, UK;
- Department of Paediatrics and Paediatric Infectious Diseases, Sechenov First Moscow State Medical University, Moscow 119991, Russia
- World-Class Research Center “Digital Biodesign and Personalized Healthcare”, Sechenov First Moscow State Medical University, Moscow 119991, Russia
| | - Rowan E. Miller
- Department of Medical Oncology, Barts Health NHS Trust, London EC1A 7BE, UK; (R.E.M.); (S.M.C.)
| | - Olivia Evans
- Wolfson Institute of Population Health, Barts CRUK Cancer Centre, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK; (D.C.); (M.S.); (O.E.); (L.S.); (F.G.)
| | - Shanthini M. Crusz
- Department of Medical Oncology, Barts Health NHS Trust, London EC1A 7BE, UK; (R.E.M.); (S.M.C.)
| | - Tina Mills-Baldock
- Department of Medical Oncology, Barking, Havering & Redbridge University Hospitals, Essex RM7 0AG, UK; (T.M.-B.); (M.Q.); (F.E.K.)
| | - Li Sun
- Wolfson Institute of Population Health, Barts CRUK Cancer Centre, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK; (D.C.); (M.S.); (O.E.); (L.S.); (F.G.)
- Department of Health Services Research, Faculty of Public Health & Policy, London School of Hygiene & Tropical Medicine, London WC1H 9SH, UK;
| | - Rory F. L. Hammond
- Department of Pathology, Barts Health NHS Trust, London E1 1FR, UK; (R.F.L.H.); (A.F.); (G.T.); (L.C.); (N.S.)
| | - Faiza Gaba
- Wolfson Institute of Population Health, Barts CRUK Cancer Centre, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK; (D.C.); (M.S.); (O.E.); (L.S.); (F.G.)
| | - Lucy A. Jenkins
- North East Thames Regional Genetics Service, Great Ormond Street Hospital, London WC1N 3JH, UK; (L.A.J.); (M.A.); (A.K.)
| | - Munaza Ahmed
- North East Thames Regional Genetics Service, Great Ormond Street Hospital, London WC1N 3JH, UK; (L.A.J.); (M.A.); (A.K.)
| | - Ajith Kumar
- North East Thames Regional Genetics Service, Great Ormond Street Hospital, London WC1N 3JH, UK; (L.A.J.); (M.A.); (A.K.)
| | - Arjun Jeyarajah
- Department of Gynaecological Oncology, Barts Health NHS Trust, London EC1 1BB, UK; (A.J.); (A.C.L.); (E.B.); (S.P.)
| | - Alexandra C. Lawrence
- Department of Gynaecological Oncology, Barts Health NHS Trust, London EC1 1BB, UK; (A.J.); (A.C.L.); (E.B.); (S.P.)
| | - Elly Brockbank
- Department of Gynaecological Oncology, Barts Health NHS Trust, London EC1 1BB, UK; (A.J.); (A.C.L.); (E.B.); (S.P.)
| | - Saurabh Phadnis
- Department of Gynaecological Oncology, Barts Health NHS Trust, London EC1 1BB, UK; (A.J.); (A.C.L.); (E.B.); (S.P.)
| | - Mary Quigley
- Department of Medical Oncology, Barking, Havering & Redbridge University Hospitals, Essex RM7 0AG, UK; (T.M.-B.); (M.Q.); (F.E.K.)
| | - Fatima El Khouly
- Department of Medical Oncology, Barking, Havering & Redbridge University Hospitals, Essex RM7 0AG, UK; (T.M.-B.); (M.Q.); (F.E.K.)
| | - Rekha Wuntakal
- Department of Gynaecology, Barking, Havering & Redbridge University Hospitals, Essex RM7 0AG, UK;
| | - Asma Faruqi
- Department of Pathology, Barts Health NHS Trust, London E1 1FR, UK; (R.F.L.H.); (A.F.); (G.T.); (L.C.); (N.S.)
| | - Giorgia Trevisan
- Department of Pathology, Barts Health NHS Trust, London E1 1FR, UK; (R.F.L.H.); (A.F.); (G.T.); (L.C.); (N.S.)
| | - Laura Casey
- Department of Pathology, Barts Health NHS Trust, London E1 1FR, UK; (R.F.L.H.); (A.F.); (G.T.); (L.C.); (N.S.)
| | - George J. Burghel
- Manchester Centre for Genomic Medicine, Saint Marys Hospital, Manchester M13 9WL, UK; (G.J.B.); (H.S.); (M.B.); (P.S.); (N.L.B.); (A.W.); (D.G.E.)
| | - Helene Schlecht
- Manchester Centre for Genomic Medicine, Saint Marys Hospital, Manchester M13 9WL, UK; (G.J.B.); (H.S.); (M.B.); (P.S.); (N.L.B.); (A.W.); (D.G.E.)
| | - Michael Bulman
- Manchester Centre for Genomic Medicine, Saint Marys Hospital, Manchester M13 9WL, UK; (G.J.B.); (H.S.); (M.B.); (P.S.); (N.L.B.); (A.W.); (D.G.E.)
