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Sandoval RL, Bottosso M, Tianyu L, Polidorio N, Bychkovsky BL, Verret B, Gennari A, Cahill S, Achatz MI, Caron O, Imbert-Bouteille M, Noguès C, Mawell KN, Fortuno C, Spurdle AB, Tayob N, Andre F, Garber JE. TP53-associated early breast cancer: new observations from a large cohort. J Natl Cancer Inst 2024; 116:1246-1254. [PMID: 38569880 PMCID: PMC11308175 DOI: 10.1093/jnci/djae074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 03/19/2024] [Accepted: 03/21/2024] [Indexed: 04/05/2024] Open
Abstract
BACKGROUND A recent large, well-annotated international cohort of patients with Li-Fraumeni syndrome and early-stage breast cancer was examined for shared features. METHODS This multicenter cohort study included women with a germline TP53 pathogenic or likely pathogenic variant and nonmetastatic breast cancer diagnosed between 2002 and 2022. Clinical and genetic data were obtained from institutional registries and clinical charts. Descriptive statistics were used to summarize proportions, and differences were assessed using χ2 or Wilcoxon rank sum tests. Metachronous contralateral breast cancer risk, radiation-induced sarcoma risk, and recurrence-free survival were analyzed using the Kaplan-Meier methodology. RESULTS Among 227 women who met study criteria, the median age of first breast cancer diagnosis was 37 years (range = 21-71), 11.9% presented with bilateral synchronous breast cancer, and 18.1% had ductal carcinoma in situ only. In total, 166 (73.1%) patients underwent mastectomies, including 67 bilateral mastectomies as first breast cancer surgery. Among those patients with retained breast tissue, the contralateral breast cancer rate was 25.3% at 5 years. Among 186 invasive tumors, 72.1% were stages I to II, 48.9% were node negative, and the most common subtypes were hormone receptor-positive/HER2-negative (40.9%) and hormone receptor positive/HER2 positive (34.4%). At a median follow-up of 69.9 months (interquartile range = 32.6-125.9), invasive hormone receptor-positive/HER2-negative disease had the highest recurrence risk among the subtypes (5-year recurrence-free survival = 61.1%, P = .001). Among those who received radiation therapy (n = 79), the 5-year radiation-induced sarcoma rate was 4.8%. CONCLUSION We observed high rates of ductal carcinoma in situ, hormone receptor-positive, and HER2-positive breast cancers, with a worse outcome in the hormone receptor-positive/HER2-negative luminal tumors, despite appropriate treatment. Confirmation of these findings in further studies could have implications for breast cancer care in those with Li-Fraumeni syndrome.
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Affiliation(s)
- Renata L Sandoval
- Medical Oncology Center, Hospital Sírio-Libanês, Brasília, DF, Brazil
- Division of Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Michele Bottosso
- Department of Surgery, Oncology and Gastroenterology, University of Padua, Padua, Italy
- Medical Oncology Department, Gustave Roussy Cancer Campus, INERM U981, Université Paris Saclay, France
| | - Li Tianyu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Natalia Polidorio
- Breast Surgery Department, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Brittany L Bychkovsky
- Division of Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, MA, USA
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA
- Harvard Medical School, Boston, MA, USA
| | - Benjamin Verret
- Medical Oncology Department, Gustave Roussy Cancer Campus, INERM U981, Université Paris Saclay, France
| | - Alessandra Gennari
- Department of Translational Medicine, University of Piemonte Orientale, Novara, Italy
| | - Sophie Cahill
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Olivier Caron
- Medical Oncology Department, Institut Gustave Roussy, Villejuif, France
| | | | - Catherine Noguès
- Cancer Risk Management Department, Clinical Oncogenetics, Institut Paoli-Calmettes, Marseille, France
- Aix Marseille Université, INSERM, IRD, SESSTIM, Marseille, France
| | - Kara N Mawell
- Department of Medicine, Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Cristina Fortuno
- Population Health Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Amanda B Spurdle
- Population Health Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Nabihah Tayob
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Fabrice Andre
- Medical Oncology Department, Gustave Roussy Cancer Campus, INERM U981, Université Paris Saclay, France
| | - Judy E Garber
- Division of Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, MA, USA
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA
- Harvard Medical School, Boston, MA, USA
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2
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Fortuno C, Michailidou K, Parsons M, Dolinsky JS, Pesaran T, Yussuf A, Mester JL, Hruska KS, Hiraki S, O’Connor R, Chan RC, Kim S, Tavtigian SV, Goldgar D, James PA, Spurdle AB. Challenges and approaches to calibrating patient phenotype as evidence for cancer gene variant classification under ACMG/AMP guidelines. Hum Mol Genet 2024; 33:724-732. [PMID: 38271184 PMCID: PMC11000651 DOI: 10.1093/hmg/ddae009] [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: 11/13/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 01/27/2024] Open
