1
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Schwartz M, Ibadioune S, Chansavang A, Vacher S, Caputo SM, Delhomelle H, Wong J, Abidallah K, Moncoutier V, Becette V, Popova T, Suybeng V, De Pauw A, Stern MH, Colas C, Mouret-Fourme E, Stoppa-Lyonnet D, Golmard L, Bieche I, Masliah-Planchon J. Mosaic BRCA1 promoter methylation contribution in hereditary breast/ovarian cancer pedigrees. J Med Genet 2024; 61:284-288. [PMID: 37748860 DOI: 10.1136/jmg-2023-109325] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 09/05/2023] [Indexed: 09/27/2023]
Abstract
PURPOSE Mosaic BRCA1 promoter methylation (BRCA1meth) increases the risk of early-onset breast cancer, triple-negative breast cancer and ovarian cancer. As mosaic BRCA1meth are believed to occur de novo, their role in family breast/ovarian cancer has not been assessed. PATIENTS Blood-derived DNA from 20 unrelated affected cases from families with aggregation of breast/ovarian cancer, but with no germline pathogenic variants in BRCA1/2, PALB2 or RAD51C/D, were screened by methylation-sensitive high-resolution melting. CpG analysis was performed by pyrosequencing on blood and buccal swab. Two probands carried a pathogenic variant in a moderate-penetrance gene (ATM and BARD1), and 8 of 18 others (44%) carried BRCA1meth (vs none of the 20 age-matched controls). Involvement of BRCA1 in tumourigenesis in methylated probands was demonstrated in most tested cases by detection of a loss of heterozygosity and a homologous recombination deficiency signature. Among the eight methylated probands, two had relatives with breast cancer with detectable BRCA1meth in blood, including one with high methylation levels in two non-tumour tissues. CONCLUSIONS The high prevalence of mosaic BRCA1meth in patients with breast/ovarian cancer with affected relatives, as well as this first description of a family aggregation of mosaic BRCA1meth, shows how this de novo event can contribute to hereditary breast/ovarian cancer pedigrees.
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Affiliation(s)
- Mathias Schwartz
- Department of genetics, Curie Institute Hospital Group, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
- UMR3244, Curie Institute, Paris, France
| | - Sabrina Ibadioune
- Department of genetics, Curie Institute Hospital Group, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
| | - Albain Chansavang
- Department of genetics, Curie Institute Hospital Group, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
| | - Sophie Vacher
- Department of genetics, Curie Institute Hospital Group, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
| | - Sandrine M Caputo
- Department of genetics, Curie Institute Hospital Group, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
| | - Hélène Delhomelle
- Department of genetics, Curie Institute Hospital Group, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
| | - Jennifer Wong
- Department of genetics, Curie Institute Hospital Group, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
| | - Khadija Abidallah
- Department of genetics, Curie Institute Hospital Group, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
| | - Virginie Moncoutier
- Department of genetics, Curie Institute Hospital Group, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
| | - Véronique Becette
- Paris Sciences & Lettres Research University, Paris, France
- Department of Pathology, Curie Institute, Saint-Cloud, France
| | - Tatiana Popova
- Paris Sciences & Lettres Research University, Paris, France
- DNA Repair and Uveal Melanoma (D.R.U.M.), Inserm U830, Curie Institute, Paris, France
| | - Voreak Suybeng
- Department of genetics, Curie Institute Hospital Group, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
| | - Antoine De Pauw
- Department of genetics, Curie Institute Hospital Group, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
| | - Marc-Henri Stern
- Department of genetics, Curie Institute Hospital Group, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
- DNA Repair and Uveal Melanoma (D.R.U.M.), Inserm U830, Curie Institute, Paris, France
| | - Chrystelle Colas
- Department of genetics, Curie Institute Hospital Group, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
- DNA Repair and Uveal Melanoma (D.R.U.M.), Inserm U830, Curie Institute, Paris, France
| | - Emmanuelle Mouret-Fourme
- Department of genetics, Curie Institute Hospital Group, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
| | - Dominique Stoppa-Lyonnet
- Department of genetics, Curie Institute Hospital Group, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
- Université de Paris Cité, Paris, France
| | - Lisa Golmard
- Department of genetics, Curie Institute Hospital Group, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
| | - Ivan Bieche
- Department of genetics, Curie Institute Hospital Group, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
- Université de Paris Cité, Paris, France
| | - Julien Masliah-Planchon
- Department of genetics, Curie Institute Hospital Group, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
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2
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Schwartz M, Ibadioune S, Vacher S, Villy MC, Trabelsi-Grati O, Le Gall J, Caputo SM, Delhomelle H, Warcoin M, Moncoutier V, Bourneix C, Boutry-Kryza N, De Pauw A, Stern MH, Buecher B, Mouret-Fourme E, Colas C, Stoppa-Lyonnet D, Masliah-Planchon J, Golmard L, Bieche I. Male breast cancer: No evidence for mosaic BRCA1 promoter methylation involvement. Breast 2024; 73:103620. [PMID: 38096711 PMCID: PMC10761895 DOI: 10.1016/j.breast.2023.103620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 12/05/2023] [Accepted: 12/07/2023] [Indexed: 01/06/2024] Open
Abstract
Breast cancers (BC) are rare in men and are often caused by constitutional predisposing factors. In women, mosaic BRCA1 promoter methylations (MBPM) are frequent events, detected in 4-8% of healthy subjects. This constitutional epimutation increases risk of early-onset and triple-negative BC. However, the role of MBPM in male BC predisposition has never been assessed. We screened 40 blood samples from men affected by BC, and performed extensive tumour analysis on MBPM-positive patients. We detected two patients carrying MBPM. Surprisingly, tumour analysis revealed that neither of these two male BCs were caused by the constitutional BRCA1 epimutations carried by the patients.
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Affiliation(s)
- Mathias Schwartz
- Department of genetics, Curie Institute, Paris, France; UMR3244, Curie Institute, Paris, France; Paris Sciences & Lettres Research University, Paris, France.
| | - Sabrina Ibadioune
- Department of genetics, Curie Institute, Paris, France; Paris Sciences & Lettres Research University, Paris, France
| | - Sophie Vacher
- Department of genetics, Curie Institute, Paris, France; Paris Sciences & Lettres Research University, Paris, France
| | - Marie-Charlotte Villy
- Department of genetics, Curie Institute, Paris, France; Université Paris Cité, Paris, France
| | - Olfa Trabelsi-Grati
- Department of genetics, Curie Institute, Paris, France; Paris Sciences & Lettres Research University, Paris, France
| | - Jessica Le Gall
- Department of genetics, Curie Institute, Paris, France; Paris Sciences & Lettres Research University, Paris, France
| | - Sandrine M Caputo
- Department of genetics, Curie Institute, Paris, France; Paris Sciences & Lettres Research University, Paris, France
| | - Hélène Delhomelle
- Department of genetics, Curie Institute, Paris, France; Paris Sciences & Lettres Research University, Paris, France
| | - Mathilde Warcoin
- Department of genetics, Curie Institute, Paris, France; Paris Sciences & Lettres Research University, Paris, France
| | - Virginie Moncoutier
- Department of genetics, Curie Institute, Paris, France; Paris Sciences & Lettres Research University, Paris, France
| | - Christine Bourneix
- Department of genetics, Curie Institute, Paris, France; Paris Sciences & Lettres Research University, Paris, France
| | | | - Antoine De Pauw
- Department of genetics, Curie Institute, Paris, France; Paris Sciences & Lettres Research University, Paris, France
| | - Marc-Henri Stern
- Department of genetics, Curie Institute, Paris, France; Paris Sciences & Lettres Research University, Paris, France; DNA Repair and Uveal Melanoma (D.R.U.M.), Inserm U830, Paris, France
| | - Bruno Buecher
- Department of genetics, Curie Institute, Paris, France; Paris Sciences & Lettres Research University, Paris, France
| | - Emmanuelle Mouret-Fourme
- Department of genetics, Curie Institute, Paris, France; Paris Sciences & Lettres Research University, Paris, France
| | - Chrystelle Colas
- Department of genetics, Curie Institute, Paris, France; Paris Sciences & Lettres Research University, Paris, France
| | - Dominique Stoppa-Lyonnet
- Department of genetics, Curie Institute, Paris, France; Université Paris Cité, Paris, France; DNA Repair and Uveal Melanoma (D.R.U.M.), Inserm U830, Paris, France
| | - Julien Masliah-Planchon
- Department of genetics, Curie Institute, Paris, France; Paris Sciences & Lettres Research University, Paris, France
| | - Lisa Golmard
- Department of genetics, Curie Institute, Paris, France; Paris Sciences & Lettres Research University, Paris, France
| | - Ivan Bieche
- Department of genetics, Curie Institute, Paris, France; Université Paris Cité, Paris, France
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3
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Alvaro-Aranda L, Petitalot A, Djeghmoum Y, Panigada D, Singh JK, Ehlén Å, Vugic D, Martin C, Miron S, Contreras-Perez A, Nhiri N, Boucherit V, Lafitte P, Dumoulin I, Rouleau E, Jacquet E, Feliubadaló L, Del Valle J, Stoppa-Lyonnet D, Zinn-Justin S, Lázaro C, Caputo SM, Carreira A. The BRCA2 R2645G variant increases DNA binding and induces hyper-recombination. Nucleic Acids Res 2023:gkad1222. [PMID: 38142462 DOI: 10.1093/nar/gkad1222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 11/30/2023] [Accepted: 12/12/2023] [Indexed: 12/26/2023] Open
Abstract
BRCA2 tumor suppressor protein ensures genome integrity by mediating DNA repair via homologous recombination (HR). This function is executed in part by its canonical DNA binding domain located at the C-terminus (BRCA2CTD), the only folded domain of the protein. Most germline pathogenic missense variants are located in this highly conserved region which binds to single-stranded DNA (ssDNA) and to the acidic protein DSS1. These interactions are essential for the HR function of BRCA2. Here, we report that the variant R2645G, identified in breast cancer and located at the DSS1 interface, unexpectedly increases the ssDNA binding activity of BRCA2CTDin vitro. Human cells expressing this variant display a hyper-recombination phenotype, chromosomal instability in the form of chromatid gaps when exposed to DNA damage, and increased PARP inhibitor sensitivity. In mouse embryonic stem cells (mES), this variant alters viability and confers sensitivity to cisplatin and Mitomycin C. These results suggest that BRCA2 interaction with ssDNA needs to be tightly regulated to limit HR and prevent chromosomal instability and we propose that this control mechanism involves DSS1. Given that several missense variants located within this region have been identified in breast cancer patients, these findings might have clinical implications for carriers.
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Affiliation(s)
- Lucia Alvaro-Aranda
- Genome Instability and Cancer Predisposition Laboratory, Centro de Biologia Molecular Severo Ochoa (CBMSO), CSIC-UAM, Madrid 28049, Spain
| | - Ambre Petitalot
- Department of Genetics, Institut Curie, Paris 75005, France
- PSL Research University, Paris 75005, France
| | - Yasmina Djeghmoum
- Institut Curie, PSL Research University, CNRS, UMR3348, F-91405 Orsay, France
- Paris-Saclay University CNRS, UMR3348, F-91405 Orsay, France
| | - Davide Panigada
- Institut Curie, PSL Research University, CNRS, UMR3348, F-91405 Orsay, France
- Paris-Saclay University CNRS, UMR3348, F-91405 Orsay, France
| | - Jenny Kaur Singh
- Institut Curie, PSL Research University, CNRS, UMR3348, F-91405 Orsay, France
- Paris-Saclay University CNRS, UMR3348, F-91405 Orsay, France
| | - Åsa Ehlén
- Institut Curie, PSL Research University, CNRS, UMR3348, F-91405 Orsay, France
- Paris-Saclay University CNRS, UMR3348, F-91405 Orsay, France
| | - Domagoj Vugic
- Institut Curie, PSL Research University, CNRS, UMR3348, F-91405 Orsay, France
- Paris-Saclay University CNRS, UMR3348, F-91405 Orsay, France
| | - Charlotte Martin
- Institut Curie, PSL Research University, CNRS, UMR3348, F-91405 Orsay, France
- Paris-Saclay University CNRS, UMR3348, F-91405 Orsay, France
| | - Simona Miron
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Paris-Saclay University, 91190 Gif-sur-Yvette, France
| | - Aida Contreras-Perez
- Genome Instability and Cancer Predisposition Laboratory, Centro de Biologia Molecular Severo Ochoa (CBMSO), CSIC-UAM, Madrid 28049, Spain
| | - Naima Nhiri
- Institut de Chimie des Substances Naturelles, Paris-Saclay University, CNRS, 91190 Gif-sur-Yvette, France
| | - Virginie Boucherit
- Institut Curie, PSL Research University, CNRS, UMR3348, F-91405 Orsay, France
- Paris-Saclay University CNRS, UMR3348, F-91405 Orsay, France
| | - Philippe Lafitte
- Department of Genetics, Institut Curie, Paris 75005, France
- PSL Research University, Paris 75005, France
| | - Isaac Dumoulin
- Institut Curie, PSL Research University, CNRS, UMR3348, F-91405 Orsay, France
- Paris-Saclay University CNRS, UMR3348, F-91405 Orsay, France
| | - Etienne Rouleau
- Department of Genetics, Institut Curie, Paris 75005, France
- PSL Research University, Paris 75005, France
| | - Eric Jacquet
- Institut de Chimie des Substances Naturelles, Paris-Saclay University, CNRS, 91190 Gif-sur-Yvette, France
| | - Lidia Feliubadaló
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO), Hereditary Cancer Group, Molecular Mechanisms and Experimental Therapy in Oncology Program, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Spain
- Ciber Oncología (CIBERONC), Instituto Salud Carlos III, Madrid, Spain
| | - Jesús Del Valle
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO), Hereditary Cancer Group, Molecular Mechanisms and Experimental Therapy in Oncology Program, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Spain
- Ciber Oncología (CIBERONC), Instituto Salud Carlos III, Madrid, Spain
| | - Dominique Stoppa-Lyonnet
- Department of Genetics, Institut Curie, Paris 75005, France
- Paris-Cité University, Paris, France
- INSERM U830, Institut Curie, Paris 75005, France
| | - Sophie Zinn-Justin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Paris-Saclay University, 91190 Gif-sur-Yvette, France
| | - Conxi Lázaro
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO), Hereditary Cancer Group, Molecular Mechanisms and Experimental Therapy in Oncology Program, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Spain
- Ciber Oncología (CIBERONC), Instituto Salud Carlos III, Madrid, Spain
| | - Sandrine M Caputo
- Department of Genetics, Institut Curie, Paris 75005, France
- PSL Research University, Paris 75005, France
| | - Aura Carreira
- Genome Instability and Cancer Predisposition Laboratory, Centro de Biologia Molecular Severo Ochoa (CBMSO), CSIC-UAM, Madrid 28049, Spain
- Institut Curie, PSL Research University, CNRS, UMR3348, F-91405 Orsay, France
- Paris-Saclay University CNRS, UMR3348, F-91405 Orsay, France
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4
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Le Gall J, Dehainault C, Boutte M, Petitalot A, Caputo SM, Courtois L, Vacher S, Bieche I, Radvanyi F, Pacquement H, Doz F, Lumbroso-Le Rouic L, Gauthier Villars M, Stoppa-Lyonnet D, Lallemand F, Houdayer C, Golmard L. Germline HPF1 retrogene insertion in RB1 gene involved in cancer predisposition. J Med Genet 2023; 61:78-83. [PMID: 37541786 DOI: 10.1136/jmg-2022-109105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 07/23/2023] [Indexed: 08/06/2023]
Abstract
About half of the human genome is composed of repeated sequences derived from mobile elements, mainly retrotransposons, generally without pathogenic effect. Familial forms of retinoblastoma are caused by germline pathogenic variants in RB1 gene. Here, we describe a family with retinoblastoma affecting a father and his son. No pathogenic variant was identified after DNA analysis of RB1 gene coding sequence and exon-intron junctions. However, RB1 mRNA analysis showed a chimeric transcript with insertion of 114 nucleotides from HPF1 gene inside RB1 gene. This chimeric transcript led to an insertion of 38 amino acids in functional domain of retinoblastoma protein. Subsequent DNA analysis in RB1 intron 17 revealed the presence of a full-length HPF1 retrogene insertion in opposite orientation. Functional assay shows that this insertion has a deleterious impact on retinoblastoma protein function. This is the first report of a full-length retrogene insertion involved in human Mendelian disease leading to a chimeric transcript and a non-functional chimeric protein. Some retrogene insertions may be missed by standard diagnostic genetic testing, so contribution of retrogene insertions to human disease may be underestimated. The increasing use of whole genome sequencing in diagnostic settings will help to get a more comprehensive view of retrogenes.
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Affiliation(s)
- Jessica Le Gall
- Department of Genetics, Institut Curie, Paris, France
- Department of Genetics, PSL University, Paris, France
| | - Catherine Dehainault
- Department of Genetics, Institut Curie, Paris, France
- Department of Genetics, PSL University, Paris, France
| | - Matteo Boutte
- Department of Genetics, Institut Curie, Paris, France
- Department of Genetics, PSL University, Paris, France
| | - Ambre Petitalot
- Department of Genetics, Institut Curie, Paris, France
- Department of Genetics, PSL University, Paris, France
| | - Sandrine M Caputo
- Department of Genetics, Institut Curie, Paris, France
- Department of Genetics, PSL University, Paris, France
| | - Laura Courtois
- Department of Genetics, Institut Curie, Paris, France
- Department of Genetics, PSL University, Paris, France
| | - Sophie Vacher
- Department of Genetics, Institut Curie, Paris, France
- Department of Genetics, PSL University, Paris, France
| | - Ivan Bieche
- Department of Genetics, Institut Curie, Paris, France
- Université de Paris, Paris, France
| | - François Radvanyi
- Department of Genetics, PSL University, Paris, France
- Molecular Oncology Team, UMR144, Paris, France
| | - Hélène Pacquement
- Department of Genetics, PSL University, Paris, France
- Oncology Center SIREDO, Institut Curie, Paris, France
| | - François Doz
- Molecular Oncology Team, UMR144, Paris, France
- Oncology Center SIREDO, Institut Curie, Paris, France
| | - Livia Lumbroso-Le Rouic
- Department of Genetics, PSL University, Paris, France
- Department of Ophthalmology, Institut Curie, Paris, France
| | - Marion Gauthier Villars
- Department of Genetics, Institut Curie, Paris, France
- Department of Genetics, PSL University, Paris, France
| | - Dominique Stoppa-Lyonnet
- Department of Genetics, Institut Curie, Paris, France
- Department of Genetics, PSL University, Paris, France
| | - François Lallemand
- Department of Genetics, Institut Curie, Paris, France
- Department of Genetics, PSL University, Paris, France
| | - Claude Houdayer
- Department of Genetics, University Hospital Centre Rouen, Rouen, France
| | - Lisa Golmard
- Department of Genetics, Institut Curie, Paris, France
- Department of Genetics, PSL University, Paris, France
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5
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Filser M, Schwartz M, Merchadou K, Hamza A, Villy MC, Decees A, Frouin E, Girard E, Caputo SM, Renault V, Becette V, Golmard L, Servant N, Stoppa-Lyonnet D, Delattre O, Colas C, Masliah-Planchon J. Adaptive nanopore sequencing to determine pathogenicity of BRCA1 exonic duplication. J Med Genet 2023; 60:1206-1209. [PMID: 37263769 DOI: 10.1136/jmg-2023-109155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 04/30/2023] [Indexed: 06/03/2023]
Abstract
BRCA1 and BRCA2 are tumour suppressor genes that have been characterised as predisposition genes for the development of hereditary breast and ovarian cancers among other malignancies. The molecular diagnosis of this predisposition syndrome is based on the detection of inactivating variants of any type in those genes. But in the case of structural variants, functional consequences can be difficult to assess using standard molecular methods, as the precise resolution of their sequence is often impossible with short-read next generation sequencing techniques. It has been recently demonstrated that Oxford Nanopore long-read sequencing technology can accurately and rapidly provide genetic diagnoses of Mendelian diseases, including those linked to pathogenic structural variants. Here, we report the accurate resolution of a germline duplication event of exons 18-20 of BRCA1 using Nanopore sequencing with adaptive sampling target enrichment. This allowed us to classify this variant as pathogenic within a short timeframe of 10 days. This study provides a proof-of-concept that nanopore adaptive sampling is a highly efficient technique for the investigation of structural variants of tumour suppressor genes in a clinical context.
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Affiliation(s)
- Mathilde Filser
- Genetics Department, Institut Curie, Paris, France
- PSL Research University, Paris, France
| | - Mathias Schwartz
- Genetics Department, Institut Curie, Paris, France
- PSL Research University, Paris, France
| | - Kevin Merchadou
- PSL Research University, Paris, France
- Clinical Bioinformatics Unit, Institut Curie, Paris, France
| | - Abderaouf Hamza
- Genetics Department, Institut Curie, Paris, France
- PSL Research University, Paris, France
| | - Marie-Charlotte Villy
- Oncogenetic Clinic Unit, Institut Curie, Paris, France
- SIREDO Oncology Centre, Institut Curie, Paris, France
| | - Antoine Decees
- Genetics Department, Institut Curie, Paris, France
- PSL Research University, Paris, France
| | - Eléonore Frouin
- PSL Research University, Paris, France
- Clinical Bioinformatics Unit, Institut Curie, Paris, France
| | - Elodie Girard
- PSL Research University, Paris, France
- INSERM U900, Institut Curie, Paris, France
| | - Sandrine M Caputo
- Genetics Department, Institut Curie, Paris, France
- PSL Research University, Paris, France
| | - Victor Renault
- PSL Research University, Paris, France
- Clinical Bioinformatics Unit, Institut Curie, Paris, France
| | - Véronique Becette
- PSL Research University, Paris, France
- Anatomo- and Cyto-pathology, Institut Curie, Saint-Cloud, France
| | - Lisa Golmard
- Genetics Department, Institut Curie, Paris, France
- PSL Research University, Paris, France
| | - Nicolas Servant
- PSL Research University, Paris, France
- INSERM U900, Institut Curie, Paris, France
| | - Dominique Stoppa-Lyonnet
- Genetics Department, Institut Curie, Paris, France
- SIREDO Oncology Centre, Institut Curie, Paris, France
| | - Olivier Delattre
- Genetics Department, Institut Curie, Paris, France
- Inserm U830, PSL University, Research Center, Institut Curie, Paris, France
| | - Chrystelle Colas
- PSL Research University, Paris, France
- Oncogenetic Clinic Unit, Institut Curie, Paris, France
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6
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Taouis K, Vacher S, Guirouilh-Barbat J, Camonis J, Formstecher E, Popova T, Hamy AS, Petitalot A, Lidereau R, Caputo SM, Zinn-Justin S, Bièche I, Driouch K, Lallemand F. WWOX binds MERIT40 and modulates its function in homologous recombination, implications in breast cancer. Cancer Gene Ther 2023; 30:1144-1155. [PMID: 37248434 PMCID: PMC10425285 DOI: 10.1038/s41417-023-00626-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 04/26/2023] [Accepted: 05/09/2023] [Indexed: 05/31/2023]
Abstract
The tumor suppressor gene WWOX is localized in an unstable chromosomal region and its expression is decreased or absent in several types of cancer. A low expression of WWOX is associated with a poor prognosis in breast cancer (BC). It has recently been shown that WWOX contributes to genome stability through its role in the DNA damage response (DDR). In breast cancer cells, WWOX inhibits homologous recombination (HR), and thus promotes the repair of DNA double-stranded breaks (DSBs) by non-homologous end joining (NHEJ). The fine-tuning modulation of HR activity is crucial. Its under or overstimulation inducing genome alterations that can induce cancer. MERIT40 is a positive regulator of the DDR. This protein is indispensable for the function of the multi-protein complex BRCA1-A, which suppresses excessive HR activity. MERIT40 also recruits Tankyrase, a positive regulator of HR, to the DSBs to stimulate DNA repair. Here, we identified MERIT40 as a new molecular partner of WWOX. We demonstrated that WWOX inhibited excessive HR activity induced by overexpression of MERIT40. We showed that WWOX impaired the MERIT40-Tankyrase interaction preventing the role of the complex on DSBs. Furthermore, we found that MERIT40 is overexpressed in BC and that this overexpression is associated to a poor prognosis. These results strongly suggest that WWOX, through its interaction with MERIT40, prevents the deleterious impact of excessive HR on BC development by inhibiting MERIT40-Tankyrase association. This inhibitory effect of WWOX would oppose MERIT40-dependent BC development.
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Affiliation(s)
- Karim Taouis
- Service de génétique, unité de pharmacogénomique, Institut Curie, 26 rue d'Ulm, Paris, France
- Paris Sciences Lettres Research University, Paris, France
| | - Sophie Vacher
- Service de génétique, unité de pharmacogénomique, Institut Curie, 26 rue d'Ulm, Paris, France
- Paris Sciences Lettres Research University, Paris, France
| | - Josée Guirouilh-Barbat
- Laboratoire Recombinaison-Réparation et Cancer UMR8200 Stabilité Génétique et Oncogenèse Institut Gustave Roussy, PR2, pièce 426114 Rue Edouard Vaillant, 94805, Villejuif, France
| | | | | | - Tatiana Popova
- Centre De Recherche, Institut Curie, Paris, F-75248, France
- INSERM U830, Paris, F-75248, France
| | - Anne-Sophie Hamy
- Residual Tumor & Response to Treatment Laboratory, RT2Lab, Translational Research Department, INSERM, U932 Immunity and Cancer, University Paris, Paris, France
- Department of Medical Oncology, Institut Curie, Paris, France
- University Paris, Paris, France
| | - Ambre Petitalot
- Service de génétique, unité de pharmacogénomique, Institut Curie, 26 rue d'Ulm, Paris, France
| | - Rosette Lidereau
- Service de génétique, unité de pharmacogénomique, Institut Curie, 26 rue d'Ulm, Paris, France
| | - Sandrine M Caputo
- Service de génétique, unité de pharmacogénomique, Institut Curie, 26 rue d'Ulm, Paris, France
- Paris Sciences Lettres Research University, Paris, France
| | - Sophie Zinn-Justin
- Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris-Sud, Gif-sur-Yvette, France
| | - Ivan Bièche
- Service de génétique, unité de pharmacogénomique, Institut Curie, 26 rue d'Ulm, Paris, France
- INSERM U1016, Université Paris Descartes, 4 avenue de l'observatoire, Paris, France
| | - Keltouma Driouch
- Service de génétique, unité de pharmacogénomique, Institut Curie, 26 rue d'Ulm, Paris, France
- Paris Sciences Lettres Research University, Paris, France
| | - François Lallemand
- Service de génétique, unité de pharmacogénomique, Institut Curie, 26 rue d'Ulm, Paris, France.
- Paris Sciences Lettres Research University, Paris, France.
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7
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Borcoman E, Santana Dos Santos E, Genestie C, Pautier P, Lacroix L, Caputo SM, Cabaret O, Guillaud-Bataille M, Michels J, Auguste A, Leary A, Rouleau E. Combined Tumor-Based BRCA1/2 and TP53 Mutation Testing in Ovarian Cancer. Int J Mol Sci 2023; 24:11570. [PMID: 37511329 PMCID: PMC10380272 DOI: 10.3390/ijms241411570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 05/26/2023] [Accepted: 06/03/2023] [Indexed: 07/30/2023] Open
Abstract
Somatic/germline BRCA1/2 mutations (m)/(likely) pathogenic variants (PV) (s/gBRCAm) remain the best predictive biomarker for PARP inhibitor efficacy. As >95% of high-grade serous ovarian cancers (HGSOC) have a somatic TP53m, combined tumor-based BRCA1/2 (tBRCA) and TP53 mutation testing (tBRCA/TP53m) may improve the quality of results in somatic BRCAm identification and interpretation of the 'second hit' event, i.e., loss of heterozygosity (LOH). A total of 237 patients with HGSOC underwent tBRCA/TP53m testing. The ratio of allelic fractions (AFs) for tBRCA/TP53m was calculated to estimate the proportion of cells carrying BRCAm and to infer LOH. Among the 142/237 gBRCA results, 16.2% demonstrated a pathogenic/deleterious variant (DEL) gBRCA1/2m. Among the 195 contributive tumor samples, 43 DEL of tBRCAm (22.1%) were identified (23 gBRCAm and 20 sBRCAm) with LOH identified in 37/41 conclusive samples. The median AF of TP53m was 0.52 (0.01-0.93), confirming huge variability in tumor cellularity. Initially, three samples were considered as wild type with <10% cellularity. However, additional testing detected a very low AF (<0.05) in both BRCA1/2m and TP53m, thus reidentifying them as sBRCA1/2m. Combined tBRCA/TP53m testing is rapid, sensitive, and identifies somatic and germline BRCA1/2m. AF TP53m is essential for interpreting sBRCA1/2m in low-cellularity samples and provides indirect evidence for LOH as the 'second hit' of BRCA1/2-related tumorigenesis.
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Affiliation(s)
- Edith Borcoman
- Department of Medical Oncology, Institut Curie, 75005 Paris, France
- Department of Drug Development and Innovation (D3i), Institut Curie, 75005 Paris, France
| | | | - Catherine Genestie
- Department of Medical Biology and Pathology, Gustave Roussy, 94805 Villejuif, France
- INSERM U981, Translational Research Laboratory, University Paris-Saclay, 94805 Villejuif, France
| | - Patricia Pautier
- Gynecology Unit, Gustave Roussy, 94805 Villejuif, France
- Groupe d'Investigateurs Nationaux pour l'Etude des Cancers Ovariens (GINECO), 94805 Villejuif, France
| | - Ludovic Lacroix
- Department of Medical Biology and Pathology, Gustave Roussy, 94805 Villejuif, France
| | - Sandrine M Caputo
- Department of Genetics, Institut Curie, PSL Research University, 75005 Paris, France
| | - Odile Cabaret
- Department of Medical Biology and Pathology, Gustave Roussy, 94805 Villejuif, France
| | | | - Judith Michels
- Gynecology Unit, Gustave Roussy, 94805 Villejuif, France
| | - Aurelie Auguste
- INSERM U981, Translational Research Laboratory, University Paris-Saclay, 94805 Villejuif, France
| | - Alexandra Leary
- INSERM U981, Translational Research Laboratory, University Paris-Saclay, 94805 Villejuif, France
- Gynecology Unit, Gustave Roussy, 94805 Villejuif, France
| | - Etienne Rouleau
- Department of Medical Biology and Pathology, Gustave Roussy, 94805 Villejuif, France
- INSERM U981, Translational Research Laboratory, University Paris-Saclay, 94805 Villejuif, France
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8
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Debbabi I, Vacher S, Neuzillet C, Cros J, Revillon F, Petitalot A, Turpin A, Antonio S, Girard E, Dupain C, Kamal M, Hammel P, Bièche I, Masliah-Planchon J, Caputo SM. Identification of a large intra-exonic deletion in BRCA2 exon 18 in a pancreatic ductal adenocarcinoma. Ther Adv Med Oncol 2023; 15:17588359221146132. [PMID: 36700131 PMCID: PMC9869184 DOI: 10.1177/17588359221146132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 11/30/2022] [Indexed: 01/19/2023] Open
Abstract
By 2030, pancreatic cancer will become the second leading cause of cancer-related deaths in the United States and in Europe. The management of patients with advanced pancreatic cancer relies on chemotherapy and poly (ADP-ribose) polymerase inhibitors for patients who carry BRCA1/2 inactivating alterations. Some variants, such as large insertion/deletions (Indels), inactivating BRCA1/2 and therefore of clinical relevance can be hard to detect by next-generation sequencing techniques. Here we report a 47-year-old patient presenting with pancreatic cancer whose tumour harbours a large somatic intra-exonic deletion of BRCA2 of 141 bp. This BRCA2 deletion, located in the C-terminal domain, can be considered as pathogenic and consequently affect tumorigenesis because it is involved in the interaction between the DSS1 protein and DNA. Thanks to the optimized bioinformatics algorithm, this intermediate size deletion in BRCA2 was identified, enabling personalized patient management via the inclusion of the patients in a clinical trial.
