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Bouras A, Guidara S, Leone M, Buisson A, Martin-Denavit T, Dussart S, Lasset C, Giraud S, Bonnet-Dupeyron MN, Kherraf ZE, Sanlaville D, Fert-Ferrer S, Lebrun M, Bonadona V, Calender A, Boutry-Kryza N. Overview of the Genetic Causes of Hereditary Breast and Ovarian Cancer Syndrome in a Large French Patient Cohort. Cancers (Basel) 2023; 15:3420. [PMID: 37444530 DOI: 10.3390/cancers15133420] [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: 05/25/2023] [Revised: 06/19/2023] [Accepted: 06/27/2023] [Indexed: 07/15/2023] Open
Abstract
The use of multigene panel testing for patients with a predisposition to Hereditary Breast and Ovarian Cancer syndrome (HBOC) is increasing as the identification of mutations is useful for diagnosis and disease management. Here, we conducted a retrospective analysis of BRCA1/2 and non-BRCA gene sequencing in 4630 French HBOC suspected patients. Patients were investigated using a germline cancer panel including the 13 genes defined by The French Genetic and Cancer Group (GGC)-Unicancer. In the patients analyzed, 528 pathogenic and likely pathogenic variants (P/LP) were identified, including BRCA1 (n = 203, 38%), BRCA2 (n = 198, 37%), PALB2 (n = 46, 9%), RAD51C (n = 36, 7%), TP53 (n = 16, 3%), and RAD51D (n = 13, 2%). In addition, 35 novel (P/LP) variants, according to our knowledge, were identified, and double mutations in two distinct genes were found in five patients. Interestingly, retesting a subset of BRCA1/2-negative individuals with an expanded panel produced clinically relevant results in 5% of cases. Additionally, combining in silico (splicing impact prediction tools) and in vitro analyses (RT-PCR and Sanger sequencing) highlighted the deleterious impact of four candidate variants on splicing and translation. Our results present an overview of pathogenic variations of HBOC genes in the southeast of France, emphasizing the clinical relevance of cDNA analysis and the importance of retesting BRCA-negative individuals with an expanded panel.
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Affiliation(s)
- Ahmed Bouras
- Laboratory of Constitutional Genetics for Frequent Cancer HCL-CLB, Centre Léon Bérard, 69008 Lyon, France
- Team 'Endocrine Resistance, Methylation and Breast Cancer' Research Center of Lyon-CRCL, UMR Inserm 1052 CNRS 5286, 69008 Lyon, France
| | - Souhir Guidara
- Department of Genetics, Groupement Hospitalier EST, Hospices Civils de Lyon, 69500 Bron, France
- Department of Genetics, CHU Hédi Chaker, Sfax 3027, Tunisia
| | - Mélanie Leone
- Department of Genetics, Groupement Hospitalier EST, Hospices Civils de Lyon, 69500 Bron, France
| | - Adrien Buisson
- Department of Biopathology, Centre Léon Bérard, 69008 Lyon, France
| | - Tanguy Martin-Denavit
- Department of Genetics, Groupement Hospitalier EST, Hospices Civils de Lyon, 69500 Bron, France
- Center for Medical Genetics, Alpigène, 69007 Lyon, France
| | - Sophie Dussart
- Centre Léon Bérard, Unité de Prévention et Epidémiologie Génétique, 69008 Lyon, France
| | - Christine Lasset
- Centre Léon Bérard, Unité de Prévention et Epidémiologie Génétique, 69008 Lyon, France
| | - Sophie Giraud
- Department of Genetics, Groupement Hospitalier EST, Hospices Civils de Lyon, 69500 Bron, France