| | - Philip Smith
- Manchester Centre for Genomic Medicine, Saint Marys Hospital, Manchester M13 9WL, UK; (G.J.B.); (H.S.); (M.B.); (P.S.); (N.L.B.); (A.W.); (D.G.E.)
| | - Naomi L. Bowers
- Manchester Centre for Genomic Medicine, Saint Marys Hospital, Manchester M13 9WL, UK; (G.J.B.); (H.S.); (M.B.); (P.S.); (N.L.B.); (A.W.); (D.G.E.)
| | - Rosa Legood
- Department of Health Services Research, Faculty of Public Health & Policy, London School of Hygiene & Tropical Medicine, London WC1H 9SH, UK;
| | - Michelle Lockley
- Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK;
| | - Andrew Wallace
- Manchester Centre for Genomic Medicine, Saint Marys Hospital, Manchester M13 9WL, UK; (G.J.B.); (H.S.); (M.B.); (P.S.); (N.L.B.); (A.W.); (D.G.E.)
| | - Naveena Singh
- Department of Pathology, Barts Health NHS Trust, London E1 1FR, UK; (R.F.L.H.); (A.F.); (G.T.); (L.C.); (N.S.)
| | - D. Gareth Evans
- Manchester Centre for Genomic Medicine, Saint Marys Hospital, Manchester M13 9WL, UK; (G.J.B.); (H.S.); (M.B.); (P.S.); (N.L.B.); (A.W.); (D.G.E.)
| | - Ranjit Manchanda
- Wolfson Institute of Population Health, Barts CRUK Cancer Centre, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK; (D.C.); (M.S.); (O.E.); (L.S.); (F.G.)
- Department of Gynaecological Oncology, Barts Health NHS Trust, London EC1 1BB, UK; (A.J.); (A.C.L.); (E.B.); (S.P.)
- Department of Health Services Research, Faculty of Public Health & Policy, London School of Hygiene & Tropical Medicine, London WC1H 9SH, UK;
- Correspondence:
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Gillyard T, Davis J. DNA double-strand break repair in cancer: A path to achieving precision medicine. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2021; 364:111-137. [PMID: 34507781 DOI: 10.1016/bs.ircmb.2021.06.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The assessment of DNA damage can be a significant diagnostic for precision medicine. DNA double strand break (DSBs) pathways in cancer are the primary targets in a majority of anticancer therapies, yet the molecular vulnerabilities that underlie each tumor can vary widely making the application of precision medicine challenging. Identifying and understanding these interindividual vulnerabilities enables the design of targeted DSB inhibitors along with evolving precision medicine approaches to selectively kill cancer cells with minimal side effects. A major challenge however, is defining exactly how to target unique differences in DSB repair pathway mechanisms. This review comprises a brief overview of the DSB repair mechanisms in cancer and includes results obtained with revolutionary advances such as CRISPR/Cas9 and machine learning/artificial intelligence, which are rapidly advancing not only our understanding of determinants of DSB repair choice, but also how it can be used to advance precision medicine. Scientific innovation in the methods used to diagnose and treat cancer is converging with advances in basic science and translational research. This revolution will continue to be a critical driver of precision medicine that will enable precise targeting of unique individual mechanisms. This review aims to lay the foundation for achieving this goal.
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Affiliation(s)
- Taneisha Gillyard
- Department of Biochemistry, Cancer Biology, Neuroscience and Pharmacology, Meharry Medical College, Nashville, TN, United States
| | - Jamaine Davis
- Department of Biochemistry, Cancer Biology, Neuroscience and Pharmacology, Meharry Medical College, Nashville, TN, United States.
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Abdel-Razeq H, Abujamous L, Abunasser M, Edaily S, Bater R. Prevalence and predictors of germline BRCA1 and BRCA2 mutations among young patients with breast cancer in Jordan. Sci Rep 2021; 11:14906. [PMID: 34290354 PMCID: PMC8295261 DOI: 10.1038/s41598-021-94403-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Accepted: 06/24/2021] [Indexed: 11/09/2022] Open
Abstract
BRCA1 and BRCA2 mutations are not uncommon in breast cancer patients. Western studies show that such mutations are more prevalent among younger patients. This study evaluates the prevalence of germline mutations in BRCA1 and BRCA2 among breast cancer patients diagnosed at age 40 or younger in Jordan. Blood samples of patients with breast cancer diagnosed at age 40 years or younger were obtained for DNA extraction and BRCA sequencing. Mutations were classified as benign/likely benign (non-carrier), pathogenic/likely pathogenic variant (carrier) and variant of uncertain significance (VUS). Genetic testing and counseling were completed on 616 eligible patients. Among the whole group, 75 (12.2%) had pathogenic or likely pathogenic variants; two of the BRCA2 mutations were novel. In multivariate analysis, triple-negative disease (Odd Ratio [OR]: 5.37; 95% CI 2.88-10.02, P < 0.0001), breast cancer in ≥ 2 family members (OR: 4.44; 95% CI 2.52-7.84, P < 0.0001), and a personal history ≥ 2 primary breast cancers (OR: 3.43; 95% CI 1.62-7.24, P = 0.001) were associated with higher mutation rates. In conclusion, among young Jordanian patients with breast cancer, mutation rates are significantly higher in patients with triple-negative disease, personal history of breast cancer and those with two or more close relatives with breast cancer.