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Affiliation(s)
- Inès Debbabi
- Department of Genetics, Institut Curie, Paris, France
| | - Sophie Vacher
- Department of Genetics, Institut Curie, Paris, France,PSL Research University, Paris, France
| | - Cindy Neuzillet
- Department of Medical Oncology, Curie Institute, Versailles Saint Quentin University, Paris, France
| | - Jérome Cros
- INSERM UMR1149, Beaujon University Hospital, Paris University, Paris, France,Department of Pathology, Beaujon University, Hospital Paris 7 Diderot University, Paris, France
| | | | - Ambre Petitalot
- Department of Genetics, Institut Curie, Paris, France,PSL Research University, Paris, France
| | - Anthony Turpin
- ULR9020-UMR-S 1277 Canther-Cancer Heterogeneity, Plasticity and Resistance to Therapies, University of Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, France,Medical Oncology Department, CHU Lille, University of Lille, France
| | - Samantha Antonio
- Department of Genetics, Institut Curie, Paris, France,PSL Research University, Paris, France
| | | | - Célia Dupain
- Department of Drug Development and Innovation, Institut Curie, PSL Research University, Paris
| | - Maud Kamal
- Department of Drug Development and Innovation, Institut Curie, PSL Research University, Paris
| | - Pascal Hammel
- Department of Digestive and Medical Oncology, Paris-Saclay University, Hôpital Paul Brousse, Villejuif, France
| | - Ivan Bièche
- Department of Genetics, Institut Curie, Paris, France,Université de Paris, Paris, France
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9
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Jiao Y, Truong T, Eon-Marchais S, Mebirouk N, Caputo SM, Dondon MG, Karimi M, Le Gal D, Beauvallet J, Le Floch É, Dandine-Roulland C, Bacq-Daian D, Olaso R, Albuisson J, Audebert-Bellanger S, Berthet P, Bonadona V, Buecher B, Caron O, Cavaillé M, Chiesa J, Colas C, Collonge-Rame MA, Coupier I, Delnatte C, De Pauw A, Dreyfus H, Fert-Ferrer S, Gauthier-Villars M, Gesta P, Giraud S, Gladieff L, Golmard L, Lasset C, Lejeune-Dumoulin S, Léoné M, Limacher JM, Lortholary A, Luporsi É, Mari V, Maugard CM, Mortemousque I, Mouret-Fourme E, Nambot S, Noguès C, Popovici C, Prieur F, Pujol P, Sevenet N, Sobol H, Toulas C, Uhrhammer N, Vaur D, Venat L, Boland-Augé A, Guénel P, Deleuze JF, Stoppa-Lyonnet D, Andrieu N, Lesueur F. Association and performance of polygenic risk scores for breast cancer among French women presenting or not a familial predisposition to the disease. Eur J Cancer 2023; 179:76-86. [PMID: 36509001 DOI: 10.1016/j.ejca.2022.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/26/2022] [Accepted: 11/06/2022] [Indexed: 11/15/2022]
Abstract
BACKGROUND Three partially overlapping breast cancer polygenic risk scores (PRS) comprising 77, 179 and 313 SNPs have been proposed for European-ancestry women by the Breast Cancer Association Consortium (BCAC) for improving risk prediction in the general population. However, the effect of these SNPs may vary from one country to another and within a country because of other factors. OBJECTIVE To assess their associated risk and predictive performance in French women from (1) the CECILE population-based case-control study, (2) BRCA1 or BRCA2 (BRCA1/2) pathogenic variant (PV) carriers from the GEMO study, and (3) familial breast cancer cases with no BRCA1/2 PV and unrelated controls from the GENESIS study. RESULTS All three PRS were associated with breast cancer in all studies, with odds ratios per standard deviation varying from 1.7 to 2.0 in CECILE and GENESIS, and hazard ratios varying from 1.1 to 1.4 in GEMO. The predictive performance of PRS313 in CECILE was similar to that reported in BCAC but lower than that in GENESIS (area under the receiver operating characteristic curve (AUC) = 0.67 and 0.75, respectively). PRS were less performant in BRCA2 and BRCA1 PV carriers (AUC = 0.58 and 0.54 respectively). CONCLUSION Our results are in line with previous validation studies in the general population and in BRCA1/2 PV carriers. Additionally, we showed that PRS may be of clinical utility for women with a strong family history of breast cancer and no BRCA1/2 PV, and for those carrying a predicted PV in a moderate-risk gene like ATM, CHEK2 or PALB2.
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Affiliation(s)
- Yue Jiao
- INSERM, U900, Paris, France; Institut Curie, Paris, France; Mines ParisTech, Fontainebleau, France; PSL Research University, Paris, France
| | - Thérèse Truong
- Université Paris-Saclay, UVSQ, INSERM, U1018, Gustave Roussy, CESP, Team Exposome and Heredity, Villejuif, France
| | - Séverine Eon-Marchais
- INSERM, U900, Paris, France; Institut Curie, Paris, France; Mines ParisTech, Fontainebleau, France; PSL Research University, Paris, France
| | - Noura Mebirouk
- INSERM, U900, Paris, France; Institut Curie, Paris, France; Mines ParisTech, Fontainebleau, France; PSL Research University, Paris, France
| | - Sandrine M Caputo
- PSL Research University, Paris, France; Department of Genetics, Institut Curie, Paris, France
| | - Marie-Gabrielle Dondon
- INSERM, U900, Paris, France; Institut Curie, Paris, France; Mines ParisTech, Fontainebleau, France; PSL Research University, Paris, France
| | - Mojgan Karimi
- Université Paris-Saclay, UVSQ, INSERM, U1018, Gustave Roussy, CESP, Team Exposome and Heredity, Villejuif, France
| | - Dorothée Le Gal
- INSERM, U900, Paris, France; Institut Curie, Paris, France; Mines ParisTech, Fontainebleau, France; PSL Research University, Paris, France
| | - Juana Beauvallet
- INSERM, U900, Paris, France; Institut Curie, Paris, France; Mines ParisTech, Fontainebleau, France; PSL Research University, Paris, France
| | - Édith Le Floch
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Claire Dandine-Roulland
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Delphine Bacq-Daian
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Robert Olaso
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Juliette Albuisson
- Centre de Lutte contre le Cancer Georges François Leclerc, Dijon, France
| | | | - Pascaline Berthet
- Département de Biopathologie, Centre François Baclesse, Caen, France; INSERM, U1245, Rouen, France
| | - Valérie Bonadona
- Université Claude Bernard Lyon 1, Villeurbanne, France; CNRS UMR 5558, Centre Léon Bérard, Unité de Prévention et épidémiologie Génétique, Lyon, France
| | - Bruno Buecher
- PSL Research University, Paris, France; Department of Genetics, Institut Curie, Paris, France
| | - Olivier Caron
- Gustave Roussy, Département de Médecine Oncologique, Villejuif, France
| | - Mathias Cavaillé
- Université Clermont Auvergne, UMR INSERM, U1240, Clermont Ferrand, France; Département d'Oncogénétique, Centre Jean Perrin, Clermont Ferrand, France
| | - Jean Chiesa
- UF de Génétique Médicale et Cytogénétique, CHRU Caremeau, Nîmes, France
| | - Chrystelle Colas
- PSL Research University, Paris, France; Department of Genetics, Institut Curie, Paris, France; INSERM, U830, Paris, France
| | - Marie-Agnès Collonge-Rame
- Service Génétique et Biologie du Développement - Histologie, CHU Hôpital Saint-Jacques, Besançon, France
| | - Isabelle Coupier
- Hôpital Arnaud de Villeneuve, CHU Montpellier, Service de Génétique Médicale et Oncogénétique, Montpellier, France; INSERM, U896, CRCM Val d'Aurelle, Montpellier, France
| | - Capucine Delnatte
- Institut de Cancérologie de l'Ouest, Unité d'Oncogénétique, Saint Herblain, France
| | - Antoine De Pauw
- PSL Research University, Paris, France; Department of Genetics, Institut Curie, Paris, France
| | - Hélène Dreyfus
- Clinique Sainte Catherine, Avignon, CHU de Grenoble, Grenoble, France; Hôpital Couple-Enfant, Département de Génétique, Grenoble, France
| | | | - Marion Gauthier-Villars
- PSL Research University, Paris, France; Department of Genetics, Institut Curie, Paris, France
| | - Paul Gesta
- CH Georges Renon, Service d'Oncogénétique Régional Poitou-Charentes, Niort, France
| | - Sophie Giraud
- Hospices Civils de Lyon, Service de Génétique, Groupement Hospitalier Est, Bron, France
| | - Laurence Gladieff
- Institut Claudius Regaud - IUCT-Oncopole, Service d'Oncologie Médicale, Toulouse, France
| | - Lisa Golmard
- PSL Research University, Paris, France; Department of Genetics, Institut Curie, Paris, France
| | - Christine Lasset
- Université Claude Bernard Lyon 1, Villeurbanne, France; CNRS UMR 5558, Centre Léon Bérard, Unité de Prévention et épidémiologie Génétique, Lyon, France
| | | | - Mélanie Léoné
- Hospices Civils de Lyon, Service de Génétique, Groupement Hospitalier Est, Bron, France
| | | | - Alain Lortholary
- Service d'Oncologie Médicale, Centre Catherine de Sienne, Nantes, France; Hôpital Privé du Confluent, Nantes, France
| | - Élisabeth Luporsi
- Service de Génétique UF4128 CHR Metz-Thionville, Hôpital de Mercy, Metz, France
| | - Véronique Mari
- Unité d'Oncogénétique, Centre Antoine Lacassagne, Nice, France
| | - Christine M Maugard
- Génétique Oncologique Moléculaire, UF1422, Département d'Oncobiologie, LBBM, Hôpitaux Universitaires de Strasbourg, Strasbourg, France; UF6948 Génétique Oncologique Clinique, évaluation Familiale et Suivi, Strasbourg, France
| | | | | | - Sophie Nambot
- Centre de Lutte contre le Cancer Georges François Leclerc, Dijon, France; Institut GIMI, CHU de Dijon, Hôpital d'Enfants, France; Oncogénétique, Dijon, France
| | - Catherine Noguès
- Département d'Anticipation et de Suivi des Cancers, Oncogénétique Clinique, Institut Paoli-Calmettes, Marseille, France; Aix Marseille Université, INSERM, IRD, SESSTIM, Marseille, France
| | - Cornel Popovici
- Département d'Anticipation et de Suivi des Cancers, Oncogénétique Clinique, Institut Paoli-Calmettes, Marseille, France
| | - Fabienne Prieur
- CHU de Saint-Etienne; Hôpital Nord, Service de Génétique, Saint-Etienne, France
| | - Pascal Pujol
- Hôpital Arnaud de Villeneuve, CHU Montpellier, Service de Génétique Médicale et Oncogénétique, Montpellier, France; INSERM, U896, CRCM Val d'Aurelle, Montpellier, France
| | | | - Hagay Sobol
- Département d'Anticipation et de Suivi des Cancers, Oncogénétique Clinique, Institut Paoli-Calmettes, Marseille, France
| | - Christine Toulas
- Institut Claudius Regaud - IUCT-Oncopole, Service d'Oncologie Médicale, Toulouse, France
| | - Nancy Uhrhammer
- Centre Jean Perrin, LBM OncoGenAuvergne, Clermont Ferrand, France
| | - Dominique Vaur
- Département de Biopathologie, Centre François Baclesse, Caen, France; INSERM, U1245, Rouen, France
| | - Laurence Venat
- Hôpital Universitaire Dupuytren, Service d'Oncologie Médicale, Limoges, France
| | - Anne Boland-Augé
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Pascal Guénel
- Université Paris-Saclay, UVSQ, INSERM, U1018, Gustave Roussy, CESP, Team Exposome and Heredity, Villejuif, France
| | - Jean-François Deleuze
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Dominique Stoppa-Lyonnet
- Department of Genetics, Institut Curie, Paris, France; Département d'Oncogénétique, Centre Jean Perrin, Clermont Ferrand, France; Université Paris-Cité, Paris, France
| | - Nadine Andrieu
- INSERM, U900, Paris, France; Institut Curie, Paris, France; Mines ParisTech, Fontainebleau, France; PSL Research University, Paris, France
| | - Fabienne Lesueur
- INSERM, U900, Paris, France; Institut Curie, Paris, France; Mines ParisTech, Fontainebleau, France; PSL Research University, Paris, France.
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10
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Leman R, Parfait B, Vidaud D, Girodon E, Pacot L, Le Gac G, Ka C, Ferec C, Fichou Y, Quesnelle C, Aucouturier C, Muller E, Vaur D, Castera L, Boulouard F, Ricou A, Tubeuf H, Soukarieh O, Gaildrat P, Riant F, Guillaud‐Bataille M, Caputo SM, Caux‐Moncoutier V, Boutry‐Kryza N, Bonnet‐Dorion F, Schultz I, Rossing M, Quenez O, Goldenberg L, Harter V, Parsons MT, Spurdle AB, Frébourg T, Martins A, Houdayer C, Krieger S. SPiP: Splicing Prediction Pipeline, a machine learning tool for massive detection of exonic and intronic variant effects on mRNA splicing. Hum Mutat 2022; 43:2308-2323. [PMID: 36273432 PMCID: PMC10946553 DOI: 10.1002/humu.24491] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 10/06/2022] [Accepted: 10/18/2022] [Indexed: 01/25/2023]
Abstract
Modeling splicing is essential for tackling the challenge of variant interpretation as each nucleotide variation can be pathogenic by affecting pre-mRNA splicing via disruption/creation of splicing motifs such as 5'/3' splice sites, branch sites, or splicing regulatory elements. Unfortunately, most in silico tools focus on a specific type of splicing motif, which is why we developed the Splicing Prediction Pipeline (SPiP) to perform, in one single bioinformatic analysis based on a machine learning approach, a comprehensive assessment of the variant effect on different splicing motifs. We gathered a curated set of 4616 variants scattered all along the sequence of 227 genes, with their corresponding splicing studies. The Bayesian analysis provided us with the number of control variants, that is, variants without impact on splicing, to mimic the deluge of variants from high-throughput sequencing data. Results show that SPiP can deal with the diversity of splicing alterations, with 83.13% sensitivity and 99% specificity to detect spliceogenic variants. Overall performance as measured by area under the receiving operator curve was 0.986, better than SpliceAI and SQUIRLS (0.965 and 0.766) for the same data set. SPiP lends itself to a unique suite for comprehensive prediction of spliceogenicity in the genomic medicine era. SPiP is available at: https://sourceforge.net/projects/splicing-prediction-pipeline/.
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Affiliation(s)
- Raphaël Leman
- Laboratoire de Biologie et Génétique du CancerCentre François BaclesseCaenFrance
- Inserm U1245, UNIROUEN, FHU‐G4 génomiqueNormandie UniversitéRouenFrance
- UNICAENNormandie UniversitéCaenFrance
| | - Béatrice Parfait
- Service de Génétique et Biologie Moléculaires, APHP, HUPCHôpital CochinParisFrance
| | - Dominique Vidaud
- Service de Génétique et Biologie Moléculaires, APHP, HUPCHôpital CochinParisFrance
| | - Emmanuelle Girodon
- Service de Génétique et Biologie Moléculaires, APHP, HUPCHôpital CochinParisFrance
| | - Laurence Pacot
- Service de Génétique et Biologie Moléculaires, APHP, HUPCHôpital CochinParisFrance
| | - Gérald Le Gac
- Inserm UMR1078, Genetics, Functional Genomics and BiotechnologyUniversité de Bretagne OccidentaleBrestFrance
| | - Chandran Ka
- Inserm UMR1078, Genetics, Functional Genomics and BiotechnologyUniversité de Bretagne OccidentaleBrestFrance
| | - Claude Ferec
- Inserm UMR1078, Genetics, Functional Genomics and BiotechnologyUniversité de Bretagne OccidentaleBrestFrance
| | - Yann Fichou
- Inserm UMR1078, Genetics, Functional Genomics and BiotechnologyUniversité de Bretagne OccidentaleBrestFrance
| | - Céline Quesnelle
- Laboratoire de Biologie et Génétique du CancerCentre François BaclesseCaenFrance
| | - Camille Aucouturier
- Laboratoire de Biologie et Génétique du CancerCentre François BaclesseCaenFrance
- Inserm U1245, UNIROUEN, FHU‐G4 génomiqueNormandie UniversitéRouenFrance
| | - Etienne Muller
- Laboratoire de Biologie et Génétique du CancerCentre François BaclesseCaenFrance
| | - Dominique Vaur
- Laboratoire de Biologie et Génétique du CancerCentre François BaclesseCaenFrance
- Inserm U1245, UNIROUEN, FHU‐G4 génomiqueNormandie UniversitéRouenFrance
| | - Laurent Castera
- Laboratoire de Biologie et Génétique du CancerCentre François BaclesseCaenFrance
- Inserm U1245, UNIROUEN, FHU‐G4 génomiqueNormandie UniversitéRouenFrance
| | - Flavie Boulouard
- Laboratoire de Biologie et Génétique du CancerCentre François BaclesseCaenFrance
- Inserm U1245, UNIROUEN, FHU‐G4 génomiqueNormandie UniversitéRouenFrance
| | - Agathe Ricou
- Laboratoire de Biologie et Génétique du CancerCentre François BaclesseCaenFrance
- Inserm U1245, UNIROUEN, FHU‐G4 génomiqueNormandie UniversitéRouenFrance
| | - Hélène Tubeuf
- Inserm U1245, UNIROUEN, FHU‐G4 génomiqueNormandie UniversitéRouenFrance
- Integrative BiosoftwareRouenFrance
| | - Omar Soukarieh
- Inserm U1245, UNIROUEN, FHU‐G4 génomiqueNormandie UniversitéRouenFrance
| | | | - Florence Riant
- Laboratoire de Génétique, AP‐HPGH Saint‐Louis‐Lariboisière‐Fernand WidalParisFrance
| | | | - Sandrine M. Caputo
- Department of Genetics, Institut CurieParis Sciences Lettres Research UniversityParisFrance
| | | | - Nadia Boutry‐Kryza
- Unité Mixte de Génétique Constitutionnelle des Cancers FréquentsHospices Civils de LyonLyonFrance
| | - Françoise Bonnet‐Dorion
- Departement de Biopathologie Unité de Génétique ConstitutionnelleInstitut Bergonie—INSERM U1218BordeauxFrance
| | - Ines Schultz
- Laboratoire d'OncogénétiqueCentre Paul StraussStrasbourgFrance
| | - Maria Rossing
- Centre for Genomic Medicine, RigshospitaletUniversity of CopenhagenCopenhagenDenmark
| | - Olivier Quenez
- Inserm U1245, UNIROUEN, FHU‐G4 génomiqueNormandie UniversitéRouenFrance
| | - Louis Goldenberg
- Inserm U1245, UNIROUEN, FHU‐G4 génomiqueNormandie UniversitéRouenFrance
| | - Valentin Harter
- Department of BiostatisticsBaclesse Unicancer CenterCaenFrance
| | - Michael T. Parsons
- Department of Genetics and Computational BiologyQIMR Berghofer Medical Research InstituteHerstonQueenslandAustralia
| | - Amanda B. Spurdle
- Department of Genetics and Computational BiologyQIMR Berghofer Medical Research InstituteHerstonQueenslandAustralia
| | - Thierry Frébourg
- Inserm U1245, UNIROUEN, FHU‐G4 génomiqueNormandie UniversitéRouenFrance
- Department of geneticsRouen University HospitalRouenFrance
| | - Alexandra Martins
- Inserm U1245, UNIROUEN, FHU‐G4 génomiqueNormandie UniversitéRouenFrance
| | - Claude Houdayer
- Inserm U1245, UNIROUEN, FHU‐G4 génomiqueNormandie UniversitéRouenFrance
- Department of geneticsRouen University HospitalRouenFrance
| | - Sophie Krieger
- Laboratoire de Biologie et Génétique du CancerCentre François BaclesseCaenFrance
- Inserm U1245, UNIROUEN, FHU‐G4 génomiqueNormandie UniversitéRouenFrance
- UNICAENNormandie UniversitéCaenFrance
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Li H, Engel C, Hoya MDL, Peterlongo P, Yannoukakos D, Livraghi L, Radice P, Thomassen M, Hansen TVO, Gerdes AM, Nielsen HR, Caputo SM, Zambelli A, Borg A, Solano A, Thomas A, Parsons MT, Antoniou AC, Leslie G, Yang X, Chenevix-Trench G, Caldes T, Kwong A, Pedersen IS, Lautrup CK, John EM, Terry MB, Hopper JL, Southey MC, Andrulis IL, Tischkowitz M, Janavicius R, Boonen SE, Kroeldrup L, Varesco L, Hamann U, Vega A, Palmero EI, Garber J, Montagna M, Van Asperen CJ, Foretova L, Greene MH, Selkirk T, Moller P, Toland AE, Domchek SM, James PA, Thorne H, Eccles DM, Nielsen SM, Manoukian S, Pasini B, Caligo MA, Lazaro C, Kirk J, Wappenschmidt B, Spurdle AB, Couch FJ, Schmutzler R, Goldgar DE. Risks of breast and ovarian cancer for women harboring pathogenic missense variants in BRCA1 and BRCA2 compared with those harboring protein truncating variants. Genet Med 2022; 24:2208. [PMID: 36205748 DOI: 10.1016/j.gim.2022.08.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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12
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Li S, Silvestri V, Leslie G, Rebbeck TR, Neuhausen SL, Hopper JL, Nielsen HR, Lee A, Yang X, McGuffog L, Parsons MT, Andrulis IL, Arnold N, Belotti M, Borg Å, Buecher B, Buys SS, Caputo SM, Chung WK, Colas C, Colonna SV, Cook J, Daly MB, de la Hoya M, de Pauw A, Delhomelle H, Eason J, Engel C, Evans DG, Faust U, Fehm TN, Fostira F, Fountzilas G, Frone M, Garcia-Barberan V, Garre P, Gauthier-Villars M, Gehrig A, Glendon G, Goldgar DE, Golmard L, Greene MH, Hahnen E, Hamann U, Hanson H, Hassan T, Hentschel J, Horvath J, Izatt L, Janavicius R, Jiao Y, John EM, Karlan BY, Kim SW, Konstantopoulou I, Kwong A, Laugé A, Lee JW, Lesueur F, Mebirouk N, Meindl A, Mouret-Fourme E, Musgrave H, Ngeow Yuen Yie J, Niederacher D, Park SK, Pedersen IS, Ramser J, Ramus SJ, Rantala J, Rashid MU, Reichl F, Ritter J, Rump A, Santamariña M, Saule C, Schmidt G, Schmutzler RK, Senter L, Shariff S, Singer CF, Southey MC, Stoppa-Lyonnet D, Sutter C, Tan Y, Teo SH, Terry MB, Thomassen M, Tischkowitz M, Toland AE, Torres D, Vega A, Wagner SA, Wang-Gohrke S, Wappenschmidt B, Weber BHF, Yannoukakos D, Spurdle AB, Easton DF, Chenevix-Trench G, Ottini L, Antoniou AC. Cancer Risks Associated With BRCA1 and BRCA2 Pathogenic Variants. J Clin Oncol 2022; 40:1529-1541. [PMID: 35077220 PMCID: PMC9084432 DOI: 10.1200/jco.21.02112] [Citation(s) in RCA: 73] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/19/2021] [Accepted: 12/20/2021] [Indexed: 12/24/2022] Open
Abstract
PURPOSE To provide precise age-specific risk estimates of cancers other than female breast and ovarian cancers associated with pathogenic variants (PVs) in BRCA1 and BRCA2 for effective cancer risk management. METHODS We used data from 3,184 BRCA1 and 2,157 BRCA2 families in the Consortium of Investigators of Modifiers of BRCA1/2 to estimate age-specific relative (RR) and absolute risks for 22 first primary cancer types adjusting for family ascertainment. RESULTS BRCA1 PVs were associated with risks of male breast (RR = 4.30; 95% CI, 1.09 to 16.96), pancreatic (RR = 2.36; 95% CI, 1.51 to 3.68), and stomach (RR = 2.17; 95% CI, 1.25 to 3.77) cancers. Associations with colorectal and gallbladder cancers were also suggested. BRCA2 PVs were associated with risks of male breast (RR = 44.0; 95% CI, 21.3 to 90.9), stomach (RR = 3.69; 95% CI, 2.40 to 5.67), pancreatic (RR = 3.34; 95% CI, 2.21 to 5.06), and prostate (RR = 2.22; 95% CI, 1.63 to 3.03) cancers. The stomach cancer RR was higher for females than males (6.89 v 2.76; P = .04). The absolute risks to age 80 years ranged from 0.4% for male breast cancer to approximately 2.5% for pancreatic cancer for BRCA1 carriers and from approximately 2.5% for pancreatic cancer to 27% for prostate cancer for BRCA2 carriers. CONCLUSION In addition to female breast and ovarian cancers, BRCA1 and BRCA2 PVs are associated with increased risks of male breast, pancreatic, stomach, and prostate (only BRCA2 PVs) cancers, but not with the risks of other previously suggested cancers. The estimated age-specific risks will refine cancer risk management in men and women with BRCA1/2 PVs.