| | | | - Zine-Eddine Kherraf
- Institute for Advanced Biosciences, University Grenoble Alpes, INSERM, CNRS, 38000 Grenoble, France
- UM GI-DPI, University Hospital Grenoble Alpes, 38000 Grenoble, France
| | - Damien Sanlaville
- Department of Genetics, Groupement Hospitalier EST, Hospices Civils de Lyon, 69500 Bron, France
| | - Sandra Fert-Ferrer
- Genetics Departement, Centre Hospitalier Métropole Savoie, 73011 Chambery, France
| | - Marine Lebrun
- Department of Genetics, Saint Etienne University Hospital, 42270 Saint Priez en Jarez, France
| | - Valerie Bonadona
- Centre Léon Bérard, Unité de Prévention et Epidémiologie Génétique, 69008 Lyon, France
| | - Alain Calender
- Department of Genetics, Groupement Hospitalier EST, Hospices Civils de Lyon, 69500 Bron, France
| | - Nadia Boutry-Kryza
- Department of Genetics, Groupement Hospitalier EST, Hospices Civils de Lyon, 69500 Bron, France
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Borja NA, Silva-Smith R, Huang M, Parekh DJ, Sussman D, Tekin M. Atypical ATMs: Broadening the phenotypic spectrum of ATM-associated hereditary cancer. Front Oncol 2023; 13:1068110. [PMID: 36865800 PMCID: PMC9971806 DOI: 10.3389/fonc.2023.1068110] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 02/03/2023] [Indexed: 02/16/2023] Open
Abstract
Heterozygous, loss-of-function germline variants in ATM have been associated with an increased lifetime risk of breast, pancreas, prostate, stomach, ovarian, colorectal, and melanoma cancers. We conducted a retrospective review of thirty-one unrelated patients found to be heterozygous for a germline pathogenic variant in ATM and identified a significant proportion of patients in this cohort with cancers not currently associated with the ATM hereditary cancer syndrome, including carcinomas of the gallbladder, uterus, duodenum, kidney, and lung as well as a vascular sarcoma. A comprehensive review of the literature found 25 relevant studies where 171 individuals with a germline deleterious ATM variant have been diagnosed with the same or similar cancers. The combined data from these studies were then used to estimate the prevalence of germline ATM pathogenic variants in these cancers, which ranged between 0.45% and 2.2%. Analysis of tumor sequencing performed in large cohorts demonstrated that the frequency of deleterious somatic ATM alterations in these atypical cancers equaled or exceeded the alteration frequency in breast cancer and occurred at a significantly higher rate than in other DNA-damage response tumor suppressors, namely BRCA1 and CHEK2. Furthermore, multi-gene analysis of somatic alterations in these atypical cancers demonstrated significant co-occurrence of pathogenic alterations in ATM with BRCA1 and CHEK2, while there was significant mutual exclusivity between pathogenic alterations in ATM and TP53. This indicates that germline ATM pathogenic variants may play a role in cancer initiation and progression in these atypical ATM malignancies, potentially influencing these cancers to be driven toward DNA-damage repair deficiency and away from loss of TP53. As such, these findings provide evidence for broadening of the ATM-cancer susceptibility syndrome phenotype to improve the recognition of affected patients and provide more efficacious, germline-directed therapies.