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Affiliation(s)
- Hikmat Abdel-Razeq
- Department of Internal Medicine, King Hussein Cancer Center, Queen Rania Al Abdullah Street, P.O. Box: 1269, Amman, 11941, Jordan.
- School of Medicine, University of Jordan, Amman, Jordan.
| | - Lama Abujamous
- Department of Cell Therapy & Applied Genomic, King Hussein Cancer Center, Amman, Jordan
| | - Mahmoud Abunasser
- Department of Internal Medicine, King Hussein Cancer Center, Queen Rania Al Abdullah Street, P.O. Box: 1269, Amman, 11941, Jordan
| | - Sara Edaily
- Department of Internal Medicine, King Hussein Cancer Center, Queen Rania Al Abdullah Street, P.O. Box: 1269, Amman, 11941, Jordan
| | - Rayan Bater
- Department of Internal Medicine, King Hussein Cancer Center, Queen Rania Al Abdullah Street, P.O. Box: 1269, Amman, 11941, Jordan
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Spizzo G, Puccini A, Xiu J, Goldberg RM, Grothey A, Shields AF, Arora SP, Khushman M, Salem ME, Battaglin F, Baca Y, El-Deiry WS, Philip PA, Nassem M, Hall M, Marshall JL, Kocher F, Amann A, Wolf D, Korn WM, Lenz HJ, Seeber A. Molecular profile of BRCA-mutated biliary tract cancers. ESMO Open 2021; 5:e000682. [PMID: 32576609 PMCID: PMC7312328 DOI: 10.1136/esmoopen-2020-000682] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 03/04/2020] [Accepted: 03/13/2020] [Indexed: 12/21/2022] Open
Abstract
Introduction Prognosis of biliary tract cancers (BTC) remains dismal and novel treatment strategies are needed to improve survival. BRCA mutations are known to occur in BTC but their frequency and the molecular landscape in which they are observed in distinct sites of BTC remain unknown. Material and methods Tumour samples from 1292 patients with BTC, comprising intrahepatic cholangiocarcinoma (IHC, n=746), extrahepatic cholangiocarcinoma (EHC, n=189) and gallbladder cancer (GBC, n=353), were analysed using next-generation sequencing (NGS). Tumour mutational burden (TMB) was calculated based on somatic non-synonymous missense mutations. Determination of tumour mismatch repair (MMR) or microsatellite instability (MSI) status was done by fragment analysis, immunohistochemistry and the evaluation of known microsatellite loci by NGS. Programmed death ligand 1 expression was analysed using immunohistochemistry. Results Overall, BRCA mutations were detected in 3.6% (n=46) of samples (BRCA1: 0.6%, BRCA2: 3%) with no significant difference in frequency observed based on tumour site. In GBC and IHC, BRCA2 mutations (4.0% and 2.7%) were more frequent than BRCA1 (0.3% and 0.4%, p<0.05) while in EHC, similar frequency was observed (2.6% for BRCA2 vs 2.1% for BRCA1). BRCA mutations were associated with a higher rate in subjects with MSI-H/deficient mismatch repair (19.5% vs 1.7%, p<0.0001) and tumours with higher TMB, regardless of the MMR or MSI status (p<0.05). Conclusions BRCA mutations are found in a subgroup of patients with BTC and are characterised by a distinct molecular profile. These data provide a rationale testing poly(ADP-ribose)polymeraseinhibitors and other targeted therapies in patients with BRCA-mutant BTC.
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Affiliation(s)
- Gilbert Spizzo
- Department of Internal Medicine, Oncologic Day Hospital, Hospital of Bressanone (SABES-ASDAA), Bressanone-Brixen, Italy
| | - Alberto Puccini
- Oncologia Medica 1, Ospedale Policlinico San Martino-IRCCS, Genoa, Italy
| | - Joanne Xiu
- Caris Life Sciences, Phoenix, Arizona, USA
| | - Richard M Goldberg
- West Virginia University Cancer Institute, Morgantown, West Virginia, USA
| | | | - Anthony F Shields
- epartment of Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, Michigan, USA
| | | | | | | | - Francesca Battaglin
- University of Southern California-Norris Comprehensive Cancer Center and Hospital, Los Angeles, California, USA
| | | | | | - Philip A Philip
- Department of Oncology, Karmanos Cancer Institute, Detroit, Michigan, USA
| | - Madiha Nassem
- University of Southern California-Norris Comprehensive Cancer Center and Hospital, Los Angeles, California, USA
| | - Michael Hall
- Fox Chase Cancer Institute, Philadelphia, Pennsylvania, USA
| | - John L Marshall
- Ruesch Center for The Cure of Gastrointestinal Cancers, Lombardi Comprehensive Cancer Center, Washington, DC, USA
| | - Florian Kocher
- Department of Hematology and Oncology, Comprehensive Cancer Center Innsbruck, Medical University of Innsbruck, Innsbruck, Austria
| | - Arno Amann
- Department of Hematology and Oncology, Comprehensive Cancer Center Innsbruck, Medical University of Innsbruck, Innsbruck, Austria
| | - Dominik Wolf
- Department of Hematology and Oncology, Comprehensive Cancer Center Innsbruck, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Heinz-Josef Lenz
- University of Southern California-Norris Comprehensive Cancer Center and Hospital, Los Angeles, California, USA
| | - Andreas Seeber
- Department of Hematology and Oncology, Comprehensive Cancer Center Innsbruck, Medical University of Innsbruck, Innsbruck, Austria.