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Affiliation(s)
- Shuai Li
- Center for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
- Center for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | | | - Goska Leslie
- Center for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Timothy R. Rebbeck
- Harvard T.H. Chan School of Public Health, Boston, MA
- Dana-Farber Cancer Institute, Boston, MA
| | - Susan L. Neuhausen
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA
| | - John L. Hopper
- Center for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | | | - Andrew Lee
- Center for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Xin Yang
- Center for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Lesley McGuffog
- Center for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Michael T. Parsons
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Irene L. Andrulis
- Fred A. Litwin Center for Cancer Genetics, Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Norbert Arnold
- Department of Gynaecology and Obstetrics, University Hospital of Schleswig-Holstein, Campus Kiel, Christian-Albrechts University Kiel, Kiel, Germany
- Institute of Clinical Molecular Biology, University Hospital of Schleswig-Holstein, Campus Kiel, Christian-Albrechts University Kiel, Kiel, Germany
| | - Muriel Belotti
- Service de Génétique, Institut Curie, Paris, France
- Paris Sciences Lettres Research University, Paris, France
| | - Åke Borg
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Bruno Buecher
- Service de Génétique, Institut Curie, Paris, France
- Paris Sciences Lettres Research University, Paris, France
| | - Saundra S. Buys
- Department of Medicine and Huntsman Cancer Institute, University of Utah Health, Salt Lake City, UT
| | - Sandrine M. Caputo
- Service de Génétique, Institut Curie, Paris, France
- Paris Sciences Lettres Research University, Paris, France
| | - Wendy K. Chung
- Departments of Pediatrics and Medicine, Columbia University, New York, NY
| | - Chrystelle Colas
- Service de Génétique, Institut Curie, Paris, France
- Paris Sciences Lettres Research University, Paris, France
| | - Sarah V. Colonna
- Department of Medicine and Huntsman Cancer Institute, University of Utah Health, Salt Lake City, UT
| | - Jackie Cook
- Sheffield Clinical Genetics Service, Sheffield Children's Hospital, Sheffield, United Kingdom
| | - Mary B. Daly
- Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, PA
| | - Miguel de la Hoya
- Molecular Oncology Laboratory, CIBERONC, Hospital Clinico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clinico San Carlos), Madrid, Spain
| | - Antoine de Pauw
- Service de Génétique, Institut Curie, Paris, France
- Paris Sciences Lettres Research University, Paris, France
| | - Hélène Delhomelle
- Service de Génétique, Institut Curie, Paris, France
- Paris Sciences Lettres Research University, Paris, France
| | - Jacqueline Eason
- Nottingham Clinical Genetics Service, Nottingham University Hospitals NHS Trust, Nottingham, United Kingdom
| | - Christoph Engel
- Institute for Medical Informatics, Statistics and Epidemiology, 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 Center, Manchester, United Kingdom
- North West Genomics Laboratory Hub, Manchester Center for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Science Center, Manchester, United Kingdom
| | - Ulrike Faust
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Tanja N. Fehm
- Department of Gynecology and Obstetrics, University Hospital Düsseldorf, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Florentia Fostira
- Molecular Diagnostics Laboratory, INRASTES, National Center for Scientific Research “Demokritos”, Athens, Greece
| | - George Fountzilas
- Aristotle University of Thessaloniki School of Medicine, Thessaloniki, Greece
- Department of Medical Oncology, German Oncology Center, Limassol, Cyprus
| | - Megan Frone
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | - Vanesa Garcia-Barberan
- Molecular Oncology Laboratory, CIBERONC, Hospital Clinico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clinico San Carlos), Madrid, Spain
| | - Pilar Garre
- Molecular Oncology Laboratory, CIBERONC, Hospital Clinico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clinico San Carlos), Madrid, Spain
| | - Marion Gauthier-Villars
- Service de Génétique, Institut Curie, Paris, France
- Paris Sciences Lettres Research University, Paris, France
| | - Andrea Gehrig
- Department of Human Genetics, University Würzburg, Würzburg, Germany
| | - Gord Glendon
- Fred A. Litwin Center for Cancer Genetics, Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, ON, Canada
| | - David E. Goldgar
- Department of Dermatology, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT
| | - Lisa Golmard
- Service de Génétique, Institut Curie, Paris, France
- Paris Sciences Lettres Research University, Paris, France
| | - Mark H. Greene
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | - 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
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Helen Hanson
- Southwest Thames Regional Genetics Service, St George's Hospital, London, United Kingdom
| | - Tiara Hassan
- Breast Cancer Research Programme, Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia
| | - Julia Hentschel
- Institute of Human Genetics, University Hospital Leipzig, Leipzig, Germany
| | - Judit Horvath
- Institute of Human Genetics, University of Münster, Münster, Germany
| | - Louise Izatt
- Clinical Genetics Department, Guy's and St Thomas' NHS Foundation Trust, London, United Kingdom
| | - Ramunas Janavicius
- Faculty of Medicine, Department of Human and Medical Genetics, Institute of Biomedical Sciences, Vilnius University, Vilnius, Lithuania
- State Research Institute Center for Innovative Medicine, Vilnius, Lithuania
| | - Yue Jiao
- Genetic Epidemiology of Cancer Team, Inserm U900, Paris, France
- Institut Curie, Paris, France
- Mines ParisTech, Fontainebleau, France
| | - Esther M. John
- Department of Epidemiology and Population Health, Stanford University School of Medicine, Stanford, CA
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA
| | - Beth Y. Karlan
- Department of Obstetrics and Gynecology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA
| | - Sung-Won Kim
- Department of Surgery, Daerim Saint Mary's Hospital, Seoul, South Korea
| | - Irene Konstantopoulou
- Molecular Diagnostics Laboratory, INRASTES, National Center for Scientific Research “Demokritos”, Athens, Greece
| | - Ava Kwong
- Hong Kong Hereditary Breast Cancer Family Registry, Hong Kong
- Department of Surgery, The University of Hong Kong, Hong Kong
- Department of Surgery and Cancer Genetics Center, Hong Kong Sanatorium and Hospital, Hong Kong
| | - Anthony Laugé
- Service de Génétique, Institut Curie, Paris, France
- Paris Sciences Lettres Research University, Paris, France
| | - Jong Won Lee
- Department of Surgery, Ulsan University College of Medicine and Asan Medical Center, Seoul, South Korea
| | - Fabienne Lesueur
- Genetic Epidemiology of Cancer Team, Inserm U900, Paris, France
- Institut Curie, Paris, France
- Mines ParisTech, Fontainebleau, France
| | - Noura Mebirouk
- Genetic Epidemiology of Cancer Team, Inserm U900, Paris, France
- Institut Curie, Paris, France
- Mines ParisTech, Fontainebleau, France
| | - Alfons Meindl
- Department of Gynecology and Obstetrics, University of Munich, Campus Großhadern, Munich, Germany
- Division of Gynaecology and Obstetrics, Klinikum rechts der Isar der Technischen Universität München, Munich, Germany
| | - Emmanuelle Mouret-Fourme
- Service de Génétique, Institut Curie, Paris, France
- Paris Sciences Lettres Research University, Paris, France
| | - Hannah Musgrave
- Yorkshire Regional Genetics Service, Leeds Teaching Hospitals NHS Trust, Leeds, United Kingdom
| | - Joanne Ngeow Yuen Yie
- Cancer Genetics Service, National Cancer Center, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Dieter Niederacher
- Department of Gynecology and Obstetrics, University Hospital Düsseldorf, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Sue K. Park
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, South Korea
- Integrated Major in Innovative Medical Science, Seoul National University College of Medicine, Seoul, South Korea
- Cancer Research Institute, Seoul National University, Seoul, South Korea
| | - Inge Sokilde Pedersen
- Molecular Diagnostics, Aalborg University Hospital, Aalborg, Denmark
- Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Juliane Ramser
- Division of Gynaecology and Obstetrics, Klinikum rechts der Isar der Technischen Universität München, Munich, Germany
| | - Susan J. Ramus
- Faculty of Medicine, School of Women's and Children's Health, University of NSW Sydney, Sydney, New South Wales, Australia
- Adult Cancer Program, Lowy Cancer Research Center, University of NSW Sydney, Sydney, New South Wales, Australia
| | | | - 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 Center (SKMCH & RC), Lahore, Pakistan
| | - Florian Reichl
- Department of OB/GYN and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Julia Ritter
- Institute of Medical and Human Genetics, Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Andreas Rump
- Faculty of Medicine Carl Gustav Carus, Institute for Clinical Genetics, TU Dresden, Dresden, Germany
| | - Marta Santamariña
- Centro de Investigación en Red de Enfermedades Raras (CIBERER), Madrid, Spain
- Fundación Pública Galega Medicina Xenómica, Santiago De Compostela, Spain
- Instituto de Investigación Sanitaria de Santiago de Compostela, Santiago De Compostela, Spain
| | - Claire Saule
- Service de Génétique, Institut Curie, Paris, France
- Paris Sciences Lettres Research University, Paris, France
| | - Gunnar Schmidt
- Institute of Human Genetics, Hannover Medical School, Hannover, Germany
| | - 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
- Faculty of Medicine, Center for Molecular Medicine Cologne (CMMC), University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Leigha Senter
- Clinical Cancer Genetics Program, Division of Human Genetics, Department of Internal Medicine, The Comprehensive Cancer Center, The Ohio State University, Columbus, OH
| | - Saba Shariff
- West Midlands Regional Genetics Service, Birmingham Women's Hospital Healthcare NHS Trust, Birmingham, United Kingdom
| | - Christian F. Singer
- Department of OB/GYN and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Melissa C. Southey
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
- Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
| | - Dominique Stoppa-Lyonnet
- Service de Génétique, Institut Curie, Paris, France
- Department of Tumour Biology, INSERM U830, Paris, France
- Université Paris Descartes, Paris, France
| | - Christian Sutter
- Institute of Human Genetics, University Hospital Heidelberg, Heidelberg, Germany
| | - Yen Tan
- Department of OB/GYN and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Soo Hwang Teo
- Breast Cancer Research Programme, Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia
- Department of Surgery, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Mary Beth Terry
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY
| | - Mads Thomassen
- Department of Clinical Genetics, Odense University Hospital, Odence, Denmark
| | - Marc Tischkowitz
- Program in Cancer Genetics, Departments of Human Genetics and Oncology, McGill University, Montréal, QC, Canada
- Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Amanda E. Toland
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH
| | - Diana Torres
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Human Genetics, Pontificia Universidad Javeriana, Bogota, Colombia
| | - Ana Vega
- Centro de Investigación en Red de Enfermedades Raras (CIBERER), Madrid, Spain
- Fundación Pública Galega Medicina Xenómica, Santiago De Compostela, Spain
- Instituto de Investigación Sanitaria de Santiago de Compostela, Santiago De Compostela, Spain
| | - Sebastian A. Wagner
- Department of Medicine, Hematology/Oncology, Goethe-University Frankfurt, Frankfurt, Germany
| | - Shan Wang-Gohrke
- Department of Gynaecology and Obstetrics, University Hospital Ulm, Ulm, Germany
| | - 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
| | - Bernhard H. F. Weber
- Institute of Human Genetics, University Regensburg, Regensburg, Germany
- Institute of Clinical Human Genetics, University Hospital Regensburg, Regensburg, Germany
| | - Drakoulis Yannoukakos
- Molecular Diagnostics Laboratory, INRASTES, National Center for Scientific Research “Demokritos”, Athens, Greece
| | - Amanda B. Spurdle
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Douglas F. Easton
- Center for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Georgia Chenevix-Trench
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Laura Ottini
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Antonis C. Antoniou
- Center for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
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13
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Li H, Engel C, de la Hoya M, Peterlongo P, Yannoukakos D, Livraghi L, Radice P, Thomassen M, Hansen TVO, Gerdes AM, Nielsen HR, Caputo SM, Zambelli A, Borg A, Solano A, Thomas A, Parsons MT, Antoniou AC, Leslie G, Yang X, Chenevix-Trench G, Caldes T, Kwong A, Pedersen IS, Lautrup CK, John EM, Terry MB, Hopper JL, Southey MC, Andrulis IL, Tischkowitz M, Janavicius R, Boonen SE, Kroeldrup L, Varesco L, Hamann U, Vega A, Palmero EI, Garber J, Montagna M, Van Asperen CJ, Foretova L, Greene MH, Selkirk T, Moller P, Toland AE, Domchek SM, James PA, Thorne H, Eccles DM, Nielsen SM, Manoukian S, Pasini B, Caligo MA, Lazaro C, Kirk J, Wappenschmidt B, Spurdle AB, Couch FJ, Schmutzler R, Goldgar DE. Risks of breast and ovarian cancer for women harboring pathogenic missense variants in BRCA1 and BRCA2 compared with those harboring protein truncating variants. Genet Med 2022; 24:119-129. [PMID: 34906479 PMCID: PMC10170303 DOI: 10.1016/j.gim.2021.08.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 07/22/2021] [Accepted: 08/25/2021] [Indexed: 12/20/2022] Open
Abstract
PURPOSE Germline genetic testing for BRCA1 and BRCA2 variants has been a part of clinical practice for >2 decades. However, no studies have compared the cancer risks associated with missense pathogenic variants (PVs) with those associated with protein truncating (PTC) variants. METHODS We collected 582 informative pedigrees segregating 1 of 28 missense PVs in BRCA1 and 153 pedigrees segregating 1 of 12 missense PVs in BRCA2. We analyzed 324 pedigrees with PTC variants in BRCA1 and 214 pedigrees with PTC variants in BRCA2. Cancer risks were estimated using modified segregation analysis. RESULTS Estimated breast cancer risks were markedly lower for women aged >50 years carrying BRCA1 missense PVs than for the women carrying BRCA1 PTC variants (hazard ratio [HR] = 3.9 [2.4-6.2] for PVs vs 12.8 [5.7-28.7] for PTC variants; P = .01), particularly for missense PVs in the BRCA1 C-terminal domain (HR = 2.8 [1.4-5.6]; P = .005). In case of BRCA2, for women aged >50 years, the HR was 3.9 (2.0-7.2) for those heterozygous for missense PVs compared with 7.0 (3.3-14.7) for those harboring PTC variants. BRCA1 p.[Cys64Arg] and BRCA2 p.[Trp2626Cys] were associated with particularly low risks of breast cancer compared with other PVs. CONCLUSION These results have important implications for the counseling of at-risk women who harbor missense PVs in the BRCA1/2 genes.
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Affiliation(s)
- Hongyan Li
- Cancer Control and Population Science, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT
| | - Christoph Engel
- Institute for Medical Informatics, Statistics and Epidemiology (IMISE), University of Leipzig, Leipzig, Germany
| | - Miguel de la Hoya
- Molecular Oncology Laboratory, CIBERONC, Hospital Clinico San Carlos, Instituto de Investigación Sanitaria San Carlos, Madrid, Spain
| | - Paolo Peterlongo
- Genome Diagnostics Program, IFOM - the FIRC Institute of Molecular Oncology, Milan, Italy
| | - Drakoulis Yannoukakos
- Molecular Diagnostics Laboratory, National Centre for Scientific Research "Demokritos", INRASTES Institute of Nuclear & Radiological Sciences & Technology, Energy & Safety, Athens, Greece
| | - Luca Livraghi
- Medical Oncology Unit, AZIENDA SOCIO SANITARIA TERRITORIALE PAPA GIOVANNI XXIII, Bergamo, Italy; University of Siena, Siena, Italy
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori (INT), Milan, Italy
| | - Mads Thomassen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Thomas V O Hansen
- Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Anne-Marie Gerdes
- Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Henriette R Nielsen
- Department of Clinical Genetics Sygehus Lillebaelt, Vejle Hospital, Vejle, Denmark
| | - Sandrine M Caputo
- Service de Génétique, Institut Curie, Paris, France; Paris Sciences and Lettres Research University, Paris, France
| | - Alberto Zambelli
- Medical Oncology Unit, AZIENDA SOCIO SANITARIA TERRITORIALE PAPA GIOVANNI XXIII, Bergamo, Italy
| | - Ake Borg
- Divisions of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Angela Solano
- INBIOMED, Faculty of Medicine, University of Buenos Aires, CONICET and Genotyping Laboratory, Department of Clinical Chemistry, CEMIC, Buenos Aires, Argentina
| | - Abigail Thomas
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN
| | - Michael T Parsons
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Antonis C Antoniou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, School of Clinical Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Goska Leslie
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, School of Clinical Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Xin Yang
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, School of Clinical Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Georgia Chenevix-Trench
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Trinidad Caldes
- Molecular Oncology Laboratory, CIBERONC, Hospital Clinico San Carlos, Instituto de Investigación Sanitaria San Carlos, Madrid, Spain
| | - Ava Kwong
- Cancer Genetics Centre, Hong Kong Sanatorium & Hospital, Happy Valley, Hong Kong; Department of Surgery, LKS Faculty of Medicine,University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Inge Søkilde Pedersen
- Molecular Diagnostics, Aalborg University Hospital, Aalborg, Denmark; Clinical Cancer Research Center and Department of Clinical Genetics, Aalborg University Hospital, Aalborg, Denmark; Department of Clinical Medicine, The Faculty of Medicine, Aalborg University of Aalborg, Aalborg, Denmark
| | - Charlotte K Lautrup
- Clinical Cancer Research Center and Department of Clinical Genetics, Aalborg University Hospital, Aalborg, Denmark; Department of Clinical Medicine, The Faculty of Medicine, Aalborg University of Aalborg, Aalborg, Denmark
| | - Esther M John
- Department of Epidemiology & Population Health and Stanford Cancer Institute, School of Medicine, Stanford University, Stanford, CA
| | - Mary Beth Terry
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY; Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Victoria, Australia
| | - Melissa C Southey
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia; Department of Clinical Pathology, Melbourne Medical School, University of Melbourne, Melbourne, Victoria, Australia; Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
| | - 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
| | - Marc Tischkowitz
- Department of Medical Genetics, NIHR Cambridge Biomedical Research Centre, Cambridge University Hospitals NHS Foundation Trust, University of Cambridge, Cambridge, United Kingdom
| | - Ramunas Janavicius
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Vilnius, Lithuania; State Research Institute Centre for Innovative Medicine, Vilnius, Lithuania
| | - Susanne E Boonen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Lone Kroeldrup
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Liliana Varesco
- Unit of Hereditary Cancer, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ana Vega
- Fundación Pública galega Medicina Xenómica-SERGAS, Grupo de Medicina Xenómica-USC, CIBERER, IDIS, Santiago de Compostela, Spain
| | - Edenir I Palmero
- Molecular Oncology Research Center, Barretos Cancer Hospital, São Paulo, Brazil; National Cancer Institute, Rio de Janeiro, Brazil
| | - Judy Garber
- Center for Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, MA
| | - Marco Montagna
- Immunology and Molecular Oncology Unit, IOV - Istituto Oncologico Veneto - IRCCS, Padova, Italy
| | - Christi J Van Asperen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Lenka Foretova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Mark H Greene
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Tina Selkirk
- NorthShore University HealthSystem, University of Chicago, Evanston, IL
| | - Pal Moller
- Department of Tumor Biology, Institute of Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway; Center for Hereditary Tumors, HELIOS-Klinikum Wuppertal, University of Witten-Herdecke, Wuppertal, Germany
| | - Amanda E Toland
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus, OH
| | - Susan M Domchek
- Basser Center for BRCA, Abramson Cancer Center, Penn Medicine, University of Pennsylvania, Philadelphia, PA
| | - Paul A James
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia; The Sir Peter MacCallum Department of Oncology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Heather Thorne
- The Sir Peter MacCallum Department of Oncology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Diana M Eccles
- Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Sarah M Nielsen
- Center for Clinical Cancer Genetics, The University of Chicago, Chicago, IL
| | - Siranoush Manoukian
- Unit of Medical Genetics, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Italy
| | - Barbara Pasini
- Medical Genetics Unit, Department of Medical Sciences, University of Torino, Torino, Italy
| | - Maria A Caligo
- SOD Genetica Molecolare, University Hospital, Pisa, Italy
| | - Conxi Lazaro
- ONCOBELL-IDIBELL-IDIBGI-IGTP, CIBERONC, Hereditary Cancer Program, Catalan Institute of Oncology, Barcelona, Spain
| | - Judy Kirk
- Familial Cancer Service, Crown Princess Mary Cancer Centre, Westmead Hospital, Sydney Medical School, University of Sydney, Centre for Cancer Research, The Westmead Institute for Medical Research, Westmead, New South Wales, Australia
| | - Barbara Wappenschmidt
- Center for Hereditary Breast and Ovarian Cancer, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany; Center for Integrated Oncology (CIO), Faculty of Medicine, University of Cologne, Cologne, Germany
| | - Amanda B Spurdle
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Fergus J Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Rita Schmutzler
- Center for Hereditary Breast and Ovarian Cancer, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany; Center for Integrated Oncology (CIO), Faculty of Medicine, University of Cologne, Cologne, Germany
| | - David E Goldgar
- Cancer Control and Population Science, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT; Department of Dermatology, University of Utah School of Medicine, Salt Lake City, UT.
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14
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Sebai M, Tulasne D, Caputo SM, Verkarre V, Fernandes M, Reinhart F, Adams S, Maugard C, Caron O, Guillaud-Bataille M, Berthet P, Bignon YJ, Bressac-de Paillerets B, Burnichon N, Chiesa J, Giraud S, Lejeune S, Limacher JM, de Pauw A, Stoppa-Lyonnet D, Zattara-Cannoni H, Deveaux S, Lidereau R, Richard S, Rouleau E. Novel germline MET pathogenic variants in French patients with papillary renal cell carcinomas type I. Hum Mutat 2021; 43:316-327. [PMID: 34882875 DOI: 10.1002/humu.24313] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 11/30/2021] [Accepted: 12/06/2021] [Indexed: 11/10/2022]
Abstract
Hereditary papillary renal cell carcinoma (HPRC) is a rare inherited renal cancer syndrome characterized by bilateral and multifocal papillary type 1 renal tumors (PRCC1). Activating germline pathogenic variants of MET gene were identified in HPRC families. We reviewed the medical and molecular records of a large French series of 158 patients screened for MET oncogenic variants. MET pathogenic and likely pathogenic variants rate was 12.4% with 40.6% among patients with familial PRCC1 and 5% among patients with sporadic PRCC1. The phenotype in cases with MET pathogenic and likely pathogenic variants was characteristic: PRCC1 tumors were mainly bilateral (84.3%) and multifocal (87.5%). Histologically, six out of seven patients with MET pathogenic variant harboured biphasic squamoid alveolar PRCC. Genetic screening identified one novel pathogenic variant MET c.3389T>C, p.(Leu1130Ser) and three novel likely pathogenic variants: MET c.3257A>T, p.(His1086Leu); MET c.3305T>C, p.(Ile1102Thr) and MET c.3373T>G, p.(Cys1125Gly). Functional assay confirmed their oncogenic effect as they induced an abnormal focus formation. The genotype-phenotype correlation between MET pathogenic variants and PRCC1 presentation should encourage to widen the screening, especially toward non-familial PRCC1. This precise phenotype also constitutes a strong argument for the classification of novel missense variants within the tyrosine kinase domain when functional assays aren't accessible. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Molka Sebai
- Department of Medical Biology and Pathology, Cancer Genetics Laboratory, Gustave Roussy, 94800, Villejuif, France
| | - David Tulasne
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, UMR9020-U1277 - CANTHER - Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000, Lille, France
| | - Sandrine M Caputo
- Department of Genetics, Institut Curie, 75005, Paris, France.,Paris Sciences Lettres Research University, 75005, Paris, France
| | - Virginie Verkarre
- Department of Pathology, Georges Pompidou European Hospital, Assistance Publique Hôpitaux de Paris, 75015, Paris, France.,French National Network for Rare Cancers in Adults PREDIR labelled by INCa, AP-HP, Hôpital Bicêtre, 94270, Le Kremlin-Bicêtre, France
| | - Marie Fernandes
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, UMR9020-U1277 - CANTHER - Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000, Lille, France
| | - Fanny Reinhart
- Department of Pathology, Georges Pompidou European Hospital, Assistance Publique Hôpitaux de Paris, 75015, Paris, France
| | - Séverine Adams
- Department of Medical Biology and Pathology, Cancer Genetics Laboratory, Gustave Roussy, 94800, Villejuif, France
| | - Christine Maugard
- Department of molecular oncogenetics, Hôpitaux Universitaires de Strasbourg, 67091, Strasbourg, France
| | - Olivier Caron
- Department of Medical Oncogenetics, Gustave Roussy, 94800, Villejuif, France
| | - Marine Guillaud-Bataille
- Department of Medical Biology and Pathology, Cancer Genetics Laboratory, Gustave Roussy, 94800, Villejuif, France
| | - Pascaline Berthet
- French National Network for Rare Cancers in Adults PREDIR labelled by INCa, AP-HP, Hôpital Bicêtre, 94270, Le Kremlin-Bicêtre, France.,Oncogenetics Department, Centre François Baclesse, 14000, Caen, France
| | - Yves-Jean Bignon
- French National Network for Rare Cancers in Adults PREDIR labelled by INCa, AP-HP, Hôpital Bicêtre, 94270, Le Kremlin-Bicêtre, France.,Oncogenetics Department, Centre Jean-Perrin, BP 392, 63011, Clermont-Ferrand, France
| | | | - Nelly Burnichon
- Université de Paris, AP-HP, Hôpital Européen Georges Pompidou, Genetics department, Paris, France
| | - Jean Chiesa
- Department of Cytogenetics, Nimes University Hospital, 30029, Nîmes, France
| | - Sophie Giraud
- French National Network for Rare Cancers in Adults PREDIR labelled by INCa, AP-HP, Hôpital Bicêtre, 94270, Le Kremlin-Bicêtre, France.,Genetics Department, Hospices Civils de LYON (HCL), 69002, Lyon, France
| | - Sophie Lejeune
- Department of genetics, CHRU Lille, 59000, Lille, France
| | | | - Antoine de Pauw
- Department of Genetics, Institut Curie, 75005, Paris, France.,Paris Sciences Lettres Research University, 75005, Paris, France
| | - Dominique Stoppa-Lyonnet
- Department of Genetics, Institut Curie, 75005, Paris, France.,INSERM U830, Institut Curie Paris, 75505, Paris, France.,Paris-University, 75006, Paris, France
| | | | - Sophie Deveaux
- French National Network for Rare Cancers in Adults PREDIR labelled by INCa, AP-HP, Hôpital Bicêtre, 94270, Le Kremlin-Bicêtre, France
| | | | - Stéphane Richard
- French National Network for Rare Cancers in Adults PREDIR labelled by INCa, AP-HP, Hôpital Bicêtre, 94270, Le Kremlin-Bicêtre, France.,EPHE, PSL University, UMR 9019 CNRS, Paris-Saclay University, Gustave Roussy, 94800, Villejuif, France
| | - Etienne Rouleau
- Department of Medical Biology and Pathology, Cancer Genetics Laboratory, Gustave Roussy, 94800, Villejuif, France
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15
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Caputo SM, Golmard L, Léone M, Damiola F, Guillaud-Bataille M, Revillion F, Rouleau E, Derive N, Buisson A, Basset N, Schwartz M, Vilquin P, Garrec C, Privat M, Gay-Bellile M, Abadie C, Abidallah K, Airaud F, Allary AS, Barouk-Simonet E, Belotti M, Benigni C, Benusiglio PR, Berthemin C, Berthet P, Bertrand O, Bézieau S, Bidart M, Bignon YJ, Birot AM, Blanluet M, Bloucard A, Bombled J, Bonadona V, Bonnet F, Bonnet-Dupeyron MN, Boulaire M, Boulouard F, Bouras A, Bourdon V, Brahimi A, Brayotel F, Bressac de Paillerets B, Bronnec N, Bubien V, Buecher B, Cabaret O, Carriere J, Chiesa J, Chieze-Valéro S, Cohen C, Cohen-Haguenauer O, Colas C, Collonge-Rame MA, Conoy AL, Coulet F, Coupier I, Crivelli L, Cusin V, De Pauw A, Dehainault C, Delhomelle H, Delnatte C, Demontety S, Denizeau P, Devulder P, Dreyfus H, d’Enghein CD, Dupré A, Durlach A, Dussart S, Fajac A, Fekairi S, Fert-Ferrer S, Fiévet A, Fouillet R, Mouret-Fourme E, Gauthier-Villars M, Gesta P, Giraud S, Gladieff L, Goldbarg V, Goussot V, Guibert V, Guillerm E, Guy C, Hardouin A, Heude C, Houdayer C, Ingster O, Jacquot-Sawka C, Jones N, Krieger S, Lacoste S, Lallaoui H, Larbre H, Laugé A, Le Guyadec G, Le Mentec M, Lecerf C, Le Gall J, Legendre B, Legrand C, Legros A, Lejeune S, Lidereau R, Lignon N, Limacher JM, Doriane Livon, Lizard S, Longy M, Lortholary A, Macquere P, Mailliez A, Malsa S, Margot H, Mari V, Maugard C, Meira C, Menjard J, Molière D, Moncoutier V, Moretta-Serra J, Muller E, Nevière Z, Nguyen Minh Tuan TV, Noguchi T, Noguès C, Oca F, Popovici C, Prieur F, Raad S, Rey JM, Ricou A, Salle L, Saule C, Sevenet N, Simaga F, Sobol H, Suybeng V, Tennevet I, Tenreiro H, Tinat J, Toulas C, Turbiez I, Uhrhammer N, Vande Perre P, Vaur D, Venat L, Viellard N, Villy MC, Warcoin M, Yvard A, Zattara H, Caron O, Lasset C, Remenieras A, Boutry-Kryza N, Castéra L, Stoppa-Lyonnet D. Classification of 101 BRCA1 and BRCA2 variants of uncertain significance by cosegregation study: A powerful approach. Am J Hum Genet 2021; 108:1907-1923. [PMID: 34597585 DOI: 10.1016/j.ajhg.2021.09.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 09/01/2021] [Indexed: 12/18/2022] Open
Abstract
Up to 80% of BRCA1 and BRCA2 genetic variants remain of uncertain clinical significance (VUSs). Only variants classified as pathogenic or likely pathogenic can guide breast and ovarian cancer prevention measures and treatment by PARP inhibitors. We report the first results of the ongoing French national COVAR (cosegregation variant) study, the aim of which is to classify BRCA1/2 VUSs. The classification method was a multifactorial model combining different associations between VUSs and cancer, including cosegregation data. At this time, among the 653 variants selected, 101 (15%) distinct variants shared by 1,624 families were classified as pathogenic/likely pathogenic or benign/likely benign by the COVAR study. Sixty-six of the 101 (65%) variants classified by COVAR would have remained VUSs without cosegregation data. Of note, among the 34 variants classified as pathogenic by COVAR, 16 remained VUSs or likely pathogenic when following the ACMG/AMP variant classification guidelines. Although the initiation and organization of cosegregation analyses require a considerable effort, the growing number of available genetic tests results in an increasing number of families sharing a particular variant, and thereby increases the power of such analyses. Here we demonstrate that variant cosegregation analyses are a powerful tool for the classification of variants in the BRCA1/2 breast-ovarian cancer predisposition genes.
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16
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Jiao Y, Lesueur F, Azencott CA, Laurent M, Mebirouk N, Laborde L, Beauvallet J, Dondon MG, Eon-Marchais S, Laugé A, Noguès C, Andrieu N, Stoppa-Lyonnet D, Caputo SM. A new hybrid record linkage process to make epidemiological databases interoperable: application to the GEMO and GENEPSO studies involving BRCA1 and BRCA2 mutation carriers. BMC Med Res Methodol 2021; 21:155. [PMID: 34325649 PMCID: PMC8320036 DOI: 10.1186/s12874-021-01299-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 04/29/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Linking independent sources of data describing the same individuals enable innovative epidemiological and health studies but require a robust record linkage approach. We describe a hybrid record linkage process to link databases from two independent ongoing French national studies, GEMO (Genetic Modifiers of BRCA1 and BRCA2), which focuses on the identification of genetic factors modifying cancer risk of BRCA1 and BRCA2 mutation carriers, and GENEPSO (prospective cohort of BRCAx mutation carriers), which focuses on environmental and lifestyle risk factors. METHODS To identify as many as possible of the individuals participating in the two studies but not registered by a shared identifier, we combined probabilistic record linkage (PRL) and supervised machine learning (ML). This approach (named "PRL + ML") combined together the candidate matches identified by both approaches. We built the ML model using the gold standard on a first version of the two databases as a training dataset. This gold standard was obtained from PRL-derived matches verified by an exhaustive manual review. Results The Random Forest (RF) algorithm showed a highest recall (0.985) among six widely used ML algorithms: RF, Bagged trees, AdaBoost, Support Vector Machine, Neural Network. Therefore, RF was selected to build the ML model since our goal was to identify the maximum number of true matches. Our combined linkage PRL + ML showed a higher recall (range 0.988-0.992) than either PRL (range 0.916-0.991) or ML (0.981) alone. It identified 1995 individuals participating in both GEMO (6375 participants) and GENEPSO (4925 participants). CONCLUSIONS Our hybrid linkage process represents an efficient tool for linking GEMO and GENEPSO. It may be generalizable to other epidemiological studies involving other databases and registries.
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Affiliation(s)
- Yue Jiao
- Department of Genetics, Institut Curie, PSL Research University, Paris, France.,Inserm, U900, Paris, France.,Institut Curie, PSL Research University, Mines ParisTech, Paris, France
| | - Fabienne Lesueur
- Inserm, U900, Paris, France.,Institut Curie, PSL Research University, Mines ParisTech, Paris, France
| | - Chloé-Agathe Azencott
- Inserm, U900, Paris, France.,Mines ParisTech, PSL Research University, CBIO-Centre for Computational Biology, Paris, France
| | - Maïté Laurent
- Department of Genetics, Institut Curie, PSL Research University, Paris, France
| | - Noura Mebirouk
- Inserm, U900, Paris, France.,Institut Curie, PSL Research University, Mines ParisTech, Paris, France
| | - Lilian Laborde
- Institut Paoli-Calmettes, Centre de Traitement des Données IPC-PACA, Département de la Recherche Clinique et de l'Innovation, Marseille, France
| | - Juana Beauvallet
- Inserm, U900, Paris, France.,Institut Curie, PSL Research University, Mines ParisTech, Paris, France
| | - Marie-Gabrielle Dondon
- Inserm, U900, Paris, France.,Institut Curie, PSL Research University, Mines ParisTech, Paris, France
| | - Séverine Eon-Marchais
- Inserm, U900, Paris, France.,Institut Curie, PSL Research University, Mines ParisTech, Paris, France
| | - Anthony Laugé
- Department of Genetics, Institut Curie, PSL Research University, Paris, France
| | | | | | - Catherine Noguès
- Institut Paoli-Calmettes, Département d'Anticipation et de Suivi du Cancer, Oncogénétique clinique, Marseille France Inserm, U830, Université Paris Descartes, Paris, France.,Aix Marseille Univ, INSERM, IRD, SESSTIM, Sciences Economiques et Sociales de la Santé & Traitement de l'Information Médicale, Marseille, France
| | - Nadine Andrieu
- Inserm, U900, Paris, France.,Institut Curie, PSL Research University, Mines ParisTech, Paris, France
| | - Dominique Stoppa-Lyonnet
- Department of Genetics, Institut Curie, PSL Research University, Paris, France.,Paris University, Paris, France.,Inserm, U830, Paris, France
| | - Sandrine M Caputo
- Department of Genetics, Institut Curie, PSL Research University, Paris, France.
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17
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Julien M, Ghouil R, Petitalot A, Caputo SM, Carreira A, Zinn-Justin S. Intrinsic Disorder and Phosphorylation in BRCA2 Facilitate Tight Regulation of Multiple Conserved Binding Events. Biomolecules 2021; 11:1060. [PMID: 34356684 PMCID: PMC8301801 DOI: 10.3390/biom11071060] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/09/2021] [Accepted: 07/13/2021] [Indexed: 12/26/2022] Open
Abstract
The maintenance of genome integrity in the cell is an essential process for the accurate transmission of the genetic material. BRCA2 participates in this process at several levels, including DNA repair by homologous recombination, protection of stalled replication forks, and cell division. These activities are regulated and coordinated via cell-cycle dependent modifications. Pathogenic variants in BRCA2 cause genome instability and are associated with breast and/or ovarian cancers. BRCA2 is a very large protein of 3418 amino acids. Most well-characterized variants causing a strong predisposition to cancer are mutated in the C-terminal 700 residues DNA binding domain of BRCA2. The rest of the BRCA2 protein is predicted to be disordered. Interactions involving intrinsically disordered regions (IDRs) remain difficult to identify both using bioinformatics tools and performing experimental assays. However, the lack of well-structured binding sites provides unique functional opportunities for BRCA2 to bind to a large set of partners in a tightly regulated manner. We here summarize the predictive and experimental arguments that support the presence of disorder in BRCA2. We describe how BRCA2 IDRs mediate self-assembly and binding to partners during DNA double-strand break repair, mitosis, and meiosis. We highlight how phosphorylation by DNA repair and cell-cycle kinases regulate these interactions. We finally discuss the impact of cancer-associated variants on the function of BRCA2 IDRs and more generally on genome stability and cancer risk.
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Affiliation(s)
- Manon Julien
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, 91190 Gif-sur-Yvette, France; (M.J.); (R.G.)
- L’Institut de Biologie Intégrative de la Cellule (I2BC), UMR 9198, Paris-Saclay University, 91190 Gif-sur-Yvette, France;
| | - Rania Ghouil
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, 91190 Gif-sur-Yvette, France; (M.J.); (R.G.)
- L’Institut de Biologie Intégrative de la Cellule (I2BC), UMR 9198, Paris-Saclay University, 91190 Gif-sur-Yvette, France;
| | - Ambre Petitalot
- Service de Génétique, Unité de Génétique Constitutionnelle, Institut Curie, 75005 Paris, France; (A.P.); (S.M.C.)