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Affiliation(s)
- Nicholas A. Borja
- Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, United States
| | - Rachel Silva-Smith
- Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, United States
| | - Marilyn Huang
- Division of Gynecologic Oncology, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, United States
| | - Dipen J. Parekh
- Desai Sethi Urology Institute, Miller School of Medicine, University of Miami, Miami, FL, United States
| | - Daniel Sussman
- Division of Digestive Health and Liver Diseases, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Mustafa Tekin
- Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, United States,John P. Hussmann Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, United States,*Correspondence: Mustafa Tekin,
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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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Laraqui A, Cavaillé M, Uhrhammer N, ElBiad O, Bidet Y, El Rhaffouli H, El Anaz H, Rahali DM, Kouach J, Guelzim K, Badaoui B, AlBouzidi A, Oukabli M, Tanz R, Sbitti Y, Ichou M, Ennibi K, Sekhsokh Y, Bignon YJ. Identification of a novel pathogenic variant in PALB2 and BARD1 genes by a multigene sequencing panel in triple negative breast cancer in Morocco. J Genomics 2021; 9:43-54. [PMID: 34646395 PMCID: PMC8490085 DOI: 10.7150/jgen.61713] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 08/21/2021] [Indexed: 12/24/2022] Open
Abstract
Pathogenic variants (PVs) in BRCA genes have been mainly associated with an increasing risk of triple negative breast cancer (TNBC). The contribution of PVs in non-BRCA genes to TNBC seems likely since the processing of homologous recombination repair of double-strand DNA breaks involves several genes. Here, we investigate the susceptibility of genetic variation of the BRCA and non-BRCA genes in 30 early-onset Moroccan women with TNBC. Methods: Targeted capture-based next generation sequencing (NGS) method was performed with a multigene panel testing (MGPT) for variant screening. Panel sequencing was performed with genes involved in hereditary predisposition to cancer and candidate genes whose involvement remains unclear using Illumina MiSeq platform. Interpretation was conducted by following the American College of Medical Genetics and Genomics-Association for Molecular Pathology (ACMG-AMP) criteria. Results: PVs were identified in 20% (6/30) of patients with TNBC. Of these, 16.7% (5/30) carried a BRCA PV [10% (3/30) in BRCA1, 6.7% (2/30) in BRCA2] and 6.6% (2/30) carried a non-BRCA PV. The identified PVs in BRCA genes (BRCA1 c.798_799delTT, BRCA1 c.3279delC, BRCA2 c.1310_1313del, and BRCA2 c.1658T>G) have been reported before and were classified as pathogenic. The identified founder PVs BRCA1 c.798_799del and BRCA2 c.1310_1313delAAGA represented 10% (3/30). Our MGPT allowed identification of several sequence variations in most investigated genes, among which we found novel truncating variations in PALB2 and BARD1 genes. The PALB2 c.3290dup and BARD1 c.1333G>T variants are classified as pathogenic. We also identified 42 variants of unknown/uncertain significance (VUS) in 70% (21/30) of patients with TNBC, including 50% (21/42) missense variants. The highest VUS rate was observed in ATM (13%, 4/30). Additionally, 35.7% (15/42) variants initially well-known as benign, likely benign or conflicting interpretations of pathogenicity have been reclassified as VUS according to ACMG-AMP. Conclusions: PALB2 and BARD1 along with BRCA genetic screening could be helpful for a larger proportion of early-onset TNBC in Morocco.
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Affiliation(s)
- Abdelilah Laraqui
- Unité de séquençage, Centre de virologie, des maladies infectieuses et tropicales, Hôpital militaire d'Instruction Mohammed V, Faculté de Médecine et de Pharmacie, Université Mohammed V, Rabat, Maroc
- Laboratoire de Recherche et de Biosécurité P3, Hôpital Militaire d'Instruction Mohammed V, Faculté de Médecine et de Pharmacie, Rabat, Maroc