Abstract
Since first publication of the American College of Medical Genetics and Genomics/Association for Medical Pathology (ACMG/AMP) variant classification guidelines, additional recommendations for application of certain criteria have been released (https://clinicalgenome.org/docs/), to improve their application in the diagnostic setting. However, none have addressed use of the PS4 and PP4 criteria, capturing patient presentation as evidence towards pathogenicity. Application of PS4 can be done through traditional case-control studies, or "proband counting" within or across clinical testing cohorts. Review of the existing PS4 and PP4 specifications for Hereditary Cancer Gene Variant Curation Expert Panels revealed substantial differences in the approach to defining specifications. Using BRCA1, BRCA2 and TP53 as exemplar genes, we calibrated different methods proposed for applying the "PS4 proband counting" criterion. For each approach, we considered limitations, non-independence with other ACMG/AMP criteria, broader applicability, and variability in results for different datasets. Our findings highlight inherent overlap of proband-counting methods with ACMG/AMP frequency codes, and the importance of calibration to derive dataset-specific code weights that can account for potential between-dataset differences in ascertainment and other factors. Our work emphasizes the advantages and generalizability of logistic regression analysis over simple proband-counting approaches to empirically determine the relative predictive capacity and weight of various personal clinical features in the context of multigene panel testing, for improved variant interpretation. We also provide a general protocol, including instructions for data formatting and a web-server for analysis of personal history parameters, to facilitate dataset-specific calibration analyses required to use such data for germline variant classification.
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Affiliation(s)
- Cristina Fortuno
- Population Health Program, QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia
| | - Kyriaki Michailidou
- Biostatistics Unit, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus
| | - Michael Parsons
- Population Health Program, QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia
| | | | - Tina Pesaran
- Ambry Genetics, Aliso Viejo, CA 92656, United States
| | - Amal Yussuf
- Ambry Genetics, Aliso Viejo, CA 92656, United States
| | | | | | | | | | - Raymond C Chan
- Color Genomics, Inc., Burlingame, CA 94010, United States
| | - Serra Kim
- Color Genomics, Inc., Burlingame, CA 94010, United States
| | - Sean V Tavtigian
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, United States
| | - David Goldgar
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, United States
| | - Paul A James
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, VIC 3052, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Amanda B Spurdle
- Population Health Program, QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia
- Faculty of Medicine, The University of Queensland, Herston, QLD 4006, Australia
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3
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Pinto EM, Ribeiro EMSF, Wang J, Phillips AH, Kriwacki RW, Zambetti GP. Clinical and functional analysis of the germline TP53 p.K164E acetylation site variant. Cold Spring Harb Mol Case Stud 2023; 9:a006290. [PMID: 38050059 PMCID: PMC10815290 DOI: 10.1101/mcs.a006290] [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: 09/12/2023] [Accepted: 11/27/2023] [Indexed: 12/06/2023] Open
Abstract
TP53 plays a critical role as a tumor suppressor by controlling cell cycle progression, DNA repair, and apoptosis. Post-translational modifications such as acetylation of specific lysine residues in the DNA binding and carboxy-terminus regulatory domains modulate its tumor suppressor activities. In this study, we addressed the functional consequences of the germline TP53 p.K164E (NM_000546.5: c.490A>G) variant identified in a patient with early-onset breast cancer and a significant family history of cancer. K164 is a conserved residue located in the L2 loop of the p53 DNA binding domain that is post-translationally modified by acetylation. In silico, in vitro, and in vivo analyses demonstrated that the glutamate substitution at K164 marginally destabilizes the p53 protein structure but significantly impairs sequence-specific DNA binding, transactivation, and tumor cell growth inhibition. Although p.K164E is currently considered a variant of unknown significance by different clinical genetic testing laboratories, the clinical and laboratory-based findings presented here provide strong evidence to reclassify TP53 p.K164E as a likely pathogenic variant.
