1
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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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2
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Bouras A, Guidara S, Leone M, Buisson A, Martin-Denavit T, Dussart S, Lasset C, Giraud S, Bonnet-Dupeyron MN, Kherraf ZE, Sanlaville D, Fert-Ferrer S, Lebrun M, Bonadona V, Calender A, Boutry-Kryza N. Overview of the Genetic Causes of Hereditary Breast and Ovarian Cancer Syndrome in a Large French Patient Cohort. Cancers (Basel) 2023; 15:3420. [PMID: 37444530 DOI: 10.3390/cancers15133420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 06/19/2023] [Accepted: 06/27/2023] [Indexed: 07/15/2023] Open
Abstract
The use of multigene panel testing for patients with a predisposition to Hereditary Breast and Ovarian Cancer syndrome (HBOC) is increasing as the identification of mutations is useful for diagnosis and disease management. Here, we conducted a retrospective analysis of BRCA1/2 and non-BRCA gene sequencing in 4630 French HBOC suspected patients. Patients were investigated using a germline cancer panel including the 13 genes defined by The French Genetic and Cancer Group (GGC)-Unicancer. In the patients analyzed, 528 pathogenic and likely pathogenic variants (P/LP) were identified, including BRCA1 (n = 203, 38%), BRCA2 (n = 198, 37%), PALB2 (n = 46, 9%), RAD51C (n = 36, 7%), TP53 (n = 16, 3%), and RAD51D (n = 13, 2%). In addition, 35 novel (P/LP) variants, according to our knowledge, were identified, and double mutations in two distinct genes were found in five patients. Interestingly, retesting a subset of BRCA1/2-negative individuals with an expanded panel produced clinically relevant results in 5% of cases. Additionally, combining in silico (splicing impact prediction tools) and in vitro analyses (RT-PCR and Sanger sequencing) highlighted the deleterious impact of four candidate variants on splicing and translation. Our results present an overview of pathogenic variations of HBOC genes in the southeast of France, emphasizing the clinical relevance of cDNA analysis and the importance of retesting BRCA-negative individuals with an expanded panel.
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Affiliation(s)
- Ahmed Bouras
- Laboratory of Constitutional Genetics for Frequent Cancer HCL-CLB, Centre Léon Bérard, 69008 Lyon, France
- Team 'Endocrine Resistance, Methylation and Breast Cancer' Research Center of Lyon-CRCL, UMR Inserm 1052 CNRS 5286, 69008 Lyon, France
| | - Souhir Guidara
- Department of Genetics, Groupement Hospitalier EST, Hospices Civils de Lyon, 69500 Bron, France
- Department of Genetics, CHU Hédi Chaker, Sfax 3027, Tunisia
| | - Mélanie Leone
- Department of Genetics, Groupement Hospitalier EST, Hospices Civils de Lyon, 69500 Bron, France
| | - Adrien Buisson
- Department of Biopathology, Centre Léon Bérard, 69008 Lyon, France
| | - Tanguy Martin-Denavit
- Department of Genetics, Groupement Hospitalier EST, Hospices Civils de Lyon, 69500 Bron, France
- Center for Medical Genetics, Alpigène, 69007 Lyon, France
| | - Sophie Dussart
- Centre Léon Bérard, Unité de Prévention et Epidémiologie Génétique, 69008 Lyon, France
| | - Christine Lasset
- Centre Léon Bérard, Unité de Prévention et Epidémiologie Génétique, 69008 Lyon, France
| | - Sophie Giraud
- Department of Genetics, Groupement Hospitalier EST, Hospices Civils de Lyon, 69500 Bron, France
| | | | - Zine-Eddine Kherraf
- Institute for Advanced Biosciences, University Grenoble Alpes, INSERM, CNRS, 38000 Grenoble, France
- UM GI-DPI, University Hospital Grenoble Alpes, 38000 Grenoble, France
| | - Damien Sanlaville
- Department of Genetics, Groupement Hospitalier EST, Hospices Civils de Lyon, 69500 Bron, France
| | - Sandra Fert-Ferrer
- Genetics Departement, Centre Hospitalier Métropole Savoie, 73011 Chambery, France
| | - Marine Lebrun
- Department of Genetics, Saint Etienne University Hospital, 42270 Saint Priez en Jarez, France
| | - Valerie Bonadona
- Centre Léon Bérard, Unité de Prévention et Epidémiologie Génétique, 69008 Lyon, France
| | - Alain Calender
- Department of Genetics, Groupement Hospitalier EST, Hospices Civils de Lyon, 69500 Bron, France
| | - Nadia Boutry-Kryza
- Department of Genetics, Groupement Hospitalier EST, Hospices Civils de Lyon, 69500 Bron, France
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3
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Bouras A, Leone M, Bonadona V, Lebrun M, Calender A, Boutry-Kryza N. Identification and Characterization of New Alu Element Insertion in the BRCA1 Exon 14 Associated with Hereditary Breast and Ovarian Cancer. Genes (Basel) 2021; 12:genes12111736. [PMID: 34828342 PMCID: PMC8623961 DOI: 10.3390/genes12111736] [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: 10/13/2021] [Revised: 10/26/2021] [Accepted: 10/28/2021] [Indexed: 11/30/2022] Open
Abstract
Hereditary breast and ovarian cancer syndrome (HBOC) is an autosomal dominant cancer predisposition syndrome characterized by an increased risk of breast and ovarian cancers. Germline pathogenic variants in BRCA1 are found in about 7–10% of all familial breast cancers and 10% of ovarian cancers. Alu elements are the most abundant mobile DNA element in the human genome and are known to affect the human genome by different mechanisms leading to human disease. We report here the detection, by next-generation sequencing (NGS) analysis coupled with a suitable bioinformatics pipeline, of an AluYb8 element in exon 14 of the BRCA1 gene in a family with HBOC history first classified as BRCA-negative by Sanger sequencing and first NGS analysis. The c.4475_c.4476insAluYb8 mutation impacts splicing and induces the skipping of exon 14. As a result, the produced mRNA contains a premature stop, leading to the production of a short and likely non-functional protein (pAla1453Glyfs*10). Overall, our study allowed us to identify a novel pathogenic variant in BRCA1 and showed the importance of bioinformatics tool improvement and versioning.
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Affiliation(s)
- Ahmed Bouras
- Department of Molecular and Medical Genetics, Hospices Civils de Lyon, University Hospital, 69500 Bron, France; (M.L.); (A.C.); (N.B.-K.)
- Correspondence:
| | - Melanie Leone
- Department of Molecular and Medical Genetics, Hospices Civils de Lyon, University Hospital, 69500 Bron, France; (M.L.); (A.C.); (N.B.-K.)
| | - Valerie Bonadona
- Unit of Prevention and Genetic Epidemiology, UMR CNRS 5558, Centre Léon Bérard, 69008 Lyon, France;
| | - Marine Lebrun
- Department of Genetics, Saint Etienne University Hospital, 42270 Saint Priez en Jarez, France;
| | - Alain Calender
- Department of Molecular and Medical Genetics, Hospices Civils de Lyon, University Hospital, 69500 Bron, France; (M.L.); (A.C.); (N.B.-K.)
| | - Nadia Boutry-Kryza
- Department of Molecular and Medical Genetics, Hospices Civils de Lyon, University Hospital, 69500 Bron, France; (M.L.); (A.C.); (N.B.-K.)
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4
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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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5
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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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6
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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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7
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Leman R, Tubeuf H, Raad S, Tournier I, Derambure C, Lanos R, Gaildrat P, Castelain G, Hauchard J, Killian A, Baert-Desurmont S, Legros A, Goardon N, Quesnelle C, Ricou A, Castera L, Vaur D, Le Gac G, Ka C, Fichou Y, Bonnet-Dorion F, Sevenet N, Guillaud-Bataille M, Boutry-Kryza N, Schultz I, Caux-Moncoutier V, Rossing M, Walker LC, Spurdle AB, Houdayer C, Martins A, Krieger S. Assessment of branch point prediction tools to predict physiological branch points and their alteration by variants. BMC Genomics 2020; 21:86. [PMID: 31992191 PMCID: PMC6988378 DOI: 10.1186/s12864-020-6484-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [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: 07/16/2019] [Accepted: 01/10/2020] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Branch points (BPs) map within short motifs upstream of acceptor splice sites (3'ss) and are essential for splicing of pre-mature mRNA. Several BP-dedicated bioinformatics tools, including HSF, SVM-BPfinder, BPP, Branchpointer, LaBranchoR and RNABPS were developed during the last decade. Here, we evaluated their capability to detect the position of BPs, and also to predict the impact on splicing of variants occurring upstream of 3'ss. RESULTS We used a large set of constitutive and alternative human 3'ss collected from Ensembl (n = 264,787 3'ss) and from in-house RNAseq experiments (n = 51,986 3'ss). We also gathered an unprecedented collection of functional splicing data for 120 variants (62 unpublished) occurring in BP areas of disease-causing genes. Branchpointer showed the best performance to detect the relevant BPs upstream of constitutive and alternative 3'ss (99.48 and 65.84% accuracies, respectively). For variants occurring in a BP area, BPP emerged as having the best performance to predict effects on mRNA splicing, with an accuracy of 89.17%. CONCLUSIONS Our investigations revealed that Branchpointer was optimal to detect BPs upstream of 3'ss, and that BPP was most relevant to predict splicing alteration due to variants in the BP area.
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Affiliation(s)
- Raphaël Leman
- Laboratoire de Biologie Clinique et Oncologique, Centre François Baclesse, Caen, France. .,Inserm U1245, Normandy Center for Genomic and Personalized Medicine, Rouen, UNIROUEN, Normandy University, Caen, France. .,Université Caen-Normandie, Caen, France.
| | - Hélène Tubeuf
- Inserm U1245, Normandy Center for Genomic and Personalized Medicine, Rouen, UNIROUEN, Normandy University, Caen, France.,Interactive Biosoftware, Rouen, France
| | - Sabine Raad
- Inserm U1245, Normandy Center for Genomic and Personalized Medicine, Rouen, UNIROUEN, Normandy University, Caen, France
| | - Isabelle Tournier
- Inserm U1245, Normandy Center for Genomic and Personalized Medicine, Rouen, UNIROUEN, Normandy University, Caen, France
| | - Céline Derambure
- Inserm U1245, Normandy Center for Genomic and Personalized Medicine, Rouen, UNIROUEN, Normandy University, Caen, France
| | - Raphaël Lanos
- Inserm U1245, Normandy Center for Genomic and Personalized Medicine, Rouen, UNIROUEN, Normandy University, Caen, France
| | - Pascaline Gaildrat
- Inserm U1245, Normandy Center for Genomic and Personalized Medicine, Rouen, UNIROUEN, Normandy University, Caen, France
| | - Gaia Castelain
- Inserm U1245, Normandy Center for Genomic and Personalized Medicine, Rouen, UNIROUEN, Normandy University, Caen, France
| | - Julie Hauchard
- Inserm U1245, Normandy Center for Genomic and Personalized Medicine, Rouen, UNIROUEN, Normandy University, Caen, France
| | - Audrey Killian
- Inserm U1245, Normandy Center for Genomic and Personalized Medicine, Rouen, UNIROUEN, Normandy University, Caen, France
| | - Stéphanie Baert-Desurmont
- Inserm U1245, Normandy Center for Genomic and Personalized Medicine, Rouen, UNIROUEN, Normandy University, Caen, France
| | - Angelina Legros
- Laboratoire de Biologie Clinique et Oncologique, Centre François Baclesse, Caen, France
| | - Nicolas Goardon
- Laboratoire de Biologie Clinique et Oncologique, Centre François Baclesse, Caen, France.,Inserm U1245, Normandy Center for Genomic and Personalized Medicine, Rouen, UNIROUEN, Normandy University, Caen, France
| | - Céline Quesnelle
- Laboratoire de Biologie Clinique et Oncologique, Centre François Baclesse, Caen, France
| | - Agathe Ricou
- Laboratoire de Biologie Clinique et Oncologique, Centre François Baclesse, Caen, France.,Inserm U1245, Normandy Center for Genomic and Personalized Medicine, Rouen, UNIROUEN, Normandy University, Caen, France
| | - Laurent Castera
- Laboratoire de Biologie Clinique et Oncologique, Centre François Baclesse, Caen, France.,Inserm U1245, Normandy Center for Genomic and Personalized Medicine, Rouen, UNIROUEN, Normandy University, Caen, France
| | - Dominique Vaur
- Laboratoire de Biologie Clinique et Oncologique, Centre François Baclesse, Caen, France.,Inserm U1245, Normandy Center for Genomic and Personalized Medicine, Rouen, UNIROUEN, Normandy University, Caen, France
| | - Gérald Le Gac
- Inserm UMR1078, Genetics, Functional Genomics and Biotechnology, Université de Bretagne Occidentale, Brest, France
| | - Chandran Ka
- Inserm UMR1078, Genetics, Functional Genomics and Biotechnology, Université de Bretagne Occidentale, Brest, France
| | - Yann Fichou
- Inserm UMR1078, Genetics, Functional Genomics and Biotechnology, Université de Bretagne Occidentale, Brest, France
| | - Françoise Bonnet-Dorion
- Inserm U916, Département de Pathologie, Laboratoire de Génétique Constitutionnelle, Institut Bergonié, Bordeaux, France
| | - Nicolas Sevenet
- Inserm U916, Département de Pathologie, Laboratoire de Génétique Constitutionnelle, Institut Bergonié, Bordeaux, France
| | | | - Nadia Boutry-Kryza
- Lyon Neuroscience Research Center-CRNL, Inserm U1028, CNRS UMR 5292, University of Lyon, Lyon, France
| | - Inès Schultz
- Laboratoire d'Oncogénétique, Centre Paul Strauss, Strasbourg, France
| | | | - Maria Rossing
- Centre for Genomic Medicine, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Logan C Walker
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Amanda B Spurdle
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Claude Houdayer
- Inserm U1245, Normandy Center for Genomic and Personalized Medicine, Rouen, UNIROUEN, Normandy University, Caen, France
| | - Alexandra Martins
- Inserm U1245, Normandy Center for Genomic and Personalized Medicine, Rouen, UNIROUEN, Normandy University, Caen, France
| | - Sophie Krieger
- Laboratoire de Biologie Clinique et Oncologique, Centre François Baclesse, Caen, France. .,Inserm U1245, Normandy Center for Genomic and Personalized Medicine, Rouen, UNIROUEN, Normandy University, Caen, France. .,Université Caen-Normandie, Caen, France. .,Present address: Laboratoire de biologie et génétique des cancers, Centre François Baclesse, Caen, France.