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Poon KS. In silico analysis of BRCA1 and BRCA2 missense variants and the relevance in molecular genetic testing. Sci Rep 2021; 11:11114. [PMID: 34045478 PMCID: PMC8160182 DOI: 10.1038/s41598-021-88586-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 04/13/2021] [Indexed: 01/12/2023] Open
Abstract
Over the years since the genetic testing of BRCA1 and BRCA2 has been conducted for research and later introduced into clinical practice, a high number of missense variants have been reported in the literature and deposited in public databases. Polymorphism Phenotyping v2 (PolyPhen-2) and Sorting Intolerant from Tolerant (SIFT) are two widely applied bioinformatics tools used to assess the functional impacts of missense variants. A total of 2605 BRCA1 and 4763 BRCA2 variants from the ClinVar database were analysed with PolyPhen2 and SIFT. When SIFT was evaluated alongside PolyPhen-2 HumDiv and HumVar, it had shown top performance in terms of negative predictive value (NPV) (100%) and sensitivity (100%) for ClinVar classified benign and pathogenic BRCA1 variants. Both SIFT and PolyPhen-2 HumDiv achieved 100% NPV and 100% sensitivity in prediction of pathogenicity of the BRCA2 variants. Agreement was achieved in prediction outcomes from the three tested approaches in 55.04% and 68.97% of the variants of unknown significance (VUS) for BRCA1 and BRCA2, respectively. The performances of PolyPhen-2 and SIFT in predicting functional impacts varied across the two genes. Due to lack of high concordance in prediction outcomes among the two tested algorithms, their usefulness in classifying the pathogenicity of VUS identified through molecular testing of BRCA1 and BRCA2 is hence limited in the clinical setting.
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Affiliation(s)
- Kok-Siong Poon
- Department of Laboratory Medicine, National University Hospital, NUH Main Building, 5 Lower Kent Ridge Road, Singapore, 119074, Singapore.
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Jimenez-Sainz J, Jensen RB. Imprecise Medicine: BRCA2 Variants of Uncertain Significance (VUS), the Challenges and Benefits to Integrate a Functional Assay Workflow with Clinical Decision Rules. Genes (Basel) 2021; 12:genes12050780. [PMID: 34065235 PMCID: PMC8161351 DOI: 10.3390/genes12050780] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 05/14/2021] [Accepted: 05/18/2021] [Indexed: 12/20/2022] Open
Abstract
Pathological mutations in homology-directed repair (HDR) genes impact both future cancer risk and therapeutic options for patients. HDR is a high-fidelity DNA repair pathway for resolving DNA double-strand breaks throughout the genome. BRCA2 is an essential protein that mediates the loading of RAD51 onto resected DNA breaks, a key step in HDR. Germline mutations in BRCA2 are associated with an increased risk for breast, ovarian, prostate, and pancreatic cancer. Clinical findings of germline or somatic BRCA2 mutations in tumors suggest treatment with platinum agents or PARP inhibitors. However, when genetic analysis reveals a variant of uncertain significance (VUS) in the BRCA2 gene, precision medicine-based decisions become complex. VUS are genetic changes with unknown pathological impact. Current statistics indicate that between 10–20% of BRCA sequencing results are VUS, and of these, more than 50% are missense mutations. Functional assays to determine the pathological outcome of VUS are urgently needed to provide clinical guidance regarding cancer risk and treatment options. In this review, we provide a brief overview of BRCA2 functions in HDR, describe how BRCA2 VUS are currently assessed in the clinic, and how genetic and biochemical functional assays could be integrated into the clinical decision process. We suggest a multi-step workflow composed of robust and accurate functional assays to correctly evaluate the potential pathogenic or benign nature of BRCA2 VUS. Success in this precision medicine endeavor will offer actionable information to patients and their physicians.
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Affiliation(s)
- Judit Jimenez-Sainz
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520, USA
- Correspondence: (J.J.-S.); (R.B.J.); Tel.:+1-203-737-6456 (R.B.J.)
| | - Ryan B. Jensen
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520, USA
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06520, USA
- Correspondence: (J.J.-S.); (R.B.J.); Tel.:+1-203-737-6456 (R.B.J.)