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Affiliation(s)
- Emilia Modolo Pinto
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA;
| | - Enilze M S F Ribeiro
- Programa de Pós-graduação em Genética, Universidade Federal do Paraná, Curitiba, Paraná, 81531-980, Brazil;
| | - Jinling Wang
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Aaron H Phillips
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Richard W Kriwacki
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Gerard P Zambetti
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA;
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4
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Fortuno C, Richardson M, Pesaran T, Yussuf A, Horton C, James PA, Spurdle AB. CHEK2 is not a Li-Fraumeni syndrome gene: time to update public resources. J Med Genet 2023; 60:1215-1217. [PMID: 37536919 DOI: 10.1136/jmg-2023-109464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 07/23/2023] [Indexed: 08/05/2023]
Abstract
The gene-disease relationship for CHEK2 remains listed as 'Li-Fraumeni syndrome 2' in public resources such as OMIM and MONDO, despite published evidence to the contrary, causing frustration among Li-Fraumeni syndrome (LFS) clinical experts. Here, we compared personal cancer characteristics of 2095 CHEK2 and 248 TP53 pathogenic variant carriers undergoing multigene panel testing at Ambry Genetics against 15 135 individuals with no known pathogenic variant. Our results from a within-cohort logistic regression approach highlight obvious differences between clinical presentation of TP53 and CHEK2 pathogenic variant carriers, with no evidence of CHEK2 being associated with any of the TP53-related core LFS cancers. These findings emphasise the need to replace 'Li-Fraumeni syndrome 2' as the CHEK2-associated disease name, thereby limiting potential confusion.
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Affiliation(s)
- Cristina Fortuno
- Population Health Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | | | | | - Amal Yussuf
- Ambry Genetics, Aliso Viejo, California, USA
| | | | - Paul A James
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Amanda B Spurdle
- Population Health Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
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5
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Schwartz A, Manning DK, Koeller DR, Chittenden A, Isidro RA, Hayes CP, Abraamyan F, Manam MD, Dwan M, Barletta JA, Sholl LM, Yurgelun MB, Rana HQ, Garber JE, Ghazani AA. An integrated somatic and germline approach to aid interpretation of germline variants of uncertain significance in cancer susceptibility genes. Front Oncol 2022; 12:942741. [PMID: 36091175 PMCID: PMC9453486 DOI: 10.3389/fonc.2022.942741] [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: 05/12/2022] [Accepted: 07/12/2022] [Indexed: 11/13/2022] Open
Abstract
Genomic profiles of tumors are often unique and represent characteristic mutational signatures defined by DNA damage or DNA repair response processes. The tumor-derived somatic information has been widely used in therapeutic applications, but it is grossly underutilized in the assessment of germline genetic variants. Here, we present a comprehensive approach for evaluating the pathogenicity of germline variants in cancer using an integrated interpretation of somatic and germline genomic data. We have previously demonstrated the utility of this integrated approach in the reassessment of pathogenic germline variants in selected cancer patients with unexpected or non-syndromic phenotypes. The application of this approach is presented in the assessment of rare variants of uncertain significance (VUS) in Lynch-related colon cancer, hereditary paraganglioma-pheochromocytoma syndrome, and Li-Fraumeni syndrome. Using this integrated method, germline VUS in PMS2, MSH6, SDHC, SHDA, and TP53 were assessed in 16 cancer patients after genetic evaluation. Comprehensive clinical criteria, somatic signature profiles, and tumor immunohistochemistry were used to re-classify VUS by upgrading or downgrading the variants to likely or unlikely actionable categories, respectively. Going forward, collation of such germline variants and creation of cross-institutional knowledgebase datasets that include integrated somatic and germline data will be crucial for the assessment of these variants in a larger cancer cohort.
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Affiliation(s)
- Alison Schwartz
- Division of Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Danielle K. Manning
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, United States
| | - Diane R. Koeller
- Division of Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Anu Chittenden
- Division of Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Raymond A. Isidro
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
| | - Connor P. Hayes
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, United States
| | - Feruza Abraamyan
- Harvard Medical School, Boston, MA, United States
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, United States
| | - Monica Devi Manam
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, United States
| | - Meaghan Dwan
- Division of Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Justine A. Barletta
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
| | - Lynette M. Sholl
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
| | - Matthew B. Yurgelun
- Division of Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
- Division of Population Sciences, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Huma Q. Rana
- Division of Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
- Division of Population Sciences, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Judy E. Garber
- Division of Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