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8
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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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9
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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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10
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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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11
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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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12
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Alfaiz AA, Müller V, Boutry-Kryza N, Ville D, Guex N, de Bellescize J, Rivier C, Labalme A, des Portes V, Edery P, Till M, Xenarios I, Sanlaville D, Herrmann JM, Lesca G, Reymond A. West syndrome caused by homozygous variant in the evolutionary conserved gene encoding the mitochondrial elongation factor GUF1. Eur J Hum Genet 2015; 24:1001-8. [PMID: 26486472 DOI: 10.1038/ejhg.2015.227] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 09/12/2015] [Accepted: 09/18/2015] [Indexed: 12/15/2022] Open
Abstract
West syndrome (WS), defined by the triad of infantile spasms, pathognomonic hypsarrhythmia and developmental regression, is a rare epileptic disease affecting about 1:3500 live births. To get better insights on the genetic of this pathology, we exome-sequenced the members of a consanguineous family affected with isolated WS. We identified a homozygous variant (c.1825G>T/p.(Ala609Ser)) in the GUF1 gene in the three affected siblings. GUF1 encodes a protein essential in conditions that counteract faithful protein synthesis: it is able to remobilize stuck ribosomes and transiently inhibit the elongation process to optimize protein synthesis. The variant identified in the WS family changes an alanine residue conserved in all eukaryotic organisms and positioned within the tRNA-binding moiety of this nuclear genome-encoded mitochondrial translational elongation factor. Yeast complementation assays show that the activity of GUF1(A609S) is modified in suboptimal environments. We suggest a new link between improper assembly of respiratory chain complexes and WS.
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Affiliation(s)
- Ali Abdullah Alfaiz
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.,King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences (KSAU-HS), Riyadh, Saudi Arabia
| | - Verena Müller
- Division of Cell Biology, Department of Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Nadia Boutry-Kryza
- Department of Constitutional Cytogenetics, Lyon Hospices Civils, Lyon, France.,Claude Bernard Lyon I University, Lyon, France.,CRNL, CNRS UMR 5292, INSERM U1028, Lyon, France
| | - Dorothée Ville
- Center of Reference for Tuberous Sclerosis and Rare Epileptic Disorders, Hospices Civils de Lyon, Lyon, France
| | - Nicolas Guex
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | | | - Clotilde Rivier
- Department of Pediatrics, Hopital Nord-Ouest, Villefranche-sur-Saône, France
| | - Audrey Labalme
- Department of Constitutional Cytogenetics, Lyon Hospices Civils, Lyon, France
| | - Vincent des Portes
- Claude Bernard Lyon I University, Lyon, France.,Center of Reference for Tuberous Sclerosis and Rare Epileptic Disorders, Hospices Civils de Lyon, Lyon, France
| | - Patrick Edery
- Department of Constitutional Cytogenetics, Lyon Hospices Civils, Lyon, France.,Claude Bernard Lyon I University, Lyon, France.,CRNL, CNRS UMR 5292, INSERM U1028, Lyon, France
| | - Marianne Till
- Department of Constitutional Cytogenetics, Lyon Hospices Civils, Lyon, France
| | - Ioannis Xenarios
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Damien Sanlaville
- Department of Constitutional Cytogenetics, Lyon Hospices Civils, Lyon, France.,Claude Bernard Lyon I University, Lyon, France.,CRNL, CNRS UMR 5292, INSERM U1028, Lyon, France
| | - Johannes M Herrmann
- Division of Cell Biology, Department of Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Gaétan Lesca
- Department of Constitutional Cytogenetics, Lyon Hospices Civils, Lyon, France.,Claude Bernard Lyon I University, Lyon, France.,CRNL, CNRS UMR 5292, INSERM U1028, Lyon, France
| | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
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13
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Dimassi S, Simonet T, Labalme A, Boutry-Kryza N, Campan-Fournier A, Lamy R, Bardel C, Elsensohn MH, Roucher-Boulez F, Chatron N, Putoux A, de Bellescize J, Ville D, Schaeffer L, Roy P, Mougou-Zerelli S, Saad A, Calender A, Sanlaville D, Lesca G. Comparison of two next-generation sequencing kits for diagnosis of epileptic disorders with a user-friendly tool for displaying gene coverage, DeCovA. Appl Transl Genom 2015; 7:19-25. [PMID: 27054081 PMCID: PMC4803767 DOI: 10.1016/j.atg.2015.10.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [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: 07/17/2015] [Revised: 09/25/2015] [Accepted: 10/06/2015] [Indexed: 11/30/2022]
Affiliation(s)
- Sarra Dimassi
- Department of Medical Genetics, Lyon University Hospital, Lyon, France
- CNRL, CNRS UMR 5292, INSERM U1028, Lyon, France
- Claude Bernard Lyon I University, Lyon, France
| | - Thomas Simonet
- Department of Cell Biotechnology, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
| | - Audrey Labalme
- Department of Medical Genetics, Lyon University Hospital, Lyon, France
| | | | | | - Raphaelle Lamy
- Department of Medical Genetics, Lyon University Hospital, Lyon, France
| | - Claire Bardel
- Claude Bernard Lyon I University, Lyon, France
- Service de Biostatistique, Hospices Civils de Lyon, Lyon, France
- CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, Equipe Biostatistique-Santé, Villeurbanne, France
| | - Mad-Hélénie Elsensohn
- Claude Bernard Lyon I University, Lyon, France
- Service de Biostatistique, Hospices Civils de Lyon, Lyon, France
- CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, Equipe Biostatistique-Santé, Villeurbanne, France
| | - Florence Roucher-Boulez
- Claude Bernard Lyon I University, Lyon, France
- CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, Equipe Biostatistique-Santé, Villeurbanne, France
- Cytogenetics and Reproductive Biology Department, Farhat Hached University Teaching Hospital, Sousse, Tunisia
| | - Nicolas Chatron
- Department of Medical Genetics, Lyon University Hospital, Lyon, France
| | - Audrey Putoux
- Department of Medical Genetics, Lyon University Hospital, Lyon, France
- CNRL, CNRS UMR 5292, INSERM U1028, Lyon, France
- Claude Bernard Lyon I University, Lyon, France
| | - Julitta de Bellescize
- Common Service Units for Research in Genetics, Faculty of Medicine of Sousse, University of Sousse, Sousse, Tunisia
| | - Dorothée Ville
- Department of Neuropediatrics, Reference Center for Tuberous Sclerosis and Rare Epileptic Syndromes, Lyon University Hospital, Lyon, France
| | - Laurent Schaeffer
- Claude Bernard Lyon I University, Lyon, France
- Department of Cell Biotechnology, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
| | - Pascal Roy
- Claude Bernard Lyon I University, Lyon, France
- Service de Biostatistique, Hospices Civils de Lyon, Lyon, France
- CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, Equipe Biostatistique-Santé, Villeurbanne, France
| | - Soumaya Mougou-Zerelli
- Cytogenetics and Reproductive Biology Department, Farhat Hached University Teaching Hospital, Sousse, Tunisia
- Common Service Units for Research in Genetics, Faculty of Medicine of Sousse, University of Sousse, Sousse, Tunisia
| | - Ali Saad
- Cytogenetics and Reproductive Biology Department, Farhat Hached University Teaching Hospital, Sousse, Tunisia
- Common Service Units for Research in Genetics, Faculty of Medicine of Sousse, University of Sousse, Sousse, Tunisia
| | - Alain Calender
- Department of Medical Genetics, Lyon University Hospital, Lyon, France
- Claude Bernard Lyon I University, Lyon, France
| | - Damien Sanlaville
- Department of Medical Genetics, Lyon University Hospital, Lyon, France
- CNRL, CNRS UMR 5292, INSERM U1028, Lyon, France
- Claude Bernard Lyon I University, Lyon, France
- Corresponding author at: Service de Génétique, Groupement Hospitalier Est, 59 Boulevard Pinel, 69677 Bron, France.Service de GénétiqueGroupement Hospitalier Est59 Boulevard PinelBron69677France
| | - Gaetan Lesca
- Department of Medical Genetics, Lyon University Hospital, Lyon, France
- CNRL, CNRS UMR 5292, INSERM U1028, Lyon, France
- Claude Bernard Lyon I University, Lyon, France
- Corresponding author at: Service de Génétique, Groupement Hospitalier Est, 59 Boulevard Pinel, 69677 Bron, France.Service de GénétiqueGroupement Hospitalier Est59 Boulevard PinelBron69677France
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14
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Dimassi S, Labalme A, Ville D, Calender A, Mignot C, Boutry-Kryza N, de Bellescize J, Rivier-Ringenbach C, Bourel-Ponchel E, Cheillan D, Simonet T, Maincent K, Rossi M, Till M, Mougou-Zerelli S, Edery P, Saad A, Heron D, des Portes V, Sanlaville D, Lesca G. Whole-exome sequencing improves the diagnosis yield in sporadic infantile spasm syndrome. Clin Genet 2015; 89:198-204. [PMID: 26138355 DOI: 10.1111/cge.12636] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [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: 05/04/2015] [Revised: 06/13/2015] [Accepted: 06/29/2015] [Indexed: 12/25/2022]
Abstract
Infantile spasms syndrome (ISs) is characterized by clinical spasms with ictal electrodecrement, usually occurring before the age of 1 year and frequently associated with cognitive impairment. Etiology is widely heterogeneous, the cause remaining elusive in 40% of patients. We searched for de novo mutations in 10 probands with ISs and their parents using whole-exome sequencing (WES). Patients had neither consanguinity nor family history of epilepsy. Common causes of ISs were excluded by brain magnetic resonance imaging (MRI), metabolic screening, array-comparative genomic hybridization (CGH) and testing for mutations in CDKL5, STXBP1, and for ARX duplications. We found a probably pathogenic mutation in four patients. Missense mutations in SCN2A (p.Leu1342Pro) and KCNQ2 (p.Ala306Thr) were found in two patients with no history of epilepsy before the onset of ISs. The p.Asn107Ser missense mutation of ALG13 had been previously reported in four females with ISs. The fourth mutation was an in-frame deletion (p.Phe110del) in NR2F1, a gene whose mutations cause intellectual disability, epilepsy, and optic atrophy. In addition, we found a possibly pathogenic variant in KIF3C that encodes a kinesin expressed during neural development. Our results confirm that WES improves significantly the diagnosis yield in patients with sporadic ISs.