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Menke C, Nagaraj CB, Dawson B, He H, Tawde S, Wakefield EG. Understanding and interpretation of a variant of uncertain significance (VUS) genetic test result by pediatric providers who do not specialize in genetics. J Genet Couns 2021; 30:1559-1569. [PMID: 33969574 DOI: 10.1002/jgc4.1422] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 03/16/2021] [Accepted: 03/17/2021] [Indexed: 11/09/2022]
Abstract
The advancement of genetic testing technologies has allowed for better diagnosis and management of patients, but also results in more variants of uncertain significance (VUSs) due to the increased number of genes being analyzed. There are more genetic tests available and more providers who do not specialize in genetics ordering genetic testing, but few studies examining how providers who do not specialize in genetics interpret VUSs. This study surveyed pediatric providers at a midwestern pediatric care center who do not specialize in genetics about their understanding of a mock genetic test report with a VUS result and whether their understanding of the result was associated with experience ordering genetic tests. Participants' preferences about content of the report and steps taken to understand the result were also examined. Of the 51 participants, 33% correctly answered both knowledge questions about the VUS result: one asking them to interpret the result and one asking them how they would explain the result to the patient. There was no association between answering both knowledge questions correctly and types of previous genetic tests ordered (p > .1 for 8 types of genetic tests), having received a genetic test report with a VUS result (p = .58), having referred patients to a genetics professional (p = .74), or feeling comfortable discussing a positive, negative, or VUS genetic test result (p > .4). This suggests that having previous experience ordering genetic tests does not contribute to the participants' knowledge about a variant of uncertain significance. Most participants reported that the amount of information in each section of the mock report was adequate. Participants were likely to reference multiple resources to better understand a VUS result, including published literature (82%), gene-specific databases (67%), and colleagues (63%). While these results cannot be generalized to all institutions, institutions can use the two knowledge questions to determine participants' understanding of genetic test results. This will help healthcare institutions determine methods that will best aide their providers who order genetic testing but do not specialize in genetics in learning more about the genetic testing process and better utilize results to improve patient care.
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Affiliation(s)
- Chelsea Menke
- Department of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Chinmayee B Nagaraj
- Department of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Brian Dawson
- Department of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Hua He
- Department of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Sanjukta Tawde
- Department of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Genetic Services Laboratory, University of Chicago, Chicago, IL, USA
| | - Emily G Wakefield
- Department of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
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Shur NE, Summerlin ML, McIntosh BJ, Shalaby-Rana E, Hinds TS. Genetic causes of fractures and subdural hematomas: fact versus fiction. Pediatr Radiol 2021; 51:1029-1043. [PMID: 33999244 DOI: 10.1007/s00247-020-04865-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 08/19/2020] [Accepted: 09/30/2020] [Indexed: 10/21/2022]
Abstract
Genetic disorders are in the differential diagnosis when young children present with unexplained fractures or intracranial hemorrhage. For medical and legal reasons, it is imperative to make the correct diagnosis and provide clear, evidence-based explanations of how alternative diagnoses were ruled out. A genetics consultation in cases of suspected child physical abuse should synthesize the history of present illness, medical history, family history, physical examination, and radiologic and laboratory findings in consultation with other specialists. The medical geneticist highlights how these disorders truly present. When the natural history of a genetic disorder is understood, it becomes clear that genetic disorders are not mysterious or difficult to diagnose. As highlighted in this case-based review, mainstream medical practice allows for differentiation among the intracranial and skeletal manifestations of osteogenesis imperfecta, Menkes disease, glutaric acidemia type 1 and child physical abuse. This review also highlights how a genetic disorder, Ehlers-Danlos syndrome, can be misused in a courtroom. Finally, this review summarizes when genetic testing is appropriate in cases of suspected child physical abuse.
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Affiliation(s)
- Natasha E Shur
- Rare Disease Institute, Division of Genetics and Metabolism, Children's National Hospital, 111 Michigan Ave., NW, Washington, DC, 20010, USA. .,George Washington University School of Medicine and Health Sciences, Washington, DC, USA.