- Division of Population Sciences, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Arezou A. Ghazani
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, United States
- *Correspondence: Arezou A. Ghazani,
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6
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Masson E, Zou WB, Génin E, Cooper DN, Le Gac G, Fichou Y, Pu N, Rebours V, Férec C, Liao Z, Chen JM. Expanding ACMG variant classification guidelines into a general framework. Hum Genomics 2022; 16:31. [PMID: 35974416 PMCID: PMC9380380 DOI: 10.1186/s40246-022-00407-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 08/10/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The American College of Medical Genetics and Genomics (ACMG)-recommended five variant classification categories (pathogenic, likely pathogenic, uncertain significance, likely benign, and benign) have been widely used in medical genetics. However, these guidelines are fundamentally constrained in practice owing to their focus upon Mendelian disease genes and their dichotomous classification of variants as being either causal or not. Herein, we attempt to expand the ACMG guidelines into a general variant classification framework that takes into account not only the continuum of clinical phenotypes, but also the continuum of the variants' genetic effects, and the different pathological roles of the implicated genes. MAIN BODY As a disease model, we employed chronic pancreatitis (CP), which manifests clinically as a spectrum from monogenic to multifactorial. Bearing in mind that any general conceptual proposal should be based upon sound data, we focused our analysis on the four most extensively studied CP genes, PRSS1, CFTR, SPINK1 and CTRC. Based upon several cross-gene and cross-variant comparisons, we first assigned the different genes to two distinct categories in terms of disease causation: CP-causing (PRSS1 and SPINK1) and CP-predisposing (CFTR and CTRC). We then employed two new classificatory categories, "predisposing" and "likely predisposing", to replace ACMG's "pathogenic" and "likely pathogenic" categories in the context of CP-predisposing genes, thereby classifying all pathologically relevant variants in these genes as "predisposing". In the case of CP-causing genes, the two new classificatory categories served to extend the five ACMG categories whilst two thresholds (allele frequency and functional) were introduced to discriminate "pathogenic" from "predisposing" variants. CONCLUSION Employing CP as a disease model, we expand ACMG guidelines into a five-category classification system (predisposing, likely predisposing, uncertain significance, likely benign, and benign) and a seven-category classification system (pathogenic, likely pathogenic, predisposing, likely predisposing, uncertain significance, likely benign, and benign) in the context of disease-predisposing and disease-causing genes, respectively. Taken together, the two systems constitute a general variant classification framework that, in principle, should span the entire spectrum of variants in any disease-related gene. The maximal compliance of our five-category and seven-category classification systems with the ACMG guidelines ought to facilitate their practical application.
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Affiliation(s)
- Emmanuelle Masson
- Univ Brest, Inserm, EFS, UMR 1078, GGB, 22 Avenue Camille Desmoulins, F-29200, Brest, France.,Service de Génétique Médicale et de Biologie de la Reproduction, CHRU Brest, F-29200, Brest, France
| | - Wen-Bin Zou
- Department of Gastroenterology, Changhai Hospital, The Secondary Military Medical University, Shanghai, China.,Shanghai Institute of Pancreatic Diseases, Shanghai, China
| | - Emmanuelle Génin
- Univ Brest, Inserm, EFS, UMR 1078, GGB, 22 Avenue Camille Desmoulins, F-29200, Brest, France
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, UK
| | - Gerald Le Gac
- Univ Brest, Inserm, EFS, UMR 1078, GGB, 22 Avenue Camille Desmoulins, F-29200, Brest, France.,Service de Génétique Médicale et de Biologie de la Reproduction, CHRU Brest, F-29200, Brest, France
| | - Yann Fichou
- Univ Brest, Inserm, EFS, UMR 1078, GGB, 22 Avenue Camille Desmoulins, F-29200, Brest, France
| | - Na Pu
- Univ Brest, Inserm, EFS, UMR 1078, GGB, 22 Avenue Camille Desmoulins, F-29200, Brest, France.,Department of Critical Care Medicine, Research Institute of General Surgery, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Vinciane Rebours
- Department of Gastroenterology and Pancreatology, Beaujon Hospital, Assistance Publique-Hôpitaux de Paris, Clichy, Université de Paris, Paris, France
| | - Claude Férec
- Univ Brest, Inserm, EFS, UMR 1078, GGB, 22 Avenue Camille Desmoulins, F-29200, Brest, France
| | - Zhuan Liao
- Department of Gastroenterology, Changhai Hospital, The Secondary Military Medical University, Shanghai, China.,Shanghai Institute of Pancreatic Diseases, Shanghai, China
| | - Jian-Min Chen
- Univ Brest, Inserm, EFS, UMR 1078, GGB, 22 Avenue Camille Desmoulins, F-29200, Brest, France.
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7
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Sandoval RL, Polidorio N, Leite ACR, Cartaxo M, Pisani JP, Quirino CV, Cezana L, Pereira NG, Pereira AAL, Rossi BM, Achatz MI. Breast Cancer Phenotype Associated With Li-Fraumeni Syndrome: A Brazilian Cohort Enriched by TP53 p.R337H Carriers. Front Oncol 2022; 12:836937. [PMID: 35371985 PMCID: PMC8966034 DOI: 10.3389/fonc.2022.836937] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 02/14/2022] [Indexed: 01/01/2023] Open
Abstract
Breast cancer (BC) is the most prevalent malignancy in women with Li-Fraumeni syndrome (LFS). The literature on BC in LFS is limited due to its rarity worldwide. A TP53 founder pathogenic variant (c.1010G>A; p.R337H) is responsible for the higher prevalence of this syndrome among women of Brazilian ancestry.