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Affiliation(s)
- S Dimassi
- Department of Medical Genetics, Lyon University Hospital, Lyon, France.,CNRS UMR 5292, INSERM U1028, CNRL, Lyon, France.,Claude Bernard Lyon I University, University of Lyon, Lyon, France.,Cytogenetics and Reproductive Biology Department, Farhat Hached University Teaching Hospital, Sousse, Tunisia.,Common Service Units for Research in Genetics, Faculty of Medicine of Sousse, Avenue Mohamed Karoui, University of Sousse, Tunisia
| | - A Labalme
- Department of Medical Genetics, Lyon University Hospital, Lyon, France
| | - D Ville
- Department of Neuropediatrics, Lyon University Hospital, Lyon, France
| | - A Calender
- Claude Bernard Lyon I University, University of Lyon, Lyon, France.,Department of Molecular Genetics, Lyon University Hospital, Lyon, France
| | - C Mignot
- Département de Génétique et Centre de Référence "Déficiences intellectuelles de causes rares", AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Paris, France.,Department of Pediatric Neurophysiology, Amiens University Hospital, Amiens, France
| | - N Boutry-Kryza
- CNRS UMR 5292, INSERM U1028, CNRL, Lyon, France.,Claude Bernard Lyon I University, University of Lyon, Lyon, France.,Department of Molecular Genetics, Lyon University Hospital, Lyon, France
| | - J de Bellescize
- Epilepsy, Sleep and Pediatric Neurophysiology Department, Lyon University Hospital, Lyon, France
| | - C Rivier-Ringenbach
- Department of Pediatrics, Nord-Ouest Hospital, Villefranche-sur-Saone, France
| | - E Bourel-Ponchel
- Department of Pediatric Neurophysiology, Amiens University Hospital, Amiens, France
| | - D Cheillan
- Claude Bernard Lyon I University, University of Lyon, Lyon, France.,Service des Maladies Héréditaires du métabolisme, INSERM U1060, Lyon University Hospital, Lyon, France
| | - T Simonet
- Department of Cell Biotechnology, ENS Lyon, Lyon University Hospital, Lyon, France
| | - K Maincent
- Department of Pediatric Neurology, Hôpital Trousseau, Assistance Publique des Hôpitaux de Paris, Paris, France
| | - M Rossi
- Department of Medical Genetics, Lyon University Hospital, Lyon, France.,CNRS UMR 5292, INSERM U1028, CNRL, Lyon, France
| | - M Till
- Department of Medical Genetics, Lyon University Hospital, Lyon, France
| | - S Mougou-Zerelli
- Cytogenetics and Reproductive Biology Department, Farhat Hached University Teaching Hospital, Sousse, Tunisia.,Common Service Units for Research in Genetics, Faculty of Medicine of Sousse, Avenue Mohamed Karoui, University of Sousse, Tunisia
| | - P Edery
- Department of Medical Genetics, Lyon University Hospital, Lyon, France.,CNRS UMR 5292, INSERM U1028, CNRL, Lyon, France.,Claude Bernard Lyon I University, University of Lyon, Lyon, France
| | - A Saad
- Cytogenetics and Reproductive Biology Department, Farhat Hached University Teaching Hospital, Sousse, Tunisia.,Common Service Units for Research in Genetics, Faculty of Medicine of Sousse, Avenue Mohamed Karoui, University of Sousse, Tunisia
| | - D Heron
- Département de Génétique et Centre de Référence "Déficiences intellectuelles de causes rares", AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Paris, France.,GRC-Génétique des Déficiences Intellectuelles de Causes rares, Université Pierre et Marie Curie, Paris, France
| | - V des Portes
- Department of Neuropediatrics, Lyon University Hospital, Lyon, France.,Department of Molecular Genetics, Lyon University Hospital, Lyon, France.,Reference Center for Tuberous Sclerosis and Rare Epileptic Syndromes, Lyon University Hospital, Lyon, France
| | - D Sanlaville
- Department of Medical Genetics, Lyon University Hospital, Lyon, France.,CNRS UMR 5292, INSERM U1028, CNRL, Lyon, France.,Claude Bernard Lyon I University, University of Lyon, Lyon, France
| | - G Lesca
- Department of Medical Genetics, Lyon University Hospital, Lyon, France.,CNRS UMR 5292, INSERM U1028, CNRL, Lyon, France.,Claude Bernard Lyon I University, University of Lyon, Lyon, France
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Rebbeck TR, Mitra N, Wan F, Sinilnikova OM, Healey S, McGuffog L, Mazoyer S, Chenevix-Trench G, Easton DF, Antoniou AC, Nathanson KL, Laitman Y, Kushnir A, Paluch-Shimon S, Berger R, Zidan J, Friedman E, Ehrencrona H, Stenmark-Askmalm M, Einbeigi Z, Loman N, Harbst K, Rantala J, Melin B, Huo D, Olopade OI, Seldon J, Ganz PA, Nussbaum RL, Chan SB, Odunsi K, Gayther SA, Domchek SM, Arun BK, Lu KH, Mitchell G, Karlan BY, Walsh C, Lester J, Godwin AK, Pathak H, Ross E, Daly MB, Whittemore AS, John EM, Miron A, Terry MB, Chung WK, Goldgar DE, Buys SS, Janavicius R, Tihomirova L, Tung N, Dorfling CM, van Rensburg EJ, Steele L, Neuhausen SL, Ding YC, Ejlertsen B, Gerdes AM, Hansen TVO, Ramón y Cajal T, Osorio A, Benitez J, Godino J, Tejada MI, Duran M, Weitzel JN, Bobolis KA, Sand SR, Fontaine A, Savarese A, Pasini B, Peissel B, Bonanni B, Zaffaroni D, Vignolo-Lutati F, Scuvera G, Giannini G, Bernard L, Genuardi M, Radice P, Dolcetti R, Manoukian S, Pensotti V, Gismondi V, Yannoukakos D, Fostira F, Garber J, Torres D, Rashid MU, Hamann U, Peock S, Frost D, Platte R, Evans DG, Eeles R, Davidson R, Eccles D, Cole T, Cook J, Brewer C, Hodgson S, Morrison PJ, Walker L, Porteous ME, Kennedy MJ, Izatt L, Adlard J, Donaldson A, Ellis S, Sharma P, Schmutzler RK, Wappenschmidt B, Becker A, Rhiem K, Hahnen E, Engel C, Meindl A, Engert S, Ditsch N, Arnold N, Plendl HJ, Mundhenke C, Niederacher D, Fleisch M, Sutter C, Bartram CR, Dikow N, Wang-Gohrke S, Gadzicki D, Steinemann D, Kast K, Beer M, Varon-Mateeva R, Gehrig A, Weber BH, Stoppa-Lyonnet D, Sinilnikova OM, Mazoyer S, Houdayer C, Belotti M, Gauthier-Villars M, Damiola F, Boutry-Kryza N, Lasset C, Sobol H, Peyrat JP, Muller D, Fricker JP, Collonge-Rame MA, Mortemousque I, Nogues C, Rouleau E, Isaacs C, De Paepe A, Poppe B, Claes K, De Leeneer K, Piedmonte M, Rodriguez G, Wakely K, Boggess J, Blank SV, Basil J, Azodi M, Phillips KA, Caldes T, de la Hoya M, Romero A, Nevanlinna H, Aittomäki K, van der Hout AH, Hogervorst FBL, Verhoef S, Collée JM, Seynaeve C, Oosterwijk JC, Gille JJP, Wijnen JT, Gómez Garcia EB, Kets CM, Ausems MGEM, Aalfs CM, Devilee P, Mensenkamp AR, Kwong A, Olah E, Papp J, Diez O, Lazaro C, Darder E, Blanco I, Salinas M, Jakubowska A, Lubinski J, Gronwald J, Jaworska-Bieniek K, Durda K, Sukiennicki G, Huzarski T, Byrski T, Cybulski C, Toloczko-Grabarek A, Złowocka-Perłowska E, Menkiszak J, Arason A, Barkardottir RB, Simard J, Laframboise R, Montagna M, Agata S, Alducci E, Peixoto A, Teixeira MR, Spurdle AB, Lee MH, Park SK, Kim SW, Friebel TM, Couch FJ, Lindor NM, Pankratz VS, Guidugli L, Wang X, Tischkowitz M, Foretova L, Vijai J, Offit K, Robson M, Rau-Murthy R, Kauff N, Fink-Retter A, Singer CF, Rappaport C, Gschwantler-Kaulich D, Pfeiler G, Tea MK, Berger A, Greene MH, Mai PL, Imyanitov EN, Toland AE, Senter L, Bojesen A, Pedersen IS, Skytte AB, Sunde L, Thomassen M, Moeller ST, Kruse TA, Jensen UB, Caligo MA, Aretini P, Teo SH, Selkirk CG, Hulick PJ, Andrulis I. Association of type and location of BRCA1 and BRCA2 mutations with risk of breast and ovarian cancer. JAMA 2015; 313:1347-61. [PMID: 25849179 PMCID: PMC4537700 DOI: 10.1001/jama.2014.5985] [Citation(s) in RCA: 347] [Impact Index Per Article: 38.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
IMPORTANCE Limited information about the relationship between specific mutations in BRCA1 or BRCA2 (BRCA1/2) and cancer risk exists. OBJECTIVE To identify mutation-specific cancer risks for carriers of BRCA1/2. DESIGN, SETTING, AND PARTICIPANTS Observational study of women who were ascertained between 1937 and 2011 (median, 1999) and found to carry disease-associated BRCA1 or BRCA2 mutations. The international sample comprised 19,581 carriers of BRCA1 mutations and 11,900 carriers of BRCA2 mutations from 55 centers in 33 countries on 6 continents. We estimated hazard ratios for breast and ovarian cancer based on mutation type, function, and nucleotide position. We also estimated RHR, the ratio of breast vs ovarian cancer hazard ratios. A value of RHR greater than 1 indicated elevated breast cancer risk; a value of RHR less than 1 indicated elevated ovarian cancer risk. EXPOSURES Mutations of BRCA1 or BRCA2. MAIN OUTCOMES AND MEASURES Breast and ovarian cancer risks. RESULTS Among BRCA1 mutation carriers, 9052 women (46%) were diagnosed with breast cancer, 2317 (12%) with ovarian cancer, 1041 (5%) with breast and ovarian cancer, and 7171 (37%) without cancer. Among BRCA2 mutation carriers, 6180 women (52%) were diagnosed with breast cancer, 682 (6%) with ovarian cancer, 272 (2%) with breast and ovarian cancer, and 4766 (40%) without cancer. In BRCA1, we identified 3 breast cancer cluster regions (BCCRs) located at c.179 to c.505 (BCCR1; RHR = 1.46; 95% CI, 1.22-1.74; P = 2 × 10(-6)), c.4328 to c.4945 (BCCR2; RHR = 1.34; 95% CI, 1.01-1.78; P = .04), and c. 5261 to c.5563 (BCCR2', RHR = 1.38; 95% CI, 1.22-1.55; P = 6 × 10(-9)). We also identified an ovarian cancer cluster region (OCCR) from c.1380 to c.4062 (approximately exon 11) with RHR = 0.62 (95% CI, 0.56-0.70; P = 9 × 10(-17)). In BRCA2, we observed multiple BCCRs spanning c.1 to c.596 (BCCR1; RHR = 1.71; 95% CI, 1.06-2.78; P = .03), c.772 to c.1806 (BCCR1'; RHR = 1.63; 95% CI, 1.10-2.40; P = .01), and c.7394 to c.8904 (BCCR2; RHR = 2.31; 95% CI, 1.69-3.16; P = .00002). We also identified 3 OCCRs: the first (OCCR1) spanned c.3249 to c.5681 that was adjacent to c.5946delT (6174delT; RHR = 0.51; 95% CI, 0.44-0.60; P = 6 × 10(-17)). The second OCCR spanned c.6645 to c.7471 (OCCR2; RHR = 0.57; 95% CI, 0.41-0.80; P = .001). Mutations conferring nonsense-mediated decay were associated with differential breast or ovarian cancer risks and an earlier age of breast cancer diagnosis for both BRCA1 and BRCA2 mutation carriers. CONCLUSIONS AND RELEVANCE Breast and ovarian cancer risks varied by type and location of BRCA1/2 mutations. With appropriate validation, these data may have implications for risk assessment and cancer prevention decision making for carriers of BRCA1 and BRCA2 mutations.
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Affiliation(s)
- Timothy R Rebbeck
- Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia2Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia
| | - Nandita Mitra
- Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia
| | - Fei Wan
- Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia
| | - Olga M Sinilnikova
- Centre de Recherche en Cancérologie de Lyon, UMR Inserm, Centre Léon Bérard, Lyon, France
| | - Sue Healey
- Department of Genetics and Computational Biology, Queensland Institute of Medical Research, Brisbane, Australia
| | - Lesley McGuffog
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Sylvie Mazoyer
- Centre de Recherche en Cancérologie de Lyon, UMR Inserm, Centre Léon Bérard, Lyon, France
| | - Georgia Chenevix-Trench
- Department of Genetics and Computational Biology, Queensland Institute of Medical Research, Brisbane, Australia
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Antonis C Antoniou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Katherine L Nathanson
- Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia6Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia
| | | | - Anya Kushnir
- Susanne Levy Gertner Oncogenetics Unit, Sheba Medical Center, Tel Hashomer, Israel
| | | | - Raanan Berger
- Oncology Institute, Sheba Medical Center, Tel Hashomer, Israel
| | - Jamal Zidan
- Oncology Institute, Rivkah Ziv Medical Center Zefat, Israel
| | | | - Hans Ehrencrona
- Department of Oncology, Lund University, Lund, Sweden12Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Marie Stenmark-Askmalm
- Division of Clinical Genetics, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Zakaria Einbeigi
- Department of Oncology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Niklas Loman
- Department of Oncology, Lund University, Lund, Sweden
| | - Katja Harbst
- Department of Oncology, Lund University, Lund, Sweden
| | - Johanna Rantala
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Beatrice Melin
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Dezheng Huo
- Center for Clinical Cancer Genetics and Global Health, University of Chicago Medical Center, Chicago, Illinois
| | - Olufunmilayo I Olopade
- Center for Clinical Cancer Genetics and Global Health, University of Chicago Medical Center, Chicago, Illinois
| | - Joyce Seldon
- UCLA Schools of Medicine and Public Health, Division of Cancer Prevention and Control Research, Jonsson Comprehensive Cancer Center, Los Angeles, California
| | - Patricia A Ganz
- UCLA Schools of Medicine and Public Health, Division of Cancer Prevention and Control Research, Jonsson Comprehensive Cancer Center, Los Angeles, California
| | - Robert L Nussbaum
- Department of Medicine and Genetics, University of California, San Francisco
| | - Salina B Chan
- Cancer Risk Program, Helen Diller Family Cancer Center, University of California, San Francisco
| | - Kunle Odunsi
- Department of Gynecologic Oncology, Roswell Park Cancer Institute, Buffalo, New York
| | - Simon A Gayther
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles
| | - Susan M Domchek
- Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia6Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia
| | - Banu K Arun
- University of Texas MD Anderson Cancer Center, Houston
| | - Karen H Lu
- University of Texas MD Anderson Cancer Center, Houston
| | - Gillian Mitchell
- Division of Cancer Medicine, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia 25Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
| | - Beth Y Karlan
- Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Christine Walsh
- Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Jenny Lester
- Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Andrew K Godwin
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City
| | - Harsh Pathak
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City
| | - Eric Ross
- Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Mary B Daly
- Department of Health Research and Policy, Stanford University School of Medicine, Stanford, California
| | - Alice S Whittemore
- Cancer Risk Program, Helen Diller Family Cancer Center, University of California, San Francisco
| | - Esther M John
- Department of Epidemiology, Cancer Prevention Institute of California, Fremont
| | | | - Mary Beth Terry
- Department of Epidemiology, Columbia University, New York, New York
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University, New York, New York
| | - David E Goldgar
- Department of Dermatology, University of Utah School of Medicine, Salt Lake City
| | - Saundra S Buys
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City
| | - Ramunas Janavicius
- Vilnius University Hospital Santariskiu Clinics, Hematology, Oncology, and Transfusion Medicine Center, Department of Molecular and Regenerative Medicine, State Research Institute Innovative Medicine Center, Vilnius, Lithuania
| | | | - Nadine Tung
- Department of Medical Oncology, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | | | | | - Linda Steele
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, California
| | - Susan L Neuhausen
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, California
| | - Yuan Chun Ding
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, California
| | - Bent Ejlertsen
- Departments of Oncology or Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Anne-Marie Gerdes
- Departments of Oncology or Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Thomas v O Hansen
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | | | - Ana Osorio
- Human Genetics Group, Spanish National Cancer Centre (CNIO), and Biomedical Network on Rare Diseases (CIBERER), Madrid, Spain
| | - Javier Benitez
- Human Genetics Group and Genotyping Unit, Spanish National Cancer Centre (CNIO), and Biomedical Network on Rare Diseases (CIBERER), Madrid, Spain
| | - Javier Godino
- Hospital clinico Universitario "Lozano Blesa," Instituto de investigación sanitaria de Aragón (IIS), Zaragoza, Spain
| | - Maria-Isabel Tejada
- Molecular Genetics Laboratory (Department of Genetics), Cruces University Hospital Barakaldo, Bizkaia, Spain
| | - Mercedes Duran