| | - Maxwell L Summerlin
- George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Bruce J McIntosh
- Child Protection Team System, Children's Medical Service, Florida Department of Health, Tallahassee, FL, USA
| | - Eglal Shalaby-Rana
- George Washington University School of Medicine and Health Sciences, Washington, DC, USA.,Diagnostic Imaging and Radiology, Children's National Hospital, Washington, DC, USA
| | - Tanya S Hinds
- George Washington University School of Medicine and Health Sciences, Washington, DC, USA.,Child & Adolescent Protection Center, Children's National Hospital, Washington, DC, USA
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Biologic behavior of resected BRCA-mutated pancreatic cancer: Comparison with sporadic pancreatic cancer and other BRCA-related cancers. Pancreatology 2021; 21:544-549. [PMID: 33612442 DOI: 10.1016/j.pan.2021.02.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 01/23/2021] [Accepted: 02/09/2021] [Indexed: 12/11/2022]
Abstract
BACKGROUND Since margin-negative resection is essential for the cure of pancreatic cancer (PC), early detection of PC is important. Although PC is the third most common cancer associated with BRCA1/2 mutations, clinical research regarding BRCA mutations in resected PC are rare. In this study, we investigated the oncologic characteristics of resected PC with BRCA mutation to suggest management strategies. METHODS We retrospectively reviewed data from 493 patients who were confirmed to be pathogenic BRCA1/2 mutation carriers between January 2007 and December 2019. We investigated the oncologic characteristics of PC patients by comparing them with resected sporadic PC and other BRCA-related cancer groups (breast cancer, ovarian cancer, and others). RESULTS Ten BRCA mutation carriers (2.0%) experienced PC, and PC onset was significantly later than that of BRCA-related breast cancer (age: breast vs. pancreas, 45.0 vs. 53.5 years, p = 0.050). Six patients underwent pancreatectomy and their long-term survival outcomes did not differ from those of sporadic PC patients (disease free survival: BRCA1/2 vs. sporadic, 10.0 months vs. 9.0 months, p = 0.504; overall survival: BRCA1/2 vs. sporadic, 29.0 months vs. 35.0 months, p = 0.520). CONCLUSION BRCA-mutated PC occurs later than BRCA-mutated breast cancer. Active genetic testing to identify BRCA1/2 mutation carriers at the onset of breast cancer and continuous long-term surveillance of these patients can provide opportunities to detect BRCA-mutated PC at a resectable stage.
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Tumour Versus Germline BRCA Testing in Ovarian Cancer: A Single-Site Institution Experience in the United Kingdom. Diagnostics (Basel) 2021; 11:diagnostics11030547. [PMID: 33808557 PMCID: PMC8003427 DOI: 10.3390/diagnostics11030547] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 03/17/2021] [Indexed: 12/04/2022] Open
Abstract
The aim of this audit was to evaluate the usefulness and serviceability of testing for pathogenic mutations in BRCA1 or BRCA2 (BRCA1/2) genes in ovarian cancer (OC) patients. One hundred and thirty-five patients with more common histological sub-types of OC were retrospectively identified between 2011 and 2019. The fail rate of the molecular analysis was 7.4% (10/135). One hundred and twenty-five records were evaluated: 99 (79.2%) patients had wild-type BRCA (both somatic and germline); tumour BRCA1/2 (tBRCA1/2) pathogenic mutations were found in 20 (16%) patients with distribution between BRCA1 and BRCA2 being 40% and 60%, respectively; 13 (10.4%) patients with pathogenic variants had germline mutations; and tBRCA1/2 with variant of unknown significance (VUS), in the absence of pathogenic BRCA1 or BRCA2 variants, was detected in 6 (4.8%) patients. Our data show that expanding the molecular service to the routine first-tumour testing for patients with OC will potentially increase the detection rate of BRCA mutations, thereby providing early benefits of PARP inhibitors therapy. The tumour testing service should continue to be offered to newly diagnosed patients with high-grade epithelial cancers, including high-grade serous carcinoma, but also with carcinosarcomas and poorly-differentiated metastatic adenocarcinomas of unknown origin.
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Ginsburg O, Ashton-Prolla P, Cantor A, Mariosa D, Brennan P. The role of genomics in global cancer prevention. Nat Rev Clin Oncol 2021; 18:116-128. [PMID: 32973296 DOI: 10.1038/s41571-020-0428-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/07/2020] [Indexed: 02/07/2023]
Abstract
Despite improvements in the understanding of cancer causation, much remains unknown regarding the mechanisms by which genomic and non-genomic factors initiate carcinogenesis, drive cell invasion and metastasis, and enable cancer to develop. Technological advances have enabled the analysis of whole genomes, comprising thousands of tumours across populations worldwide, with the aim of identifying mutation signatures associated with particular tumour types. Large collaborative efforts have resulted in the identification and improved understanding of causal factors, and have shed light on new opportunities to prevent cancer. In this new era in cancer genomics, discoveries from studies conducted on an international scale can inform evidence-based strategies in cancer control along the cancer care continuum, from prevention to treatment. In this Review, we present the relevant history and emerging frontiers of cancer genetics and genomics from the perspective of global cancer prevention. We highlight the importance of local context in the adoption of new technologies and emergent evidence, with illustrative examples from worldwide. We emphasize the challenges in implementing important genomic findings in clinical settings with disparate resource availability and present a conceptual framework for the translation of such findings into clinical practice, and evidence-based policies in order to maximize the utility for a population.
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Affiliation(s)
- Ophira Ginsburg
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA.