| | - Mathias Cavaillé
- Laboratoire Diagnostic Génétique et Moléculaire, Centre Jean Perrin, 58 rue Montalembert, Clermont-Ferrand, France
- INSERM, U1240 Imagerie Moléculaire et Stratégies Théranostiques, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Nancy Uhrhammer
- Laboratoire Diagnostic Génétique et Moléculaire, Centre Jean Perrin, 58 rue Montalembert, Clermont-Ferrand, France
- INSERM, U1240 Imagerie Moléculaire et Stratégies Théranostiques, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Oubaida ElBiad
- Unité de séquençage, Centre de virologie, des maladies infectieuses et tropicales, Hôpital militaire d'Instruction Mohammed V, Faculté de Médecine et de Pharmacie, Université Mohammed V, Rabat, Maroc
- Laboratoire de Biodiversité, Ecologie et Génome, Faculté des Sciences, Université Mohammed V, Rabat, Maroc
| | - Yannick Bidet
- Laboratoire Diagnostic Génétique et Moléculaire, Centre Jean Perrin, 58 rue Montalembert, Clermont-Ferrand, France
- INSERM, U1240 Imagerie Moléculaire et Stratégies Théranostiques, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Hicham El Rhaffouli
- Laboratoire de Recherche et de Biosécurité P3, Hôpital Militaire d'Instruction Mohammed V, Faculté de Médecine et de Pharmacie, Rabat, Maroc
| | - Hicham El Anaz
- Unité de séquençage, Centre de virologie, des maladies infectieuses et tropicales, Hôpital militaire d'Instruction Mohammed V, Faculté de Médecine et de Pharmacie, Université Mohammed V, Rabat, Maroc
| | - Driss Moussaoui Rahali
- Service de Gynécologie Obstétrique, Hôpital Militaire d'Instruction Mohammed V, Faculté de Médecine et de Pharmacie, Rabat, Maroc
| | - Jaouad Kouach
- Service de Gynécologie Obstétrique, Hôpital Militaire d'Instruction Mohammed V, Faculté de Médecine et de Pharmacie, Rabat, Maroc
| | - Khaled Guelzim
- Service de Gynécologie Obstétrique, Hôpital Militaire d'Instruction Mohammed V, Faculté de Médecine et de Pharmacie, Rabat, Maroc
| | - Bouabid Badaoui
- Laboratoire de Biodiversité, Ecologie et Génome, Faculté des Sciences, Université Mohammed V, Rabat, Maroc
| | - Abderrahman AlBouzidi
- Laboratoire d'Anatomopathologie, Hôpital Militaire d'Instruction Mohammed V, Faculté de Médecine et de Pharmacie, Rabat 10000, Maroc
| | - Mohammed Oukabli
- Laboratoire d'Anatomopathologie, Hôpital Militaire d'Instruction Mohammed V, Faculté de Médecine et de Pharmacie, Rabat 10000, Maroc
| | - Rachid Tanz
- Service d'Oncologie Médicale, Hôpital Militaire d'Instruction Mohammed V, Faculté de Médecine et de Pharmacie, Rabat, Maroc
| | - Yasser Sbitti
- Service d'Oncologie Médicale, Hôpital Militaire d'Instruction Mohammed V, Faculté de Médecine et de Pharmacie, Rabat, Maroc
| | - Mohammed Ichou
- Service d'Oncologie Médicale, Hôpital Militaire d'Instruction Mohammed V, Faculté de Médecine et de Pharmacie, Rabat, Maroc
| | - Khaled Ennibi
- Unité de séquençage, Centre de virologie, des maladies infectieuses et tropicales, Hôpital militaire d'Instruction Mohammed V, Faculté de Médecine et de Pharmacie, Université Mohammed V, Rabat, Maroc
| | - Yassine Sekhsokh
- Laboratoire de Recherche et de Biosécurité P3, Hôpital Militaire d'Instruction Mohammed V, Faculté de Médecine et de Pharmacie, Rabat, Maroc
| | - Yves-Jean Bignon
- Laboratoire Diagnostic Génétique et Moléculaire, Centre Jean Perrin, 58 rue Montalembert, Clermont-Ferrand, France
- INSERM, U1240 Imagerie Moléculaire et Stratégies Théranostiques, Université Clermont Auvergne, Clermont-Ferrand, France
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5
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Boland CR, Yurgelun MB, Mraz KA, Boland PM. Managing gastric cancer risk in lynch syndrome: controversies and recommendations. Fam Cancer 2021; 21:75-78. [PMID: 33611683 PMCID: PMC8799584 DOI: 10.1007/s10689-021-00235-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 02/09/2021] [Indexed: 01/01/2023]
Affiliation(s)
- C Richard Boland
- Department of Medicine, University of California San Diego, San Diego, CA, USA.