- Institut Curie, Paris Sciences Lettres Research University, 75005 Paris, France
| | - Sandrine M. Caputo
- Service de Génétique, Unité de Génétique Constitutionnelle, Institut Curie, 75005 Paris, France; (A.P.); (S.M.C.)
- Institut Curie, Paris Sciences Lettres Research University, 75005 Paris, France
| | - Aura Carreira
- L’Institut de Biologie Intégrative de la Cellule (I2BC), UMR 9198, Paris-Saclay University, 91190 Gif-sur-Yvette, France;
- Institut Curie, Paris Sciences Lettres Research University, 75005 Paris, France
- Unité Intégrité du Génome, ARN et Cancer, Institut Curie, CNRS UMR3348, 91405 Orsay, France
| | - Sophie Zinn-Justin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, 91190 Gif-sur-Yvette, France; (M.J.); (R.G.)
- L’Institut de Biologie Intégrative de la Cellule (I2BC), UMR 9198, Paris-Saclay University, 91190 Gif-sur-Yvette, France;
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18
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Campos FAB, Rouleau E, Torrezan GT, Carraro DM, Casali da Rocha JC, Mantovani HK, da Silva LR, Osório CABDT, Moraes Sanches S, Caputo SM, Santana dos Santos E. Genetic Landscape of Male Breast Cancer. Cancers (Basel) 2021; 13:3535. [PMID: 34298749 PMCID: PMC8305894 DOI: 10.3390/cancers13143535] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/06/2021] [Accepted: 07/08/2021] [Indexed: 12/20/2022] Open
Abstract
Male breast cancer (MBC) is now considered molecularly different from female breast cancer (FBC). Evidence from studies indicates that common genetic and epigenetic features of FBC are not shared with those diagnosed in men. Genetic predisposition is likely to play a significant role in the tumorigenesis of this rare disease. Inherited germline variants in BRCA1 and BRCA2 account for around 2% and 10% of MBC cases, respectively, and the lifetime risk of breast cancer for men harboring BRCA1 and BRCA2 mutations is 1.2% and 6.8%. As for FBC, pathogenic mutations in other breast cancer genes have also been recently associated with an increased risk of MBC, such as PALB2 and CHEK2 mutations. However, while multigene germline panels have been extensively performed for BC female patients, the rarity of MBC has resulted in limited data to allow the understanding of the magnitude of risk and the contribution of recently identified moderate penetrance genes of FBC for MBC predisposition. This review gathers available data about the germline genetic landscape of men affected by breast cancer, estimated risk associated with these genetic variants, and current guidelines for clinical management.
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Affiliation(s)
| | - Etienne Rouleau
- Department of Medical Biology and Pathology, Gustave Roussy, Cancer Genetics Laboratory, Gustave Roussy, 94805 Villejuif, France;
| | - Giovana Tardin Torrezan
- Genomics and Molecular Biology Group, International Center of Research CIPE, A.C.Camargo Cancer Center, Sao Paulo 01509-010, Brazil; (G.T.T.); (D.M.C.)
- National Institute of Science and Technology in Oncogenomics (INCITO), Sao Paulo 01508-010, Brazil
| | - Dirce Maria Carraro
- Genomics and Molecular Biology Group, International Center of Research CIPE, A.C.Camargo Cancer Center, Sao Paulo 01509-010, Brazil; (G.T.T.); (D.M.C.)
- National Institute of Science and Technology in Oncogenomics (INCITO), Sao Paulo 01508-010, Brazil
| | | | - Higor Kassouf Mantovani
- Department of Obstetrics and Gynecology, Faculty of Medical Sciences, State University of Campinas (UNICAMP), Campinas 13083-881, Brazil; (H.K.M.); (L.R.d.S.)
| | - Leonardo Roberto da Silva
- Department of Obstetrics and Gynecology, Faculty of Medical Sciences, State University of Campinas (UNICAMP), Campinas 13083-881, Brazil; (H.K.M.); (L.R.d.S.)
| | | | - Solange Moraes Sanches
- Deparment of Medical Oncology, A.C.Camargo Cancer Center, Sao Paulo 01509-010, Brazil; (S.M.S.); (E.S.d.S.)
| | - Sandrine M. Caputo
- Department of Genetics, Institut Curie, 75248 Paris, France;
- Institut Curie, PSL Research University, 75005 Paris, France
| | - Elizabeth Santana dos Santos
- Deparment of Medical Oncology, A.C.Camargo Cancer Center, Sao Paulo 01509-010, Brazil; (S.M.S.); (E.S.d.S.)
- Centro de Oncologia, Hospital Sírio Libanês, Sao Paulo 01308-050, Brazil
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19
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Caputo SM, Telly D, Briaux A, Sesen J, Ceppi M, Bonnet F, Bourdon V, Coulet F, Castera L, Delnatte C, Hardouin A, Mazoyer S, Schultz I, Sevenet N, Uhrhammer N, Bonnet C, Tilkin-Mariamé AF, Houdayer C, Moncoutier V, Andrieu C, Bièche I, Stern MH, Stoppa-Lyonnet D, Lidereau R, Toulas C, Rouleau E. 5' Region Large Genomic Rearrangements in the BRCA1 Gene in French Families: Identification of a Tandem Triplication and Nine Distinct Deletions with Five Recurrent Breakpoints. Cancers (Basel) 2021; 13:cancers13133171. [PMID: 34202044 PMCID: PMC8268747 DOI: 10.3390/cancers13133171] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/11/2021] [Accepted: 06/17/2021] [Indexed: 12/28/2022] Open
Abstract
Simple Summary Large genomic rearrangements in BRCA1 consisting of deletions/duplications of one or several exons are complex events, often occurring in the 5′ region. We characterized 10 events in 20 families: one large triplication classified as benign and nine large deletions classified as pathogenic. The breakpoint localization will certainly help to further understand the chromatin structure in regions sensitive to rearrangement. Abstract Background: Large genomic rearrangements (LGR) in BRCA1 consisting of deletions/duplications of one or several exons have been found throughout the gene with a large proportion occurring in the 5′ region from the promoter to exon 2. The aim of this study was to better characterize those LGR in French high-risk breast/ovarian cancer families. Methods: DNA from 20 families with one apparent duplication and nine deletions was analyzed with a dedicated comparative genomic hybridization (CGH) array, high-resolution BRCA1 Genomic Morse Codes analysis and Sanger sequencing. Results: The apparent duplication was in fact a tandem triplication of exons 1 and 2 and part of intron 2 of BRCA1, fully characterized here for the first time. We calculated a causality score with the multifactorial model from data obtained from six families, classifying this variant as benign. Among the nine deletions detected in this region, eight have never been identified. The breakpoints fell in six recurrent regions and could confirm some specific conformation of the chromatin. Conclusions: Taken together, our results firmly establish that the BRCA1 5′ region is a frequent site of different LGRs and highlight the importance of the segmental duplication and Alu sequences, particularly the very high homologous region, in the mechanism of a recombination event. This also confirmed that those events are not systematically deleterious.
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Affiliation(s)
- Sandrine M. Caputo
- Department of Genetics, Institut Curie, F-75248 Paris, France; (S.M.C.); (A.B.); (V.M.); (C.A.); (I.B.); (M.-H.S.); (D.S.-L.); (R.L.)
- Institut Curie, PSL Research University, F-75005 Paris, France
| | - Dominique Telly
- Laboratoire d’Oncogénétique, Institut Claudius Regaud, IUCT-O, F-31059 Toulouse, France;
| | - Adrien Briaux
- Department of Genetics, Institut Curie, F-75248 Paris, France; (S.M.C.); (A.B.); (V.M.); (C.A.); (I.B.); (M.-H.S.); (D.S.-L.); (R.L.)
- Institut Curie, PSL Research University, F-75005 Paris, France
| | - Julie Sesen
- Department of Neurosurgery, Boston Children’s Hospital, Boston, MA 02115, USA;
| | - Maurizio Ceppi
- Roche Innovation Center Basel (RICB), Roche Pharma Research and Early Development, CH-4052 Basel, Switzerland;
| | - Françoise Bonnet
- Laboratoire de Génétique Constitutionnelle et INSERM U916 VINCO, Institut Bergonié, CEDEX, F-33076 Bordeaux, France; (F.B.); (N.S.)
| | - Violaine Bourdon
- Laboratoire d’Oncogénétique Moléculaire, Département de Biologie du Cancer, Institut Paoli-Calmettes, F-13273 Marseille, France;
| | - Florence Coulet
- Department of Genetics, Pitié-Salpêtriere Hospital, Assistance Publique-Hopitaux de Paris, Sorbonne University, F-75013 Paris, France;
| | - Laurent Castera
- Laboratoire de Biologie et de Génétique du Cancer, CLCC François Baclesse, INSERM 1079 Centre Normand de Génomique et de Médecine Personnalisée, F-14076 Caen, France; (L.C.); (A.H.)
| | - Capucine Delnatte
- Service de Génétique Médicale, Unité de Génétique Moléculaire, CHU Nantes, F-44093 Nantes, France;
| | - Agnès Hardouin
- Laboratoire de Biologie et de Génétique du Cancer, CLCC François Baclesse, INSERM 1079 Centre Normand de Génomique et de Médecine Personnalisée, F-14076 Caen, France; (L.C.); (A.H.)
| | - Sylvie Mazoyer
- Centre de Recherche en Neurosciences de Lyon, INSERM, U1028, CNRS, UMR5292, Université de Lyon, F-69008 Lyon, France;
| | - Inès Schultz
- Centre Paul Strauss, Laboratoire de Biologie Tumorale—Oncogénétique, F-67000 Strasbourg, France;
| | - Nicolas Sevenet
- Laboratoire de Génétique Constitutionnelle et INSERM U916 VINCO, Institut Bergonié, CEDEX, F-33076 Bordeaux, France; (F.B.); (N.S.)
| | - Nancy Uhrhammer
- Biologie Clinique et Oncologique, Biologie Moléculaire—Centre Jean Perrin, F-63000 Clermont-Ferrand, France;
| | - Céline Bonnet
- Institut de Cancérologie, 6 Avenue de Bourgogne, F-54519 Vandœuvre-lès-Nancy, France;
| | - Anne-Françoise Tilkin-Mariamé
- Cancer Research Center of Toulouse (CRCT), Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1037, F-31000 Toulouse, France;
| | - Claude Houdayer
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, F-76183 Rouen, France;
- Normandy Centre for Genomic and 41 Personalized Medicine, Department of Genetics, University Hospital, F-76183 Rouen, France
| | - Virginie Moncoutier
- Department of Genetics, Institut Curie, F-75248 Paris, France; (S.M.C.); (A.B.); (V.M.); (C.A.); (I.B.); (M.-H.S.); (D.S.-L.); (R.L.)
- Institut Curie, PSL Research University, F-75005 Paris, France
| | - Catherine Andrieu
- Department of Genetics, Institut Curie, F-75248 Paris, France; (S.M.C.); (A.B.); (V.M.); (C.A.); (I.B.); (M.-H.S.); (D.S.-L.); (R.L.)
- Institut Curie, PSL Research University, F-75005 Paris, France
| | | | - Ivan Bièche
- Department of Genetics, Institut Curie, F-75248 Paris, France; (S.M.C.); (A.B.); (V.M.); (C.A.); (I.B.); (M.-H.S.); (D.S.-L.); (R.L.)
- Faculty of Pharmaceutical and Biological Sciences, University of Paris, F-75006 Paris, France
| | - Marc-Henri Stern
- Department of Genetics, Institut Curie, F-75248 Paris, France; (S.M.C.); (A.B.); (V.M.); (C.A.); (I.B.); (M.-H.S.); (D.S.-L.); (R.L.)
- Institut Curie, INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), PSL Research University, F-75005 Paris, France
| | - Dominique Stoppa-Lyonnet
- Department of Genetics, Institut Curie, F-75248 Paris, France; (S.M.C.); (A.B.); (V.M.); (C.A.); (I.B.); (M.-H.S.); (D.S.-L.); (R.L.)
- Institut Curie, INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), PSL Research University, F-75005 Paris, France
- Faculty of Medicine, University of Paris, F-75005 Paris, France
| | - Rosette Lidereau
- Department of Genetics, Institut Curie, F-75248 Paris, France; (S.M.C.); (A.B.); (V.M.); (C.A.); (I.B.); (M.-H.S.); (D.S.-L.); (R.L.)
- Institut Curie, PSL Research University, F-75005 Paris, France
| | - Christine Toulas
- Laboratoire d’Oncogénétique, Institut Claudius Regaud, IUCT-O, F-31059 Toulouse, France;
- Correspondence: (C.T.); (E.R.)
| | - Etienne Rouleau
- Department of Biology, Gustave Roussy, Université Paris-Saclay, F-94805 Villejuif, France
- Correspondence: (C.T.); (E.R.)
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20
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Tubeuf H, Caputo SM, Sullivan T, Rondeaux J, Krieger S, Caux-Moncoutier V, Hauchard J, Castelain G, Fiévet A, Meulemans L, Révillion F, Léoné M, Boutry-Kryza N, Delnatte C, Guillaud-Bataille M, Cleveland L, Reid S, Southon E, Soukarieh O, Drouet A, Di Giacomo D, Vezain M, Bonnet-Dorion F, Bourdon V, Larbre H, Muller D, Pujol P, Vaz F, Audebert-Bellanger S, Colas C, Venat-Bouvet L, Solano AR, Stoppa-Lyonnet D, Houdayer C, Frebourg T, Gaildrat P, Sharan SK, Martins A. Calibration of Pathogenicity Due to Variant-Induced Leaky Splicing Defects by Using BRCA2 Exon 3 as a Model System. Cancer Res 2020; 80:3593-3605. [PMID: 32641407 DOI: 10.1158/0008-5472.can-20-0895] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/14/2020] [Accepted: 07/02/2020] [Indexed: 12/25/2022]
Abstract
BRCA2 is a clinically actionable gene implicated in breast and ovarian cancer predisposition that has become a high priority target for improving the classification of variants of unknown significance (VUS). Among all BRCA2 VUS, those causing partial/leaky splicing defects are the most challenging to classify because the minimal level of full-length (FL) transcripts required for normal function remains to be established. Here, we explored BRCA2 exon 3 (BRCA2e3) as a model for calibrating variant-induced spliceogenicity and estimating thresholds for BRCA2 haploinsufficiency. In silico predictions, minigene splicing assays, patients' RNA analyses, a mouse embryonic stem cell (mESC) complementation assay and retrieval of patient-related information were combined to determine the minimal requirement of FL BRCA2 transcripts. Of 100 BRCA2e3 variants tested in the minigene assay, 64 were found to be spliceogenic, causing mild to severe RNA defects. Splicing defects were also confirmed in patients' RNA when available. Analysis of a neutral leaky variant (c.231T>G) showed that a reduction of approximately 60% of FL BRCA2 transcripts from a mutant allele does not cause any increase in cancer risk. Moreover, data obtained from mESCs suggest that variants causing a decline in FL BRCA2 with approximately 30% of wild-type are not pathogenic, given that mESCs are fully viable and resistant to DNA-damaging agents in those conditions. In contrast, mESCs producing lower relative amounts of FL BRCA2 exhibited either null or hypomorphic phenotypes. Overall, our findings are likely to have broader implications on the interpretation of BRCA2 variants affecting the splicing pattern of other essential exons. SIGNIFICANCE: These findings demonstrate that BRCA2 tumor suppressor function tolerates substantial reduction in full-length transcripts, helping to determine the pathogenicity of BRCA2 leaky splicing variants, some of which may not increase cancer risk.
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Affiliation(s)
- Hélène Tubeuf
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France.,Interactive Biosoftware, Rouen, France
| | - Sandrine M Caputo
- Department of Genetics, Institut Curie, Paris, France.,PSL Research University, Paris, France
| | - Teresa Sullivan
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland
| | - Julie Rondeaux
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Sophie Krieger
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France.,Laboratory of Cancer Biology and Genetics, Centre François Baclesse, Caen, France - Normandie University, UNICAEN, Caen, France
| | | | - Julie Hauchard
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Gaia Castelain
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Alice Fiévet
- Department of Genetics, Institut Curie, Paris, France.,INSERM U830, University Paris Descartes, Paris, France.,Service Génétique des Tumeurs, Gustave Roussy, Villejuif, France
| | - Laëtitia Meulemans
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | | | | | | | | | | | - Linda Cleveland
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland
| | - Susan Reid
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland
| | - Eileen Southon
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland
| | - Omar Soukarieh
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Aurélie Drouet
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Daniela Di Giacomo
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Myriam Vezain
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | | | - Violaine Bourdon
- Department of Genetics, Institut Paoli-Calmettes, Marseille, France
| | - Hélène Larbre
- Laboratoire d'Oncogénétique Moléculaire, Institut Godinot, Reims, France
| | - Danièle Muller
- Unité d'Oncogénétique, Centre Paul Strauss, Strasbourg, France
| | - Pascal Pujol
- Unité d'Oncogénétique, CHU Arnaud de Villeneuve, Montpellier, France
| | - Fátima Vaz
- Breast Cancer Risk Evaluation Clinic, Portuguese Institute of Oncology of Lisbon, Lisbon, Portugal
| | | | - Chrystelle Colas
- Department of Genetics, Institut Curie, Paris, France.,PSL Research University, Paris, France
| | | | - Angela R Solano
- Genotipificacion y Cancer Hereditario, Departmento de Analisis Clinicos, Centro de Educacion Medica e Investigaciones Clinicas (CEMIC), Ciudad Autonoma de Buenos Aires, Argentina
| | - Dominique Stoppa-Lyonnet
- Department of Genetics, Institut Curie, Paris, France.,INSERM U830, University Paris Descartes, Paris, France
| | - Claude Houdayer
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France.,Department of Genetics, University Hospital, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Thierry Frebourg
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France.,Department of Genetics, University Hospital, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Pascaline Gaildrat
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Shyam K Sharan
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland
| | - Alexandra Martins
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France.
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21
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Santana dos Santos E, Lallemand F, Petitalot A, Caputo SM, Rouleau E. HRness in Breast and Ovarian Cancers. Int J Mol Sci 2020; 21:E3850. [PMID: 32481735 PMCID: PMC7312125 DOI: 10.3390/ijms21113850] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/25/2020] [Accepted: 04/28/2020] [Indexed: 02/06/2023] Open
Abstract
Ovarian and breast cancers are currently defined by the main pathways involved in the tumorigenesis. The majority are carcinomas, originating from epithelial cells that are in constant division and subjected to cyclical variations of the estrogen stimulus during the female hormonal cycle, therefore being vulnerable to DNA damage. A portion of breast and ovarian carcinomas arises in the context of DNA repair defects, in which genetic instability is the backdrop for cancer initiation and progression. For these tumors, DNA repair deficiency is now increasingly recognized as a target for therapeutics. In hereditary breast/ovarian cancers (HBOC), tumors with BRCA1/2 mutations present an impairment of DNA repair by homologous recombination (HR). For many years, BRCA1/2 mutations were only screened on germline DNA, but now they are also searched at the tumor level to personalize treatment. The reason of the inactivation of this pathway remains uncertain for most cases, even in the presence of a HR-deficient signature. Evidence indicates that identifying the mechanism of HR inactivation should improve both genetic counseling and therapeutic response, since they can be useful as new biomarkers of response.
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Affiliation(s)
- Elizabeth Santana dos Santos
- Department of Medical Biology and Pathology, Gustave Roussy, Cancer Genetics Laboratory, Gustave Roussy, 94800 Villejuif, France;
- Department of Clinical Oncology, A.C. Camargo Cancer Center, São Paulo 01509-010, Brazil
| | - François Lallemand
- Department of Genetics, Institut Curie, 75005 Paris, France; (F.L.); (A.P.); (S.M.C.)
- PSL Research University, 75005 Paris, France
| | - Ambre Petitalot
- Department of Genetics, Institut Curie, 75005 Paris, France; (F.L.); (A.P.); (S.M.C.)
- PSL Research University, 75005 Paris, France
| | - Sandrine M. Caputo
- Department of Genetics, Institut Curie, 75005 Paris, France; (F.L.); (A.P.); (S.M.C.)
- PSL Research University, 75005 Paris, France
| | - Etienne Rouleau
- Department of Medical Biology and Pathology, Gustave Roussy, Cancer Genetics Laboratory, Gustave Roussy, 94800 Villejuif, France;
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22
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Meulemans L, Mesman RLS, Caputo SM, Krieger S, Guillaud-Bataille M, Caux-Moncoutier V, Léone M, Boutry-Kryza N, Sokolowska J, Révillion F, Delnatte C, Tubeuf H, Soukarieh O, Bonnet-Dorion F, Guibert V, Bronner M, Bourdon V, Lizard S, Vilquin P, Privat M, Drouet A, Grout C, Calléja FMGR, Golmard L, Vrieling H, Stoppa-Lyonnet D, Houdayer C, Frebourg T, Vreeswijk MPG, Martins A, Gaildrat P. Skipping Nonsense to Maintain Function: The Paradigm of BRCA2 Exon 12. Cancer Res 2020; 80:1374-1386. [PMID: 32046981 DOI: 10.1158/0008-5472.can-19-2491] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 12/18/2019] [Accepted: 02/06/2020] [Indexed: 11/16/2022]
Abstract
Germline nonsense and canonical splice site variants identified in disease-causing genes are generally considered as loss-of-function (LoF) alleles and classified as pathogenic. However, a fraction of such variants could maintain function through their impact on RNA splicing. To test this hypothesis, we used the alternatively spliced BRCA2 exon 12 (E12) as a model system because its in-frame skipping leads to a potentially functional protein. All E12 variants corresponding to putative LoF variants or predicted to alter splicing (n = 40) were selected from human variation databases and characterized for their impact on splicing in minigene assays and, when available, in patient lymphoblastoid cell lines. Moreover, a selection of variants was analyzed in a mouse embryonic stem cell-based functional assay. Using these complementary approaches, we demonstrate that a subset of variants, including nonsense variants, induced in-frame E12 skipping through the modification of splice sites or regulatory elements and, consequently, led to an internally deleted but partially functional protein. These data provide evidence, for the first time in a cancer-predisposition gene, that certain presumed null variants can retain function due to their impact on splicing. Further studies are required to estimate cancer risk associated with these hypomorphic variants. More generally, our findings highlight the need to exercise caution in the interpretation of putative LoF variants susceptible to induce in-frame splicing modifications. SIGNIFICANCE: This study presents evidence that certain presumed loss-of-function variants in a cancer predisposition gene can retain function due to their direct impact on RNA splicing.
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Affiliation(s)
- Laëtitia Meulemans
- Normandie Univ, UNIROUEN, Inserm U1245, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Romy L S Mesman
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Sandrine M Caputo
- Department of Genetics, Institut Curie, Paris, France.,PSL Research University, Paris, France
| | - Sophie Krieger
- Normandie Univ, UNIROUEN, Inserm U1245, Normandy Centre for Genomic and Personalized Medicine, Rouen, France.,Laboratory of Cancer Biology and Genetics, Centre François Baclesse, Caen, France.,Normandie University, UNICAEN, Caen, France
| | | | | | | | | | | | | | | | - Hélène Tubeuf
- Normandie Univ, UNIROUEN, Inserm U1245, Normandy Centre for Genomic and Personalized Medicine, Rouen, France.,Interactive Biosoftware, Rouen, France
| | - Omar Soukarieh
- Normandie Univ, UNIROUEN, Inserm U1245, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | | | - Virginie Guibert
- Department of Genetics, Nantes University Hospital, Nantes, France
| | - Myriam Bronner
- Department of Genetics, Nancy University Hospital, Nancy, France
| | - Violaine Bourdon
- Department of Genetics, Institut Paoli-Calmettes, Marseille, France
| | - Sarab Lizard
- Department of Genetics, Nancy University Hospital, Nancy, France
| | - Paul Vilquin
- Department of Pathology and Oncobiology, Montpellier University Hospital, Montpellier, France
| | - Maud Privat
- University of Clermont Auvergne, Inserm U1240, Clermont Ferrand, France.,Department of Oncogenetics, Centre Jean Perrin, Clermont Ferrand, France
| | - Aurélie Drouet
- Normandie Univ, UNIROUEN, Inserm U1245, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Charlotte Grout
- Normandie Univ, UNIROUEN, Inserm U1245, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | | | - Lisa Golmard
- Department of Genetics, Institut Curie, Paris, France.,PSL Research University, Paris, France
| | - Harry Vrieling
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Dominique Stoppa-Lyonnet
- Department of Genetics, Institut Curie, Paris, France.,Inserm U830, University Paris Descartes, Paris, France
| | - Claude Houdayer
- Normandie Univ, UNIROUEN, Inserm U1245, Normandy Centre for Genomic and Personalized Medicine, Rouen, France.,Department of Genetics, Institut Curie, Paris, France.,Department of Genetics, Rouen University Hospital, Rouen, France
| | - Thierry Frebourg
- Normandie Univ, UNIROUEN, Inserm U1245, Normandy Centre for Genomic and Personalized Medicine, Rouen, France.,Department of Genetics, Rouen University Hospital, Rouen, France
| | - Maaike P G Vreeswijk
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Alexandra Martins
- Normandie Univ, UNIROUEN, Inserm U1245, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Pascaline Gaildrat
- Normandie Univ, UNIROUEN, Inserm U1245, Normandy Centre for Genomic and Personalized Medicine, Rouen, France.