- Section for Global Health, Division of Health and Behavior, Department of Population Health, NYU Grossman School of Medicine, New York, NY, USA.
| | - Patricia Ashton-Prolla
- Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre and Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Anna Cantor
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | | | - Paul Brennan
- International Agency for Research on Cancer, Lyon, France
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Shur N, Summerlin ML, Robin NH, Moreno-Mendelson A, Shalaby-Rana E, Hinds T. Genetic consultations in cases of unexplained fractures and haemorrhage: an evidence-based approach. Curr Opin Pediatr 2021; 33:3-18. [PMID: 33337606 DOI: 10.1097/mop.0000000000000986] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
PURPOSE OF REVIEW When infants and young children present with suspected physical abuse, it is critical to follow standard guidelines and rule out alternative causes of fracture and haemorrhage. A multidisciplinary team involved in the initial evaluation typically includes paediatrics, radiology, child protective services and/or law enforcement, and in complex cases, haematology, neurology, and genetics. A comprehensive genetics consultation includes review of the history of present illness, birth and past medical history, review of growth curves, family history, physical examination, radiological findings, and when indicated, biochemical and/ or genetic testing. RECENT FINDINGS A number of reports have mischaracterized several genetic disorders as child abuse mimics. There is a difference between a differential diagnosis, which includes every condition that can cause a fracture and/or subdural haemorrhage, and a mimic, so called because it can be difficult to differentiate from child abuse. In this review, we discuss the differential diagnosis for infantile fractures and subdural bleeds, highlight cardinal signs and symptoms of genetic disorders, and demonstrate that these genetic disorders can be readily differentiated and diagnosed using a stepwise approach. Genetic disorders rarely, if ever, are truly mimics of child physical abuse. SUMMARY In cases of suspected child physical abuse, multidisciplinary evaluations by paediatric specialists, keen clinical judgment, complete physical examinations, and judicious testing provides an evidence-based, time tested approach to excluding genetic disorders and diagnosing suspected child physical abuse.
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Affiliation(s)
- Natasha Shur
- George Washington University School of Medicine and Health Sciences
- Division of Genetics and Metabolism, Rare Disease Institute, Children's National Hospital
| | | | | | | | - Eglal Shalaby-Rana
- George Washington University School of Medicine and Health Sciences
- Diagnostic Imaging and Radiology
| | - Tanya Hinds
- George Washington University School of Medicine and Health Sciences
- Child & Adolescent Protection Center, Children's National Hospital, Washington DC
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Sundar S, Manchanda R, Gourley C, George A, Wallace A, Balega J, Williams S, Wallis Y, Edmondson R, Nicum S, Frost J, Attygalle A, Fotopoulou C, Bowen R, Bell D, Gajjar K, Ramsay B, Wood NJ, Ghaem-Maghami S, Miles T, Ganesan R. British Gynaecological Cancer Society/British Association of Gynaecological Pathology consensus for germline and tumor testing for BRCA1/2 variants in ovarian cancer in the United Kingdom. Int J Gynecol Cancer 2021; 31:272-278. [PMID: 33468564 DOI: 10.1136/ijgc-2020-002112] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 12/06/2020] [Accepted: 12/09/2020] [Indexed: 11/04/2022] Open
Abstract
The British Gynecological Cancer Society and the British Association of Gynecological Pathologists established a multidisciplinary consensus group comprising experts in surgical gynecological oncology, medical oncology, genetics, and laboratory science, and clinical nurse specialists to identify the optimal pathways to BRCA germline and tumor testing in patients with ovarian cancer in routine clinical practice. In particular, the group explored models of consent, quality standards identified at pathology laboratories, and experience and data from pioneering cancer centers. The group liaised with representatives from ovarian cancer charities to also identify patient perspectives that would be important to implementation. Recommendations from these consensus group deliberations are presented in this manuscript.
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Affiliation(s)
- Sudha Sundar
- Gynaecological Oncology, Pan-Birmingham Gynaecological Cancer Centre, Birmingham, UK .,Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Ranjit Manchanda
- Gynaecological Oncology, Barts Health NHS Trust, Barts Cancer Institute, London, UK
| | - Charlie Gourley
- University of Edinburgh Cancer Research UK Centre, Edinburgh, UK
| | | | - Andrew Wallace
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester, UK
| | - Janos Balega
- Gynaecological Oncology, Pan-Birmingham Gynaecological Cancer Centre, Birmingham, UK
| | - Sarah Williams
- University Hospital Birmingham Foundation NHS Trust, Birmingham, UK
| | - Yvonne Wallis
- Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | | | | | - Jonathan Frost
- Royal United Hospitals Bath NHS Foundation Trust, Bath, UK
| | | | | | - Rebecca Bowen
- Royal United Hospitals Bath NHS Foundation Trust, Bath, UK