- Institute of Biology and Molecular Genetics. Universidad de Valladolid (IBGM-UVA), Valladolid, Spain
| | - Jeffrey N Weitzel
- Clinical Cancer Genetics, City of Hope Clinical Cancer Genetics Community Research Network, Duarte, California
| | - Kristie A Bobolis
- Clinical Cancer Genetics, City of Hope Clinical Cancer Genetics Community Research Network, Duarte, California
| | - Sharon R Sand
- Clinical Cancer Genetics, City of Hope Clinical Cancer Genetics Community Research Network, Duarte, California
| | - Annette Fontaine
- Clinical Cancer Genetics, City of Hope Clinical Cancer Genetics Community Research Network, Duarte, California
| | - Antonella Savarese
- Unit of Genetic Counselling, Medical Oncology Department, Istituto Nazionale Tumori Regina Elena, Rome, Italy
| | - Barbara Pasini
- Department of Medical Science, University of Turin, and AO Città della Salute e della Scienza, Turin, Italy
| | - Bernard Peissel
- Unit of Medical Genetics, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori (INT), Milan, Italy
| | - Bernardo Bonanni
- Division of Cancer Prevention and Genetics, Istituto Europeo di Oncologia, Milan, Italy
| | - Daniela Zaffaroni
- Unit of Medical Genetics, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori (INT), Milan, Italy
| | | | - Giulietta Scuvera
- Unit of Medical Genetics, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori (INT), Milan, Italy
| | - Giuseppe Giannini
- Department of Molecular Medicine, University La Sapienza, Rome, Italy
| | - Loris Bernard
- Department of Experimental Oncology, Istituto Europeo di Oncologia, Milan, Italy57Cogentech Cancer Genetic Test Laboratory, Milan, Italy
| | - Maurizio Genuardi
- Institute of Medical Genetics, Catholic University, "A. Gemelli" Hospital, Rome, Italy
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale Tumori (INT), Milan, Italy60IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy
| | - Riccardo Dolcetti
- Cancer Bioimmunotherapy Unit, Centro di Riferimento Oncologico, IRCCSCRO Aviano National Cancer Institute, Aviano (PN), Italy
| | - Siranoush Manoukian
- Unit of Medical Genetics, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori (INT), Milan, Italy
| | - Valeria Pensotti
- Cogentech Cancer Genetic Test Laboratory, Milan, Italy60IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy
| | - Viviana Gismondi
- Unit of Hereditary Cancer, IRCCS AOU San Martino-IST Istituto Nazionale per la Ricerca sul Cancro, Genoa, Italy
| | - Drakoulis Yannoukakos
- Molecular Diagnostics Laboratory, IRRP, National Centre for Scientific Research "Demokritos" Aghia Paraskevi Attikis, Athens, Greece
| | - Florentia Fostira
- Molecular Diagnostics Laboratory, IRRP, National Centre for Scientific Research "Demokritos" Aghia Paraskevi Attikis, Athens, Greece
| | - Judy Garber
- Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Diana Torres
- Instituto de Genética Humana, Pontificia Universidad Javeriana, Bogotá, Colombia65Molecular Genetics of Breast Cancer, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | - Muhammad Usman Rashid
- Molecular Genetics of Breast Cancer, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany 66Department of Basic Sciences, Shaukat Khanum Memorial Cancer Hospital and Research Centre (SKMCH & RC), Lahore, Pakistan
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | - Susan Peock
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Debra Frost
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Radka Platte
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - D Gareth Evans
- Genetic Medicine, Manchester Academic Health Sciences Centre, Central Manchester University Hospitals, NHS Foundation Trust, Manchester, United Kingdom
| | - Rosalind Eeles
- Oncogenetics Team, Institute of Cancer Research and Royal Marsden, NHS Foundation Trust, London, United Kingdom
| | - Rosemarie Davidson
- Ferguson-Smith Centre for Clinical Genetics, Yorkhill Hospitals, Glasgow, United Kingdom
| | - Diana Eccles
- Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, United Kingdom
| | - Trevor Cole
- West Midlands Regional Genetics Service, Birmingham Women's Hospital Healthcare NHS Trust, Edgbaston, Birmingham, United Kingdom
| | - Jackie Cook
- Sheffield Clinical Genetics Service, Sheffield Children's Hospital, Sheffield, United Kingdom
| | - Carole Brewer
- Department of Clinical Genetics, Royal Devon and Exeter Hospital, Exeter, United Kingdom
| | - Shirley Hodgson
- Clinical Genetics Department, St Georges Hospital, University of London, United Kingdom
| | - Patrick J Morrison
- Northern Ireland Regional Genetics Centre, Belfast City Hospital, Belfast, United Kingdom
| | - Lisa Walker
- Oxford Regional Genetics Service, Churchill Hospital, Oxford, United Kingdom
| | - Mary E Porteous
- South East of Scotland Regional Genetics Service, Western General Hospital, Edinburgh, United Kingdom
| | - M John Kennedy
- Academic Unit of Clinical and Molecular Oncology, Trinity College Dublin and St James's Hospital, Dublin, Eire
| | - Louise Izatt
- South East Thames Regional Genetics Service, Guy's Hospital London, United Kingdom
| | - Julian Adlard
- Yorkshire Regional Genetics Service, Leeds, United Kingdom
| | - Alan Donaldson
- South West Regional Genetics Service, Bristol, United Kingdom
| | - Steve Ellis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Priyanka Sharma
- Department of Hematology and Oncology, University of Kansas Medical Center, Kansas City
| | - Rita Katharina Schmutzler
- Center for Hereditary Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), and Center for Molecular Medicine Cologne (CMMC), Medical Faculty, University of Cologne and University Hospital Cologne, Cologne, Germany
| | - Barbara Wappenschmidt
- Center for Hereditary Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), and Center for Molecular Medicine Cologne (CMMC), Medical Faculty, University of Cologne and University Hospital Cologne, Cologne, Germany
| | - Alexandra Becker
- Center for Hereditary Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), and Center for Molecular Medicine Cologne (CMMC), Medical Faculty, University of Cologne and University Hospital Cologne, Cologne, Germany
| | - Kerstin Rhiem
- Center for Hereditary Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), and Center for Molecular Medicine Cologne (CMMC), Medical Faculty, University of Cologne and University Hospital Cologne, Cologne, Germany
| | - Eric Hahnen
- Center for Hereditary Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), and Center for Molecular Medicine Cologne (CMMC), Medical Faculty, University of Cologne and University Hospital Cologne, Cologne, Germany
| | - Christoph Engel
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
| | - Alfons Meindl
- Department of Gynaecology and Obstetrics, Division of Tumor Genetics, Klinikum rechts der Isar, Technical University Munich, Munich, Germany
| | - Stefanie Engert
- Department of Gynaecology and Obstetrics, Division of Tumor Genetics, Klinikum rechts der Isar, Technical University Munich, Munich, Germany
| | - Nina Ditsch
- Department of Gynaecology and Obstetrics, Division of Tumor Genetics, Klinikum rechts der Isar, Technical University Munich, Munich, Germany
| | - Norbert Arnold
- Department of Gynecology and Obstetrics, University Medical Center Schleswig-Holstein, Campus Kiel, Germany
| | - Hans Jörg Plendl
- Institute of Human Genetics, University Medical Center Schleswig-Holstein, Campus Kiel, Germany
| | - Christoph Mundhenke
- Department of Gynecology and Obstetrics, University Medical Center Schleswig-Holstein, Campus Kiel, Germany
| | - Dieter Niederacher
- Department of Gynaecology and Obstetrics, University Hospital Düsseldorf, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Markus Fleisch
- Department of Gynaecology and Obstetrics, University Hospital Düsseldorf, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Christian Sutter
- Institute of Human Genetics, Department of Human Genetics, University Hospital Heidelberg, Heidelberg, Germany
| | - C R Bartram
- Institute of Human Genetics, Department of Human Genetics, University Hospital Heidelberg, Heidelberg, Germany
| | - Nicola Dikow
- Institute of Human Genetics, Department of Human Genetics, University Hospital Heidelberg, Heidelberg, Germany
| | - Shan Wang-Gohrke
- Department of Gynaecology and Obstetrics, University Hospital Ulm, Ulm, Germany
| | - Dorothea Gadzicki
- Institute of Cell and Molecular Pathology, Hannover Medical School, Hannover, Germany
| | - Doris Steinemann
- Institute of Cell and Molecular Pathology, Hannover Medical School, Hannover, Germany
| | - Karin Kast
- Department of Gynaecology and Obstetrics, University Hospital Carl Gustav Carus, Technical University Dresden, Dresden, Germany
| | - Marit Beer
- Institute of Human Genetics, Technical University Dresden, Dresden, Germany
| | | | - Andrea Gehrig
- Centre of Familial Breast and Ovarian Cancer, Department of Medical Genetics, Institute of Human Genetics, University of Würzburg, Würzburg, Germany
| | - Bernhard H Weber
- Institute of Human Genetics, University of Regensburg, Regensburg, Germany
| | - Dominique Stoppa-Lyonnet
- Institut Curie, Department of Tumour Biology, Paris, France98Institut Curie, INSERM U830, Paris, France99Université Paris Descartes, Sorbonne Paris Cité, France
| | - Olga M Sinilnikova
- Unité Mixte de Génétique Constitutionnelle des Cancers Fréquents, Hospices Civils de Lyon-Centre Léon Bérard, Lyon, France101INSERM U1052, CNRS UMR5286, Université Lyon 1, Centre de Recherche en Cancérologie de Lyon, Lyon, France
| | - Sylvie Mazoyer
- INSERM U1052, CNRS UMR5286, Université Lyon 1, Centre de Recherche en Cancérologie de Lyon, Lyon, France
| | - Claude Houdayer
- Institut Curie, Department of Tumour Biology, Paris, France99Université Paris Descartes, Sorbonne Paris Cité, France
| | - Muriel Belotti
- Institut Curie, Department of Tumour Biology, Paris, France
| | | | - Francesca Damiola
- INSERM U1052, CNRS UMR5286, Université Lyon 1, Centre de Recherche en Cancérologie de Lyon, Lyon, France
| | - Nadia Boutry-Kryza
- Unité Mixte de Génétique Constitutionnelle des Cancers Fréquents, Hospices Civils de Lyon-Centre Léon Bérard, Lyon, France
| | - Christine Lasset
- Université Lyon 1, CNRS UMR5558, Lyon, France103Unité de Prévention et d'Epidémiologie Génétique, Centre Léon Bérard, Lyon, France
| | - Hagay Sobol
- Département Oncologie Génétique, Prévention et Dépistage, INSERM CIC-P9502, Institut Paoli-Calmettes/Université d'Aix-Marseille II, Marseille, France
| | - Jean-Philippe Peyrat
- Laboratoire d'Oncologie Moléculaire Humaine, Centre Oscar Lambret, Lille, France
| | - Danièle Muller
- Unité d'Oncogénétique, CLCC Paul Strauss, Strasbourg, France
| | | | - Marie-Agnès Collonge-Rame
- Service de Génétique Biologique-Histologie-Biologie du Développement et de la Reproduction, Centre Hospitalier Universitaire de Besançon, Besançon, France
| | | | - Catherine Nogues
- Oncogénétique Clinique, Hôpital René Huguenin/Institut Curie, Saint-Cloud, France
| | - Etienne Rouleau
- Laboratoire d'Oncogénétique, Hôpital René Huguenin/Institut Curie, Saint-Cloud, France
| | - Claudine Isaacs
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC
| | - Anne De Paepe
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Bruce Poppe
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Kathleen Claes
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Kim De Leeneer
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | | | | | | | | | | | - Jack Basil
- Ohio State, Good Samaritan Hospital, Cincinnati
| | - Masoud Azodi
- Yale University School of Medicine, New Haven, Connecticut
| | - Kelly-Anne Phillips
- Division of Cancer Medicine, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia 25Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
| | - Trinidad Caldes
- Molecular Oncology Laboratory, Hospital Clinico San Carlos, IdISSC, Madrid, Spain
| | - Miguel de la Hoya
- Molecular Oncology Laboratory, Hospital Clinico San Carlos, IdISSC, Madrid, Spain
| | - Atocha Romero
- Molecular Oncology Laboratory, Hospital Clinico San Carlos, IdISSC, Madrid, Spain
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - Kristiina Aittomäki
- Department of Clinical Genetics, Helsinki University Central Hospital, Helsinki, Finland
| | - Annemarie H van der Hout
- Department of Genetics, University Medical Center, Groningen University, Groningen, The Netherlands
| | | | - Senno Verhoef
- Family Cancer Clinic, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - J Margriet Collée
- Department of Clinical Genetics, Family Cancer Clinic, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Caroline Seynaeve
- Department of Medical Oncology, Family Cancer Clinic, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jan C Oosterwijk
- Department of Genetics, University Medical Center, Groningen University, Groningen, The Netherlands
| | - Johannes J P Gille
- Department of Clinical Genetics, VU University Medical Centre, Amsterdam, The Netherlands
| | - Juul T Wijnen
- Department of Human Genetics and Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Encarna B Gómez Garcia
- Department of Clinical Genetics and GROW, School for Oncology and Developmental Biology, MUMC, Maastricht, The Netherlands
| | - Carolien M Kets
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Margreet G E M Ausems
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Cora M Aalfs
- Department of Clinical Genetics, Academic Medical Center, Amsterdam, The Netherlands
| | - Peter Devilee
- Department of Human Genetics and Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Arjen R Mensenkamp
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Ava Kwong
- Hong Kong Hereditary Breast Cancer Family Registry, Hong Kong135Cancer Genetics Center, Hong Kong Sanatorium and Hospital, Hong Kong136Department of Surgery, University of Hong Kong, Hong Kong
| | - Edith Olah
- Department of Molecular Genetics, National Institute of Oncology, Budapest, Hungary
| | - Janos Papp
- Department of Molecular Genetics, National Institute of Oncology, Budapest, Hungary
| | - Orland Diez
- Oncogenetics Laboratory, Vall d'Hebron Institute of Oncology (VHIO), Universitat Autonoma de Barcelona, Barcelona, Spain139University Hospital of Vall d'Hebron, Barcelona, Spain
| | - Conxi Lazaro
- Molecular Diagnostic Unit, Hereditary Cancer Program, IDIBELL-Catalan Institute of Oncology, Barcelona, Spain
| | - Esther Darder
- Genetic Counseling Unit, Hereditary Cancer Program, IDIBGI-Catalan Institute of Oncology, Girona, Spain
| | - Ignacio Blanco
- Genetic Counseling Unit, Hereditary Cancer Program, IDIBELL-Catalan Institute of Oncology, Barcelona, Spain
| | - Mónica Salinas
- Genetic Counseling Unit, Hereditary Cancer Program, IDIBELL-Catalan Institute of Oncology, Barcelona, Spain
| | - Anna Jakubowska
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Jan Lubinski
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Jacek Gronwald
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Katarzyna Jaworska-Bieniek
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland144Postgraduate School of Molecular Medicine, Warsaw Medical University, Warsaw, Poland
| | - Katarzyna Durda
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Grzegorz Sukiennicki
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Tomasz Huzarski
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Tomasz Byrski
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Cezary Cybulski
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | | | | | - Janusz Menkiszak
- Department of Surgical Gynecology and Gynecological Oncology of Adults and Adolescents, Pomeranian Medical University, Szczecin, Poland
| | - Adalgeir Arason
- Department of Pathology, Landspitali University Hospital, Reykjavík, Iceland147BMC, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Rosa B Barkardottir
- Department of Pathology, Landspitali University Hospital, Reykjavík, Iceland147BMC, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Jacques Simard
- Canada Research Chair in Oncogenetics, Cancer Genomics Laboratory, Centre Hospitalier Universitaire de Québec Research Center, Quebec City, Quebec, Canada149Laval University, Quebec City, Quebec, Canada
| | - Rachel Laframboise