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23
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Gay-Bellile M, Privat M, Martins A, Caputo SM, Pebrel-Richard C, Cavaillé M, Viala S, Corsini C, Rodrigues M, Barnich N, Bidet Y, Uhrhammer N, Bignon YJ. Is BRCA2 involved in early onset colorectal cancer risk? Clin Genet 2019; 97:668-669. [PMID: 31875949 PMCID: PMC7078894 DOI: 10.1111/cge.13679] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 10/23/2019] [Accepted: 10/24/2019] [Indexed: 12/27/2022]
Affiliation(s)
- Mathilde Gay-Bellile
- Université Clermont Auvergne, INSERM, U1240 Imagerie Moléculaire et Stratégies Théranostiques, Clermont Ferrand, France.,Département d'Oncogénétique, Centre Jean Perrin, Clermont-Ferrand, France
| | - Maud Privat
- Université Clermont Auvergne, INSERM, U1240 Imagerie Moléculaire et Stratégies Théranostiques, Clermont Ferrand, France.,Département d'Oncogénétique, Centre Jean Perrin, Clermont-Ferrand, France
| | - Alexandra Martins
- INSERM U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, UNIROUEN, Normandie Université, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | | | - Céline Pebrel-Richard
- Université Clermont Auvergne, INSERM, U1240 Imagerie Moléculaire et Stratégies Théranostiques, Clermont Ferrand, France.,Service de Cytogénétique Médicale, CHU Clermont-Ferrand, Clermont-Ferrand, France
| | - Mathias Cavaillé
- Université Clermont Auvergne, INSERM, U1240 Imagerie Moléculaire et Stratégies Théranostiques, Clermont Ferrand, France.,Département d'Oncogénétique, Centre Jean Perrin, Clermont-Ferrand, France
| | - Sandrine Viala
- Université Clermont Auvergne, INSERM, U1240 Imagerie Moléculaire et Stratégies Théranostiques, Clermont Ferrand, France.,Département d'Oncogénétique, Centre Jean Perrin, Clermont-Ferrand, France
| | - Carole Corsini
- Département de Génétique Médicale, unité d'oncogénétique clinique, Hôpital Arnaud de Villeneuve, CHRU de Montpellier, France
| | - Michael Rodrigues
- Université Clermont Auvergne, Laboratoire Microbes Intestin Inflammation et Susceptibilité de l'Hôte (M2iSH), Clermont-Ferrand, France
| | - Nicolas Barnich
- Université Clermont Auvergne, Laboratoire Microbes Intestin Inflammation et Susceptibilité de l'Hôte (M2iSH), Clermont-Ferrand, France
| | - Yannick Bidet
- Université Clermont Auvergne, INSERM, U1240 Imagerie Moléculaire et Stratégies Théranostiques, Clermont Ferrand, France.,Département d'Oncogénétique, Centre Jean Perrin, Clermont-Ferrand, France
| | - Nancy Uhrhammer
- Université Clermont Auvergne, INSERM, U1240 Imagerie Moléculaire et Stratégies Théranostiques, Clermont Ferrand, France.,Département d'Oncogénétique, Centre Jean Perrin, Clermont-Ferrand, France
| | - Yves-Jean Bignon
- Université Clermont Auvergne, INSERM, U1240 Imagerie Moléculaire et Stratégies Théranostiques, Clermont Ferrand, France.,Département d'Oncogénétique, Centre Jean Perrin, Clermont-Ferrand, France
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24
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Leman R, Gaildrat P, Le Gac G, Ka C, Fichou Y, Audrezet MP, Caux-Moncoutier V, Caputo SM, Boutry-Kryza N, Léone M, Mazoyer S, Bonnet-Dorion F, Sevenet N, Guillaud-Bataille M, Rouleau E, Bressac-de Paillerets B, Wappenschmidt B, Rossing M, Muller D, Bourdon V, Revillon F, Parsons MT, Rousselin A, Davy G, Castelain G, Castéra L, Sokolowska J, Coulet F, Delnatte C, Férec C, Spurdle AB, Martins A, Krieger S, Houdayer C. Novel diagnostic tool for prediction of variant spliceogenicity derived from a set of 395 combined in silico/in vitro studies: an international collaborative effort. Nucleic Acids Res 2019; 48:1600-1601. [PMID: 31863589 PMCID: PMC7026662 DOI: 10.1093/nar/gkz1212] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
- Raphaël Leman
- Laboratoire de Biologie Clinique et Oncologique, Centre François Baclesse, 14000 Caen, France.,Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, 76031 Rouen, France.,Normandie Univ, UNICAEN, 14000 Caen, France
| | - Pascaline Gaildrat
- Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, 76031 Rouen, France
| | - Gérald Le Gac
- Inserm UMR1078, Genetics, Functional Genomics and Biotechnology, Université de Bretagne Occidentale, 29200 Brest, France
| | - Chandran Ka
- Inserm UMR1078, Genetics, Functional Genomics and Biotechnology, Université de Bretagne Occidentale, 29200 Brest, France
| | - Yann Fichou
- Inserm UMR1078, Genetics, Functional Genomics and Biotechnology, Université de Bretagne Occidentale, 29200 Brest, France
| | - Marie-Pierre Audrezet
- Inserm UMR1078, Genetics, Functional Genomics and Biotechnology, Université de Bretagne Occidentale, 29200 Brest, France
| | - Virginie Caux-Moncoutier
- Inserm U830, Institut Curie Centre de Recherches, 75005 Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, 75005 Paris, France.,Service de Génétique, Institut Curie, 75005 Paris, France
| | | | - Nadia Boutry-Kryza
- Unité Mixte de Génétique Constitutionnelle des Cancers Fréquents, Hospices Civils de Lyon, 69000 Lyon, France
| | - Mélanie Léone
- Unité Mixte de Génétique Constitutionnelle des Cancers Fréquents, Hospices Civils de Lyon, 69000 Lyon, France
| | - Sylvie Mazoyer
- Lyon Neuroscience Research Center-CRNL, Inserm U1028, CNRS UMR 5292, University of Lyon, 69008 Lyon, France
| | - Françoise Bonnet-Dorion
- Inserm U916, Département de Pathologie, Laboratoire de Génétique Constitutionnelle, Institut Bergonié, 33000 Bordeaux, France
| | - Nicolas Sevenet
- Inserm U916, Département de Pathologie, Laboratoire de Génétique Constitutionnelle, Institut Bergonié, 33000 Bordeaux, France
| | | | - Etienne Rouleau
- Gustave Roussy, Université Paris-Saclay, Département de Biopathologie, 94805 Villejuif, France
| | | | - Barbara Wappenschmidt
- Division of Molecular Gynaeco-Oncology, Department of Gynaecology and Obstetrics, University Hospital of Cologne, 50937 Cologne, Germany
| | - Maria Rossing
- Centre for Genomic Medicine, Rigshospitalet, University of Copenhagen, 1017 Copenhagen, Denmark
| | - Danielle Muller
- Laboratoire d'Oncogénétique, Centre Paul Strauss, 67000 Strasbourg, France
| | - Violaine Bourdon
- Laboratoire d'Oncogénétique Moléculaire, Institut Paoli-Calmettes, 13009 Marseille, France
| | - Françoise Revillon
- Laboratoire d'Oncogénétique Moléculaire Humaine, Centre Oscar Lambret, 59000 Lille, France
| | - Michael T Parsons
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, 4006 Herston, Queensland, Australia
| | - Antoine Rousselin
- Laboratoire de Biologie Clinique et Oncologique, Centre François Baclesse, 14000 Caen, France.,Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, 76031 Rouen, France
| | - Grégoire Davy
- Laboratoire de Biologie Clinique et Oncologique, Centre François Baclesse, 14000 Caen, France.,Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, 76031 Rouen, France
| | - Gaia Castelain
- Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, 76031 Rouen, France
| | - Laurent Castéra
- Laboratoire de Biologie Clinique et Oncologique, Centre François Baclesse, 14000 Caen, France.,Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, 76031 Rouen, France
| | | | - Florence Coulet
- Service de génétique, Hôpital Pitié Salpétrière, AP-HP, 75013 Paris, France
| | - Capucine Delnatte
- Laboratoire de génétique moléculaire, CHU Nantes, 44000 Nantes, France
| | - Claude Férec
- Inserm UMR1078, Genetics, Functional Genomics and Biotechnology, Université de Bretagne Occidentale, 29200 Brest, France
| | - Amanda B Spurdle
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, 4006 Herston, Queensland, Australia
| | - Alexandra Martins
- Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, 76031 Rouen, France
| | - Sophie Krieger
- Laboratoire de Biologie Clinique et Oncologique, Centre François Baclesse, 14000 Caen, France.,Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, 76031 Rouen, France.,Normandie Univ, UNICAEN, 14000 Caen, France
| | - Claude Houdayer
- Inserm U830, Institut Curie Centre de Recherches, 75005 Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, 75005 Paris, France.,Service de Génétique, Institut Curie, 75005 Paris, France
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25
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Parsons MT, Tudini E, Li H, Hahnen E, Wappenschmidt B, Feliubadaló L, Aalfs CM, Agata S, Aittomäki K, Alducci E, Alonso‐Cerezo MC, Arnold N, Auber B, Austin R, Azzollini J, Balmaña J, Barbieri E, Bartram CR, Blanco A, Blümcke B, Bonache S, Bonanni B, Borg Å, Bortesi B, Brunet J, Bruzzone C, Bucksch K, Cagnoli G, Caldés T, Caliebe A, Caligo MA, Calvello M, Capone GL, Caputo SM, Carnevali I, Carrasco E, Caux‐Moncoutier V, Cavalli P, Cini G, Clarke EM, Concolino P, Cops EJ, Cortesi L, Couch FJ, Darder E, de la Hoya M, Dean M, Debatin I, Del Valle J, Delnatte C, Derive N, Diez O, Ditsch N, Domchek SM, Dutrannoy V, Eccles DM, Ehrencrona H, Enders U, Evans DG, Farra C, Faust U, Felbor U, Feroce I, Fine M, Foulkes WD, Galvao HC, Gambino G, Gehrig A, Gensini F, Gerdes A, Germani A, Giesecke J, Gismondi V, Gómez C, Gómez Garcia EB, González S, Grau E, Grill S, Gross E, Guerrieri‐Gonzaga A, Guillaud‐Bataille M, Gutiérrez‐Enríquez S, Haaf T, Hackmann K, Hansen TV, Harris M, Hauke J, Heinrich T, Hellebrand H, Herold KN, Honisch E, Horvath J, Houdayer C, Hübbel V, Iglesias S, Izquierdo A, James PA, Janssen LA, Jeschke U, Kaulfuß S, Keupp K, Kiechle M, Kölbl A, Krieger S, Kruse TA, Kvist A, Lalloo F, Larsen M, Lattimore VL, Lautrup C, Ledig S, Leinert E, Lewis AL, Lim J, Loeffler M, López‐Fernández A, Lucci‐Cordisco E, Maass N, Manoukian S, Marabelli M, Matricardi L, Meindl A, Michelli RD, Moghadasi S, Moles‐Fernández A, Montagna M, Montalban G, Monteiro AN, Montes E, Mori L, Moserle L, Müller CR, Mundhenke C, Naldi N, Nathanson KL, Navarro M, Nevanlinna H, Nichols CB, Niederacher D, Nielsen HR, Ong K, Pachter N, Palmero EI, Papi L, Pedersen IS, Peissel B, Perez‐Segura P, Pfeifer K, Pineda M, Pohl‐Rescigno E, Poplawski NK, Porfirio B, Quante AS, Ramser J, Reis RM, Revillion F, Rhiem K, Riboli B, Ritter J, Rivera D, Rofes P, Rump A, Salinas M, Sánchez de Abajo AM, Schmidt G, Schoenwiese U, Seggewiß J, Solanes A, Steinemann D, Stiller M, Stoppa‐Lyonnet D, Sullivan KJ, Susman R, Sutter C, Tavtigian SV, Teo SH, Teulé A, Thomassen M, Tibiletti MG, Tischkowitz M, Tognazzo S, Toland AE, Tornero E, Törngren T, Torres‐Esquius S, Toss A, Trainer AH, Tucker KM, van Asperen CJ, van Mackelenbergh MT, Varesco L, Vargas‐Parra G, Varon R, Vega A, Velasco Á, Vesper A, Viel A, Vreeswijk MPG, Wagner SA, Waha A, Walker LC, Walters RJ, Wang‐Gohrke S, Weber BHF, Weichert W, Wieland K, Wiesmüller L, Witzel I, Wöckel A, Woodward ER, Zachariae S, Zampiga V, Zeder‐Göß C, Investigators KC, Lázaro C, De Nicolo A, Radice P, Engel C, Schmutzler RK, Goldgar DE, Spurdle AB. Large scale multifactorial likelihood quantitative analysis of BRCA1 and BRCA2 variants: An ENIGMA resource to support clinical variant classification. Hum Mutat 2019; 40:1557-1578. [PMID: 31131967 PMCID: PMC6772163 DOI: 10.1002/humu.23818] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 05/08/2019] [Accepted: 05/12/2019] [Indexed: 12/24/2022]
Abstract
The multifactorial likelihood analysis method has demonstrated utility for quantitative assessment of variant pathogenicity for multiple cancer syndrome genes. Independent data types currently incorporated in the model for assessing BRCA1 and BRCA2 variants include clinically calibrated prior probability of pathogenicity based on variant location and bioinformatic prediction of variant effect, co-segregation, family cancer history profile, co-occurrence with a pathogenic variant in the same gene, breast tumor pathology, and case-control information. Research and clinical data for multifactorial likelihood analysis were collated for 1,395 BRCA1/2 predominantly intronic and missense variants, enabling classification based on posterior probability of pathogenicity for 734 variants: 447 variants were classified as (likely) benign, and 94 as (likely) pathogenic; and 248 classifications were new or considerably altered relative to ClinVar submissions. Classifications were compared with information not yet included in the likelihood model, and evidence strengths aligned to those recommended for ACMG/AMP classification codes. Altered mRNA splicing or function relative to known nonpathogenic variant controls were moderately to strongly predictive of variant pathogenicity. Variant absence in population datasets provided supporting evidence for variant pathogenicity. These findings have direct relevance for BRCA1 and BRCA2 variant evaluation, and justify the need for gene-specific calibration of evidence types used for variant classification.
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Affiliation(s)
- Michael T. Parsons
- Department of Genetics and Computational BiologyQIMR Berghofer Medical Research InstituteBrisbaneQueenslandAustralia
| | - Emma Tudini
- Department of Genetics and Computational BiologyQIMR Berghofer Medical Research InstituteBrisbaneQueenslandAustralia
| | - Hongyan Li
- Cancer Control and Population Science, Huntsman Cancer InstituteUniversity of UtahSalt Lake CityUtah
| | - Eric Hahnen
- Center for Familial Breast and Ovarian Cancer, Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
- Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
| | - Barbara Wappenschmidt
- Center for Familial Breast and Ovarian Cancer, Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
- Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
| | - Lidia Feliubadaló
- Hereditary Cancer Program, ONCOBELL‐IDIBELL‐IDIBGI‐IGTP, Catalan Institute of OncologyCIBERONCBarcelonaSpain
| | - Cora M. Aalfs
- Department of Clinical GeneticsAmsterdam UMCAmsterdamThe Netherlands
| | - Simona Agata
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOVIRCCSPaduaItaly
| | - Kristiina Aittomäki
- Department of Clinical Genetics, Helsinki University HospitalUniversity of HelsinkiHelsinkiFinland
| | - Elisa Alducci
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOVIRCCSPaduaItaly
| | | | - Norbert Arnold
- Department of Gynaecology and Obstetrics, University Hospital of Schleswig‐Holstein, Campus KielChristian‐Albrechts University KielKielGermany
- Institute of Clinical Molecular Biology, University Hospital of Schleswig‐Holstein, Campus KielChristian‐Albrechts University KielKielGermany
| | - Bernd Auber
- Institute of Human GeneticsHannover Medical SchoolHannoverGermany
| | - Rachel Austin
- Genetic Health QueenslandRoyal Brisbane and Women's HospitalBrisbaneAustralia
| | - Jacopo Azzollini
- Unit of Medical Genetics, Department of Medical Oncology and HematologyFondazione IRCCS Istituto Nazionale dei Tumori di MilanoMilanItaly
| | - Judith Balmaña
- High Risk and Cancer Prevention GroupVall d'Hebron Institute of OncologyBarcelonaSpain
- Department of Medical OncologyUniversity Hospital of Vall d'HebronBarcelonaSpain
| | - Elena Barbieri
- Department of Oncology and HaematologyUniversity of Modena and Reggio EmiliaModenaItaly
| | - Claus R. Bartram
- Institute of Human GeneticsUniversity Hospital HeidelbergHeidelbergGermany
| | - Ana Blanco
- Fundación Pública galega Medicina Xenómica‐SERGASGrupo de Medicina Xenómica‐USC, CIBERER, IDISSantiago de CompostelaSpain
| | - Britta Blümcke
- Center for Familial Breast and Ovarian Cancer, Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
- Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
| | - Sandra Bonache
- Oncogenetics GroupVall d'Hebron Institute of Oncology (VHIO)BarcelonaSpain
| | - Bernardo Bonanni
- Division of Cancer Prevention and Genetics, IEOEuropean Institute of Oncology IRCCSMilanItaly
| | - Åke Borg
- Division of Oncology and Pathology, Department of Clinical Sciences LundLund UniversityLundSweden
| | | | - Joan Brunet
- Hereditary Cancer Program, ONCOBELL‐IDIBELL‐IDIBGI‐IGTP, Catalan Institute of OncologyCIBERONCBarcelonaSpain
| | - Carla Bruzzone
- Unit of Hereditary CancerIRCCS Ospedale Policlinico San MartinoGenoaItaly
| | - Karolin Bucksch
- Institute for Medical Informatics, Statistics and EpidemiologyUniversity of LeipzigLeipzigGermany
| | - Giulia Cagnoli
- Unit of Medical Genetics, Department of Medical Oncology and HematologyFondazione IRCCS Istituto Nazionale dei Tumori di MilanoMilanItaly
| | - Trinidad Caldés
- Molecular Oncology Laboratory, CIBERONC, Hospital Clinico San CarlosIdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos)MadridSpain
| | - Almuth Caliebe
- Institute of Human Genetics, University Hospital of Schleswig‐Holstein, Campus KielChristian‐Albrechts University KielKielGermany
| | | | - Mariarosaria Calvello
- Division of Cancer Prevention and Genetics, IEOEuropean Institute of Oncology IRCCSMilanItaly
| | - Gabriele L. Capone
- Department of Experimental and Clinical Biomedical Sciences 'Mario Serio', Medical Genetics UnitUniversity of FlorenceFlorenceItaly
| | - Sandrine M. Caputo
- Service de GénétiqueInstitut CurieParisFrance
- Paris Sciences Lettres Research UniversityParisFrance
| | - Ileana Carnevali
- UO Anatomia PatologicaOspedale di Circolo ASST SettelaghiVareseItaly
| | - Estela Carrasco
- High Risk and Cancer Prevention GroupVall d'Hebron Institute of OncologyBarcelonaSpain
| | | | | | - Giulia Cini
- Division of Functional Onco‐genomics and Genetics, Centro di Riferimento Oncologico di Aviano (CRO)IRCCSAvianoItaly
| | - Edward M. Clarke
- Department of Genetics and Computational BiologyQIMR Berghofer Medical Research InstituteBrisbaneQueenslandAustralia
| | - Paola Concolino
- Fondazione Policlinico Universitario A.GemelliIRCCSRomeItaly
| | - Elisa J. Cops
- Parkville Familial Cancer CentrePeter MacCallum Cancer CenterMelbourneVictoriaAustralia
| | - Laura Cortesi
- Department of Oncology and HaematologyUniversity of Modena and Reggio EmiliaModenaItaly
| | - Fergus J. Couch
- Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesota
| | - Esther Darder
- Hereditary Cancer Program, ONCOBELL‐IDIBELL‐IDIBGI‐IGTP, Catalan Institute of OncologyCIBERONCBarcelonaSpain
| | - Miguel de la Hoya
- Molecular Oncology Laboratory, CIBERONC, Hospital Clinico San CarlosIdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos)MadridSpain
| | - Michael Dean
- Laboratory of Translational Genomics, DCEGNational Cancer InstituteGaithersburgMaryland
| | - Irmgard Debatin
- Institute of Human GeneticsUniversity Hospital UlmUlmGermany
| | - Jesús Del Valle
- Hereditary Cancer Program, ONCOBELL‐IDIBELL‐IDIBGI‐IGTP, Catalan Institute of OncologyCIBERONCBarcelonaSpain
| | | | - Nicolas Derive
- Service de GénétiqueInstitut CurieParisFrance
- Paris Sciences Lettres Research UniversityParisFrance
| | - Orland Diez
- Oncogenetics GroupVall d'Hebron Institute of Oncology (VHIO)BarcelonaSpain
- Clinical and Molecular Genetics AreaUniversity Hospital Vall d'HebronBarcelonaSpain
| | - Nina Ditsch
- Department of Gynecology and ObstetricsUniversity of MunichMunichGermany
| | - Susan M. Domchek
- Basser Center for BRCA, Abramson Cancer CenterUniversity of PennsylvaniaPhiladelphiaPennsylvania
| | - Véronique Dutrannoy
- Institute of Medical and Human GeneticsCharité –Universitätsmedizin BerlinBerlinGermany
| | | | - Hans Ehrencrona
- Department of Clinical Genetics and Pathology, Laboratory MedicineOffice for Medical Services ‐ Region SkåneLundSweden
- Division of Clinical Genetics, Department of Laboratory MedicineLund UniversityLundSweden
| | - Ute Enders
- Institute for Medical Informatics, Statistics and EpidemiologyUniversity of LeipzigLeipzigGermany
| | - D. Gareth Evans
- Genomic Medicine, Division of Evolution and Genomic Sciences, The University of Manchester, Manchester Academic Health Science Centre, Manchester Universities Foundation TrustSt. Mary's HospitalManchesterUK
- Genomic Medicine, North West Genomics hub, Manchester Academic Health Science Centre, Manchester Universities Foundation TrustSt. Mary's HospitalManchesterUK
| | - Chantal Farra
- Medical GeneticsAmerican University of Beirut Medical CenterBeirutLebanon
| | - Ulrike Faust
- Institute of Medical Genetics and Applied GenomicsUniversity of TübingenTübingenGermany
| | - Ute Felbor
- Institute of Human GeneticsUniversity Medicine GreifswaldGreifswaldGermany
| | - Irene Feroce
- Division of Cancer Prevention and Genetics, IEOEuropean Institute of Oncology IRCCSMilanItaly
| | - Miriam Fine
- Adult Genetics UnitRoyal Adelaide HospitalAdelaideAustralia
| | - William D. Foulkes
- Program in Cancer Genetics, Departments of Human Genetics and OncologyMcGill UniversityMontréalQCCanada
| | | | | | - Andrea Gehrig
- Department of Human GeneticsUniversity of WürzburgWürzburgGermany
| | - Francesca Gensini
- Department of Experimental and Clinical Biomedical Sciences 'Mario Serio', Medical Genetics UnitUniversity of FlorenceFlorenceItaly
| | - Anne‐Marie Gerdes
- Department of Clinical Genetics, RigshospitaletCopenhagen University HospitalCopenhagenDenmark
| | - Aldo Germani
- Department of Clinical and Molecular Medicine, Sant'Andrea University HospitalSapienza UniversityRomeItaly
| | - Jutta Giesecke
- Center for Familial Breast and Ovarian Cancer, Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
- Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
| | - Viviana Gismondi
- Unit of Hereditary CancerIRCCS Ospedale Policlinico San MartinoGenoaItaly
| | - Carolina Gómez
- Hereditary Cancer Program, ONCOBELL‐IDIBELL‐IDIBGI‐IGTP, Catalan Institute of OncologyCIBERONCBarcelonaSpain
| | - Encarna B. Gómez Garcia
- Department of Clinical GeneticsMaastricht University Medical CenterMaastrichtThe Netherlands
| | - Sara González
- Hereditary Cancer Program, ONCOBELL‐IDIBELL‐IDIBGI‐IGTP, Catalan Institute of OncologyCIBERONCBarcelonaSpain
| | - Elia Grau
- Hereditary Cancer Program, ONCOBELL‐IDIBELL‐IDIBGI‐IGTP, Catalan Institute of OncologyCIBERONCBarcelonaSpain
| | - Sabine Grill
- Division of Gynaecology and Obstetrics, Klinikum rechts der Isar der TechnischenUniversität MünchenMunichGermany
| | - Eva Gross
- Department of Gynecology and ObstetricsUniversity of MunichMunichGermany
| | | | | | | | - Thomas Haaf
- Department of Human GeneticsUniversity of WürzburgWürzburgGermany
| | - Karl Hackmann
- Institute for Clinical Genetics, Faculty of Medicine Carl Gustav CarusTU DresdenDresdenGermany
| | - Thomas V.O. Hansen
- Department of Clinical Genetics, RigshospitaletCopenhagen University HospitalCopenhagenDenmark
| | | | - Jan Hauke
- Center for Familial Breast and Ovarian Cancer, Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
- Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
| | - Tilman Heinrich
- Institute of Medical Genetics and Applied GenomicsUniversity of TübingenTübingenGermany
| | - Heide Hellebrand
- Division of Gynaecology and Obstetrics, Klinikum rechts der Isar der TechnischenUniversität MünchenMunichGermany
| | | | - Ellen Honisch
- Department of Gynecology and Obstetrics, University Hospital DüsseldorfHeinrich‐Heine University DüsseldorfDüsseldorfGermany
| | - Judit Horvath
- Institute of Human GeneticsUniversity of MünsterMünsterGermany
| | - Claude Houdayer
- Department of Genetics, F76000 and Normandy University, UNIROUEN, Inserm U1245, Normandy Centre for Genomic and Personalized MedicineRouen University HospitalRouenFrance
| | - Verena Hübbel
- Center for Familial Breast and Ovarian Cancer, Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
- Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
| | - Silvia Iglesias
- Hereditary Cancer Program, ONCOBELL‐IDIBELL‐IDIBGI‐IGTP, Catalan Institute of OncologyCIBERONCBarcelonaSpain
| | - Angel Izquierdo
- Hereditary Cancer Program, ONCOBELL‐IDIBELL‐IDIBGI‐IGTP, Catalan Institute of OncologyCIBERONCBarcelonaSpain
| | - Paul A. James
- Parkville Familial Cancer CentrePeter MacCallum Cancer CenterMelbourneVictoriaAustralia
- Sir Peter MacCallum Department of OncologyThe University of MelbourneMelbourneVictoriaAustralia
| | - Linda A.M. Janssen
- Department of Clinical GeneticsLeiden University Medical CenterLeidenThe Netherlands
| | - Udo Jeschke
- Department of Gynecology and ObstetricsUniversity of MunichMunichGermany
| | - Silke Kaulfuß
- Institute of Human GeneticsUniversity Medical Center GöttingenGöttingenGermany
| | - Katharina Keupp
- Center for Familial Breast and Ovarian Cancer, Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
- Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
| | - Marion Kiechle
- Division of Gynaecology and Obstetrics, Klinikum rechts der Isar der TechnischenUniversität MünchenMunichGermany
| | - Alexandra Kölbl
- Department of Gynecology and ObstetricsUniversity of MunichMunichGermany
| | - Sophie Krieger
- Laboratoire de Biologie Clinique et OncologiqueCentre Francois BaclesseCaenFrance
- Genomics and Personalized Medecine in Cancer and Neurological DisordersNormandy Centre for Genomic and Personalized MedicineRouenFrance
- Normandie UniversitéUNICAENCaenFrance
| | - Torben A. Kruse
- Department of Clinical GeneticsOdense University HospitalOdense CDenmark
| | - Anders Kvist
- Division of Oncology and Pathology, Department of Clinical Sciences LundLund UniversityLundSweden
| | - Fiona Lalloo
- Genomic Medicine, North West Genomics hub, Manchester Academic Health Science Centre, Manchester Universities Foundation TrustSt. Mary's HospitalManchesterUK
| | - Mirjam Larsen
- Center for Familial Breast and Ovarian Cancer, Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
- Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
| | - Vanessa L. Lattimore
- Department of Pathology and Biomedical ScienceUniversity of OtagoChristchurchNew Zealand
| | - Charlotte Lautrup
- Department of Clinical GeneticsAalborg University HospitalAalborgDenmark
- Clinical Cancer Research CenterAalborg University HospitalAalborgDenmark
| | - Susanne Ledig
- Institute of Human GeneticsUniversity of MünsterMünsterGermany
| | - Elena Leinert
- Department of Gynaecology and ObstetricsUniversity Hospital UlmUlmGermany
| | | | - Joanna Lim
- Breast Cancer Research ProgrammeCancer Research MalaysiaSubang JayaSelangorMalaysia
| | - Markus Loeffler
- Institute for Medical Informatics, Statistics and EpidemiologyUniversity of LeipzigLeipzigGermany
| | - Adrià López‐Fernández
- High Risk and Cancer Prevention GroupVall d'Hebron Institute of OncologyBarcelonaSpain
| | - Emanuela Lucci‐Cordisco
- UOC Genetica Medica, Fondazione Policlinico Universitario A.Gemelli IRCCS and Istituto di Medicina GenomicaUniversità Cattolica del Sacro CuoreRomeItaly
| | - Nicolai Maass
- Department of Gynaecology and Obstetrics, University Hospital of Schleswig‐Holstein, Campus KielChristian‐Albrechts University KielKielGermany
| | - Siranoush Manoukian
- Unit of Medical Genetics, Department of Medical Oncology and HematologyFondazione IRCCS Istituto Nazionale dei Tumori di MilanoMilanItaly
| | - Monica Marabelli
- Division of Cancer Prevention and Genetics, IEOEuropean Institute of Oncology IRCCSMilanItaly
| | - Laura Matricardi
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOVIRCCSPaduaItaly
| | - Alfons Meindl
- Department of Gynecology and ObstetricsUniversity of MunichMunichGermany
| | | | - Setareh Moghadasi
- Department of Clinical GeneticsLeiden University Medical CenterLeidenThe Netherlands
| | | | - Marco Montagna
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOVIRCCSPaduaItaly
| | - Gemma Montalban
- Oncogenetics GroupVall d'Hebron Institute of Oncology (VHIO)BarcelonaSpain
| | | | - Eva Montes
- Hereditary Cancer Program, ONCOBELL‐IDIBELL‐IDIBGI‐IGTP, Catalan Institute of OncologyCIBERONCBarcelonaSpain
| | - Luigi Mori
- Department of Clinical and Experimental Science, University of Brescia c/o 2nd Internal MedicineHospital of BresciaBresciaItaly
| | - Lidia Moserle
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOVIRCCSPaduaItaly
| | | | - Christoph Mundhenke
- Department of Gynaecology and Obstetrics, University Hospital of Schleswig‐Holstein, Campus KielChristian‐Albrechts University KielKielGermany
| | - Nadia Naldi
- Division of OncologyUniversity Hospital of ParmaParmaItaly
| | - Katherine L. Nathanson
- Basser Center for BRCA, Abramson Cancer CenterUniversity of PennsylvaniaPhiladelphiaPennsylvania
| | - Matilde Navarro
- Hereditary Cancer Program, ONCOBELL‐IDIBELL‐IDIBGI‐IGTP, Catalan Institute of OncologyCIBERONCBarcelonaSpain
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, Helsinki University HospitalUniversity of HelsinkiHelsinkiFinland
| | - Cassandra B. Nichols
- Genetic Services of Western AustraliaKing Edward Memorial HospitalPerthAustralia
| | - Dieter Niederacher
- Department of Gynecology and Obstetrics, University Hospital DüsseldorfHeinrich‐Heine University DüsseldorfDüsseldorfGermany
| | | | - Kai‐ren Ong
- West Midlands Regional Genetics ServiceBirmingham Women's Hospital Healthcare NHS TrustBirminghamUK
| | - Nicholas Pachter
- Genetic Services of Western AustraliaKing Edward Memorial HospitalPerthAustralia
- Faculty of Health and Medical SciencesUniversity of Western AustraliaPerthAustralia
| | - Edenir I. Palmero
- Molecular Oncology Research CenterBarretos Cancer HospitalSão PauloBrazil
- Barretos School of Health SciencesDr. Paulo Prata ‐ FACISBSão PauloBrazil
| | - Laura Papi
- Department of Experimental and Clinical Biomedical Sciences 'Mario Serio', Medical Genetics UnitUniversity of FlorenceFlorenceItaly
| | - Inge Sokilde Pedersen
- Clinical Cancer Research CenterAalborg University HospitalAalborgDenmark
- Molecular DiagnosticsAalborg University HospitalAalborgDenmark
- Department of Clinical MedicineAalborg UniversityAalborgDenmark
| | - Bernard Peissel
- Unit of Medical Genetics, Department of Medical Oncology and HematologyFondazione IRCCS Istituto Nazionale dei Tumori di MilanoMilanItaly
| | - Pedro Perez‐Segura
- Molecular Oncology Laboratory, CIBERONC, Hospital Clinico San CarlosIdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos)MadridSpain
| | - Katharina Pfeifer
- Division of Gynaecology and Obstetrics, Klinikum rechts der Isar der TechnischenUniversität MünchenMunichGermany
| | - Marta Pineda
- Hereditary Cancer Program, ONCOBELL‐IDIBELL‐IDIBGI‐IGTP, Catalan Institute of OncologyCIBERONCBarcelonaSpain
| | - Esther Pohl‐Rescigno
- Center for Familial Breast and Ovarian Cancer, Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
- Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
| | - Nicola K. Poplawski
- Adult Genetics UnitRoyal Adelaide HospitalAdelaideAustralia
- School of Paediatrics and Reproductive HealthUniversity of AdelaideAdelaideAustralia
| | - Berardino Porfirio
- Department of Experimental and Clinical Biomedical Sciences 'Mario Serio', Medical Genetics UnitUniversity of FlorenceFlorenceItaly
| | - Anne S. Quante
- Division of Gynaecology and Obstetrics, Klinikum rechts der Isar der TechnischenUniversität MünchenMunichGermany
| | - Juliane Ramser
- Division of Gynaecology and Obstetrics, Klinikum rechts der Isar der TechnischenUniversität MünchenMunichGermany
| | - Rui M. Reis
- Molecular Oncology Research CenterBarretos Cancer HospitalSão PauloBrazil
- Health Sciences SchoolUniversity of MinhoBragaPortugal
- ICVS/3B's‐PT Government Associate LaboratoryBragaPortugal
| | - Françoise Revillion
- Laboratoire d'Oncogenetique Moleculaire HumaineCentre Oscar LambretLilleFrance
| | - Kerstin Rhiem
- Center for Familial Breast and Ovarian Cancer, Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
- Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
| | | | - Julia Ritter
- Institute of Medical and Human GeneticsCharité –Universitätsmedizin BerlinBerlinGermany
| | - Daniela Rivera
- Unit of Hereditary CancerIRCCS Ospedale Policlinico San MartinoGenoaItaly
| | - Paula Rofes
- Hereditary Cancer Program, ONCOBELL‐IDIBELL‐IDIBGI‐IGTP, Catalan Institute of OncologyCIBERONCBarcelonaSpain
| | - Andreas Rump
- Institute for Clinical Genetics, Faculty of Medicine Carl Gustav CarusTU DresdenDresdenGermany
| | - Monica Salinas
- Hereditary Cancer Program, ONCOBELL‐IDIBELL‐IDIBGI‐IGTP, Catalan Institute of OncologyCIBERONCBarcelonaSpain
| | - Ana María Sánchez de Abajo
- Servicio de Análisis Clínicos y Bioquímica Clínica, Complejo HospitalarioUniversitario Insular Materno‐Infantil de Gran CanariaLas Palmas de Gran CanaríaSpain
| | - Gunnar Schmidt
- Institute of Human GeneticsHannover Medical SchoolHannoverGermany
| | - Ulrike Schoenwiese
- Institute for Medical Informatics, Statistics and EpidemiologyUniversity of LeipzigLeipzigGermany
| | - Jochen Seggewiß
- Institute of Human GeneticsUniversity of MünsterMünsterGermany
| | - Ares Solanes
- Hereditary Cancer Program, ONCOBELL‐IDIBELL‐IDIBGI‐IGTP, Catalan Institute of OncologyCIBERONCBarcelonaSpain
| | - Doris Steinemann
- Institute of Human GeneticsHannover Medical SchoolHannoverGermany
| | - Mathias Stiller
- Institute of Human GeneticsUniversity Hospital LeipzigLeipzigGermany
| | - Dominique Stoppa‐Lyonnet
- Service de GénétiqueInstitut CurieParisFrance
- Department of Tumour BiologyINSERM U830ParisFrance
- Université Paris DescartesParisFrance
| | - Kelly J. Sullivan
- Genetic Health Service NZ‐ Northern HubAuckland District Health BoardAucklandNew Zealand
| | - Rachel Susman
- Genetic Health QueenslandRoyal Brisbane and Women's HospitalBrisbaneAustralia
| | - Christian Sutter
- Institute of Human GeneticsUniversity Hospital HeidelbergHeidelbergGermany
| | - Sean V. Tavtigian
- Department of Oncological ServicesUniversity of Utah School of MedicineSalt Lake CityUtah
- Huntsman Cancer InstituteUniversity of UtahSalt Lake CityUtah
| | - Soo H. Teo
- Breast Cancer Research ProgrammeCancer Research MalaysiaSubang JayaSelangorMalaysia
- Department of Surgery, Faculty of MedicineUniversity MalayaKuala LumpurMalaysia
| | - Alex Teulé
- Hereditary Cancer Program, ONCOBELL‐IDIBELL‐IDIBGI‐IGTP, Catalan Institute of OncologyCIBERONCBarcelonaSpain
| | - Mads Thomassen
- Department of Clinical GeneticsOdense University HospitalOdense CDenmark
| | | | - Marc Tischkowitz
- Department of Medical GeneticsUniversity of CambridgeCambridgeUK
| | - Silvia Tognazzo
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOVIRCCSPaduaItaly
| | - Amanda E. Toland
- Department of Cancer Biology and GeneticsThe Ohio State UniversityColumbusOhio
| | - Eva Tornero
- Hereditary Cancer Program, ONCOBELL‐IDIBELL‐IDIBGI‐IGTP, Catalan Institute of OncologyCIBERONCBarcelonaSpain
| | - Therese Törngren
- Division of Oncology and Pathology, Department of Clinical Sciences LundLund UniversityLundSweden
| | - Sara Torres‐Esquius
- High Risk and Cancer Prevention GroupVall d'Hebron Institute of OncologyBarcelonaSpain
| | - Angela Toss
- Department of Oncology and HaematologyUniversity of Modena and Reggio EmiliaModenaItaly
| | - Alison H. Trainer
- Parkville Familial Cancer CentrePeter MacCallum Cancer CenterMelbourneVictoriaAustralia
- Department of medicineUniversity of MelbourneMelbourneVictoriaAustralia
| | - Katherine M. Tucker
- Prince of Wales Clinical SchoolUniversity of NSWSydneyNew South WalesAustralia
- Hereditary Cancer Clinic, Department of Medical OncologyPrince of Wales HospitalRandwickNew South WalesAustralia
| | | | - Marion T. van Mackelenbergh
- Department of Gynaecology and Obstetrics, University Hospital of Schleswig‐Holstein, Campus KielChristian‐Albrechts University KielKielGermany
| | - Liliana Varesco
- Unit of Hereditary CancerIRCCS Ospedale Policlinico San MartinoGenoaItaly
| | - Gardenia Vargas‐Parra
- Hereditary Cancer Program, ONCOBELL‐IDIBELL‐IDIBGI‐IGTP, Catalan Institute of OncologyCIBERONCBarcelonaSpain
| | - Raymonda Varon
- Institute of Medical and Human GeneticsCharité –Universitätsmedizin BerlinBerlinGermany
| | - Ana Vega
- Fundación Pública galega Medicina Xenómica‐SERGASGrupo de Medicina Xenómica‐USC, CIBERER, IDISSantiago de CompostelaSpain
| | - Ángela Velasco
- Hereditary Cancer Program, ONCOBELL‐IDIBELL‐IDIBGI‐IGTP, Catalan Institute of OncologyCIBERONCBarcelonaSpain
| | - Anne‐Sophie Vesper
- Department of Gynecology and Obstetrics, University Hospital DüsseldorfHeinrich‐Heine University DüsseldorfDüsseldorfGermany
| | - Alessandra Viel
- Division of Functional Onco‐genomics and Genetics, Centro di Riferimento Oncologico di Aviano (CRO)IRCCSAvianoItaly
| | | | - Sebastian A. Wagner
- Department of MedicineHematology/Oncology, Goethe‐University FrankfurtFrankfurtGermany
| | - Anke Waha
- Center for Familial Breast and Ovarian Cancer, Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
- Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
| | - Logan C. Walker
- Department of Pathology and Biomedical ScienceUniversity of OtagoChristchurchNew Zealand
| | - Rhiannon J. Walters
- Department of Genetics and Computational BiologyQIMR Berghofer Medical Research InstituteBrisbaneQueenslandAustralia
| | - Shan Wang‐Gohrke
- Department of Gynaecology and ObstetricsUniversity Hospital UlmUlmGermany
| | | | - Wilko Weichert
- Institute of PathologyTechnische Universität MünchenMunichGermany
| | - Kerstin Wieland
- Institute for Medical Informatics, Statistics and EpidemiologyUniversity of LeipzigLeipzigGermany
| | - Lisa Wiesmüller
- Department of Gynaecology and ObstetricsUniversity Hospital UlmUlmGermany
| | - Isabell Witzel
- Department of GynecologyUniversity Medical Center HamburgHamburgGermany
| | - Achim Wöckel
- Department of Gynecology and ObstetricsUniversity Hospital WürzburgWürzburgGermany
| | - Emma R. Woodward
- Genomic Medicine, Division of Evolution and Genomic Sciences, The University of Manchester, Manchester Academic Health Science Centre, Manchester Universities Foundation TrustSt. Mary's HospitalManchesterUK
- Genomic Medicine, North West Genomics hub, Manchester Academic Health Science Centre, Manchester Universities Foundation TrustSt. Mary's HospitalManchesterUK
| | - Silke Zachariae
- Institute for Medical Informatics, Statistics and EpidemiologyUniversity of LeipzigLeipzigGermany
| | - Valentina Zampiga
- Biosciences LaboratoryIstituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCSMeldolaItaly
| | | | - KConFab Investigators
- Sir Peter MacCallum Department of OncologyThe University of MelbourneMelbourneVictoriaAustralia
- Research DepartmentPeter MacCallum Cancer CenterMelbourneVictoriaAustralia
| | - Conxi Lázaro
- Hereditary Cancer Program, ONCOBELL‐IDIBELL‐IDIBGI‐IGTP, Catalan Institute of OncologyCIBERONCBarcelonaSpain
| | | | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of ResearchFondazione IRCCS Istituto Nazionale dei Tumori (INT)MilanItaly
| | - Christoph Engel
- Institute for Medical Informatics, Statistics and EpidemiologyUniversity of LeipzigLeipzigGermany
| | - Rita K. Schmutzler
- Center for Familial Breast and Ovarian Cancer, Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
- Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
| | - David E. Goldgar
- Department of Dermatology, Huntsman Cancer InstituteUniversity of Utah School of MedicineSalt Lake CityUtah
| | - Amanda B. Spurdle
- Department of Genetics and Computational BiologyQIMR Berghofer Medical Research InstituteBrisbaneQueenslandAustralia
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Leman R, Gaildrat P, Le Gac G, Ka C, Fichou Y, Audrezet MP, Caux-Moncoutier V, Caputo SM, Boutry-Kryza N, Léone M, Mazoyer S, Bonnet-Dorion F, Sevenet N, Guillaud-Bataille M, Rouleau E, Bressac-de Paillerets B, Wappenschmidt B, Rossing M, Muller D, Bourdon V, Revillon F, Parsons MT, Rousselin A, Davy G, Castelain G, Castéra L, Sokolowska J, Coulet F, Delnatte C, Férec C, Spurdle AB, Martins A, Krieger S, Houdayer C. Novel diagnostic tool for prediction of variant spliceogenicity derived from a set of 395 combined in silico/in vitro studies: an international collaborative effort. Nucleic Acids Res 2019; 46:7913-7923. [PMID: 29750258 PMCID: PMC6125621 DOI: 10.1093/nar/gky372] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 04/27/2018] [Indexed: 12/17/2022] Open
Abstract
Variant interpretation is the key issue in molecular diagnosis. Spliceogenic variants exemplify this issue as each nucleotide variant can be deleterious via disruption or creation of splice site consensus sequences. Consequently, reliable in silico prediction of variant spliceogenicity would be a major improvement. Thanks to an international effort, a set of 395 variants studied at the mRNA level and occurring in 5′ and 3′ consensus regions (defined as the 11 and 14 bases surrounding the exon/intron junction, respectively) was collected for 11 different genes, including BRCA1, BRCA2, CFTR and RHD, and used to train and validate a new prediction protocol named Splicing Prediction in Consensus Elements (SPiCE). SPiCE combines in silico predictions from SpliceSiteFinder-like and MaxEntScan and uses logistic regression to define optimal decision thresholds. It revealed an unprecedented sensitivity and specificity of 99.5 and 95.2%, respectively, and the impact on splicing was correctly predicted for 98.8% of variants. We therefore propose SPiCE as the new tool for predicting variant spliceogenicity. It could be easily implemented in any diagnostic laboratory as a routine decision making tool to help geneticists to face the deluge of variants in the next-generation sequencing era. SPiCE is accessible at (https://sourceforge.net/projects/spicev2-1/).