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Affiliation(s)
| | | | | | - Mariana Cartaxo
- Oncology Center, Hospital Nossa Senhora das Neves, João Pessoa, Brazil
| | | | | | - Loureno Cezana
- Oncology Center, Hospital Santa Rita de Cássia, Vitoria, Brazil
| | | | | | - Benedito Mauro Rossi
- Oncology Center, Hospital Sírio-Libanês, São Paulo, Brazil.,Genetics and Genomics Department, Beneficência Portuguesa, São Paulo, Brazil
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8
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Rippinger N, Fischer C, Sinn HP, Dikow N, Sutter C, Rhiem K, Grill S, Cremer FW, Nguyen HP, Ditsch N, Kast K, Hettmer S, Kratz CP, Schott S. Breast cancer characteristics and surgery among women with Li-Fraumeni syndrome in Germany-A retrospective cohort study. Cancer Med 2021; 10:7747-7758. [PMID: 34569185 PMCID: PMC8559485 DOI: 10.1002/cam4.4300] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 08/16/2021] [Accepted: 08/30/2021] [Indexed: 12/26/2022] Open
Abstract
Background Women with Li‐Fraumeni syndrome (LFS) have elevated breast cancer (BC) risk. Optimal BC treatment strategies in this population are yet unknown. Methods BC subtypes and treatment were retrospectively investigated between December 2016 and January 2019 in a multicentre study. BC risks were evaluated according to the type of surgery. Results Thirty‐five women of our study population (35/44; 79.5%) had developed 36 breast lesions at first diagnosis at a mean age of 34 years. Those breast lesions comprised 32 invasive BCs (89%), three ductal carcinoma in situ alone (8%) and one malignant phyllodes tumour (3%). BCs were mainly high‐grade (18/32), of no special type (NST; 31/32), HER2‐enriched (11/32) or luminal‐B‐(like)‐type (10/32). Affected women (n = 35) received breast‐conserving surgery (BCS, n = 17) or a mastectomy (ME, n = 18) including seven women with simultaneous contralateral prophylactic mastectomy (CPM) at first diagnosis. Nineteen women suffered 20 breast or locoregional axillary lesions at second diagnosis with mean age of 36. Median time between first and second diagnosis was 57 months; median time to contra‐ and ipsilateral recurrence depended on surgical strategies (BCS: 46 vs. unilateral ME: 93 vs. bilateral ME > 140 months). Women with a primary treatment of solitaire therapeutic ME suffered from contralateral BC earlier compared to those with therapeutic ME and CPM (median: 93 vs. >140 months). Conclusion Aggressive BC subtypes occur among women with LFS. Surgical treatment, i.e. ME and CPM, may prolong time to a second BC diagnosis. Conclusion on long‐term survival benefit is pending. Individual competing tumour risks and long‐term outcomes need to be taken into consideration.
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Affiliation(s)
- Nathalie Rippinger
- Department of Gynecology and Obstetrics, University Hospital Heidelberg, Heidelberg, Germany
| | - Christine Fischer
- Institute of Human Genetics, University Hospital Heidelberg, Heidelberg, Germany
| | - Hans-Peter Sinn
- Department of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Nicola Dikow
- Institute of Human Genetics, University Hospital Heidelberg, Heidelberg, Germany
| | - Christian Sutter
- Institute of Human Genetics, University Hospital Heidelberg, Heidelberg, Germany
| | - Kerstin Rhiem
- Center for Hereditary Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Medical Faculty, University Hospital Cologne, Cologne, Germany
| | - Sabine Grill
- Department of Gynecology and Centre for Hereditary Breast and Ovarian Cancer, Comprehensive Cancer Center (CCC TUM), University Hospital Rechts der Isar, Technical University of Munich (TUM), Munich, Germany
| | | | - Huu P Nguyen
- Institute of Medical Genetics and Applied Genomics, University Hospital of Tuebingen, Tuebingen, Germany.,Department of Human Genetics, University of Bochum, Bochum, Germany
| | - Nina Ditsch
- Department of Gynecology and Obstetrics, Ludwig-Maximilians University (LMU), University Hospital of Munich, Munich, Germany.,Department of Gynecology and Obstretrics, University Hospital Augsburg, Augsburg, Germany
| | - Karin Kast
- Center for Hereditary Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Medical Faculty, University Hospital Cologne, Cologne, Germany.,Department of Gynecology and Obstetrics, Medical Faculty, University Hospital Carl Gustav Carus, Technical University Dresden, Dresden, Germany.,National Center for Tumour Diseases (NCT), Partner Site Dresden, Dresden, Germany
| | - Simone Hettmer
- Department of Paediatrics and Adolescent Medicine, Division of Paediatric Haematology and Oncology Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Christian P Kratz
- Paediatric Haematology and Oncology and Rare Disease Program, Hannover Medical School, Hannover, Germany
| | - Sarah Schott