| | - Matthew B Yurgelun
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Patrick M Boland
- Department of Medical Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
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6
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Cavaillé M, Uhrhammer N, Privat M, Ponelle-Chachuat F, Gay-Bellile M, Lepage M, Viala S, Bidet Y, Bignon YJ. Feedback of extended panel sequencing in 1530 patients referred for suspicion of hereditary predisposition to adult cancers. Clin Genet 2020; 99:166-175. [PMID: 33047316 PMCID: PMC7821123 DOI: 10.1111/cge.13864] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 10/09/2020] [Accepted: 10/10/2020] [Indexed: 12/12/2022]
Abstract
High‐throughput sequencing analysis represented both a medical diagnosis and technological revolution. Gene panel analysis is now routinely performed in the exploration of hereditary predisposition to cancer, which is becoming increasingly heterogeneous, both clinically and molecularly. We present 1530 patients with suspicion of hereditary predisposition to cancer, for which two types of analyses were performed: a) oriented according to the clinical presentation (n = 417), or b) extended to genes involved in hereditary predisposition to adult cancer (n = 1113). Extended panel analysis had a higher detection rate compared to oriented analysis in hereditary predisposition to breast / ovarian cancer (P < .001) and in digestive cancers (P < .094) (respectively 15% vs 5% and 19.3%, vs 12.5%). This higher detection is explained by the inclusion of moderate penetrance genes, as well as the identification of incident mutations and double mutations. Our study underscores the utility of proposing extended gene panel analysis to patients with suspicion of hereditary predisposition to adult cancer.
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Affiliation(s)
- Mathias Cavaillé
- Département d'Oncogénétique, Centre Jean Perrin, Clermont-Ferrand, France.,Université Clermont Auvergne, INSERM, U1240 Imagerie Moléculaire et Stratégies, Clermont Ferrand, France
| | - Nancy Uhrhammer
- Département d'Oncogénétique, Centre Jean Perrin, Clermont-Ferrand, France.,Université Clermont Auvergne, INSERM, U1240 Imagerie Moléculaire et Stratégies, Clermont Ferrand, France
| | - Maud Privat
- Département d'Oncogénétique, Centre Jean Perrin, Clermont-Ferrand, France.,Université Clermont Auvergne, INSERM, U1240 Imagerie Moléculaire et Stratégies, Clermont Ferrand, France
| | - Flora Ponelle-Chachuat
- Département d'Oncogénétique, Centre Jean Perrin, Clermont-Ferrand, France.,Université Clermont Auvergne, INSERM, U1240 Imagerie Moléculaire et Stratégies, Clermont Ferrand, France
| | - Mathilde Gay-Bellile
- Département d'Oncogénétique, Centre Jean Perrin, Clermont-Ferrand, France.,Université Clermont Auvergne, INSERM, U1240 Imagerie Moléculaire et Stratégies, Clermont Ferrand, France
| | - Mathis Lepage
- Département d'Oncogénétique, Centre Jean Perrin, Clermont-Ferrand, France
| | - Sandrine Viala
- Département d'Oncogénétique, Centre Jean Perrin, Clermont-Ferrand, France.,Université Clermont Auvergne, INSERM, U1240 Imagerie Moléculaire et Stratégies, Clermont Ferrand, France
| | - Yannick Bidet
- Département d'Oncogénétique, Centre Jean Perrin, Clermont-Ferrand, France.,Université Clermont Auvergne, INSERM, U1240 Imagerie Moléculaire et Stratégies, Clermont Ferrand, France
| | - Yves-Jean Bignon
- Département d'Oncogénétique, Centre Jean Perrin, Clermont-Ferrand, France.,Université Clermont Auvergne, INSERM, U1240 Imagerie Moléculaire et Stratégies, Clermont Ferrand, France
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