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Affiliation(s)
- Raphaël Leman
- Laboratoire de Biologie Clinique et Oncologique, Centre François Baclesse, 14000 Caen, France.,Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, 76031 Rouen, France.,Normandie Univ, UNICAEN, 14000 Caen, France
| | - Pascaline Gaildrat
- Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, 76031 Rouen, France
| | - Gérald Le Gac
- Inserm UMR1078, Genetics, Functional Genomics and Biotechnology, Université de Bretagne Occidentale, 29200 Brest, France
| | - Chandran Ka
- Inserm UMR1078, Genetics, Functional Genomics and Biotechnology, Université de Bretagne Occidentale, 29200 Brest, France
| | - Yann Fichou
- Inserm UMR1078, Genetics, Functional Genomics and Biotechnology, Université de Bretagne Occidentale, 29200 Brest, France
| | - Marie-Pierre Audrezet
- Inserm UMR1078, Genetics, Functional Genomics and Biotechnology, Université de Bretagne Occidentale, 29200 Brest, France
| | - Virginie Caux-Moncoutier
- Inserm U830, Institut Curie Centre de Recherches, 75005 Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, 75005 Paris, France.,Service de Génétique, Institut Curie, 75005 Paris, France
| | | | - Nadia Boutry-Kryza
- Unité Mixte de Génétique Constitutionnelle des Cancers Fréquents, Hospices Civils de Lyon, 69000 Lyon, France
| | - Mélanie Léone
- Unité Mixte de Génétique Constitutionnelle des Cancers Fréquents, Hospices Civils de Lyon, 69000 Lyon, France
| | - Sylvie Mazoyer
- Lyon Neuroscience Research Center-CRNL, Inserm U1028, CNRS UMR 5292, University of Lyon, 69008 Lyon, France
| | - Françoise Bonnet-Dorion
- Inserm U916, Département de Pathologie, Laboratoire de Génétique Constitutionnelle, Institut Bergonié, 33000 Bordeaux, France
| | - Nicolas Sevenet
- Inserm U916, Département de Pathologie, Laboratoire de Génétique Constitutionnelle, Institut Bergonié, 33000 Bordeaux, France
| | | | - Etienne Rouleau
- Gustave Roussy, Université Paris-Saclay, Département de Biopathologie, 94805 Villejuif, France
| | | | - Barbara Wappenschmidt
- Division of Molecular Gynaeco-Oncology, Department of Gynaecology and Obstetrics, University Hospital of Cologne, 50937 Cologne, Germany
| | - Maria Rossing
- Centre for Genomic Medicine, Rigshospitalet, University of Copenhagen, 1017 Copenhagen, Denmark
| | - Danielle Muller
- Laboratoire d'Oncogénétique, Centre Paul Strauss, 67000 Strasbourg, France
| | - Violaine Bourdon
- Laboratoire d'Oncogénétique Moléculaire, Institut Paoli-Calmettes, 13009 Marseille, France
| | - Françoise Revillon
- Laboratoire d'Oncogénétique Moléculaire Humaine, Centre Oscar Lambret, 59000 Lille, France
| | - Michael T Parsons
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, 4006 Herston, Queensland, Australia
| | - Antoine Rousselin
- Laboratoire de Biologie Clinique et Oncologique, Centre François Baclesse, 14000 Caen, France.,Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, 76031 Rouen, France
| | - Grégoire Davy
- Laboratoire de Biologie Clinique et Oncologique, Centre François Baclesse, 14000 Caen, France.,Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, 76031 Rouen, France
| | - Gaia Castelain
- Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, 76031 Rouen, France
| | - Laurent Castéra
- Laboratoire de Biologie Clinique et Oncologique, Centre François Baclesse, 14000 Caen, France.,Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, 76031 Rouen, France
| | | | - Florence Coulet
- Service de génétique, Hôpital Pitié Salpétrière, AP-HP, 75013 Paris, France
| | - Capucine Delnatte
- Laboratoire de génétique moléculaire, CHU Nantes, 44000 Nantes, France
| | - Claude Férec
- Inserm UMR1078, Genetics, Functional Genomics and Biotechnology, Université de Bretagne Occidentale, 29200 Brest, France
| | - Amanda B Spurdle
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, 4006 Herston, Queensland, Australia
| | - Alexandra Martins
- Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, 76031 Rouen, France
| | - Sophie Krieger
- Laboratoire de Biologie Clinique et Oncologique, Centre François Baclesse, 14000 Caen, France.,Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, 76031 Rouen, France.,Normandie Univ, UNICAEN, 14000 Caen, France
| | - Claude Houdayer
- Inserm U830, Institut Curie Centre de Recherches, 75005 Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, 75005 Paris, France.,Service de Génétique, Institut Curie, 75005 Paris, France
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27
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Qian F, Wang S, Mitchell J, McGuffog L, Barrowdale D, Leslie G, Oosterwijk JC, Chung WK, Evans DG, Engel C, Kast K, Aalfs CM, Adank MA, Adlard J, Agnarsson BA, Aittomäki K, Alducci E, Andrulis IL, Arun BK, Ausems MGEM, Azzollini J, Barouk-Simonet E, Barwell J, Belotti M, Benitez J, Berger A, Borg A, Bradbury AR, Brunet J, Buys SS, Caldes T, Caligo MA, Campbell I, Caputo SM, Chiquette J, Claes KBM, Margriet Collée J, Couch FJ, Coupier I, Daly MB, Davidson R, Diez O, Domchek SM, Donaldson A, Dorfling CM, Eeles R, Feliubadaló L, Foretova L, Fowler J, Friedman E, Frost D, Ganz PA, Garber J, Garcia-Barberan V, Glendon G, Godwin AK, Gómez Garcia EB, Gronwald J, Hahnen E, Hamann U, Henderson A, Hendricks CB, Hopper JL, Hulick PJ, Imyanitov EN, Isaacs C, Izatt L, Izquierdo Á, Jakubowska A, Kaczmarek K, Kang E, Karlan BY, Kets CM, Kim SW, Kim Z, Kwong A, Laitman Y, Lasset C, Hyuk Lee M, Won Lee J, Lee J, Lester J, Lesueur F, Loud JT, Lubinski J, Mebirouk N, Meijers-Heijboer HEJ, Meindl A, Miller A, Montagna M, Mooij TM, Morrison PJ, Mouret-Fourme E, Nathanson KL, Neuhausen SL, Nevanlinna H, Niederacher D, Nielsen FC, Nussbaum RL, Offit K, Olah E, Ong KR, Ottini L, Park SK, Peterlongo P, Pfeiler G, Phelan CM, Poppe B, Pradhan N, Radice P, Ramus SJ, Rantala J, Robson M, Rodriguez GC, Schmutzler RK, Hutten Selkirk CG, Shah PD, Simard J, Singer CF, Sokolowska J, Stoppa-Lyonnet D, Sutter C, Yen Tan Y, Teixeira RM, Teo SH, Terry MB, Thomassen M, Tischkowitz M, Toland AE, Tucker KM, Tung N, van Asperen CJ, van Engelen K, van Rensburg EJ, Wang-Gohrke S, Wappenschmidt B, Weitzel JN, Yannoukakos D, Greene MH, Rookus MA, Easton DF, Chenevix-Trench G, Antoniou AC, Goldgar DE, Olopade OI, Rebbeck TR, Huo D. Height and Body Mass Index as Modifiers of Breast Cancer Risk in BRCA1/2 Mutation Carriers: A Mendelian Randomization Study. J Natl Cancer Inst 2019; 111:350-364. [PMID: 30312457 PMCID: PMC6449171 DOI: 10.1093/jnci/djy132] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 06/03/2018] [Accepted: 06/29/2018] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND BRCA1/2 mutations confer high lifetime risk of breast cancer, although other factors may modify this risk. Whether height or body mass index (BMI) modifies breast cancer risk in BRCA1/2 mutation carriers remains unclear. METHODS We used Mendelian randomization approaches to evaluate the association of height and BMI on breast cancer risk, using data from the Consortium of Investigators of Modifiers of BRCA1/2 with 14 676 BRCA1 and 7912 BRCA2 mutation carriers, including 11 451 cases of breast cancer. We created a height genetic score using 586 height-associated variants and a BMI genetic score using 93 BMI-associated variants. We examined both observed and genetically determined height and BMI with breast cancer risk using weighted Cox models. All statistical tests were two-sided. RESULTS Observed height was positively associated with breast cancer risk (HR = 1.09 per 10 cm increase, 95% confidence interval [CI] = 1.0 to 1.17; P = 1.17). Height genetic score was positively associated with breast cancer, although this was not statistically significant (per 10 cm increase in genetically predicted height, HR = 1.04, 95% CI = 0.93 to 1.17; P = .47). Observed BMI was inversely associated with breast cancer risk (per 5 kg/m2 increase, HR = 0.94, 95% CI = 0.90 to 0.98; P = .007). BMI genetic score was also inversely associated with breast cancer risk (per 5 kg/m2 increase in genetically predicted BMI, HR = 0.87, 95% CI = 0.76 to 0.98; P = .02). BMI was primarily associated with premenopausal breast cancer. CONCLUSION Height is associated with overall breast cancer and BMI is associated with premenopausal breast cancer in BRCA1/2 mutation carriers. Incorporating height and BMI, particularly genetic score, into risk assessment may improve cancer management.
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Affiliation(s)
- Frank Qian
- Department of Medicine, The University of Chicago, Chicago, IL
| | - Shengfeng Wang
- Center for Clinical Cancer Genetics, The University of Chicago, Chicago, IL
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing, China
| | - Jonathan Mitchell
- Division of Gastroenterology, Department of Hepatology and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Lesley McGuffog
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Daniel Barrowdale
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Goska Leslie
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Jan C Oosterwijk
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University, New York, NY
| | - D Gareth Evans
- Division of Evolution and Genomic Sciences, Genomic Medicine, Manchester Academic Health Sciences Centre, University of Manchester, Central Manchester University Hospitals, NHS Foundation Trust, Manchester, 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
| | - Karin Kast
- Department of Gynecology and Obstetrics, Technical University of Dresden, Dresden, Germany
- Department of Clinical Genetics and GROW, School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Cora M Aalfs
- Department of Clinical Genetics, Academic Medical Center, Amsterdam, the Netherlands
- Center for Medical Genetics, NorthShore University HealthSystem, Evanston, IL
- The University of Chicago Pritzker School of Medicine, Chicago, IL
| | - Muriel A Adank
- Family Cancer Clinic, Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Julian Adlard
- Yorkshire Regional Genetics Service, Chapel Allerton Hospital, Leeds, UK
- Department of Clinical Genetics and GROW, School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Bjarni A Agnarsson
- Department of Pathology, National Institute of Oncology, Budapest, Hungary
- School of Medicine, University of Iceland, Reykjavik, Iceland
| | - Kristiina Aittomäki
- Department of Clinical Genetics, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Elisa Alducci
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV - IRCCS, Padua, Italy
- Department of Clinical Genetics and GROW, School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Irene L Andrulis
- Fred A. Litwin Center for Cancer Genetics, Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Banu K Arun
- Department of Breast Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Jacopo Azzollini
- Unit of Medical Genetics, Department of Medical Oncology and Hematology, Fondazione IRCCS (Istituto Di Ricovero e Cura a Carattere Scientifico) Istituto Nazionale dei Tumori (INT), Milan, Italy
| | - Emmanuelle Barouk-Simonet
- Oncogénétique, Institut Bergonié, Bordeaux, France
- Department of Pathology and Laboratory Medicine, Kansas University Medical Center, Kansas City, KS
| | - Julian Barwell
- Leicestershire Clinical Genetics Service, University Hospitals of Leicester NHS Trust, Leicester, UK
- Genetic Counseling Unit, Hereditary Cancer Program, IDIBGI (Institut d'Investigació Biomèdica de Girona), Catalan Institute of Oncology, CIBERONC, Girona, Spain
| | | | - Javier Benitez
- Schools of Medicine and Public Health, Division of Cancer Prevention & Control Research, Jonsson Comprehensive Cancer Center, University of California Los Angeles, CA
| | - Andreas Berger
- Department of Oncology, Lund University and Skåne University Hospital, Lund, Sweden
| | - Ake Borg
- Cancer Risk and Prevention Clinic, Dana-Farber Cancer Institute, Boston, MA
- Institute of Genetic Medicine, Centre for Life, Newcastle Upon Tyne Hospitals NHS Trust, Newcastle upon Tyne, UK
| | - Angela R Bradbury
- Department of Medicine, Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Joan Brunet
- Service de Génétique, Institut Curie, Paris, France
- Human Cancer Genetics Program, Spanish National Cancer Research Centre, Madrid, Spain
- Centro de Investigación en Red de Enfermedades Raras (CIBERER), Valencia, Spain, Department of Obstetrics and Gynecology, Medical University of Vienna, Vienna, Austria
| | - Saundra S Buys
- Department of Medicine, Huntsman Cancer Institute at the University of Utah, Salt Lake City, UT
| | - Trinidad Caldes
- Molecular Oncology Laboratory, Hospital Clinico San Carlos, IdISSC, CIBERONC, Madrid, Spain
| | - Maria A Caligo
- Section of Genetic Oncology, Department of Laboratory Medicine, University and University Hospital of Pisa, Pisa, Italy
| | - Ian Campbell
- Peter MacCallum Cancer Center, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Sandrine M Caputo
- Leicestershire Clinical Genetics Service, University Hospitals of Leicester NHS Trust, Leicester, UK
- Service de Génétique, Institut Curie, Paris, France
| | - Jocelyne Chiquette
- Unité de recherche en santé des populations, Centre des maladies du sein Deschênes-Fabia, Hôpital du Saint-Sacrement, Québec, QC, Canada
| | | | - J Margriet Collée
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Fergus J Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Isabelle Coupier
- Unité d'Oncogénétique, CHU Arnaud de Villeneuve, Montpellier, France
| | - Mary B Daly
- Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, PA
| | - Rosemarie Davidson
- Department of Clinical Genetics, South Glasgow University Hospitals, Glasgow, UK
| | - Orland Diez
- N.N. Petrov Institute of Oncology, St. Petersburg, Russia
| | - Susan M Domchek
- Department of Medicine, Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Alan Donaldson
- Oncogenetics Group, Clinical and Molecular Genetics Area, Vall d'Hebron Institute of Oncology (VHIO), University Hospital, Vall d'Hebron, Barcelona, Spain (OD); Clinical Genetics Department, St Michael's Hospital, Bristol, UK
| | - Cecilia M Dorfling
- Department of Genetics, University of Pretoria, Arcadia, South Africa
- City of Hope Clinical Cancer Genetics Community Research Network, Duarte, CA
| | - Ros Eeles
- Ocogenetics Team, The Institute of Cancer Research and Royal Marsden NHS Foundation Trust, London, UK
| | - Lidia Feliubadaló
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Lenka Foretova
- Molecular Diagnostic Unit, Hereditary Cancer Program, ICO-IDIBELL (Catalan Institute of Oncology, Bellvitge Biomedical Research Institute), CIBERONC, Barcelona, Spain
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Jeffrey Fowler
- The Ohio State University, Columbus Cancer Council, Columbus, OH
| | - Eitan Friedman
- The Susanne Levy Gertner Oncogenetics Unit, Chaim Sheba Medical Center, Ramat Gan, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv, Israel
| | - Debra Frost
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Patricia A Ganz
- Schools of Medicine and Public Health, Division of Cancer Prevention & Control Research, Jonsson Comprehensive Cancer Center, University of California Los Angeles, CA
| | - Judy Garber
- Cancer Risk and Prevention Clinic, Dana-Farber Cancer Institute, Boston, MA
| | - Vanesa Garcia-Barberan
- Molecular Oncology Laboratory, Hospital Clinico San Carlos, IdISSC, CIBERONC, Madrid, Spain
| | - Gord Glendon
- Fred A. Litwin Center for Cancer Genetics, Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, ON, Canada
| | - Andrew K Godwin
- Department of Pathology and Laboratory Medicine, Kansas University Medical Center, Kansas City, KS
| | - Encarna B Gómez Garcia
- Department of Clinical Genetics and GROW, School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Jacek Gronwald
- Department of Clinical Genetics and GROW, School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Eric Hahnen
- Centers for Hereditary Breast and Ovarian Cancer, Integrated Oncology and Molecular Medicine, University Hospital of Cologne, Cologne, Germany Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Alex Henderson
- Institute of Genetic Medicine, Centre for Life, Newcastle Upon Tyne Hospitals NHS Trust, Newcastle upon Tyne, UK
| | - Carolyn B Hendricks
- City of Hope Clinical Cancer Genetics Community Research Network, Duarte, CA
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Peter J Hulick
- Center for Medical Genetics, NorthShore University HealthSystem, Evanston, IL
- The University of Chicago Pritzker School of Medicine, Chicago, IL
| | | | - Claudine Isaacs
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC (CI)
| | - Louise Izatt
- Clinical Genetics, Guy’s and St Thomas’ NHS Foundation Trust, London, UK
| | - Ángel Izquierdo
- Genetic Counseling Unit, Hereditary Cancer Program, IDIBGI (Institut d'Investigació Biomèdica de Girona), Catalan Institute of Oncology, CIBERONC, Girona, Spain
| | - Anna Jakubowska
- Department of Clinical Genetics and GROW, School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Katarzyna Kaczmarek
- Department of Clinical Genetics and GROW, School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Eunyoung Kang
- Department of Surgery, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Beth Y Karlan
- Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Carolien M Kets
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Sung-Won Kim
- Department of Surgery, Daerim Saint Mary's Hospital, Seoul, Korea
| | - Zisun Kim
- Department of Surgery, Soonchunhyang University Hospital Bucheon, Bucheon, Korea
| | - Ava Kwong
- Hong Kong Hereditary Breast Cancer Family Registry, Happy Valley, Hong Kong
- Department of Surgery, The University of Hong Kong, Pok Fu Lam, Hong Kong
- Department of Surgery, Hong Kong Sanatorium and Hospital, Happy Valley, Hong Kong
| | - Yael Laitman
- The Susanne Levy Gertner Oncogenetics Unit, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Christine Lasset
- Unité de Prévention et d’Epidémiologie Génétique, Centre Léon Bérard, Lyon, France
| | - Min Hyuk Lee
- Department of Surgery, Soonchunhyang University College of Medicine and Soonchunhyang University Hospital, Seoul, Korea
| | - Jong Won Lee
- Department of Surgery, Ulsan University College of Medicine and Asan Medical Center, Seoul, Korea
| | - Jihyoun Lee
- Department of Clinical Genetics and GROW, School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands
- Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA
- Department of Surgery, Soonchunhyang University College of Medicine and Soonchunhyang University Hospital, Seoul, Korea
| | - Jenny Lester
- Department of Clinical Genetics and GROW, School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Fabienne Lesueur
- Genetic Epidemiology of Cancer team, Institut Curie, Paris, France
- U900, INSERM, Paris, France
- PSL University, Paris, France
- Mines ParisTech, Fontainebleau, France
| | - Jennifer T Loud
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD
| | - Jan Lubinski
- Department of Clinical Genetics and GROW, School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Noura Mebirouk
- Genetic Epidemiology of Cancer team, Institut Curie, Paris, France
- U900, INSERM, Paris, France
- PSL University, Paris, France
- Mines ParisTech, Fontainebleau, France
| | | | - Alfons Meindl
- Division of Gynaecology and Obstetrics, Technische Universität München, Munich, Germany
- NRG Oncology, Statistics and Data Management Center, Roswell Park Cancer Institute, Buffalo, NY
| | - Austin Miller
- Division of Gynaecology and Obstetrics, Technische Universität München, Munich, Germany
| | - Marco Montagna
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Thea M Mooij
- Department of Epidemiology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Patrick J Morrison
- Centre for Cancer Research and Cell Biology, Queens University Belfast, Belfast, UK
| | | | | | - Susan L Neuhausen
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Dieter Niederacher
- Department of Gynecology and Obstetrics, University Hospital Düsseldorf, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Finn C Nielsen
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Robert L Nussbaum
- Cancer Genetics and Prevention Program, University of California San Francisco, San Francisco, CA
| | - Kenneth Offit
- Clinical Genetics Research Laboratory, Department of Cancer Biology and Genetics, Memorial Sloan-Kettering Cancer Center, New York, NY
- Clinical Genetics Service, Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY
| | - Edith Olah
- Department of Molecular Genetics, National Institute of Oncology, Budapest, Hungary
| | - Kai-Ren Ong
- West Midlands Regional Genetics Service, Birmingham Women’s Hospital Healthcare NHS Trust, Birmingham, UK
| | - Laura Ottini
- Department of Molecular Medicine, University La Sapienza, Rome, Italy
| | - Sue K Park
- Departments of Preventive Medicine and Biomedical Sciences, and Cancer Research Institute, Seoul National University, Seoul, Korea
| | - Paolo Peterlongo
- IFOM, The FIRC (Italian Foundation for Cancer Research) Institute of Molecular Oncology, Milan, Italy
| | - Georg Pfeiler
- Department of Urology, Medical University of Vienna, Vienna, Austria
| | | | - Bruce Poppe
- Centre for Medical Genetics, Ghent University, Ghent, Belgium
| | - Nisha Pradhan
- Clinical Genetics Research Laboratory, Department of Cancer Biology and Genetics, Memorial Sloan-Kettering Cancer Center, New York, NY
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Research, Fondazione IRCCS (Istituto Di Ricovero e Cura a Carattere Scientifico) Istituto Nazionale dei Tumori (INT), Milan, Italy
| | - Susan J Ramus
- School of Women's and Children's Health, University of New South Wales Sydney, New South Wales, Australia
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | | | - Mark Robson
- Clinical Genetics Service, Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY
| | - Gustavo C Rodriguez
- Division of Gynecologic Oncology, NorthShore University HealthSystem, University of Chicago, Evanston, IL
| | - Rita K Schmutzler
- Centers for Hereditary Breast and Ovarian Cancer, Integrated Oncology and Molecular Medicine, University Hospital of Cologne, Cologne, Germany Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Payal D Shah
- Department of Medicine, Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Jacques Simard
- Laboratoire de génétique médicale, Nancy Université, Centre Hospitalier Régional et Universitaire, Vandoeuvre-les-Nancy, France
| | - Christian F Singer
- Department of Obstetrics and Gynecology and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Johanna Sokolowska
- Genomics Center, Centre Hospitalier Universitaire de Québec Research Center, Laval University, Québec City, QC, Canada
| | - Dominique Stoppa-Lyonnet
- Department of Tumour Biology, Institut Curie, INSERM U830, Paris, France
- Université Paris Descartes, Paris, France
| | - Christian Sutter
- Institute of Human Genetics, University Hospital Heidelberg, Heidelberg, Germany
| | - Yen Yen Tan
- Centro de Investigación en Red de Enfermedades Raras (CIBERER), Valencia, Spain, Department of Obstetrics and Gynecology, Medical University of Vienna, Vienna, Austria
| | - R Manuel Teixeira
- Department of Genetics, Portuguese Oncology Institute, Porto, Portugal
- Biomedical Sciences Institute (ICBAS), University of Porto, Porto, Portugal
| | - Soo H Teo
- Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia
- Breast Cancer Research Unit, Cancer Research Institute, University Malaya Medical Centre, Kuala Lumpur, Malaysia
| | - Mary Beth Terry
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY
| | - Mads Thomassen
- Department of Clinical Genetics, Odense University Hospital, Odense C, Denmark
| | - Marc Tischkowitz
- Program in Cancer Genetics, Departments of Human Genetics and Oncology, McGill University, Montréal, QC, Canada
- Department of Medical Genetics, Addenbrooke's Hospital, Cambridge, UK
| | - Amanda E Toland
- Department of Cancer Biology and Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH
| | - Katherine M Tucker
- School of Medicine, University of New South Wales, Sydney, New South Wales, Australia
- Hereditary Cancer Centre, Prince of Wales Hospital, Sydney, New South Wales, Australia
| | - Nadine Tung
- Department of Medical Oncology, Beth Israel Deaconess Medical Center, Boston, MA
| | - Christi J van Asperen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Klaartje van Engelen
- Department of Clinical Genetics, Academic Medical Center, Amsterdam, the Netherlands
| | | | - Shan Wang-Gohrke
- Department of Gynaecology and Obstetrics, University of Ulm, Ulm, Germany
| | - Barbara Wappenschmidt
- Centers for Hereditary Breast and Ovarian Cancer, Integrated Oncology and Molecular Medicine, University Hospital of Cologne, Cologne, Germany Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Drakoulis Yannoukakos
- Molecular Diagnostics Laboratory, INRASTES, National Centre for Scientific Research ‘Demokritos’, Athens, Greece
| | - GEMO Study Collaborators
- Department of Tumour Biology, Institut Curie, INSERM U830, Paris, France
- Université Paris Descartes, Paris, France
| | - HEBON
- The Hereditary Breast and Ovarian Cancer Research Group Netherlands
- Coordinating Center, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - EMBRACE
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Mark H Greene
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD
| | - Matti A Rookus
- Department of Epidemiology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Douglas F Easton
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Georgia Chenevix-Trench
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Antonis C Antoniou
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - David E Goldgar
- Department of Dermatology, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT
| | | | - Timothy R Rebbeck
- Harvard T.H. Chan School of Public Health, Boston, MA
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Dezheng Huo
- Department of Medicine, The University of Chicago, Chicago, IL
- Department of Public Health Sciences, The University of Chicago, Chicago, IL (DH)
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Burke LJ, Sevcik J, Gambino G, Tudini E, Mucaki EJ, Shirley BC, Whiley P, Parsons MT, De Leeneer K, Gutiérrez‐Enríquez S, Santamariña M, Caputo SM, Santana dos Santos E, Soukupova J, Janatova M, Zemankova P, Lhotova K, Stolarova L, Borecka M, Moles‐Fernández A, Manoukian S, Bonanni B, Edwards SL, Blok MJ, van Overeem Hansen T, Rossing M, Diez O, Vega A, Claes KB, Goldgar DE, Rouleau E, Radice P, Peterlongo P, Rogan PK, Caligo M, Spurdle AB, Brown MA. BRCA1 and BRCA2 5' noncoding region variants identified in breast cancer patients alter promoter activity and protein binding. Hum Mutat 2018; 39:2025-2039. [PMID: 30204945 PMCID: PMC6282814 DOI: 10.1002/humu.23652] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 09/01/2018] [Accepted: 09/07/2018] [Indexed: 12/13/2022]
Abstract
The widespread use of next generation sequencing for clinical testing is detecting an escalating number of variants in noncoding regions of the genome. The clinical significance of the majority of these variants is currently unknown, which presents a significant clinical challenge. We have screened over 6,000 early-onset and/or familial breast cancer (BC) cases collected by the ENIGMA consortium for sequence variants in the 5' noncoding regions of BC susceptibility genes BRCA1 and BRCA2, and identified 141 rare variants with global minor allele frequency < 0.01, 76 of which have not been reported previously. Bioinformatic analysis identified a set of 21 variants most likely to impact transcriptional regulation, and luciferase reporter assays detected altered promoter activity for four of these variants. Electrophoretic mobility shift assays demonstrated that three of these altered the binding of proteins to the respective BRCA1 or BRCA2 promoter regions, including NFYA binding to BRCA1:c.-287C>T and PAX5 binding to BRCA2:c.-296C>T. Clinical classification of variants affecting promoter activity, using existing prediction models, found no evidence to suggest that these variants confer a high risk of disease. Further studies are required to determine if such variation may be associated with a moderate or low risk of BC.