- Department of Gynecology and Obstetrics, University Hospital Heidelberg, Heidelberg, Germany
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9
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Prejac J, Dedić Plavetić N, Gotovac Jerčić K, Borovečki F. A first report of a rare TP53 variant associated with Li-Fraumeni syndrome manifesting as invasive breast cancer and malignant solitary fibrous tumor. World J Surg Oncol 2021; 19:254. [PMID: 34452612 PMCID: PMC8399826 DOI: 10.1186/s12957-021-02370-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 08/12/2021] [Indexed: 01/01/2023] Open
Abstract
Background Li-Fraumeni is a rare autosomal dominant cancer predisposition syndrome. The basis is a germline mutation of TP53 gene which encodes tumor suppressor protein resulting in early onset of tumors, most often breast cancer, soft tissue sarcomas, brain tumors, adrenocortical carcinomas, and leukemia. Case report We present a case of a young woman with a positive family history for cancer diagnosed with malignant solitary fibrous tumor and luminal B-like invasive breast cancer. Breast cancer and sarcomas account for the majority of tumors associated with Li-Fraumeni syndrome, yet solitary fibrous tumor is a rare clinical entity with no established guidelines for treatment. Even though both primary tumors were successfully resected, the sarcoma relapsed in the form of lung metastases. The NGS analysis revealed single nucleotide variant (c.1101-1G>A) in TP53 gene, affecting the acceptor splice site at intron 10. Until now, only one case of this genetic variant has been documented with conflicting interpretations of pathogenicity. Conclusions The knowledge of TP53 mutation status is essential since the management of these patients requires different approach to avoid excessive toxicity due to the risk of developing secondary malignancy. Using the clinical criteria to screen for affected individuals facilitates appropriate early genetic counseling of patients and their families. Following the American College of Medical Genetics criteria, we believe that the reported single nucleotide variant (c.1101-1G>A) in TP53 gene should be considered pathogenic. Supplementary Information The online version contains supplementary material available at 10.1186/s12957-021-02370-8.
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Affiliation(s)
- Juraj Prejac
- Department of Oncology, University Hospital Centre Zagreb, Kišpatićeva 12, 10000, Zagreb, Croatia.,School of Dental Medicine, University of Zagreb, Gundulićeva 5, 10000, Zagreb, Croatia
| | - Natalija Dedić Plavetić
- Department of Oncology, University Hospital Centre Zagreb, Kišpatićeva 12, 10000, Zagreb, Croatia. .,School of Medicine, University of Zagreb, Šalata 3, 10000, Zagreb, Croatia.
| | - Kristina Gotovac Jerčić
- Department of Neurology, University Hospital Centre Zagreb, Kišpatićeva 12, 10000, Zagreb, Croatia
| | - Fran Borovečki
- Department of Neurology, University Hospital Centre Zagreb, Kišpatićeva 12, 10000, Zagreb, Croatia.,Center for Translational and Clinical Research, Department for Functional Genomics, School of Medicine, University Hospital Centre Zagreb, University of Zagreb, Šalata 2, 10000, Zagreb, Croatia
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10
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Fortuno C, Pesaran T, Dolinsky J, Yussuf A, McGoldrick K, Tavtigian SV, Goldgar D, Spurdle AB, James PA. An updated quantitative model to classify missense variants in the TP53 gene: A novel multifactorial strategy. Hum Mutat 2021; 42:1351-1361. [PMID: 34273903 DOI: 10.1002/humu.24264] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 06/25/2021] [Accepted: 07/15/2021] [Indexed: 11/07/2022]
Abstract
Multigene panel testing has led to an increase in the number of variants of uncertain significance identified in the TP53 gene, associated with Li-Fraumeni syndrome. We previously developed a quantitative model for predicting the pathogenicity of P53 missense variants based on the combination of calibrated bioinformatic information and somatic to germline ratio. Here, we extended this quantitative model for the classification of P53 predicted missense variants by adding new pieces of evidence (personal and family history parameters, loss-of-function results, population allele frequency, healthy individual status by age 60, and breast tumor pathology). We also annotated which missense variants might have an effect on splicing based on bioinformatic predictions. This updated model plus annotation led to the classification of 805 variants into a clinically relevant class, which correlated well with existing ClinVar classifications, and resolved a large number of conflicting and uncertain classifications. We propose this model as a reliable approach to TP53 germline variant classification and emphasize its use in contributing to optimize TP53-specific ACMG/AMP guidelines.