| | - Dani Bell
- Macmillan Cancer Support, London, UK
| | | | - Bruce Ramsay
- Peterborough City Hospital, Peterborough, Cambridgeshire, UK
| | - Nicholas J Wood
- Obstetrics and Gynaecology, Lancashire Teaching Hospitals NHS Foundation Trust, Preston, UK
| | | | - Tracie Miles
- Gynaecological Oncology, Royal United Hospitals, Bath, UK
| | - Raji Ganesan
- Birmingham Women's and Children's NHS Trust, Birmingham, UK
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Sanoguera-Miralles L, Valenzuela-Palomo A, Bueno-Martínez E, Llovet P, Díez-Gómez B, Caloca MJ, Pérez-Segura P, Fraile-Bethencourt E, Colmena M, Carvalho S, Allen J, Easton DF, Devilee P, Vreeswijk MPG, de la Hoya M, Velasco EA. Comprehensive Functional Characterization and Clinical Interpretation of 20 Splice-Site Variants of the RAD51C Gene. Cancers (Basel) 2020; 12:E3771. [PMID: 33333735 PMCID: PMC7765170 DOI: 10.3390/cancers12123771] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 12/08/2020] [Accepted: 12/09/2020] [Indexed: 12/12/2022] Open
Abstract
Hereditary breast and/or ovarian cancer is a highly heterogeneous disease with more than 10 known disease-associated genes. In the framework of the BRIDGES project (Breast Cancer Risk after Diagnostic Gene Sequencing), the RAD51C gene has been sequenced in 60,466 breast cancer patients and 53,461 controls. We aimed at functionally characterizing all the identified genetic variants that are predicted to disrupt the splicing process. Forty RAD51C variants of the intron-exon boundaries were bioinformatically analyzed, 20 of which were selected for splicing functional assays. To test them, a splicing reporter minigene with exons 2 to 8 was designed and constructed. This minigene generated a full-length transcript of the expected size (1062 nucleotides), sequence, and structure (Vector exon V1- RAD51C exons_2-8- Vector exon V2). The 20 candidate variants were genetically engineered into the wild type minigene and functionally assayed in MCF-7 cells. Nineteen variants (95%) impaired splicing, while 18 of them produced severe splicing anomalies. At least 35 transcripts were generated by the mutant minigenes: 16 protein-truncating, 6 in-frame, and 13 minor uncharacterized isoforms. According to ACMG/AMP-based standards, 15 variants could be classified as pathogenic or likely pathogenic variants: c.404G > A, c.405-6T > A, c.571 + 4A > G, c.571 + 5G > A, c.572-1G > T, c.705G > T, c.706-2A > C, c.706-2A > G, c.837 + 2T > C, c.905-3C > G, c.905-2A > C, c.905-2_905-1del, c.965 + 5G > A, c.1026 + 5_1026 + 7del, and c.1026 + 5G > T.
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Affiliation(s)
- Lara Sanoguera-Miralles
- Splicing and Genetic Susceptibility to Cancer, Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC-UVa), 47003 Valladolid, Spain; (L.S.-M.); (A.V.-P.); (E.B.-M.); (B.D.-G.); (E.F.-B.)
| | - Alberto Valenzuela-Palomo
- Splicing and Genetic Susceptibility to Cancer, Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC-UVa), 47003 Valladolid, Spain; (L.S.-M.); (A.V.-P.); (E.B.-M.); (B.D.-G.); (E.F.-B.)
| | - Elena Bueno-Martínez
- Splicing and Genetic Susceptibility to Cancer, Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC-UVa), 47003 Valladolid, Spain; (L.S.-M.); (A.V.-P.); (E.B.-M.); (B.D.-G.); (E.F.-B.)
| | - Patricia Llovet
- Molecular Oncology Laboratory CIBERONC, Hospital Clinico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), 28040 Madrid, Spain; (P.L.); (P.P.-S.); (M.C.)
| | - Beatriz Díez-Gómez
- Splicing and Genetic Susceptibility to Cancer, Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC-UVa), 47003 Valladolid, Spain; (L.S.-M.); (A.V.-P.); (E.B.-M.); (B.D.-G.); (E.F.-B.)
| | - María José Caloca
- Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC-UVa), 47003 Valladolid, Spain;
| | - Pedro Pérez-Segura
- Molecular Oncology Laboratory CIBERONC, Hospital Clinico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), 28040 Madrid, Spain; (P.L.); (P.P.-S.); (M.C.)
| | - Eugenia Fraile-Bethencourt
- Splicing and Genetic Susceptibility to Cancer, Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC-UVa), 47003 Valladolid, Spain; (L.S.-M.); (A.V.-P.); (E.B.-M.); (B.D.-G.); (E.F.-B.)
- Knight Cancer Research Building, 2720 S Moody Ave, Portland, OR 97201, USA
| | - Marta Colmena
- Molecular Oncology Laboratory CIBERONC, Hospital Clinico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), 28040 Madrid, Spain; (P.L.); (P.P.-S.); (M.C.)
| | - Sara Carvalho
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; (S.C.); (J.A.); (D.F.E.)
| | - Jamie Allen
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; (S.C.); (J.A.); (D.F.E.)
| | - Douglas F. Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; (S.C.); (J.A.); (D.F.E.)
| | - Peter Devilee
- Leiden University Medical Center, Department of Human Genetics, 2300RC Leiden, The Netherlands; (P.D.); (M.P.G.V.)
| | - Maaike P. G. Vreeswijk
- Leiden University Medical Center, Department of Human Genetics, 2300RC Leiden, The Netherlands; (P.D.); (M.P.G.V.)
| | - Miguel de la Hoya
- Molecular Oncology Laboratory CIBERONC, Hospital Clinico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), 28040 Madrid, Spain; (P.L.); (P.P.-S.); (M.C.)
| | - Eladio A. Velasco
- Splicing and Genetic Susceptibility to Cancer, Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC-UVa), 47003 Valladolid, Spain; (L.S.-M.); (A.V.-P.); (E.B.-M.); (B.D.-G.); (E.F.-B.)
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