- Medical Genetics Division, Centre Hospitalier Universitaire de Québec, Quebec City, Quebec, Canada151Immunology and Molecular Oncology Unit, Veneto Institute of Oncology, IOV-IRCCS, Padua, Italy
| | - Marco Montagna
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology, IOV-IRCCS, Padua, Italy
| | - Simona Agata
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology, IOV-IRCCS, Padua, Italy
| | - Elisa Alducci
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology, IOV-IRCCS, Padua, Italy
| | - Ana Peixoto
- Department of Genetics, Portuguese Oncology Institute, Porto, Portugal
| | - Manuel R Teixeira
- Department of Genetics, Portuguese Oncology Institute, Porto, Portugal153Biomedical Sciences Institute (ICBAS), University of Porto, Portugal
| | - Amanda B Spurdle
- Department of Genetics and Computational Biology, Queensland Institute of Medical Research, Brisbane, Australia
| | - Min Hyuk Lee
- Department of Surgery, Soonchunhyang University and Hospital, Seoul, Korea
| | - Sue K Park
- Department of Preventive Medicine, Seoul National University College of Medicine and Cancer Research Institute, Seoul National University, Seoul, Korea
| | - Sung-Won Kim
- Department of Surgery, Daerim St Mary's Hospital, Seoul, Korea
| | - Tara M Friebel
- Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia
| | - Fergus J Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota159Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Noralane M Lindor
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Vernon S Pankratz
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Lucia Guidugli
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Xianshu Wang
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Marc Tischkowitz
- Program in Cancer Genetics, Departments of Human Genetics and Oncology, McGill University, Montreal, Quebec, Canada161Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Lenka Foretova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute and MF MU, Brno, Czech Republic
| | - Joseph Vijai
- Clinical Genetics Service, Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Kenneth Offit
- Clinical Genetics Service, Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Mark Robson
- Clinical Genetics Service, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Rohini Rau-Murthy
- Clinical Genetics Service, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Noah Kauff
- Clinical Genetics Service, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Anneliese Fink-Retter
- Department of OB/GYN and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Christian F Singer
- Department of OB/GYN and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Christine Rappaport
- Department of OB/GYN and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | | | - Georg Pfeiler
- Department of OB/GYN and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Muy-Kheng Tea
- Department of OB/GYN and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Andreas Berger
- Department of OB/GYN and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Mark H Greene
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland
| | - Phuong L Mai
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland
| | | | - Amanda Ewart Toland
- Divison of Human Cancer Genetics, Departments of Internal Medicine and Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, Ohio State University, Columbus
| | - Leigha Senter
- Divison of Human Genetics, Department of Internal Medicine, Comprehensive Cancer Center, Ohio State University, Columbus
| | - Anders Bojesen
- Department of Clinical Genetics, Vejle Hospital, Vejle, Denmark
| | - Inge Sokilde Pedersen
- Section of Molecular Diagnostics, Department of Clinical Biochemistry, Aalborg University Hospital, Aalborg, Denmark
| | | | - Lone Sunde
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus N, Denmark
| | - Mads Thomassen
- Department of Clinical Genetics, Odense University Hospital, Odense C, Denmark
| | | | - Torben A Kruse
- Department of Clinical Genetics, Odense University Hospital, Odense C, Denmark
| | - Uffe Birk Jensen
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus N, Denmark
| | - Maria Adelaide Caligo
- Section of Genetic Oncology, Department of Oncology, University of Pisa and University Hospital of Pisa, Pisa, Italy
| | - Paolo Aretini
- Section of Genetic Oncology, Department of Oncology, University of Pisa and University Hospital of Pisa, Pisa, Italy
| | - Soo-Hwang Teo
- Cancer Research Initiatives Foundation, Sime Darby Medical Centre, Subang Jaya, Malaysia176Department of Surgery, Faculty of Medicine, University Malaya Cancer Research Institute, University Malaya, Kuala Lumpur, Malaysia
| | - Christina G Selkirk
- NorthShore University HealthSystem, Department of Medicine, Evanston, Illinois
| | - Peter J Hulick
- NorthShore University HealthSystem, Department of Medicine, Evanston, Illinois
| | - Irene Andrulis
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital and University of Toronto, Toronto, Ontario, Canada
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16
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Peterlongo P, Chang-Claude J, Moysich KB, Rudolph A, Schmutzler RK, Simard J, Soucy P, Eeles RA, Easton DF, Hamann U, Wilkening S, Chen B, Rookus MA, Schmidt MK, van der Baan FH, Spurdle AB, Walker LC, Lose F, Maia AT, Montagna M, Matricardi L, Lubinski J, Jakubowska A, Gómez Garcia EB, Olopade OI, Nussbaum RL, Nathanson KL, Domchek SM, Rebbeck TR, Arun BK, Karlan BY, Orsulic S, Lester J, Chung WK, Miron A, Southey MC, Goldgar DE, Buys SS, Janavicius R, Dorfling CM, van Rensburg EJ, Ding YC, Neuhausen SL, Hansen TVO, Gerdes AM, Ejlertsen B, Jønson L, Osorio A, Martínez-Bouzas C, Benitez J, Conway EE, Blazer KR, Weitzel JN, Manoukian S, Peissel B, Zaffaroni D, Scuvera G, Barile M, Ficarazzi F, Mariette F, Fortuzzi S, Viel A, Giannini G, Papi L, Martayan A, Tibiletti MG, Radice P, Vratimos A, Fostira F, Garber JE, Donaldson A, Brewer C, Foo C, Evans DGR, Frost D, Eccles D, Brady A, Cook J, Tischkowitz M, Adlard J, Barwell J, Walker L, Izatt L, Side LE, Kennedy MJ, Rogers MT, Porteous ME, Morrison PJ, Platte R, Davidson R, Hodgson SV, Ellis S, Cole T, Godwin AK, Claes K, Van Maerken T, Meindl A, Gehrig A, Sutter C, Engel C, Niederacher D, Steinemann D, Plendl H, Kast K, Rhiem K, Ditsch N, Arnold N, Varon-Mateeva R, Wappenschmidt B, Wang-Gohrke S, Bressac-de Paillerets B, Buecher B, Delnatte C, Houdayer C, Stoppa-Lyonnet D, Damiola F, Coupier I, Barjhoux L, Venat-Bouvet L, Golmard L, Boutry-Kryza N, Sinilnikova OM, Caron O, Pujol P, Mazoyer S, Belotti M, Piedmonte M, Friedlander ML, Rodriguez GC, Copeland LJ, de la Hoya M, Segura PP, Nevanlinna H, Aittomäki K, van Os TAM, Meijers-Heijboer HEJ, van der Hout AH, Vreeswijk MPG, Hoogerbrugge N, Ausems MGEM, van Doorn HC, Collée JM, Olah E, Diez O, Blanco I, Lazaro C, Brunet J, Feliubadalo L, Cybulski C, Gronwald J, Durda K, Jaworska-Bieniek K, Sukiennicki G, Arason A, Chiquette J, Teixeira MR, Olswold C, Couch FJ, Lindor NM, Wang X, Szabo CI, Offit K, Corines M, Jacobs L, Robson ME, Zhang L, Joseph V, Berger A, Singer CF, Rappaport C, Kaulich DG, Pfeiler G, Tea MKM, Phelan CM, Greene MH, Mai PL, Rennert G, Mulligan AM, Glendon G, Tchatchou S, Andrulis IL, Toland AE, Bojesen A, Pedersen IS, Thomassen M, Jensen UB, Laitman Y, Rantala J, von Wachenfeldt A, Ehrencrona H, Askmalm MS, Borg Å, Kuchenbaecker KB, McGuffog L, Barrowdale D, Healey S, Lee A, Pharoah PDP, Chenevix-Trench G, Antoniou AC, Friedman E. Candidate genetic modifiers for breast and ovarian cancer risk in BRCA1 and BRCA2 mutation carriers. Cancer Epidemiol Biomarkers Prev 2015; 24:308-16. [PMID: 25336561 PMCID: PMC4294951 DOI: 10.1158/1055-9965.epi-14-0532] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [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] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND BRCA1 and BRCA2 mutation carriers are at substantially increased risk for developing breast and ovarian cancer. The incomplete penetrance coupled with the variable age at diagnosis in carriers of the same mutation suggests the existence of genetic and nongenetic modifying factors. In this study, we evaluated the putative role of variants in many candidate modifier genes. METHODS Genotyping data from 15,252 BRCA1 and 8,211 BRCA2 mutation carriers, for known variants (n = 3,248) located within or around 445 candidate genes, were available through the iCOGS custom-designed array. Breast and ovarian cancer association analysis was performed within a retrospective cohort approach. RESULTS The observed P values of association ranged between 0.005 and 1.000. None of the variants was significantly associated with breast or ovarian cancer risk in either BRCA1 or BRCA2 mutation carriers, after multiple testing adjustments. CONCLUSION There is little evidence that any of the evaluated candidate variants act as modifiers of breast and/or ovarian cancer risk in BRCA1 or BRCA2 mutation carriers. IMPACT Genome-wide association studies have been more successful at identifying genetic modifiers of BRCA1/2 penetrance than candidate gene studies.
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Affiliation(s)
- Paolo Peterlongo
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy. Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale Tumori (INT), Milan, Italy.
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kirsten B Moysich
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, New York
| | - Anja Rudolph
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Rita K Schmutzler
- Center for Hereditary Breast and Ovarian Cancer, Medical Faculty, University Hospital Cologne, Germany. Center for Integrated Oncology (CIO), Medical Faculty, University Hospital Cologne, Germany. Center for Molecular Medicine Cologne (CMMC), University of Cologne, Germany, on behalf of the German Consortium of Hereditary Breast and Ovarian Cancer (GC-HBOC)
| | - Jacques Simard
- Centre Hospitalier Universitaire de Québec Research Center and Laval University, Quebec City, Canada
| | - Penny Soucy
- Centre Hospitalier Universitaire de Québec Research Center and Laval University, Quebec City, Canada
| | - Rosalind A Eeles
- Oncogenetics Team, The Institute of Cancer Research and Royal Marsden NHS Foundation Trust, Surrey, United Kingdom
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefan Wilkening
- Genomic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Bowang Chen
- Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Matti A Rookus
- Department of Epidemiology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Marjanka K Schmidt
- Division of Psychosocial Research and Epidemiology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | | | - Amanda B Spurdle
- Department of Genetics and Computational Biology, QIMR Berghofer, Brisbane, Australia
| | - Logan C Walker
- Department of Pathology, University of Otago, Christchurch, New Zealand
| | - Felicity Lose
- Department of Genetics and Computational Biology, QIMR Berghofer, Brisbane, Australia
| | - Ana-Teresa Maia
- Department of Biomedical Sciences and Medicine, Gambelas Campus, University of Algarve, Portugal
| | - Marco Montagna
- Immunology and Molecular Oncology Unit, Istituto Oncologico Veneto IOV - IRCCS, Padua, Italy
| | - Laura Matricardi
- Immunology and Molecular Oncology Unit, Istituto Oncologico Veneto IOV - IRCCS, Padua, Italy
| | - Jan Lubinski
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Anna Jakubowska
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | | | - Olufunmilayo I Olopade
- Center for Clinical Cancer Genetics, Department of Medicine and Human Genetics, University of Chicago Medical Center, Chicago, Illinois
| | - Robert L Nussbaum
- Department of Medicine and Institute for Human Genetics, University of California, San Francisco, San Francisco, California
| | - Katherine L Nathanson
- Department of Medicine, Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadephia, Pennsylvania
| | - Susan M Domchek
- Department of Medicine, Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadephia, Pennsylvania
| | - Timothy R Rebbeck
- Department of Epidemiology and Biostatistics, Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadephia, Pennsylvania
| | - Banu K Arun
- University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Beth Y Karlan
- Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Sandra Orsulic
- Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Jenny Lester
- Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University, New York, New York
| | - Alex Miron
- Department of Genetics and Genomics at Case Western Reserve Medical School, Cleveland, Ohio
| | - Melissa C Southey
- Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Parkville, Australia
| | - David E Goldgar
- Department of Dermatology, University of Utah School of Medicine, Salt Lake City, Utah
| | - Saundra S Buys
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah
| | - Ramunas Janavicius
- Vilnius University Hospital Santariskiu Clinics, Hematology, Oncology, and Transfusion Medicine Center, Dept. of Molecular and Regenerative Medicine; State Research Institute Centre for Innovative Medicine, Vilnius, Lithuania
| | | | | | - Yuan Chun Ding
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, California
| | - Susan L Neuhausen
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, California
| | - Thomas V O Hansen
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Anne-Marie Gerdes
- Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Bent Ejlertsen
- Department of Oncology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Lars Jønson
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Ana Osorio
- Biomedical Network on Rare Diseases (CIBERER), Madrid, Spain. Human Genetics Group, Spanish National Cancer Centre (CNIO), Madrid, Spain
| | - Cristina Martínez-Bouzas
- Molecular Genetics Laboratory, Department of Biochemistry, Cruces Hospital Barakaldo, 48903-Barakaldo-Bizkaia, Spain
| | - Javier Benitez
- Biomedical Network on Rare Diseases (CIBERER), Madrid, Spain. Human Genetics Group and Genotyping Unit, Spanish National Cancer Centre (CNIO), Madrid, Spain
| | - Edye E Conway
- Saint Alphonsus Regional Medical Center, care of City of Hope Clinical Cancer Genetics Community Research Network, Duarte, California
| | | | - Jeffrey N Weitzel
- Clinical Cancer Genetics, City of Hope, Duarte, California (for the City of Hope Clinical Cancer Genetics Community Research Network)
| | - Siranoush Manoukian
- Unit of Medical Genetics, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale Tumori (INT), Milan, Italy
| | - Bernard Peissel
- Unit of Medical Genetics, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale Tumori (INT), Milan, Italy
| | - Daniela Zaffaroni
- Unit of Medical Genetics, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale Tumori (INT), Milan, Italy
| | - Giulietta Scuvera
- Unit of Medical Genetics, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale Tumori (INT), Milan, Italy
| | - Monica Barile
- Division of Cancer Prevention and Genetics, Istituto Europeo di Oncologia, Milan, Italy
| | - Filomena Ficarazzi
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy. Cogentech Cancer Genetic Test Laboratory, Milan, Italy
| | - Frederique Mariette
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy. Cogentech Cancer Genetic Test Laboratory, Milan, Italy
| | - Stefano Fortuzzi
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy. Cogentech Cancer Genetic Test Laboratory, Milan, Italy
| | - Alessandra Viel
- Division of Experimental Oncology 1, CRO Aviano National Cancer Institute, Aviano (PN), Italy
| | | | - Laura Papi
- Unit of Medical Genetics, Department of Biomedical, Experimental, and Clinical Sciences, University of Florence, Florence, Italy
| | - Aline Martayan
- Unit of Genetic Counseling, Medical Oncology Department, Istituto Nazionale Tumori Regina Elena, Rome, Italy
| | - Maria Grazia Tibiletti
- UO Anatomia Patologica Ospedale di Circolo e Fondazione Macchi, Polo Universitario Varese, Italy
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale Tumori (INT), Milan, Italy
| | - Athanassios Vratimos
- Molecular Diagnostics Laboratory, INRASTES, National Centre for Scientific Research "Demokritos", Aghia Paraskevi Attikis, Athens, Greece