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Affiliation(s)
- Cristina Fortuno
- Genetics and Computational Division, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | | | | | - Amal Yussuf
- Ambry Genetics, Aliso Viejo, California, USA
| | | | - Sean V Tavtigian
- Huntsman Cancer Institute and Department of Dermatology, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - David Goldgar
- Huntsman Cancer Institute and Department of Dermatology, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Amanda B Spurdle
- Genetics and Computational Division, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Paul A James
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, Australia
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11
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Fortuno C, Lee K, Olivier M, Pesaran T, Mai PL, de Andrade KC, Attardi LD, Crowley S, Evans DG, Feng BJ, Major Foreman AK, Frone MN, Huether R, James PA, McGoldrick K, Mester J, Seifert BA, Slavin TP, Witkowski L, Zhang L, Plon SE, Spurdle AB, Savage SA. Specifications of the ACMG/AMP variant interpretation guidelines for germline TP53 variants. Hum Mutat 2021; 42:223-236. [PMID: 33300245 PMCID: PMC8374922 DOI: 10.1002/humu.24152] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 11/05/2020] [Accepted: 12/07/2020] [Indexed: 12/28/2022]
Abstract
Germline pathogenic variants in TP53 are associated with Li-Fraumeni syndrome, a cancer predisposition disorder inherited in an autosomal dominant pattern associated with a high risk of malignancy, including early-onset breast cancers, sarcomas, adrenocortical carcinomas, and brain tumors. Intense cancer surveillance for individuals with TP53 germline pathogenic variants is associated with reduced cancer-related mortality. Accurate and consistent classification of germline variants across clinical and research laboratories is important to ensure appropriate cancer surveillance recommendations. Here, we describe the work performed by the Clinical Genome Resource TP53 Variant Curation Expert Panel (ClinGen TP53 VCEP) focused on specifying the American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG/AMP) guidelines for germline variant classification to the TP53 gene. Specifications were developed for 20 ACMG/AMP criteria, while nine were deemed not applicable. The original strength level for the 10 criteria was also adjusted due to current evidence. Use of TP53-specific guidelines and sharing of clinical data among experts and clinical laboratories led to a decrease in variants of uncertain significance from 28% to 12% compared with the original guidelines. The ClinGen TP53 VCEP recommends the use of these TP53-specific ACMG/AMP guidelines as the standard strategy for TP53 germline variant classification.
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Affiliation(s)
- Cristina Fortuno
- QIMR Berghofer Medical Research Institute, Brisbane City, Australia, AUS
| | - Kristy Lee
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | | | - Phuong L. Mai
- Magee-Womens Hospital, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Kelvin C. de Andrade
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Laura D. Attardi
- Departments of Radiation-Oncology and Genetics, Stanford University, Stanford, CA, USA
| | - Stephanie Crowley
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | | | | | - Megan N. Frone
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | | | - Paul A. James
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
| | | | | | - Bryce A. Seifert
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Leora Witkowski
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, MA, USA
| | - Liying Zhang
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sharon E. Plon
- Department of Pediatrics/Hematology-Oncology, Baylor College of Medicine, Houston, TX, USA
| | - Amanda B. Spurdle
- QIMR Berghofer Medical Research Institute, Brisbane City, Australia, AUS
| | - Sharon A. Savage
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
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12
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Evans DG, Woodward ER, Bajalica-Lagercrantz S, Oliveira C, Frebourg T. Germline TP53 Testing in Breast Cancers: Why, When and How? Cancers (Basel) 2020; 12:cancers12123762. [PMID: 33327514 PMCID: PMC7764913 DOI: 10.3390/cancers12123762] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 12/05/2020] [Accepted: 12/08/2020] [Indexed: 12/13/2022] Open
Abstract
Simple Summary TP53 variants detected in blood represent a main genetic cause of breast cancers occurring before 31 years of age. TP53 being included in most of the cancer gene panels, patients with breast cancer are offered germline TP53 testing, independently of the age of tumour onset and familial history. Interpretation of TP53 variants is remarkably complex, and detection of a germline disease-causing TP53 variant in a breast cancer patient has drastic medical consequences: radiotherapy contributing to the development of subsequent tumours should be, if possible, avoided. In her family, variant carriers should be offered annual follow-up, including whole-body MRI. Therefore, we consider that, in breast cancer patients, germline TP53 testing should be performed before treatment and that the decision of TP53 testing should not be systematic but based on the age of tumour onset, type of breast cancer, personal and familial history of cancer. Abstract Germline TP53 variants represent a main genetic cause of breast cancers before 31 years of age. Development of cancer multi-gene panels has resulted in an exponential increase of germline TP53 testing in breast cancer patients. Interpretation of TP53 variants, which are mostly missense, is complex and requires excluding clonal haematopoiesis and circulating tumour DNA. In breast cancer patients harbouring germline disease-causing TP53 variants, radiotherapy contributing to the development of subsequent tumours should be, if possible, avoided and, within families, annual follow-up including whole-body MRI should be offered to carriers. We consider that, in breast cancer patients, germline TP53 testing should be performed before treatment and offered systematically only to patients with: (i) invasive breast carcinoma or ductal carcinoma in situ (DCIS) before 31; or (ii) bilateral or multifocal or HER2+ invasive breast carcinoma/DCIS or phyllode tumour before 36; or (iii) invasive breast carcinoma before 46 and another TP53 core tumour (breast cancer, soft-tissue sarcoma, osteosarcoma, central nervous system tumour, adrenocortical carcinoma); or (iv) invasive breast carcinoma before 46 and one first- or second-degree relative with a TP53 core tumour before 56. In contrast, women presenting with breast cancer after 46, without suggestive personal or familial history, should not be tested for TP53.