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Affiliation(s)
- Leslie J. Burke
- School of Chemistry and Molecular BiosciencesUniversity of QueenslandBrisbaneAustralia
| | - Jan Sevcik
- School of Chemistry and Molecular BiosciencesUniversity of QueenslandBrisbaneAustralia
- Institute of Biochemistry and Experimental Oncology, First Faculty of MedicineCharles UniversityPragueCzech Republic
| | - Gaetana Gambino
- School of Chemistry and Molecular BiosciencesUniversity of QueenslandBrisbaneAustralia
- Section of Molecular GeneticsDepartment of Laboratory MedicineUniversity Hospital of PisaPisaItaly
| | - Emma Tudini
- School of Chemistry and Molecular BiosciencesUniversity of QueenslandBrisbaneAustralia
- Department of Genetics and Computational BiologyQIMR Berghofer Medical Research InstituteBrisbaneAustralia
| | - Eliseos J. Mucaki
- University of Western Ontario, Department of BiochemistrySchulich School of Medicine and DentistryLondonOntarioCanada
| | | | - Phillip Whiley
- School of Chemistry and Molecular BiosciencesUniversity of QueenslandBrisbaneAustralia
- Department of Genetics and Computational BiologyQIMR Berghofer Medical Research InstituteBrisbaneAustralia
| | - Michael T. Parsons
- Department of Genetics and Computational BiologyQIMR Berghofer Medical Research InstituteBrisbaneAustralia
| | - Kim De Leeneer
- Center for Medical GeneticsGhent University Hospitaland Cancer Research Institute Ghent (CRIG)Ghent UniversityGhentBelgium
| | | | - Marta Santamariña
- Fundación Pública Galega de Medicina Xenómica‐SERGASGrupo de Medicina Xenómica‐USC, CIBERER, IDISSantiago de CompostelaSpain
| | - Sandrine M. Caputo
- Service de GénétiqueDepartment de Biologie des TumeursInstitut CurieParisFrance
| | - Elizabeth Santana dos Santos
- Service de GénétiqueDepartment de Biologie des TumeursInstitut CurieParisFrance
- Department of oncologyCenter for Translational OncologyCancer Institute of the State of São Paulo ‐ ICESPSão PauloBrazil
- A.C.Camargo Cancer CenterSão PauloBrazil
| | - Jana Soukupova
- Institute of Biochemistry and Experimental Oncology, First Faculty of MedicineCharles UniversityPragueCzech Republic
| | - Marketa Janatova
- Institute of Biochemistry and Experimental Oncology, First Faculty of MedicineCharles UniversityPragueCzech Republic
| | - Petra Zemankova
- Institute of Biochemistry and Experimental Oncology, First Faculty of MedicineCharles UniversityPragueCzech Republic
| | - Klara Lhotova
- Institute of Biochemistry and Experimental Oncology, First Faculty of MedicineCharles UniversityPragueCzech Republic
| | - Lenka Stolarova
- Institute of Biochemistry and Experimental Oncology, First Faculty of MedicineCharles UniversityPragueCzech Republic
| | - Mariana Borecka
- Institute of Biochemistry and Experimental Oncology, First Faculty of MedicineCharles UniversityPragueCzech Republic
| | | | - Siranoush Manoukian
- Unit of Medical GeneticsDepartment of Medical Oncology and HematologyFondazione IRCCS (Istituto di Ricovero e Cura a Carattere Scientifico) Istituto Nazionale dei Tumori (INT)MilanItaly
| | - Bernardo Bonanni
- Division of Cancer Prevention and GeneticsIstituto Europeo di OncologiaMilanItaly
| | - ENIGMA Consortium
- School of Chemistry and Molecular BiosciencesUniversity of QueenslandBrisbaneAustralia
| | - Stacey L. Edwards
- Department of Genetics and Computational BiologyQIMR Berghofer Medical Research InstituteBrisbaneAustralia
| | - Marinus J. Blok
- Department of Clinical GeneticsMaastricht University Medical CentreMaastrichtThe Netherlands
| | | | - Maria Rossing
- Center for Genomic MedicineCopenhagen University Hospital, RigshospitaletCopenhagenDenmark
| | - Orland Diez
- Oncogenetics GroupVall d'Hebron Institute of Oncology (VHIO)BarcelonaSpain
- Area of Clinical and Molecular GeneticsUniversity Hospital Vall d'Hebron (UHVH)BarcelonaSpain
| | - Ana Vega
- Fundación Pública Galega de Medicina Xenómica‐SERGASGrupo de Medicina Xenómica‐USC, CIBERER, IDISSantiago de CompostelaSpain
| | - Kathleen B.M. Claes
- Center for Medical GeneticsGhent University Hospitaland Cancer Research Institute Ghent (CRIG)Ghent UniversityGhentBelgium
| | | | | | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic TestingDepartment of ResearchFondazione IRCCS Istituto Nazionale dei Tumori di MilanoMilanItaly
| | | | - Peter K. Rogan
- University of Western Ontario, Department of BiochemistrySchulich School of Medicine and DentistryLondonOntarioCanada
- CytoGnomix Inc.LondonOntarioCanada
| | - Maria Caligo
- Section of Molecular GeneticsDepartment of Laboratory MedicineUniversity Hospital of PisaPisaItaly
| | - Amanda B. Spurdle
- Department of Genetics and Computational BiologyQIMR Berghofer Medical Research InstituteBrisbaneAustralia
| | - Melissa A. Brown
- School of Chemistry and Molecular BiosciencesUniversity of QueenslandBrisbaneAustralia
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29
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Lesueur F, Mebirouk N, Jiao Y, Barjhoux L, Belotti M, Laurent M, Léone M, Houdayer C, Bressac-de Paillerets B, Vaur D, Sobol H, Noguès C, Longy M, Mortemousque I, Fert-Ferrer S, Mouret-Fourme E, Pujol P, Venat-Bouvet L, Bignon YJ, Leroux D, Coupier I, Berthet P, Mari V, Delnatte C, Gesta P, Collonge-Rame MA, Giraud S, Bonadona V, Baurand A, Faivre L, Buecher B, Lasset C, Gauthier-Villars M, Damiola F, Mazoyer S, Caputo SM, Andrieu N, Stoppa-Lyonnet D. GEMO, a National Resource to Study Genetic Modifiers of Breast and Ovarian Cancer Risk in BRCA1 and BRCA2 Pathogenic Variant Carriers. Front Oncol 2018; 8:490. [PMID: 30430080 PMCID: PMC6220051 DOI: 10.3389/fonc.2018.00490] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Accepted: 10/11/2018] [Indexed: 02/03/2023] Open
Affiliation(s)
- Fabienne Lesueur
- INSERM, U900, Institut Curie, PSL Research University, Mines ParisTech, Paris, France
| | - Noura Mebirouk
- INSERM, U900, Institut Curie, PSL Research University, Mines ParisTech, Paris, France
| | - Yue Jiao
- Service de Génétique, Institut Curie, Paris, France
| | | | | | | | - Mélanie Léone
- Hospices Civils de Lyon, Groupement Hospitalier EST, Bron, France
| | | | | | - Dominique Vaur
- Département de Biopathologie, Centre François Baclesse, Caen, France
| | - Hagay Sobol
- Institut Paoli Calmette, Département d'Anticipation et de Suivi des Cancers, Oncogénétique, Faculté de Médecine, Université d'Aix-Marseille, Marseille, France
| | - Catherine Noguès
- Institut Paoli Calmette, Département d'Anticipation et de Suivi des Cancers, Oncogénétique, Faculté de Médecine, Université d'Aix-Marseille, Marseille, France
| | - Michel Longy
- Biopathologie, Institut Bergonié, Bordeaux, France
| | | | | | | | - Pascal Pujol
- Service de Génétique Médicale et Oncogénétique, Hôpital Arnaud de Villeneuve, CHU Montpellier, INSERM 896, CRCM Val d'Aurelle, Montpellier, France
| | | | - Yves-Jean Bignon
- Université Clermont Auvergne, INSERM, U1240, Centre Jean Perrin, Clermont-Ferrand, France
| | - Dominique Leroux
- Département de Génétique, CHU de Grenoble, Hôpital Couple-Enfant, Grenoble, France
| | - Isabelle Coupier
- Service de Génétique Médicale et Oncogénétique, Hôpital Arnaud de Villeneuve, CHU Montpellier, INSERM 896, CRCM Val d'Aurelle, Montpellier, France
| | - Pascaline Berthet
- Département de Biopathologie, Centre François Baclesse, Caen, France
| | - Véronique Mari
- Unité d'Oncogénétique, Centre Antoine Lacassagne, Nice, France
| | | | - Paul Gesta
- Service d'Oncogénétique Régional Poitou-Charentes, Niort, France
| | - Marie-Agnès Collonge-Rame
- Service Génétique et Biologie du Développement-Histologie, CHU Hôpital Saint-Jacques, Besançon, France
| | - Sophie Giraud
- Hospices Civils de Lyon, Groupement Hospitalier EST, Bron, France
| | - Valérie Bonadona
- Université Claude Bernard Lyon 1, Villeurbanne, France.,CNRS UMR 5558; Unité de Prévention et Epidémiologie Génétique, Centre Léon Bérard, Lyon, France
| | - Amandine Baurand
- Institut GIMI, CHU de Dijon et Centre de Lutte contre le Cancer Georges François Leclerc, Dijon, France
| | - Laurence Faivre
- Institut GIMI, CHU de Dijon et Centre de Lutte contre le Cancer Georges François Leclerc, Dijon, France
| | | | - Christine Lasset
- Université Claude Bernard Lyon 1, Villeurbanne, France.,CNRS UMR 5558; Unité de Prévention et Epidémiologie Génétique, Centre Léon Bérard, Lyon, France
| | | | | | - Sylvie Mazoyer
- INSERM, U1028, CNRS, UMR5292, Centre de Recherche en Neurosciences de Lyon, Lyon, France
| | | | - Nadine Andrieu
- INSERM, U900, Institut Curie, PSL Research University, Mines ParisTech, Paris, France
| | - Dominique Stoppa-Lyonnet
- Service de Génétique, Institut Curie, Paris, France.,INSERM, U830, Université Paris Descartes, Paris, France
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30
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Leman R, Gaildrat P, Gac GL, Ka C, Fichou Y, Audrezet MP, Caux-Moncoutier V, Caputo SM, Boutry-Kryza N, Léone M, Mazoyer S, Bonnet-Dorion F, Sevenet N, Guillaud-Bataille M, Rouleau E, Paillerets BBD, Wappenschmidt B, Rossing M, Muller D, Bourdon V, Revillon F, Parsons MT, Rousselin A, Davy G, Castelain G, Castéra L, Sokolowska J, Coulet F, Delnatte C, Férec C, Spurdle AB, Martins A, Krieger S, Houdayer C. Corrigendum: Novel diagnostic tool for prediction of variant spliceogenicity derived from a set of 395 combined in silico/in vitro studies: an international collaborative effort. Nucleic Acids Res 2018; 46:11656-11657. [PMID: 30321405 PMCID: PMC6277085 DOI: 10.1093/nar/gky979] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Raphaël Leman
- Laboratoire de Biologie Clinique et Oncologique, Centre François Baclesse, 14000 Caen, France.,Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, 76031 Rouen, France.,Normandie Univ, UNICAEN, 14000 Caen, France
| | - Pascaline Gaildrat
- Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, 76031 Rouen, France
| | - Gérald L Gac
- Inserm UMR1078, Genetics, Functional Genomics and Biotechnology, Université de Bretagne Occidentale, 29200 Brest, France
| | - Chandran Ka
- Inserm UMR1078, Genetics, Functional Genomics and Biotechnology, Université de Bretagne Occidentale, 29200 Brest, France
| | - Yann Fichou
- Inserm UMR1078, Genetics, Functional Genomics and Biotechnology, Université de Bretagne Occidentale, 29200 Brest, France
| | - Marie-Pierre Audrezet
- Inserm UMR1078, Genetics, Functional Genomics and Biotechnology, Université de Bretagne Occidentale, 29200 Brest, France
| | - Virginie Caux-Moncoutier
- Inserm U830, Institut Curie Centre de Recherches, 75005 Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, 75005 Paris, France.,Service de Génétique, Institut Curie, 75005 Paris, France
| | | | - Nadia Boutry-Kryza
- Unité Mixte de Génétique Constitutionnelle des Cancers Fréquents, Hospices Civils de Lyon, 69000 Lyon, France
| | - Mélanie Léone
- Unité Mixte de Génétique Constitutionnelle des Cancers Fréquents, Hospices Civils de Lyon, 69000 Lyon, France
| | - Sylvie Mazoyer
- Lyon Neuroscience Research Center-CRNL, Inserm U1028, CNRS UMR 5292, University of Lyon, 69008 Lyon, France
| | - Françoise Bonnet-Dorion
- Inserm U916, Département de Pathologie, Laboratoire de Génétique Constitutionnelle, Institut Bergonié, 33000 Bordeaux, France
| | - Nicolas Sevenet
- Inserm U916, Département de Pathologie, Laboratoire de Génétique Constitutionnelle, Institut Bergonié, 33000 Bordeaux, France
| | | | - Etienne Rouleau
- Gustave Roussy, Université Paris-Saclay, Département de Biopathologie, 94805 Villejuif, France
| | | | - Barbara Wappenschmidt
- Division of Molecular Gynaeco-Oncology, Department of Gynaecology and Obstetrics, University Hospital of Cologne, 50937 Cologne, Germany
| | - Maria Rossing
- Centre for Genomic Medicine, Rigshospitalet, University of Copenhagen, 1017 Copenhagen, Denmark
| | - Danielle Muller
- Laboratoire d'Oncogénétique, Centre Paul Strauss, 67000 Strasbourg, France
| | - Violaine Bourdon
- Laboratoire d'Oncogénétique Moléculaire, Institut Paoli-Calmettes, 13009 Marseille, France
| | - Françoise Revillon
- Laboratoire d'Oncogénétique Moléculaire Humaine, Centre Oscar Lambret, 59000 Lille, France
| | - Michael T Parsons
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, 4006 Herston, Queensland, Australia
| | - Antoine Rousselin
- Laboratoire de Biologie Clinique et Oncologique, Centre François Baclesse, 14000 Caen, France.,Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, 76031 Rouen, France
| | - Grégoire Davy
- Laboratoire de Biologie Clinique et Oncologique, Centre François Baclesse, 14000 Caen, France.,Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, 76031 Rouen, France
| | - Gaia Castelain
- Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, 76031 Rouen, France
| | - Laurent Castéra
- Laboratoire de Biologie Clinique et Oncologique, Centre François Baclesse, 14000 Caen, France.,Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, 76031 Rouen, France
| | | | - Florence Coulet
- Service de génétique, Hôpital Pitié Salpétrière, AP-HP, 75013 Paris, France
| | - Capucine Delnatte
- Laboratoire de génétique moléculaire, CHU Nantes, 44000 Nantes, France
| | - Claude Férec
- Inserm UMR1078, Genetics, Functional Genomics and Biotechnology, Université de Bretagne Occidentale, 29200 Brest, France
| | - Amanda B Spurdle
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, 4006 Herston, Queensland, Australia
| | - Alexandra Martins
- Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, 76031 Rouen, France
| | - Sophie Krieger
- Laboratoire de Biologie Clinique et Oncologique, Centre François Baclesse, 14000 Caen, France.,Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, 76031 Rouen, France.,Normandie Univ, UNICAEN, 14000 Caen, France
| | - Claude Houdayer
- Inserm U830, Institut Curie Centre de Recherches, 75005 Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, 75005 Paris, France.,Service de Génétique, Institut Curie, 75005 Paris, France
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31
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Petitalot A, Dardillac E, Jacquet E, Nhiri N, Guirouilh-Barbat J, Julien P, Bouazzaoui I, Bonte D, Feunteun J, Schnell JA, Lafitte P, Aude JC, Noguès C, Rouleau E, Lidereau R, Lopez BS, Zinn-Justin S, Caputo SM. Combining Homologous Recombination and Phosphopeptide-binding Data to Predict the Impact of BRCA1 BRCT Variants on Cancer Risk. Mol Cancer Res 2018; 17:54-69. [PMID: 30257991 DOI: 10.1158/1541-7786.mcr-17-0357] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 02/07/2018] [Accepted: 09/11/2018] [Indexed: 11/16/2022]
Abstract
BRCA1 mutations have been identified that increase the risk of developing hereditary breast and ovarian cancers. Genetic screening is now offered to patients with a family history of cancer, to adapt their treatment and the management of their relatives. However, a large number of BRCA1 variants of uncertain significance (VUS) are detected. To better understand the significance of these variants, a high-throughput structural and functional analysis was performed on a large set of BRCA1 VUS. Information on both cellular localization and homology-directed DNA repair (HR) capacity was obtained for 78 BRCT missense variants in the UMD-BRCA1 database and measurement of the structural stability and phosphopeptide-binding capacities was performed for 42 mutated BRCT domains. This extensive and systematic analysis revealed that most characterized causal variants affect BRCT-domain solubility in bacteria and all impair BRCA1 HR activity in cells. Furthermore, binding to a set of 5 different phosphopeptides was tested: all causal variants showed phosphopeptide-binding defects and no neutral variant showed such defects. A classification is presented on the basis of mutated BRCT domain solubility, phosphopeptide-binding properties, and VUS HR capacity. These data suggest that HR-defective variants, which present, in addition, BRCT domains either insoluble in bacteria or defective for phosphopeptide binding, lead to an increased cancer risk. Furthermore, the data suggest that variants with a WT HR activity and whose BRCT domains bind with a WT affinity to the 5 phosphopeptides are neutral. The case of variants with WT HR activity and defective phosphopeptide binding should be further characterized, as this last functional defect might be sufficient per se to lead to tumorigenesis. IMPLICATIONS: The analysis of the current study on BRCA1 structural and functional defects on cancer risk and classification presented may improve clinical interpretation and therapeutic selection.
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Affiliation(s)
- Ambre Petitalot
- Service de Génétique, Département de Biologie des Tumeurs, Institut Curie, Paris, France.,Institut de Biologie Intégrative de la Cellule, CEA, CNRS, Université Paris Sud, UMR 9198, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Elodie Dardillac
- Institut Gustave Roussy, CNRS UMR 8200, Université Paris-Saclay, Villejuif, France.,Team labeled "Ligue 2014," Villejuif, France
| | - Eric Jacquet
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Naima Nhiri
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Josée Guirouilh-Barbat
- Institut Gustave Roussy, CNRS UMR 8200, Université Paris-Saclay, Villejuif, France.,Team labeled "Ligue 2014," Villejuif, France
| | - Patrick Julien
- Service de Génétique, Département de Biologie des Tumeurs, Institut Curie, Paris, France
| | - Isslam Bouazzaoui
- Institut de Biologie Intégrative de la Cellule, CEA, CNRS, Université Paris Sud, UMR 9198, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Dorine Bonte
- Institut Gustave Roussy, CNRS UMR 8200, Université Paris-Saclay, Villejuif, France
| | - Jean Feunteun
- Institut Gustave Roussy, CNRS UMR 8200, Université Paris-Saclay, Villejuif, France
| | - Jeff A Schnell
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Philippe Lafitte
- Service de Génétique, Département de Biologie des Tumeurs, Institut Curie, Paris, France
| | - Jean-Christophe Aude
- Institut de Biologie Intégrative de la Cellule, CEA, CNRS, Université Paris Sud, UMR 9198, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Catherine Noguès
- Service de Génétique, Département de Biologie des Tumeurs, Institut Curie, Paris, France
| | - Etienne Rouleau
- Service de Génétique, Département de Biologie des Tumeurs, Institut Curie, Paris, France
| | - Rosette Lidereau
- Service de Génétique, Département de Biologie des Tumeurs, Institut Curie, Paris, France
| | - Bernard S Lopez
- Institut Gustave Roussy, CNRS UMR 8200, Université Paris-Saclay, Villejuif, France.,Team labeled "Ligue 2014," Villejuif, France
| | - Sophie Zinn-Justin
- Institut de Biologie Intégrative de la Cellule, CEA, CNRS, Université Paris Sud, UMR 9198, Université Paris-Saclay, Gif-sur-Yvette, France.
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32
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Caputo SM, Léone M, Damiola F, Ehlen A, Carreira A, Gaidrat P, Martins A, Brandão RD, Peixoto A, Vega A, Houdayer C, Delnatte C, Bronner M, Muller D, Castera L, Guillaud-Bataille M, Søkilde I, Uhrhammer N, Demontety S, Tubeuf H, Castelain G, Jensen UB, Petitalot A, Krieger S, Lefol C, Moncoutier V, Boutry-Kryza N, Nielsen HR, Sinilnikova O, Stoppa-Lyonnet D, Spurdle AB, Teixeira MR, Coulet F, Thomassen M, Rouleau E. Full in-frame exon 3 skipping of BRCA2 confers high risk of breast and/or ovarian cancer. Oncotarget 2018; 9:17334-17348. [PMID: 29707112 PMCID: PMC5915120 DOI: 10.18632/oncotarget.24671] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 02/24/2018] [Indexed: 12/18/2022] Open
Abstract
Germline pathogenic variants in the BRCA2 gene are associated with a cumulative high risk of breast/ovarian cancer. Several BRCA2 variants result in complete loss of the exon-3 at the transcript level. The pathogenicity of these variants and the functional impact of loss of exon 3 have yet to be established. As a collaboration of the COVAR clinical trial group (France), and the ENIGMA consortium for investigating breast cancer gene variants, this study evaluated 8 BRCA2 variants resulting in complete deletion of exon 3. Clinical information for 39 families was gathered from Portugal, France, Denmark and Sweden. Multifactorial likelihood analyses were conducted using information from 293 patients, for 7 out of the 8 variants (including 6 intronic). For all variants combined the likelihood ratio in favor of causality was 4.39*1025. These results provide convincing evidence for the pathogenicity of all examined variants that lead to a total exon 3 skipping, and suggest that other variants that result in complete loss of exon 3 at the molecular level could be associated with a high risk of cancer comparable to that associated with classical pathogenic variants in BRCA1 or BRCA2 gene. In addition, our functional study shows, for the first time, that deletion of exon 3 impairs the ability of cells to survive upon Mitomycin-C treatment, supporting lack of function for the altered BRCA2 protein in these cells. Finally, this study demonstrates that any variant leading to expression of only BRCA2 delta-exon 3 will be associated with an increased risk of breast and ovarian cancer.
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Affiliation(s)
| | - Mélanie Léone
- Unité Mixte de Génétique Constitutionnelle des Cancers Fréquents, Hospices Civils de Lyon/Centre Léon Bérard, Lyon, France
| | | | - Asa Ehlen
- Institut Curie, PSL Research University, CNRS UMR3348, Orsay, France.,Université Paris Sud, Université Paris-Saclay, CNRS UMR3348, Orsay, France
| | - Aura Carreira
- Institut Curie, PSL Research University, CNRS UMR3348, Orsay, France.,Université Paris Sud, Université Paris-Saclay, CNRS UMR3348, Orsay, France
| | - Pascaline Gaidrat
- Inserm-U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Alexandra Martins
- Inserm-U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | | | - Ana Peixoto
- Department of Genetics, Portuguese Oncology Institute, Porto, Portugal
| | - Ana Vega
- Department of Genetics, Portuguese Oncology Institute, Porto, Portugal
| | - Claude Houdayer
- Institut Curie, Service de Génétique, Paris, France.,Université Paris Descartes, Paris, France
| | | | | | - Danièle Muller
- Laboratoire d'Oncogénétique, Centre Paul Strauss, Strasbourg, France
| | - Laurent Castera
- Laboratoire de biologie et de génétique du cancer, CLCC François Baclesse, INSERM 1079 Centre Normand de Génomique et de Médecine Personnalisée, Caen, France
| | | | - Inge Søkilde
- Section of Molecular Diagnostics, Department of Clinical Biochemistry, Aalborg University Hospital, Aalborg, Denmark
| | - Nancy Uhrhammer
- Laboratoire de Biologie Médicale, CLCC Jean Perrin, Clermont-Ferrand, France
| | | | - Hélène Tubeuf
- Inserm-U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France.,Interactive Biosoftware, Rouen, France
| | - Gaïa Castelain
- Inserm-U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | | | - Uffe Birk Jensen
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | | | - Sophie Krieger
- Laboratoire de biologie et de génétique du cancer, CLCC François Baclesse, INSERM 1079 Centre Normand de Génomique et de Médecine Personnalisée, Caen, France
| | | | | | - Nadia Boutry-Kryza
- Unité Mixte de Génétique Constitutionnelle des Cancers Fréquents, Hospices Civils de Lyon/Centre Léon Bérard, Lyon, France
| | | | - Olga Sinilnikova
- Unité Mixte de Génétique Constitutionnelle des Cancers Fréquents, Hospices Civils de Lyon/Centre Léon Bérard, Lyon, France
| | | | - Amanda B Spurdle
- Genetics and Comp utational Biology Division, QIMR Berghofer Medical Research Institute, Herston, Brisbane, Australia
| | - Manuel R Teixeira
- Department of Genetics, Portuguese Oncology Institute, Porto, Portugal.,Institute of Biomedical Sciences, University of Porto, Porto, Portugal
| | - Florence Coulet
- Laboratoire d'Oncogénétique et d'Angiogénétique Moléculaire, Groupe Hospitalier Pitié-Salpêtrière, Paris, France
| | - Mads Thomassen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
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Lallemand F, Petitalot A, Vacher S, de Koning L, Taouis K, Lopez BS, Zinn-Justin S, Dalla-Venezia N, Chemlali W, Schnitzler A, Lidereau R, Bieche I, Caputo SM. Involvement of the FOXO6 transcriptional factor in breast carcinogenesis. Oncotarget 2017; 9:7464-7475. [PMID: 29484124 PMCID: PMC5800916 DOI: 10.18632/oncotarget.23779] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 12/22/2017] [Indexed: 01/17/2023] Open
Abstract
In mammals, FOXO transcriptional factors form a family of four members (FOXO1, 3, 4, and 6) involved in the modulation proliferation, apoptosis, and carcinogenesis. The role of the FOXO family in breast cancer remains poorly elucidated. According to the cellular context and the stage of the disease, FOXOs can have opposite effects on carcinogenesis. To study the role of FOXOs in breast carcinogenesis in more detail, we examined their expression in normal tissues, breast cell lines, and a large series of breast tumours of human origin. We found a very low physiological level of FOXO6 expression in normal adult tissues and high levels of expression in foetal brain. FOXO gene expressions fluctuate specifically in breast cancer cells compared to normal cells, suggesting that these genes may have different roles in breast carcinogenesis. For the first time, we have shown that, among the various FOXO genes, only FOXO6 was frequently highly overexpressed in breast cell lines and tumours. We also found that inhibition of the endogenous expression of FOXO6 by a specific siRNA inhibited the growth of the human breast cell lines MDA-MB-468 and HCC-38. FACS and Western blot analysis showed that inhibition of endogenous expression of FOXO6 induced accumulation of cells in G0/G1 phase of the cell cycle, but not apoptosis. These results tend to demonstrate that the overexpression of the human FOXO6 gene that we highlighted in the breast tumors stimulates breast carcinogenesis by activating breast cancer cell proliferation.