| | - Florentia Fostira
- Molecular Diagnostics Laboratory, INRASTES, National Centre for Scientific Research "Demokritos", Aghia Paraskevi Attikis, Athens, Greece
| | | | - Alan Donaldson
- Clinical Genetics Department, St. Michael's Hospital, Bristol, United Kingdom
| | - Carole Brewer
- Department of Clinical Genetics, Royal Devon & Exeter Hospital, Exeter, United Kingdom
| | - Claire Foo
- Cheshire & Merseyside Clinical Genetics Service, Liverpool Women's NHS Foundation Trust, Liverpool, United Kingdom
| | - D Gareth R Evans
- Genetic Medicine, Manchester Academic Health Sciences Centre, Central Manchester University Hospitals NHS Foundation Trust, Manchester, United Kingdom
| | - Debra Frost
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Diana Eccles
- University of Southampton, Faculty of Medicine, Southampton University Hospitals NHS Trust, Southampton, United Kingdom
| | - Angela Brady
- North West Thames Regional Genetics Service, Kennedy-Galton Centre, Harrow, United Kingdom
| | - Jackie Cook
- Sheffield Clinical Genetics Service, Sheffield Children's Hospital, Sheffield, United Kingdom
| | - Marc Tischkowitz
- Department of Clinical Genetics, East Anglian Regional Genetics Service, Addenbrookes Hospital, Cambridge, United Kingdom
| | - Julian Adlard
- Yorkshire Regional Genetics Service, Leeds, United Kingdom
| | - Julian Barwell
- Leicestershire Clinical Genetics Service, University Hospitals of Leicester NHS Trust, Leicester, United Kingdom
| | - Lisa Walker
- Oxford Regional Genetics Service, Churchill Hospital, Oxford, United Kingdom
| | - Louise Izatt
- Clinical Genetics, Guy's and St. Thomas' NHS Foundation Trust, London, United Kingdom
| | - Lucy E Side
- North East Thames Regional Genetics Service, Great Ormond Street Hospital for Children NHS Trust, London, United Kingdom
| | - M John Kennedy
- Academic Unit of Clinical and Molecular Oncology, Trinity College Dublin, Ireland. St. James's Hospital, Dublin, Ireland
| | - Mark T Rogers
- All Wales Medical Genetics Services, University Hospital of Wales, Cardiff, United Kingdom
| | - Mary E Porteous
- South East of Scotland Regional Genetics Service, Western General Hospital, Edinburgh, United Kingdom
| | - Patrick J Morrison
- Centre for Cancer Research and Cell Biology, Queens University of Belfast, Department of Medical Genetics, Belfast HSC Trust, Belfast, United Kingdom
| | - Radka Platte
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Rosemarie Davidson
- West of Scotland Regional Genetics Service, Southern General Hospital, Glasgow, United Kingdom
| | - Shirley V Hodgson
- Medical Genetics Unit, St. George's, University of London, London, United Kingdom
| | - Steve Ellis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Trevor Cole
- West Midlands Regional Genetics Service, Birmingham Women's Hospital Healthcare NHS Trust, Edgbaston, Birmingham, United Kingdom
| | - Andrew K Godwin
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Missouri
| | - Kathleen Claes
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Tom Van Maerken
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Alfons Meindl
- Department of Gynaecology and Obstetrics, Division of Tumor Genetics, Klinikum rechts der Isar, Technical University Munich, Germany
| | - Andrea Gehrig
- Institute of Human Genetics, University Würzburg, Wurzburg, Germany
| | | | - Christoph Engel
- Institute for Medical Informatics, Statistics, and Epidemiology, University of Leipzig, Leipzig, Germany
| | | | | | - Hansjoerg Plendl
- Institute of Human Genetics, University Hospital of Schleswig-Holstein/University Kiel, Kiel, Germany
| | - Karin Kast
- Department of Gynecology and Obstetrics, University Hospital Carl Gustav Carus, Technische Universität Dresden, Germany
| | - Kerstin Rhiem
- Center for Hereditary Breast and Ovarian Cancer, Medical Faculty, University Hospital Cologne, Germany. Center for Integrated Oncology (CIO), Medical Faculty, University Hospital Cologne, Germany. Center for Molecular Medicine Cologne (CMMC), University of Cologne, Germany
| | - Nina Ditsch
- Department of Gynaecology and Obstetrics, University Munich, Munich, Germany
| | - Norbert Arnold
- Department of Gynecology and Obstetrics, University Hospital of Schleswig-Holstein/University Kiel, Kiel, Germany
| | | | - Barbara Wappenschmidt
- Center for Hereditary Breast and Ovarian Cancer, Medical Faculty, University Hospital Cologne, Germany. Center for Integrated Oncology (CIO), Medical Faculty, University Hospital Cologne, Germany. Center for Molecular Medicine Cologne (CMMC), University of Cologne, Germany
| | - Shan Wang-Gohrke
- Department of Gynaecology and Obstetrics, University Hospital Ulm, Germany
| | - Brigitte Bressac-de Paillerets
- INSERM U946, Fondation Jean Dausset, Paris, France. Service de Génétique, Institut de Cancérologie Gustave Roussy, Villejuif, France
| | - Bruno Buecher
- Institut Curie, Department of Tumour Biology, Paris, France
| | | | - Claude Houdayer
- Institut Curie, Department of Tumour Biology, Paris, France. Université Paris Descartes, Sorbonne Paris Cité, France
| | - Dominique Stoppa-Lyonnet
- Institut Curie, Department of Tumour Biology, Paris, France. Université Paris Descartes, Sorbonne Paris Cité, France. Institut Curie, INSERM U830, Paris, France
| | - Francesca Damiola
- INSERM U1052, CNRS UMR5286, Université Lyon 1, Centre de Recherche en Cancérologie de Lyon, Lyon, France
| | - Isabelle Coupier
- Unité d'Oncogénétique, CHU Arnaud de Villeneuve, Montpellier, France. Unité d'Oncogénétique, CRLCC Val d'Aurelle, Montpellier, France
| | - Laure Barjhoux
- Unité d'Oncogénétique, CRLCC Val d'Aurelle, Montpellier, France
| | - Laurence Venat-Bouvet
- Department of Medical Oncology, Centre Hospitalier Universitaire Dupuytren, Limoges, France
| | - Lisa Golmard
- Institut Curie, Department of Tumour Biology, Paris, France
| | - Nadia Boutry-Kryza
- Unité Mixte de Génétique Constitutionnelle des Cancers Fréquents, Hospices Civils de Lyon - Centre Léon Bérard, Lyon, France
| | - Olga M Sinilnikova
- INSERM U1052, CNRS UMR5286, Université Lyon 1, Centre de Recherche en Cancérologie de Lyon, Lyon, France. Unité Mixte de Génétique Constitutionnelle des Cancers Fréquents, Hospices Civils de Lyon - Centre Léon Bérard, Lyon, France. IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy
| | - Olivier Caron
- Consultation de Génétique, Département de Médecine, Institut de Cancérologie Gustave Roussy, Villejuif, France
| | - Pascal Pujol
- Unité d'Oncogénétique, CHU Arnaud de Villeneuve, Montpellier, France. INSERM 896, CRCM Val d'Aurelle, Montpellier, France
| | - Sylvie Mazoyer
- INSERM U1052, CNRS UMR5286, Université Lyon 1, Centre de Recherche en Cancérologie de Lyon, Lyon, France
| | - Muriel Belotti
- Institut Curie, Department of Tumour Biology, Paris, France
| | - Marion Piedmonte
- Gynecologic Oncology Group Statistical and Data Center, Roswell Park Cancer Institute, Buffalo, New York
| | - Michael L Friedlander
- Australia New Zealand Gynaecological Oncology Group (ANZGOG), Coordinating Centre, Camperdown, Australia
| | - Gustavo C Rodriguez
- Division of Gynecologic Oncology, NorthShore University HealthSystem, Evanston, Illinois
| | - Larry J Copeland
- Ohio State University, Department of Obstetrics and Gynecology, Hilliard, Ohio
| | - Miguel de la Hoya
- Molecular Oncology Laboratory, Hospital Clinico San Carlos, IdISSC, Madrid, Spain
| | - Pedro Perez Segura
- Department of Oncology, Hospital Clinico San Carlos, IdISSC, Madrid, Spain
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, Helsinki University Central Hospital, Helsinki, Finland. University of Helsinki, Helsinki, Finland
| | - Kristiina Aittomäki
- Department of Clinical Genetics, Helsinki University Central Hospital, Helsinki, Finland
| | - Theo A M van Os
- Department of Clinical Genetics, Academic Medical Center, Amsterdam, the Netherlands
| | | | - Annemarie H van der Hout
- Department of Genetics, University Medical Center, Groningen University, Groningen, the Netherlands
| | - Maaike P G Vreeswijk
- Department of Human Genetics, Leiden University Medical Center (LUMC), Leiden, the Netherlands
| | - Nicoline Hoogerbrugge
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Margreet G E M Ausems
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Helena C van Doorn
- Department of Obstetrics and Gynecology, Division of Gynecologic Oncology, Erasmus University MC Cancer Institute, Rotterdam, the Netherlands
| | - J Margriet Collée
- Department of Clinical Genetics, Family Cancer Clinic, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Edith Olah
- Department of Molecular Genetics, National Institute of Oncology, Budapest, Hungary
| | - Orland Diez
- Oncogenetics Group, University Hospital Vall d'Hebron, Barcelona, Spain. Universitat Autònoma de Barcelona, Barcelona, Spain. Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain. Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | - Ignacio Blanco
- Genetic Counseling Unit, Hereditary Cancer Program, IDIBELL-Catalan Institute of Oncology, Barcelona, Spain
| | - Conxi Lazaro
- Molecular Diagnostic Unit, Hereditary Cancer Program, IDIBELL-Catalan Institute of Oncology, Barcelona, Spain
| | - Joan Brunet
- Genetic Counseling Unit, Hereditary Cancer Program, IDIBGI-Catalan Institute of Oncology, Girona, Spain
| | | | - Cezary Cybulski
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Jacek Gronwald
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Katarzyna Durda
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | | | - Grzegorz Sukiennicki
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Adalgeir Arason
- BMC, Faculty of Medicine, University of Iceland, Reykjavik, Iceland. Department of Pathology, Landspitali University Hospital, Reykjavik, Iceland
| | - Jocelyne Chiquette
- Unité de Recherche en Santé des Populations, Centre des Maladies du Sein Deschênes-Fabia, Centre de Recherche FRSQ du Centre Hospitalier Affilié Universitaire de Québec, Québec, Canada
| | - Manuel R Teixeira
- Biomedical Sciences Institute (ICBAS), Porto University, Porto, Portugal. Department of Genetics, Portuguese Oncology Institute, Porto, Portugal
| | - Curtis Olswold
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnessotta
| | - Fergus J Couch
- Department of Laboratory Medicine and Pathology, and Health Sciences Research, Mayo Clinic, Rochester, Minnessotta
| | | | - Xianshu Wang
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnessotta
| | - Csilla I Szabo
- National Human Genome Research Institute, NIH, Bethesda, Maryland
| | - Kenneth Offit
- Clinical Genetics Research Laboratory, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Marina Corines
- Clinical Genetics Service, Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Lauren Jacobs
- Clinical Genetics Service, Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Mark E Robson
- Clinical Genetics Research Laboratory, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Liying Zhang
- Diagnostic Molecular Genetics Laboratory, Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Vijai Joseph
- Clinical Genetics Research Laboratory, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Andreas Berger
- Department of OB/GYN and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Christian F Singer
- Department of OB/GYN and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Christine Rappaport
- Department of OB/GYN and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | | | - Georg Pfeiler
- Department of OB/GYN and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Muy-Kheng M Tea
- Department of OB/GYN and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Catherine M Phelan
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, Florida
| | - Mark H Greene
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, Maryland
| | - Phuong L Mai
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, Maryland
| | - Gad Rennert
- Clalit National Cancer Control Center, Haifa, Israel
| | - Anna Marie Mulligan
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada. Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada
| | - Gord Glendon
- Ontario Cancer Genetics Network: Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Sandrine Tchatchou
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Irene L Andrulis
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada. Departments of Molecular Genetics and Laboratory Medicine and Pathobiology, University of Toronto, Ontario, Canada
| | - Amanda Ewart Toland
- Division of Human Cancer Genetics, Departments of Internal Medicine and Molecular Virology, Immunology, and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | - Anders Bojesen
- Department of Clinical Genetics, Vejle Hospital, Vejle, Denmark
| | - Inge Sokilde Pedersen
- Section of Molecular Diagnostics, Department of Biochemistry, Aalborg University Hospital, Aalborg, Denmark
| | - Mads Thomassen
- Department of Clinical Genetics, Odense University Hospital, Odense C, Denmark
| | - Uffe Birk Jensen
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | | | - Johanna Rantala
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | | | - Hans Ehrencrona
- Department of Clinical Genetics, Lund University Hospital, Lund, Sweden. Department of Immunology, Genetics, and Pathology, Uppsala University, Uppsala, Sweden
| | - Marie Stenmark Askmalm
- Division of Clinical Genetics, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Åke Borg
- Department of Oncology, Lund University, Lund, Sweden
| | - Karoline B Kuchenbaecker
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Lesley McGuffog
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Daniel Barrowdale
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Sue Healey
- Department of Genetics and Computational Biology, QIMR Berghofer, Brisbane, Australia
| | - Andrew Lee
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Paul D P Pharoah
- Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | | | - Antonis C Antoniou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
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17
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Boutry-Kryza N, Labalme A, Ville D, de Bellescize J, Touraine R, Prieur F, Dimassi S, Poulat AL, Till M, Rossi M, Bourel-Ponchel E, Delignières A, Le Moing AG, Rivier C, des Portes V, Edery P, Calender A, Sanlaville D, Lesca G. Molecular characterization of a cohort of 73 patients with infantile spasms syndrome. Eur J Med Genet 2014; 58:51-8. [PMID: 25497044 DOI: 10.1016/j.ejmg.2014.11.007] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [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: 05/12/2014] [Accepted: 11/30/2014] [Indexed: 01/10/2023]
Abstract
Infantile Spasms syndrome (ISs) is a characterized by epileptic spasms occurring in clusters with an onset in the first year of life. West syndrome represents a subset of ISs that associates spasms in clusters, a hypsarrhythmia EEG pattern and a developmental arrest or regression. Aetiology of ISs is widely heterogeneous including many genetic causes. Many patients, however, remain without etiological diagnosis, which is critical for prognostic purpose and genetic counselling. In the present study, we performed genetic screening of 73 patients with different types of ISs by array-CGH and molecular analysis of 5 genes: CDKL5, STXBP1, KCNQ2, and GRIN2A, whose mutations cause different types of epileptic encephalopathies, including ISs, as well as MAGI2, which was suggested to be related to a subset of ISs. In total, we found a disease-causing mutation or CNV (Copy Number Variation) in 15% of the patients. These included 6 point mutations found in CDKL5 (n = 3) and STXBP1 (n = 3), 3 microdeletions (10 Mb in 2q24.3, 3.2 Mb in 5q14.3 including the region upstream to MEF2C, and 256 kb in 9q34 disrupting EHMT1), and 2 microduplications (671 kb in 2q24.3 encompassing SCN2A, and 11.93 Mb in Xq28). In addition, we discuss 3 CNVs as potential risk factors, including one 16p12.1 deletion, one intronic deletion of the NEDD4 gene, and one intronic deletion of CALN1 gene. The present findings highlight the efficacy of combined cytogenetic and targeted mutation screening to improve the diagnostic yield in patient with ISs.