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Affiliation(s)
- D. Gareth Evans
- Manchester Centre for Genomic Medicine, Division of Evolution and Genomic Sciences, University of Manchester, Manchester M13 9WL, UK;
- Manchester Centre for Genomic Medicine St Mary’s Hospital, Manchester University Hospitals NHS Foundation Trust, Manchester M13 9WL, UK
- Correspondence: (D.G.E.); (T.F.)
| | - Emma R. Woodward
- Manchester Centre for Genomic Medicine, Division of Evolution and Genomic Sciences, University of Manchester, Manchester M13 9WL, UK;
- Manchester Centre for Genomic Medicine St Mary’s Hospital, Manchester University Hospitals NHS Foundation Trust, Manchester M13 9WL, UK
| | - Svetlana Bajalica-Lagercrantz
- Hereditary Cancer Unit, Department of Clinical Genetics, Karolinska University Hospital, SE-17176 Stockholm, Sweden;
| | - Carla Oliveira
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal;
- Ipatimup-Institute of Molecular Pathology and Immunology of the University of Porto, 4200-135 Porto, Portugal
- Porto Comprehensive Cancer Center, 4200-072 Porto, Portugal
| | - Thierry Frebourg
- Department of Genetics, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine, 76000 Rouen, France
- Inserm U1245, Normandie University, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, 76183 Rouen, France
- Correspondence: (D.G.E.); (T.F.)
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The role of TP53 pathogenic variants in early-onset HER2-positive breast cancer. Fam Cancer 2020; 20:173-180. [PMID: 33051812 DOI: 10.1007/s10689-020-00212-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 10/08/2020] [Indexed: 12/21/2022]
Abstract
Breast cancer is the most frequent event in Li-Fraumeni syndrome associated with germline TP53 variants. Some studies have shown that breast cancers in women with Li-Fraumeni syndrome are commonly HER2-positive, suggesting that HER2 amplification or over-expression in a young woman may be a useful criterion to test for germline variants in the TP53 gene. We assessed the prevalence of germline TP53 variants by Sanger sequencing or next-generation sequencing in 149 women with HER2-positive breast cancer diagnosed until age 40. The pattern of HER2 amplification was evaluated with dual-probe FISH in a subset of breast carcinomas from patients with germline TP53 variants as compared with those of noncarriers. Among 149 women tested, three presented a deleterious TP53 germline variant (2%), with one patient diagnosed at age 31 and the other two with bilateral breast cancer at ages 29/33 and 28/32, respectively. Three of the 36 patients (8.3%) with the first breast cancer diagnosed at age 31 or younger presented a pathogenic TP53 variant. Additionally, all TP53 deleterious variant carriers had a first degree relative diagnosed with different early-onset cancers (frequently not belonging to the Li-Fraumeni syndrome tumor spectrum) diagnosed at age 45 or younger. Higher levels of HER2 amplification were found in breast carcinomas of TP53 pathogenic variant carriers than in those of noncarriers. Deleterious germline TP53 variants account for a small proportion of early-onset HER2-positive breast cancers, but these seem to have higher HER2 amplification ratios. All TP53 pathogenic variant carriers found in this study had the first breast carcinoma diagnosed at age 31 or younger and a first-degree relative with early-onset cancer. Further studies are needed to clarify if HER2 status in early-onset breast cancer patients, in combination with other personal and/or familial cancer history, is useful to update the TP53 testing criteria.
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