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Affiliation(s)
- François Lallemand
- Service de génétique, unité de pharmacogénomique, Institut Curie, Paris, France
| | - Ambre Petitalot
- Service de génétique, unité de pharmacogénomique, Institut Curie, Paris, France.,Service de génétique, unité de génétique constitutionnelle, Institut Curie, Paris, France
| | - Sophie Vacher
- Service de génétique, unité de pharmacogénomique, Institut Curie, Paris, France
| | | | - Karim Taouis
- Service de génétique, unité de pharmacogénomique, Institut Curie, Paris, France
| | - Bernard S Lopez
- CNRS UMR 8200, Gustave Roussy Cancer Institute, Université Paris-Saclay, équipe labélisée par la Ligue contre le cancer, Villejuif, France
| | - Sophie Zinn-Justin
- Laboratoire de biologie structurale et radiobiologie, IBITEC-S (CEA) and I2BC (UMR 9198, CEA, CNRS, Univ. Paris South), Gif-sur-Yvette, France
| | - Nicole Dalla-Venezia
- Centre de Recherche en Cancérologie de Lyon (CRCL)/INSERM U1052-CNRS UMR5286, Lyon, France
| | - Walid Chemlali
- Service de génétique, unité de pharmacogénomique, Institut Curie, Paris, France
| | - Anne Schnitzler
- Service de génétique, unité de pharmacogénomique, Institut Curie, Paris, France
| | - Rosette Lidereau
- Service de génétique, unité de pharmacogénomique, Institut Curie, Paris, France
| | - Ivan Bieche
- Service de génétique, unité de pharmacogénomique, Institut Curie, Paris, France.,EA7331, Université Paris Descartes, Paris, France
| | - Sandrine M Caputo
- Service de génétique, unité de génétique constitutionnelle, Institut Curie, Paris, France
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34
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Dos Santos ES, Caputo SM, Castera L, Gendrot M, Briaux A, Breault M, Krieger S, Rogan PK, Mucaki EJ, Burke LJ, Bièche I, Houdayer C, Vaur D, Stoppa-Lyonnet D, Brown MA, Lallemand F, Rouleau E. Assessment of the functional impact of germline BRCA1/2 variants located in non-coding regions in families with breast and/or ovarian cancer predisposition. Breast Cancer Res Treat 2017; 168:311-325. [PMID: 29236234 DOI: 10.1007/s10549-017-4602-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 11/28/2017] [Indexed: 12/19/2022]
Abstract
PURPOSE The molecular mechanism of breast and/or ovarian cancer susceptibility remains unclear in the majority of patients. While germline mutations in the regulatory non-coding regions of BRCA1 and BRCA2 genes have been described, screening has generally been limited to coding regions. The aim of this study was to evaluate the contribution of BRCA1/2 non-coding variants. METHODS Four BRCA1/2 non-coding regions were screened using high-resolution melting analysis/Sanger sequencing or next-generation sequencing on DNA extracted from index cases with breast and ovarian cancer predisposition (3926 for BRCA1 and 3910 for BRCA2). The impact of a set of variants on BRCA1/2 gene regulation was evaluated by site-directed mutagenesis, transfection, followed by Luciferase gene reporter assay. RESULTS We identified a total of 117 variants and tested twelve BRCA1 and 8 BRCA2 variants mapping to promoter and intronic regions. We highlighted two neighboring BRCA1 promoter variants (c.-130del; c.-125C > T) and one BRCA2 promoter variants (c.-296C > T) inhibiting significantly the promoter activity. In the functional assays, a regulating region within the intron 12 was found with the same enhancing impact as within the intron 2. Furthermore, the variants c.81-3980A > G and c.4186-2022C > T suppress the positive effect of the introns 2 and 12, respectively, on the BRCA1 promoter activity. We also found some variants inducing the promoter activities. CONCLUSION In this study, we highlighted some variants among many, modulating negatively the promoter activity of BRCA1 or 2 and thus having a potential impact on the risk of developing cancer. This selection makes it possible to conduct future validation studies on a limited number of variants.
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Affiliation(s)
- E Santana Dos Santos
- Department of Oncology, Center for Translational Oncology, Cancer Institute of the State of São Paulo - ICESP, São Paulo, Brazil
- Service de Génétique, Institut Curie, Paris, France
- A.C.Camargo Cancer Center, São Paulo, Brazil
| | - S M Caputo
- Service de Génétique, Institut Curie, Paris, France
| | - L Castera
- Laboratoire de Biologie et de Génétique du Cancer, CLCC François Baclesse, INSERM 1079 Centre Normand de Génomique et de MédecinePersonnalisée, Caen, France
| | - M Gendrot
- Service de Génétique, Institut Curie, Paris, France
| | - A Briaux
- Service de Génétique, Institut Curie, Paris, France
| | - M Breault
- Service de Génétique, Institut Curie, Paris, France
| | - S Krieger
- Laboratoire de Biologie et de Génétique du Cancer, CLCC François Baclesse, INSERM 1079 Centre Normand de Génomique et de MédecinePersonnalisée, Caen, France
| | - P K Rogan
- Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Canada
| | - E J Mucaki
- Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Canada
| | - L J Burke
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - I Bièche
- Service de Génétique, Institut Curie, Paris, France
- Université Paris Descartes, Paris, France
| | - C Houdayer
- Service de Génétique, Institut Curie, Paris, France
- Université Paris Descartes, Paris, France
| | - D Vaur
- Laboratoire de Biologie et de Génétique du Cancer, CLCC François Baclesse, INSERM 1079 Centre Normand de Génomique et de MédecinePersonnalisée, Caen, France
| | - D Stoppa-Lyonnet
- Service de Génétique, Institut Curie, Paris, France
- Université Paris Descartes, Paris, France
| | - M A Brown
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - F Lallemand
- Service de Génétique, Institut Curie, Paris, France.
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35
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Moghadasi S, Meeks HD, Vreeswijk MP, Janssen LA, Borg Å, Ehrencrona H, Paulsson-Karlsson Y, Wappenschmidt B, Engel C, Gehrig A, Arnold N, Hansen TVO, Thomassen M, Jensen UB, Kruse TA, Ejlertsen B, Gerdes AM, Pedersen IS, Caputo SM, Couch F, Hallberg EJ, van den Ouweland AM, Collée MJ, Teugels E, Adank MA, van der Luijt RB, Mensenkamp AR, Oosterwijk JC, Blok MJ, Janin N, Claes KB, Tucker K, Viassolo V, Toland AE, Eccles DE, Devilee P, Van Asperen CJ, Spurdle AB, Goldgar DE, García EG. The BRCA1 c. 5096G>A p.Arg1699Gln (R1699Q) intermediate risk variant: breast and ovarian cancer risk estimation and recommendations for clinical management from the ENIGMA consortium. J Med Genet 2017; 55:15-20. [PMID: 28490613 DOI: 10.1136/jmedgenet-2017-104560] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Revised: 04/11/2017] [Accepted: 04/17/2017] [Indexed: 12/18/2022]
Abstract
BACKGROUND We previously showed that the BRCA1 variant c.5096G>A p.Arg1699Gln (R1699Q) was associated with an intermediate risk of breast cancer (BC) and ovarian cancer (OC). This study aimed to assess these cancer risks for R1699Q carriers in a larger cohort, including follow-up of previously studied families, to further define cancer risks and to propose adjusted clinical management of female BRCA1*R1699Q carriers. METHODS Data were collected from 129 BRCA1*R1699Q families ascertained internationally by ENIGMA (Evidence-based Network for the Interpretation of Germline Mutant Alleles) consortium members. A modified segregation analysis was used to calculate BC and OC risks. Relative risks were calculated under both monogenic model and major gene plus polygenic model assumptions. RESULTS In this cohort the cumulative risk of BC and OC by age 70 years was 20% and 6%, respectively. The relative risk for developing cancer was higher when using a model that included the effects of both the R1699Q variant and a residual polygenic component compared with monogenic model (for BC 3.67 vs 2.83, and for OC 6.41 vs 5.83). CONCLUSION Our results confirm that BRCA1*R1699Q confers an intermediate risk for BC and OC. Breast surveillance for female carriers based on mammogram annually from age 40 is advised. Bilateral salpingo-oophorectomy should be considered based on family history.
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Affiliation(s)
- Setareh Moghadasi
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Huong D Meeks
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, USA
| | - Maaike Pg Vreeswijk
- Department of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Linda Am Janssen
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Åke Borg
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Hans Ehrencrona
- Department of Clinical Genetics, Lund University, Lund, Sweden.,Department of Clinical Genetics, Laboratory Medicine, Office for Medical Services, Lund University, Lund, Sweden
| | | | - Barbara Wappenschmidt
- Centre of Familial Breast and Ovarian Cancer, University Hospital of Cologne, Cologne, Germany.,Department of Gynaecology and Obstetrics and Centre for Integrated Oncology (CIO), University Hospital of Cologne, Cologne, Germany.,Centre for Molecular Medicine Cologne (CMMC), University Hospital of Cologne, Cologne, Germany
| | - Christoph Engel
- Institute for Medical Informatics, University of Leipzig, Leipzig, Germany.,Department of Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
| | - Andrea Gehrig
- Centre of Familial Breast and Ovarian Cancer, University Würzburg, Würzburg, Germany.,Department of Medical Genetics, University Würzburg, Würzburg, Germany.,Institute of Human Genetics, University Würzburg, Würzburg, Germany
| | - Norbert Arnold
- Department of Gynaecology and Obstetrics, University Hospital of Schleswig-Holstein, Campus Kiel, Christian-Albrechts University Kiel, Kiel, Germany
| | - Thomas Van Overeem Hansen
- Center for Genomic Medicine, University of Copenhagen, Copenhagen, DenmarK.,Department of Rigshospitalet, University of Copenhagen, Copenhagen, DenmarK
| | - Mads Thomassen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Uffe Birk Jensen
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | - Torben A Kruse
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Bent Ejlertsen
- Department of Rigshospitalet, University of Copenhagen, Copenhagen, DenmarK.,Department of Oncology, University of Copenhagen, Copenhagen, Denmark
| | - Anne-Marie Gerdes
- Department of Rigshospitalet, University of Copenhagen, Copenhagen, DenmarK.,Department of Clinical Genetics, University of Copenhagen, Copenhagen, Denmark
| | - Inge Søkilde Pedersen
- Section of Molecular Diagnostics, Aalborg University Hospital, Aalborg, Denmark.,Department of Clinical Biochemistry, Aalborg University Hospital, Aalborg, Denmark
| | | | - Fergus Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Emily J Hallberg
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | | | - Margriet J Collée
- Department of Clinical Genetics, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Erik Teugels
- Familial Cancer Clinic and Medical Oncology, University Hospital Brussels, Belgium
| | - Muriel A Adank
- Department of Clinical Genetics, VU Medical Centre, Amsterdam, The Netherlands
| | - Rob B van der Luijt
- Division of Biomedical Genetics, University Medical Centre Utrecht, Utrecht, The Netherlands.,Department of Genetics, University Medical Centre Utrecht, Utrecht, The Netherlands
| | | | - Jan C Oosterwijk
- Department of Genetics, University of Groningen, University Medical Centre, Groningen, The Netherlands
| | - Marinus J Blok
- Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Nicolas Janin
- Department of Service de Génétique, Cliniques universitaires Saint-Luc, Bruxelles, Belgium
| | | | - Kathy Tucker
- Hereditary Cancer Service, Prince of Wales (and St George Hospitals) Hospital, Randwick, New South Wales, Australia
| | - Valeria Viassolo
- Department of Oncogenetics and Cancer Prevention Unit, Geneva University Hospitals, Geneva, Switzerland.,Division of Oncology, Geneva University Hospitals, Geneva, Switzerland
| | - Amanda Ewart Toland
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, Ohio, USA
| | - Diana E Eccles
- Faculty of Medicine, University of Southampton, Southampton, UK
| | - Peter Devilee
- Department of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Christie J Van Asperen
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Amanda B Spurdle
- Genetics and Computational Biology Division, QIMR Berghofer Medical Research Institute, Herston, Brisbane, Australia
| | - David E Goldgar
- Huntsman Cancer Institute and Department of Dermatology, University of Utah School of Medicine Salt Lake City, Salt Lake City, Utah, USA
| | - Encarna Gómez García
- Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, The Netherlands
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Béroud C, Letovsky SI, Braastad CD, Caputo SM, Beaudoux O, Bignon YJ, Bressac-De Paillerets B, Bronner M, Buell CM, Collod-Béroud G, Coulet F, Derive N, Divincenzo C, Elzinga CD, Garrec C, Houdayer C, Karbassi I, Lizard S, Love A, Muller D, Nagan N, Nery CR, Rai G, Revillion F, Salgado D, Sévenet N, Sinilnikova O, Sobol H, Stoppa-Lyonnet D, Toulas C, Trautman E, Vaur D, Vilquin P, Weymouth KS, Willis A, Eisenberg M, Strom CM. BRCA Share: A Collection of Clinical BRCA Gene Variants. Hum Mutat 2016; 37:1318-1328. [DOI: 10.1002/humu.23113] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 09/02/2016] [Indexed: 12/12/2022]
Affiliation(s)
- Christophe Béroud
- Aix Marseille Univ; INSERM, GMGF Marseille France
- APHM; Hôpital TIMONE Enfants; Laboratoire de Génétique Moléculaire; Marseille France
| | | | | | - Sandrine M. Caputo
- Service de Génétique; Department de Biologie des Tumeurs; Institut Curie; Paris France
| | | | | | | | | | | | | | - Florence Coulet
- Groupe hospitalier Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, Laboratoire d'Oncogénétique et Angiogénétique moléculaire; Université Pierre et Marie Curie; Paris France
| | - Nicolas Derive
- Service de Génétique; Department de Biologie des Tumeurs; Institut Curie; Paris France
| | | | | | | | - Claude Houdayer
- Service de Génétique; Department de Biologie des Tumeurs; Institut Curie; Paris France
- Université Paris Descartes; Paris France
| | | | - Sarab Lizard
- CHU de Dijon; Hôpital d'Enfants; Service de Génétique Médicale Dijon France
| | - Angela Love
- Quest Diagnostics; Marlborough Massachusetts
| | | | | | | | - Ghadi Rai
- Aix Marseille Univ; INSERM, GMGF Marseille France
| | | | | | | | | | | | - Dominique Stoppa-Lyonnet
- Service de Génétique; Department de Biologie des Tumeurs; Institut Curie; Paris France
- Université Paris Descartes; Paris France
| | | | - Edwin Trautman
- Laboratory Corporation of America; Westborough Massachusetts
| | - Dominique Vaur
- Laboratoire de biologie et de génétique du cancer; CLCC François Baclesse; INSERM 1079 Centre Normand de Génomique et de Médecine Personnalisée; Caen France
| | - Paul Vilquin
- Laboratoire de Biologie Cellulaire et Hormonale (CHU Arnaud de Villeneuve); Montpellier France
| | | | - Alecia Willis
- Laboratory Corporation of America; Research Triangle Park North Carolina
| | - Marcia Eisenberg
- Laboratory Corporation of America; Research Triangle Park North Carolina
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37
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de la Hoya M, Soukarieh O, López-Perolio I, Vega A, Walker LC, van Ierland Y, Baralle D, Santamariña M, Lattimore V, Wijnen J, Whiley P, Blanco A, Raponi M, Hauke J, Wappenschmidt B, Becker A, Hansen TVO, Behar R, Investigators KC, Niederacher D, Arnold N, Dworniczak B, Steinemann D, Faust U, Rubinstein W, Hulick PJ, Houdayer C, Caputo SM, Castera L, Pesaran T, Chao E, Brewer C, Southey MC, van Asperen CJ, Singer CF, Sullivan J, Poplawski N, Mai P, Peto J, Johnson N, Burwinkel B, Surowy H, Bojesen SE, Flyger H, Lindblom A, Margolin S, Chang-Claude J, Rudolph A, Radice P, Galastri L, Olson JE, Hallberg E, Giles GG, Milne RL, Andrulis IL, Glendon G, Hall P, Czene K, Blows F, Shah M, Wang Q, Dennis J, Michailidou K, McGuffog L, Bolla MK, Antoniou AC, Easton DF, Couch FJ, Tavtigian S, Vreeswijk MP, Parsons M, Meeks HD, Martins A, Goldgar DE, Spurdle AB. Combined genetic and splicing analysis of BRCA1 c.[594-2A>C; 641A>G] highlights the relevance of naturally occurring in-frame transcripts for developing disease gene variant classification algorithms. Hum Mol Genet 2016; 25:2256-2268. [PMID: 27008870 PMCID: PMC5081057 DOI: 10.1093/hmg/ddw094] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 02/10/2016] [Accepted: 03/17/2016] [Indexed: 12/13/2022] Open
Abstract
A recent analysis using family history weighting and co-observation classification modeling indicated that BRCA1 c.594-2A > C (IVS9-2A > C), previously described to cause exon 10 skipping (a truncating alteration), displays characteristics inconsistent with those of a high risk pathogenic BRCA1 variant. We used large-scale genetic and clinical resources from the ENIGMA, CIMBA and BCAC consortia to assess pathogenicity of c.594-2A > C. The combined odds for causality considering case-control, segregation and breast tumor pathology information was 3.23 × 10-8 Our data indicate that c.594-2A > C is always in cis with c.641A > G. The spliceogenic effect of c.[594-2A > C;641A > G] was characterized using RNA analysis of human samples and splicing minigenes. As expected, c.[594-2A > C; 641A > G] caused exon 10 skipping, albeit not due to c.594-2A > C impairing the acceptor site but rather by c.641A > G modifying exon 10 splicing regulatory element(s). Multiple blood-based RNA assays indicated that the variant allele did not produce detectable levels of full-length transcripts, with a per allele BRCA1 expression profile composed of ≈70-80% truncating transcripts, and ≈20-30% of in-frame Δ9,10 transcripts predicted to encode a BRCA1 protein with tumor suppression function.We confirm that BRCA1c.[594-2A > C;641A > G] should not be considered a high-risk pathogenic variant. Importantly, results from our detailed mRNA analysis suggest that BRCA-associated cancer risk is likely not markedly increased for individuals who carry a truncating variant in BRCA1 exons 9 or 10, or any other BRCA1 allele that permits 20-30% of tumor suppressor function. More generally, our findings highlight the importance of assessing naturally occurring alternative splicing for clinical evaluation of variants in disease-causing genes.
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Affiliation(s)
- Miguel de la Hoya
- Molecular Oncology Laboratory, Instituto de Investigacion Sanitaria San Carlos (IdISSC), Hospital Clinico San Carlos, Madrid, Spain
| | - Omar Soukarieh
- Inserm U1079-IRIB, University of Rouen, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Irene López-Perolio
- Molecular Oncology Laboratory, Instituto de Investigacion Sanitaria San Carlos (IdISSC), Hospital Clinico San Carlos, Madrid, Spain
| | - Ana Vega
- Fundacion Publica Galega de Medicina Xenómica-SERGAS Grupo de Medicina Xenómica-USC, IDIS, CIBERER, Santiago de Compostela 15706, Spain
| | - Logan C Walker
- Department of Pathology, University of Otago, Christchurch 8140, New Zealand
| | - Yvette van Ierland
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden 2300, The Netherlands
| | - Diana Baralle
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton S016 5YA, UK
| | - Marta Santamariña
- CIBERER, Grupo de Medicina Xenómica-USC, Universidade de Santiago de Compostela, Fundacion Galega de Medicina Xenómica (SERGAS), Santiago de Compostela 15706, Spain
| | - Vanessa Lattimore
- Department of Pathology, University of Otago, Christchurch 8140, New Zealand
| | - Juul Wijnen
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden 2300, The Netherlands Department of Clinical Genetics, Leiden University Medical Centre, Leiden 2300, The Netherlands
| | - Philip Whiley
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Ana Blanco
- Fundacion Publica Galega de Medicina Xenómica-SERGAS Grupo de Medicina Xenómica-USC, IDIS, CIBERER, Santiago de Compostela 15706, Spain
| | - Michela Raponi
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton S016 5YA, UK
| | - Jan Hauke
- Center for Hereditary Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Medical Faculty, University Hosptial Cologne, Cologne 50931, Germany
| | - Barbara Wappenschmidt
- Center for Hereditary Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Medical Faculty, University Hosptial Cologne, Cologne 50931, Germany
| | - Alexandra Becker
- Center for Hereditary Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Medical Faculty, University Hosptial Cologne, Cologne 50931, Germany
| | - Thomas V O Hansen
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen DK-2100, Denmark
| | - Raquel Behar
- Molecular Oncology Laboratory, Instituto de Investigacion Sanitaria San Carlos (IdISSC), Hospital Clinico San Carlos, Madrid, Spain
| | - KConFaB Investigators
- Peter MacCallum Cancer Center, University of Melbourne, Melbourne, VIC 3002, Australia
| | - Diether Niederacher
- Department of Gynaecology and Obstetrics, University Hospital Düsseldorf, Heinrich-Heine University Düsseldorf, Düsseldorf 40225, Germany
| | - Norbert Arnold
- Department of Gynaecology and Obstetrics, University Hospital of Schleswig-Holstein, Campus Kiel, Christian-Albrechts University Kiel, Kiel 24105, Germany
| | - Bernd Dworniczak
- Institute of Human Genetics, University of Münster, Münster 48149, Germany
| | - Doris Steinemann
- Institute of Human Genetics, Hannover Medical School, Hannover 30625, Germany
| | - Ulrike Faust
- Institute of Medical Genetics and Applied Genomics, University Hospital Tuebingen, Tuebingen 72076, Germany
| | | | - Peter J Hulick
- Center for Medical Genetics, NorthShore University Health System, University of Chicago Pritzker School of Medicine, Evanston, IL 60201, USA
| | - Claude Houdayer
- Service de Génétique, Department de Biologie des Tumeurs, Institut Curie and INSERM U830, Centre de Recherche de l'Institut Curie, Paris, and Universite Paris Descartes, Sorbonne Paris Cite, Paris 75248, France
| | - Sandrine M Caputo
- Service de Génétique, Department de Biologie des Tumeurs, Institut Curie, Paris 75248, France
| | - Laurent Castera
- Centre Francois Baclesse, Laboratoire de Biologie et de Genetique du Cancer, 14076 Caen, Paris 75248, France
| | | | | | - Carole Brewer
- Department of Clinical Genetics, Royal Devon and Exeter Hospital, Exeter, UK
| | - Melissa C Southey
- Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Christi J van Asperen
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden 2300, The Netherlands
| | - Christian F Singer
- Department of Obstetrics and Gynaecology, Medical University of Vienna, Vienna, Austria, Waehringer Guertel 18-20, A 1090 Vienna, Austria
| | - Jan Sullivan
- Genetic Health Service NZ, South Island Hub, Christchurch Hospital, Christchurch 8140, New Zealand
| | - Nicola Poplawski
- Adult Genetics Unit, South Australian Clinical Genetics Service, SA Pathology at the Women's and Children's Hospital, North Adelaide, SA 5067, Australia University Department of Paediatrics, University of Adelaide, North Terrace, Adelaide, SA 5000, Australia
| | - Phuong Mai
- Clinical Genetics Branch, DCEG, NCI, NIH, Bethesda, MD, USA
| | - Julian Peto
- London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Nichola Johnson
- Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London SW3 6JB, UK Division of Breast Cancer Research, Institute of Cancer Research, London SW3 6JB, UK
| | - Barbara Burwinkel
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, Heidelberg 69120, Germany Molecular Epidemiology Group, German Cancer Research Center, DKFZ, Heidelberg 69120, Germany
| | - Harald Surowy
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, Heidelberg 69120, Germany Molecular Epidemiology Group, German Cancer Research Center, DKFZ, Heidelberg 69120, Germany
| | - Stig E Bojesen
- Copenhagen General Population Study, Herlev and Gentofte Hospital, Copenhagen 2730, Denmark Department of Clinical Biochemistry, Herlev Hospital, Copenhagen University Hospital, Herlev 2730, Denmark Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 1165, Denmark
| | - Henrik Flyger
- Department of Breast Surgery, Herlev and Gentofte Hospital, Copenhagen University Hospital, 2730 Denmark
| | - Annika Lindblom
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm SE-171 77, Sweden
| | - Sara Margolin
- Department of Oncology Pathology, Karolinska Institutet, Stockholm SE-171 77, Sweden
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg 20246, Germany
| | - Anja Rudolph
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Paolo Radice
- Unit of "Molecular bases of genetic risk and genetic testing", Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano 20139, Italy
| | - Laura Galastri
- Associazione Volontari Italiani Sangue (AVIS) comunale di Milano, Milano 20139, Italy
| | - Janet E Olson
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Emily Hallberg
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Graham G Giles
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, VIC 3010, Australia Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, VIC 3004, Australia
| | - Roger L Milne
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, VIC 3010, Australia Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, VIC 3004, Australia
| | - Irene L Andrulis
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada Department of Molecular Genetics, University of Toronto, M5B 1W8, Canada
| | - Gord Glendon
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm SE-171 77, Sweden
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm SE-171 77, Sweden
| | - Fiona Blows
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Mitul Shah
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Qin Wang
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Kyriaki Michailidou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK Department of Electron Microscopy/Molecular Pathology, The Cyprus Institute of Neurology and Genetics, 1683, Nicosia, Cyprus
| | - Lesley McGuffog
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Manjeet K Bolla
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, 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
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Fergus J Couch
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | | | - Maaike P Vreeswijk
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden 2300, The Netherlands
| | - Michael Parsons
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | | | - Alexandra Martins
- Inserm U1079-IRIB, University of Rouen, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - David E Goldgar
- Department of Dermatology, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84132, USA
| | - Amanda B Spurdle
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
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38
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Jhuraney A, Velkova A, Johnson RC, Kessing B, Carvalho RS, Whiley P, Spurdle AB, Vreeswijk MPG, Caputo SM, Millot GA, Vega A, Coquelle N, Galli A, Eccles D, Blok MJ, Pal T, van der Luijt RB, Santamariña Pena M, Neuhausen SL, Donenberg T, Machackova E, Thomas S, Vallée M, Couch FJ, Tavtigian SV, Glover JNM, Carvalho MA, Brody LC, Sharan SK, Monteiro AN. BRCA1 Circos: a visualisation resource for functional analysis of missense variants. J Med Genet 2015; 52:224-30. [PMID: 25643705 PMCID: PMC4392196 DOI: 10.1136/jmedgenet-2014-102766] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 11/29/2014] [Accepted: 12/05/2014] [Indexed: 11/17/2022]
Abstract
BACKGROUND Inactivating germline mutations in the tumour suppressor gene BRCA1 are associated with a significantly increased risk of developing breast and ovarian cancer. A large number (>1500) of unique BRCA1 variants have been identified in the population and can be classified as pathogenic, non-pathogenic or as variants of unknown significance (VUS). Many VUS are rare missense variants leading to single amino acid changes. Their impact on protein function cannot be directly inferred from sequence information, precluding assessment of their pathogenicity. Thus, functional assays are critical to assess the impact of these VUS on protein activity. BRCA1 is a multifunctional protein and different assays have been used to assess the impact of variants on different biochemical activities and biological processes. METHODS AND RESULTS To facilitate VUS analysis, we have developed a visualisation resource that compiles and displays functional data on all documented BRCA1 missense variants. BRCA1 Circos is a web-based visualisation tool based on the freely available Circos software package. The BRCA1 Circos web tool (http://research.nhgri.nih.gov/bic/circos/) aggregates data from all published BRCA1 missense variants for functional studies, harmonises their results and presents various functionalities to search and interpret individual-level functional information for each BRCA1 missense variant. CONCLUSIONS This research visualisation tool will serve as a quick one-stop publically available reference for all the BRCA1 missense variants that have been functionally assessed. It will facilitate meta-analysis of functional data and improve assessment of pathogenicity of VUS.
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Affiliation(s)
- Ankita Jhuraney
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
- University of South Florida Cancer Biology PhD Program, Tampa, Florida, USA
| | - Aneliya Velkova
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
- Genome Technology Branch, National Human Genome Research Institute, Bethesda, Maryland, USA
| | - Randall C Johnson
- Frederick National Laboratory for Cancer Research, National Cancer Institute, Fredrick, Maryland, USA
| | - Bailey Kessing
- Frederick National Laboratory for Cancer Research, National Cancer Institute, Fredrick, Maryland, USA
| | - Renato S Carvalho
- Instituto Federal de Educação, Ciência e Tecnologia, Rio de Janeiro, RJ, Brazil
- Instituto Nacional de Câncer, Divisão de Farmacologia, Rio de Janeiro, Brazil
| | - Phillip Whiley
- Genetics and Population Health Division, QIMR, BNE, Brisbane, Queensland, Australia
| | - Amanda B Spurdle
- Genetics and Population Health Division, QIMR, BNE, Brisbane, Queensland, Australia
| | - Maaike P G Vreeswijk
- Department of Human Genetics, Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Sandrine M Caputo
- Service de Génétique, Institut Curie, Hôpital René Huguenin, Paris, France
| | - Gael A Millot
- Institut Curie, Université Pierre et Marie Curie, Paris, France
| | - Ana Vega
- Fundación Pública Galega de Medicina Xenómica, Santiago, Spain
| | - Nicolas Coquelle
- Department of Biochemistry, University of Alberta, Alberta, Canada
| | - Alvaro Galli
- Instituto di Fisiologia Clinica, Consiglio Nazionale delle Ricerche, Pisa, Italy
| | | | - Marinus J Blok
- Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Tuya Pal
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Rob B van der Luijt
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | | | - Susan L Neuhausen
- Department of Population Sciences, Beckman Research Institute of the City of Hope, Duarte, California, USA
| | | | - Eva Machackova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Simon Thomas
- Salisbury District Hospital, Salisbury, Wiltshire, UK
| | - Maxime Vallée
- International Agency for Research on Cancer, Lyon, France
| | - Fergus J Couch
- Department of Laboratory Medicine and Pathology, and Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Sean V Tavtigian
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - J N Mark Glover
- Department of Biochemistry, University of Alberta, Alberta, Canada
| | - Marcelo A Carvalho
- Instituto Federal de Educação, Ciência e Tecnologia, Rio de Janeiro, RJ, Brazil
- Instituto Nacional de Câncer, Divisão de Farmacologia, Rio de Janeiro, Brazil
| | - Lawrence C Brody
- Genome Technology Branch, National Human Genome Research Institute, Bethesda, Maryland, USA
| | - Shyam K Sharan
- Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Alvaro N Monteiro
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
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39
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Guidugli L, Carreira A, Caputo SM, Ehlen A, Galli A, Monteiro ANA, Neuhausen SL, Hansen TVO, Couch FJ, Vreeswijk MPG. Functional assays for analysis of variants of uncertain significance in BRCA2. Hum Mutat 2013; 35:151-64. [PMID: 24323938 DOI: 10.1002/humu.22478] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Accepted: 10/28/2013] [Indexed: 01/11/2023]
Abstract
Missense variants in the BRCA2 gene are routinely detected during clinical screening for pathogenic mutations in patients with a family history of breast and ovarian cancer. These subtle changes frequently remain of unknown clinical significance because of the lack of genetic information that may help establish a direct correlation with cancer predisposition. Therefore, alternative ways of predicting the pathogenicity of these variants are urgently needed. Since BRCA2 is a protein involved in important cellular mechanisms such as DNA repair, replication, and cell cycle control, functional assays have been developed that exploit these cellular activities to explore the impact of the variants on protein function. In this review, we summarize assays developed and currently utilized for studying missense variants in BRCA2. We specifically depict details of each assay, including variants of uncertain significance analyzed, and describe a validation set of (genetically) proven pathogenic and neutral missense variants to serve as a golden standard for the validation of each assay. Guidelines are proposed to enable implementation of laboratory-based methods to assess the impact of the variant on cancer risk.
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Affiliation(s)
- Lucia Guidugli
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
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40
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Millot GA, Carvalho MA, Caputo SM, Vreeswijk MPG, Brown MA, Webb M, Rouleau E, Neuhausen SL, Hansen TVO, Galli A, Brandão RD, Blok MJ, Velkova A, Couch FJ, Monteiro ANA. A guide for functional analysis of BRCA1 variants of uncertain significance. Hum Mutat 2012; 33:1526-37. [PMID: 22753008 DOI: 10.1002/humu.22150] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Accepted: 05/29/2012] [Indexed: 12/12/2022]
Abstract
Germline mutations in the tumor suppressor gene BRCA1 confer an estimated lifetime risk of 56-80% for breast cancer and 15-60% for ovarian cancer. Since the mid 1990s when BRCA1 was identified, genetic testing has revealed over 1,500 unique germline variants. However, for a significant number of these variants, the effect on protein function is unknown making it difficult to infer the consequences on risks of breast and ovarian cancers. Thus, many individuals undergoing genetic testing for BRCA1 mutations receive test results reporting a variant of uncertain clinical significance (VUS), leading to issues in risk assessment, counseling, and preventive care. Here, we describe functional assays for BRCA1 to directly or indirectly assess the impact of a variant on protein conformation or function and how these results can be used to complement genetic data to classify a VUS as to its clinical significance. Importantly, these methods may provide a framework for genome-wide pathogenicity assignment.
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Affiliation(s)
- Gaël A Millot
- Institut Curie, CNRS, UMR 3244 Université Pierre et Marie Curie, Paris, France
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