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Affiliation(s)
- Nadia Boutry-Kryza
- Department of Molecular Genetics, Lyon University Hospital, Lyon, France; CRNL, CNRS UMR 5292, INSERM U1028, Lyon, France
| | - Audrey Labalme
- Department of Genetics, Lyon University Hospital, Lyon, France
| | - Dorothee Ville
- Reference Center for Tuberous Sclerosis and Rare Epileptic Syndromes, Lyon University Hospital, Lyon, France
| | - Julitta de Bellescize
- Epilepsy, Sleep and Pediatric Neurophysiology Department, Lyon University Hospital, Lyon, France
| | - Renaud Touraine
- Department of Genetics, Hospital Nord, Saint-Etienne University Hospital, France
| | - Fabienne Prieur
- Department of Genetics, Hospital Nord, Saint-Etienne University Hospital, France
| | - Sarra Dimassi
- CRNL, CNRS UMR 5292, INSERM U1028, Lyon, France; Department of Genetics, Lyon University Hospital, Lyon, France; Claude Bernard Lyon I University, Lyon, France
| | - Anne-Lise Poulat
- Reference Center for Tuberous Sclerosis and Rare Epileptic Syndromes, Lyon University Hospital, Lyon, France
| | - Marianne Till
- Department of Genetics, Lyon University Hospital, Lyon, France
| | - Massimiliano Rossi
- CRNL, CNRS UMR 5292, INSERM U1028, Lyon, France; Department of Genetics, Lyon University Hospital, Lyon, France
| | - Emilie Bourel-Ponchel
- Pediatric Functional Exploration of the Nervous System Service, Hospital Nord, Amiens University Hospital, Amiens, France
| | - Aline Delignières
- Department of Neurology, Hospital Nord, Amiens University Hospital, Amiens, France
| | - Anne-Gaelle Le Moing
- Department of Neurology, Hospital Nord, Amiens University Hospital, Amiens, France
| | - Clotilde Rivier
- Department of Pediatrics, Hospital Nord-Ouest, Villefranche sur Saone, France
| | - Vincent des Portes
- Reference Center for Tuberous Sclerosis and Rare Epileptic Syndromes, Lyon University Hospital, Lyon, France; Claude Bernard Lyon I University, Lyon, France; CNRS UMR 5403, Institut des Sciences Cognitives, L2C2, Bron, France
| | - Patrick Edery
- CRNL, CNRS UMR 5292, INSERM U1028, Lyon, France; Department of Genetics, Lyon University Hospital, Lyon, France; Claude Bernard Lyon I University, Lyon, France
| | - Alain Calender
- Department of Molecular Genetics, Lyon University Hospital, Lyon, France; Claude Bernard Lyon I University, Lyon, France; INSERM U1052, Lyon, France
| | - Damien Sanlaville
- CRNL, CNRS UMR 5292, INSERM U1028, Lyon, France; Department of Genetics, Lyon University Hospital, Lyon, France; Claude Bernard Lyon I University, Lyon, France
| | - Gaetan Lesca
- CRNL, CNRS UMR 5292, INSERM U1028, Lyon, France; Department of Genetics, Lyon University Hospital, Lyon, France; Claude Bernard Lyon I University, Lyon, France.
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18
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Boutry-Kryza N, Ville D, Labalme A, Calender A, Dupont JM, Touraine R, Edery P, des Portes V, Sanlaville D, Lesca G. Complex mosaic CDKL5 deletion with two distinct mutant alleles in a 4-year-old girl. Am J Med Genet A 2014; 164A:2025-8. [PMID: 24715584 DOI: 10.1002/ajmg.a.36547] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [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: 08/01/2013] [Accepted: 03/01/2014] [Indexed: 11/08/2022]
Abstract
Mutations of the CDKL5 gene cause early epileptic encephalopathy. Patients manifest refractory epilepsy, beginning before the age of 3 months, which is associated with severe psychomotor delay and features that overlap with Rett syndrome. We report here a patient with mosaicism for CDKL5 exonic deletion, with the presence of two mutant alleles. The affected 4-year-old girl presented with infantile spasms, beginning at the age of 9 months, but subsequent progression of the disease was consistent with the classical CDKL5-related phenotype. A deletion of exons 17 and 18 was suspected on the basis of Multiplex Ligation Probe Amplification analysis, but unexpected results for cDNA analysis, which showed the presence of an abnormal transcript with the deletion of exon 18 only, led us to suspect that two distinct events might have occurred. We used custom array-CGH to determine the size and breakpoints of these deletions. Exon 18 was deleted from one of the abnormal alleles, and exon 17 was deleted from the other. A Fork Stalling and Template Switching (FoSTeS) mechanism was proposed to explain the two events, given the presence of regions of microhomology at the breakpoints. We propose here an original involvement of the FoSTeS mechanism to explain the co-occurrence of these two events in the CDKL5 gene in a single patient. This patient highlights the difficulties involved in the detection of such abnormalities, particularly when they occur in a mosaic state and involve two distinct mutational events in a single gene.
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Affiliation(s)
- Nadia Boutry-Kryza
- Department of Molecular Genetics, Lyon University Hospital, Lyon, France; Claude Bernard Lyon I University, Lyon, France; CRNL, CNRS UMR 5292, INSERM U1028, Lyon, France
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19
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Soldovieri MV, Boutry-Kryza N, Milh M, Doummar D, Heron B, Bourel E, Ambrosino P, Miceli F, De Maria M, Dorison N, Auvin S, Echenne B, Oertel J, Riquet A, Lambert L, Gerard M, Roubergue A, Calender A, Mignot C, Taglialatela M, Lesca G. NovelKCNQ2andKCNQ3Mutations in a Large Cohort of Families with Benign Neonatal Epilepsy: First Evidence for an Altered Channel Regulation by Syntaxin-1A. Hum Mutat 2014; 35:356-67. [DOI: 10.1002/humu.22500] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2013] [Accepted: 12/12/2013] [Indexed: 11/06/2022]
Affiliation(s)
| | - Nadia Boutry-Kryza
- Department of Medical Genetics; Hospices Civils de Lyon; France
- Claude Bernard Lyon I University; Lyon France
- CRNL, CNRS UMR 5292, INSERM U1028; Lyon France
| | - Mathieu Milh
- INSERM, UMR_S910; Marseille France
- Department of Neuropediatrics; CHU Timone, APHM; Marseille France
| | - Diane Doummar
- Department of Neuropediatrics; Armand Trousseau Hospital; APHP Paris France
| | - Benedicte Heron
- Department of Neuropediatrics; Armand Trousseau Hospital; APHP Paris France
| | - Emilie Bourel
- Department of Neuropediatrics; Hôpital Nord, CHU d'Amiens; Amiens France
| | - Paolo Ambrosino
- Department of Medicine and Health Science; University of Molise; Campobasso Italy
| | - Francesco Miceli
- Department of Neuroscience; University of Naples Federico II; Naples Italy
| | - Michela De Maria
- Department of Medicine and Health Science; University of Molise; Campobasso Italy
| | - Nathalie Dorison
- Department of Neuropediatrics; Armand Trousseau Hospital; APHP Paris France
| | - Stephane Auvin
- Department of Neuropediatrics; Robert Debré Hospital; APHP Paris France
- INSERM U676; Paris France
| | - Bernard Echenne
- Department of Neuropediatrics; Gui de Chauliac Hospital, CHU de Montpellier; Montpellier France
| | - Julie Oertel
- Department of Medical Genetics; Hopital de l'Archet 2, CHU de Nice; Nice France
| | - Audrey Riquet
- Department of Neuropediatrics; Roger Salengro Hospital; Lille France
| | - Laetitia Lambert
- Department of Medical Genetics; Maternité de Nancy and CHU de Nancy; Nancy France
- INSERM UMR954, Vandoeuvre-les-Nancy; France
| | - Marion Gerard
- Department of Medical Genetics; CHU de Caen; Caen France
| | - Anne Roubergue
- Department of Neuropediatrics; Armand Trousseau Hospital; APHP Paris France
| | - Alain Calender
- Department of Medical Genetics; Hospices Civils de Lyon; France
- Claude Bernard Lyon I University; Lyon France
| | - Cyril Mignot
- Department of Genetics; Clinical Genetics Unit, Hôpital de la Pitié-Salpêtrière; APHP Paris France
- Centre de Référence des Déficiences Intellectuelles de Causes Rares; APHP Paris France
| | - Maurizio Taglialatela
- Department of Medicine and Health Science; University of Molise; Campobasso Italy
- Department of Neuroscience; University of Naples Federico II; Naples Italy
- Unidad de Biofísica; Consejo Superior de Investigaciones Cientificas - Universidad del Pais Vasco; Leioa Spain
| | - Gaetan Lesca
- Department of Medical Genetics; Hospices Civils de Lyon; France
- Claude Bernard Lyon I University; Lyon France
- CRNL, CNRS UMR 5292, INSERM U1028; Lyon France
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20
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Dimassi S, Labalme A, Lesca G, Rudolf G, Bruneau N, Hirsch E, Arzimanoglou A, Motte J, de Saint Martin A, Boutry-Kryza N, Cloarec R, Benitto A, Ameil A, Edery P, Ryvlin P, De Bellescize J, Szepetowski P, Sanlaville D. A subset of genomic alterations detected in rolandic epilepsies contains candidate or known epilepsy genes includingGRIN2AandPRRT2. Epilepsia 2013; 55:370-8. [DOI: 10.1111/epi.12502] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/31/2013] [Indexed: 01/08/2023]
Affiliation(s)
- Sarra Dimassi
- Department of Genetics; Lyon University Hospital; Lyon France
- Claude Bernard Lyon I University; Lyon France
- CRNL; CNRS UMR 5292; INSERM U1028; Lyon France
| | - Audrey Labalme
- Department of Genetics; Lyon University Hospital; Lyon France
- The French EPILAND (Epilepsy, Language and Development) Consortium; Marseille France
| | - Gaetan Lesca
- Department of Genetics; Lyon University Hospital; Lyon France
- Claude Bernard Lyon I University; Lyon France
- CRNL; CNRS UMR 5292; INSERM U1028; Lyon France
- The French EPILAND (Epilepsy, Language and Development) Consortium; Marseille France
| | - Gabrielle Rudolf
- The French EPILAND (Epilepsy, Language and Development) Consortium; Marseille France
- Department of Neurology; Strasbourg University Hospital; Strasbourg France
- UMR_S; INSERM U1119; Strasbourg France
| | - Nadine Bruneau
- The French EPILAND (Epilepsy, Language and Development) Consortium; Marseille France
- INSERM Unit U901; Marseille France
- Mediterranean Institute of Neurobiology (INMED); Marseille France
- UMR_S901; Aix-Marseille University; Marseille France
| | - Edouard Hirsch
- The French EPILAND (Epilepsy, Language and Development) Consortium; Marseille France
- Department of Neurology; Strasbourg University Hospital; Strasbourg France
| | - Alexis Arzimanoglou
- CRNL; CNRS UMR 5292; INSERM U1028; Lyon France
- The French EPILAND (Epilepsy, Language and Development) Consortium; Marseille France
- Departments of Epilepsy, Sleep and Pediatric Neurophysiology (ESEFNP); University Hospitals of Lyon (HCL); Lyon France
| | - Jacques Motte
- The French EPILAND (Epilepsy, Language and Development) Consortium; Marseille France
- Department of Pediatry A; American Memorial Hospital; Reims University Hospital; Reims France
| | - Anne de Saint Martin
- The French EPILAND (Epilepsy, Language and Development) Consortium; Marseille France
- Department of Pediatry I; Strasbourg University Hospital; Strasbourg France
| | - Nadia Boutry-Kryza
- Claude Bernard Lyon I University; Lyon France
- CRNL; CNRS UMR 5292; INSERM U1028; Lyon France
- The French EPILAND (Epilepsy, Language and Development) Consortium; Marseille France
- Department of Molecular Genetics; Lyon University Hospital; Lyon France
| | - Robin Cloarec
- The French EPILAND (Epilepsy, Language and Development) Consortium; Marseille France
- INSERM Unit U901; Marseille France
- Mediterranean Institute of Neurobiology (INMED); Marseille France
- UMR_S901; Aix-Marseille University; Marseille France
| | - Afaf Benitto
- Department of Pediatry A; American Memorial Hospital; Reims University Hospital; Reims France
| | - Agnès Ameil
- Department of Pediatry A; American Memorial Hospital; Reims University Hospital; Reims France
| | - Patrick Edery
- Department of Genetics; Lyon University Hospital; Lyon France
- Claude Bernard Lyon I University; Lyon France
- CRNL; CNRS UMR 5292; INSERM U1028; Lyon France
| | - Philippe Ryvlin
- Claude Bernard Lyon I University; Lyon France
- CRNL; CNRS UMR 5292; INSERM U1028; Lyon France
- The French EPILAND (Epilepsy, Language and Development) Consortium; Marseille France
- Department of Neurology; Lyon University Hospital; Lyon France
| | - Julitta De Bellescize
- The French EPILAND (Epilepsy, Language and Development) Consortium; Marseille France
- Departments of Epilepsy, Sleep and Pediatric Neurophysiology (ESEFNP); University Hospitals of Lyon (HCL); Lyon France
| | - Pierre Szepetowski
- The French EPILAND (Epilepsy, Language and Development) Consortium; Marseille France
- INSERM Unit U901; Marseille France
- Mediterranean Institute of Neurobiology (INMED); Marseille France
- UMR_S901; Aix-Marseille University; Marseille France
| | - Damien Sanlaville
- Department of Genetics; Lyon University Hospital; Lyon France
- Claude Bernard Lyon I University; Lyon France
- CRNL; CNRS UMR 5292; INSERM U1028; Lyon France
- The French EPILAND (Epilepsy, Language and Development) Consortium; Marseille France
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21
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Lesca G, Rudolf G, Bruneau N, Lozovaya N, Labalme A, Boutry-Kryza N, Salmi M, Tsintsadze T, Addis L, Motte J, Wright S, Tsintsadze V, Michel A, Doummar D, Lascelles K, Strug L, Waters P, de Bellescize J, Vrielynck P, de Saint Martin A, Ville D, Ryvlin P, Arzimanoglou A, Hirsch E, Vincent A, Pal D, Burnashev N, Sanlaville D, Szepetowski P. GRIN2A mutations in acquired epileptic aphasia and related childhood focal epilepsies and encephalopathies with speech and language dysfunction. Nat Genet 2013; 45:1061-6. [PMID: 23933820 DOI: 10.1038/ng.2726] [Citation(s) in RCA: 296] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Accepted: 07/18/2013] [Indexed: 12/20/2022]
Abstract
Epileptic encephalopathies are severe brain disorders with the epileptic component contributing to the worsening of cognitive and behavioral manifestations. Acquired epileptic aphasia (Landau-Kleffner syndrome, LKS) and continuous spike and waves during slow-wave sleep syndrome (CSWSS) represent rare and closely related childhood focal epileptic encephalopathies of unknown etiology. They show electroclinical overlap with rolandic epilepsy (the most frequent childhood focal epilepsy) and can be viewed as different clinical expressions of a single pathological entity situated at the crossroads of epileptic, speech, language, cognitive and behavioral disorders. Here we demonstrate that about 20% of cases of LKS, CSWSS and electroclinically atypical rolandic epilepsy often associated with speech impairment can have a genetic origin sustained by de novo or inherited mutations in the GRIN2A gene (encoding the N-methyl-D-aspartate (NMDA) glutamate receptor α2 subunit, GluN2A). The identification of GRIN2A as a major gene for these epileptic encephalopathies provides crucial insights into the underlying pathophysiology.
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Affiliation(s)
- Gaetan Lesca
- Department of Genetics, University Hospitals of Lyon, Lyon, France
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Lauxmann S, Boutry-Kryza N, Rivier C, Mueller S, Hedrich UBS, Maljevic S, Szepetowski P, Lerche H, Lesca G. An SCN2A mutation in a family with infantile seizures from Madagascar reveals an increased subthreshold Na(+) current. Epilepsia 2013; 54:e117-21. [PMID: 23758435 DOI: 10.1111/epi.12241] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/01/2013] [Indexed: 11/29/2022]
Abstract
Missense mutations in SCN2A, encoding the brain sodium channel NaV 1.2, have been described in benign familial neonatal-infantile seizures (BFNIS), a self-limiting disorder, whereas several SCN2A de novo nonsense mutations have been found in patients with more severe phenotypes including epileptic encephalopathy. We report a family with BFNIS originating from Madagascar. Onset extended from 3 to 9 months of age. Interictal EEGs were normal. In two patients, ictal electroencephalography (EEG) studies showed partial seizure patterns with secondary generalization in one. Seizures remitted before 18 months of age, with or without medication. Intellectual development was normal. A novel missense mutation of SCN2A, c.4766A>G/p.Tyr1589Cys, was found in a highly conserved region of NaV 1.2 (D4/S2-S3). Functional studies using heterologous expression in tsA201 cells and whole-cell patch clamping revealed a depolarizing shift of steady-state inactivation, increased persistent Na(+) current, a slowing of fast inactivation and an acceleration of its recovery, thus a gain-of-function. Using an action potential waveform in a voltage-clamp experiment we indicated an increased inward Na(+) current at subthreshold voltages, which can explain a neuronal hyperexcitability. Our results suggest that this mutation induces neuronal hyperexcitability, resulting in infantile epilepsy with favorable outcome.
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Affiliation(s)
- Stephan Lauxmann
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tuebingen, Tuebingen, Germany
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Milh M, Boutry-Kryza N, Sutera-Sardo J, Mignot C, Auvin S, Lacoste C, Villeneuve N, Roubertie A, Heron B, Carneiro M, Kaminska A, Altuzarra C, Blanchard G, Ville D, Barthez MA, Heron D, Gras D, Afenjar A, Dorison N, Doummar D, Billette de Villemeur T, An I, Jacquette A, Charles P, Perrier J, Isidor B, Vercueil L, Chabrol B, Badens C, Lesca G, Villard L. Similar early characteristics but variable neurological outcome of patients with a de novo mutation of KCNQ2. Orphanet J Rare Dis 2013; 8:80. [PMID: 23692823 PMCID: PMC3670812 DOI: 10.1186/1750-1172-8-80] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [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: 03/08/2013] [Accepted: 05/15/2013] [Indexed: 11/14/2022] Open
Abstract
Background Early onset epileptic encephalopathies (EOEEs) are dramatic heterogeneous conditions in which aetiology, seizures and/or interictal EEG have a negative impact on neurological development. Several genes have been associated with EOEE and a molecular diagnosis workup is challenging since similar phenotypes are associated with mutations in different genes and since mutations in one given gene can be associated with very different phenotypes. Recently, de novo mutations in KCNQ2, have been found in about 10% of EOEE patients. Our objective was to confirm that KCNQ2 was an important gene to include in the diagnosis workup of EOEEs and to fully describe the clinical and EEG features of mutated patients. Methods We have screened KCNQ2 in a cohort of 71 patients with an EOEE, without any brain structural abnormality. To be included in the cohort, patient’s epilepsy should begin before three months of age and be associated with abnormal interictal EEG and neurological impairment. Brain MRI should not show any structural abnormality that could account for the epilepsy. Results Out of those 71 patients, 16 had a de novo mutation in KCNQ2 (23%). Interestingly, in the majority of the cases, the initial epileptic features of these patients were comparable to those previously described in the case of benign familial neonatal epilepsy (BFNE) also caused by KCNQ2 mutations. However, in contrast to BFNE, the interictal background EEG was altered and displayed multifocal spikes or a suppression-burst pattern. The ongoing epilepsy and development were highly variable but overall severe: 15/16 had obvious cognitive impairment, half of the patients became seizure-free, 5/16 could walk before the age of 3 and only 2/16 patient acquired the ability to speak. Conclusion This study confirms that KCNQ2 is frequently mutated de novo in neonatal onset epileptic encephalopathy. We show here that despite a relatively stereotyped beginning of the condition, the neurological and epileptic evolution is variable.
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Affiliation(s)
- Mathieu Milh
- INSERM, UMR_S 910 Faculté de médecine, Marseille, France.
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Milh M, Sutera-Sardo J, Boutry-Kryza N, Auvin S, Mignot C, Lacoste C, Villeneuve N, Roubertie A, Carneiro M, Kaminska A, Altuzzara C, Blanchard G, Ville D, Barthez MA, Heron D, Afenjar A, Dorison N, Billette T, Girard N, Vercueil L, Chabrol B, Lesca G, Villard L. Encéphalopathies épileptiques précoces et mutations de novo de KCNQ2 : large spectre phénotypique. Une étude multicentrique de 15 patients. Arch Pediatr 2013. [DOI: 10.1016/j.arcped.2013.01.045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Weckhuysen S, Holmgren P, Hendrickx R, Jansen AC, Hasaerts D, Dielman C, de Bellescize J, Boutry-Kryza N, Lesca G, Von Spiczak S, Helbig I, Gill D, Yendle S, Møller RS, Klitten L, Korff C, Godfraind C, Van Rijckevorsel K, De Jonghe P, Hjalgrim H, Scheffer IE, Suls A. Reduction of seizure frequency after epilepsy surgery in a patient with STXBP1 encephalopathy and clinical description of six novel mutation carriers. Epilepsia 2013; 54:e74-80. [PMID: 23409955 DOI: 10.1111/epi.12124] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/17/2013] [Indexed: 01/10/2023]
Abstract
Mutations in STXBP1 have been identified in a subset of patients with early onset epileptic encephalopathy (EE), but the full phenotypic spectrum remains to be delineated. Therefore, we screened a cohort of 160 patients with an unexplained EE, including patients with early myoclonic encephalopathy (EME), Ohtahara syndrome, West syndrome, nonsyndromic EE with onset in the first year, and Lennox-Gastaut syndrome (LGS). We found six de novo mutations in six patients presenting as Ohtahara syndrome (2/6, 33%), West syndrome (1/65, 2%), and nonsyndromic early onset EE (3/64, 5%). No mutations were found in LGS or EME. Only two of four mutation carriers with neonatal seizures had Ohtahara syndrome. Epileptic spasms were present in five of six patients. One patient with normal magnetic resonance imaging (MRI) but focal seizures underwent epilepsy surgery and seizure frequency dropped drastically. Neuropathology showed a focal cortical dysplasia type 1a. There is a need for additional neuropathologic studies to explore whether STXBP1 mutations can lead to structural brain abnormalities.
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Affiliation(s)
- Sarah Weckhuysen
- Neurogenetics Group, Department of Molecular Genetics, VIB, Antwerp, Belgium
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Schluth-Bolard C, Labalme A, Cordier MP, Till M, Nadeau G, Tevissen H, Lesca G, Boutry-Kryza N, Rossignol S, Rocas D, Dubruc E, Edery P, Sanlaville D. Breakpoint mapping by next generation sequencing reveals causative gene disruption in patients carrying apparently balanced chromosome rearrangements with intellectual deficiency and/or congenital malformations. J Med Genet 2013; 50:144-50. [PMID: 23315544 DOI: 10.1136/jmedgenet-2012-101351] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
BACKGROUND Apparently balanced chromosomal rearrangements (ABCR) are associated with an abnormal phenotype in 6% of cases. This may be due to cryptic genomic imbalances or to the disruption of genes at the breakpoint. However, breakpoint cloning using conventional methods (ie, fluorescent in situ hybridisation (FISH), Southern blot) is often laborious and time consuming. In this work, we used next generation sequencing (NGS) to locate breakpoints at the molecular level in four patients with multiple congenital abnormalities and/or intellectual deficiency (MCA/ID) who were carrying ABCR (one translocation, one complex chromosomal rearrangement and two inversions), which corresponded to nine breakpoints. METHODS Genomic imbalance was previously excluded by array comparative genomic hybridisation (CGH) in all four patients. Whole genome paired-end protocol was used to identify breakpoints. The results were verified by FISH and by PCR with Sanger sequencing. RESULTS We were able to map all nine breakpoints. NGS revealed an additional breakpoint due to a cryptic inversion at a breakpoint junction in one patient. Nine of 10 breakpoints occurred in repetitive elements and five genes were disrupted in their intronic sequence (TCF4, SHANK2, PPFIA1, RAB19, KCNQ1). CONCLUSIONS NGS is a powerful tool allowing rapid breakpoint cloning of ABCR at the molecular level. We showed that in three out of four patients, gene disruption could account for the phenotype, allowing adapted genetic counselling and stopping unnecessary investigations. We propose that patients carrying ABCR with an abnormal phenotype should be explored systematically by NGS once a genomic imbalance has been excluded by array CGH.
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Affiliation(s)
- Caroline Schluth-Bolard
- Laboratoire de Cytogénétique Constitutionnelle, Service de Génétique, Centre de Biologie et de Pathologie Est, 59, boulevard Pinel, BRON 69677 Cedex, France.
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Lesca G, Rudolf G, Labalme A, Hirsch E, Arzimanoglou A, Genton P, Motte J, de Saint Martin A, Valenti MP, Boulay C, De Bellescize J, Kéo-Kosal P, Boutry-Kryza N, Edery P, Sanlaville D, Szepetowski P. Epileptic encephalopathies of the Landau-Kleffner and continuous spike and waves during slow-wave sleep types: genomic dissection makes the link with autism. Epilepsia 2012; 53:1526-38. [PMID: 22738016 DOI: 10.1111/j.1528-1167.2012.03559.x] [Citation(s) in RCA: 121] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
PURPOSE The continuous spike and waves during slow-wave sleep syndrome (CSWSS) and the Landau-Kleffner (LKS) syndrome are two rare epileptic encephalopathies sharing common clinical features including seizures and regression. Both CSWSS and LKS can be associated with the electroencephalography pattern of electrical status epilepticus during slow-wave sleep and are part of a clinical continuum that at its benign end also includes rolandic epilepsy (RE) with centrotemporal spikes. The CSWSS and LKS patients can also have behavioral manifestations that overlap the spectrum of autism disorders (ASD). An impairment of brain development and/or maturation with complex interplay between genetic predisposition and nongenetic factors has been suspected. A role for autoimmunity has been proposed but the pathophysiology of CSWSS and of LKS remains uncharacterized. METHODS In recent years, the participation of rare genomic alterations in the susceptibility to epileptic and autistic disorders has been demonstrated. The involvement of copy number variations (CNVs) in 61 CSWSS and LKS patients was questioned using comparative genomic hybridization assays coupled with validation by quantitative polymerase chain reaction (PCR). KEY FINDINGS Whereas the patients showed highly heterogeneous in genomic architecture, several potentially pathogenic alterations were detected. A large number of these corresponded to genomic regions or genes (ATP13A4, CDH9, CDH13, CNTNAP2, CTNNA3, DIAPH3, GRIN2A, MDGA2, SHANK3) that have been either associated with ASD for most of them, or involved in speech or language impairment, or in RE. Particularly, CNVs encoding cell adhesion proteins (cadherins, protocadherins, contactins, catenins) were detected with high frequency (≈20% of the patients) and significant enrichment (cell adhesion: p = 0.027; cell adhesion molecule binding: p = 9.27 × 10(-7)). SIGNIFICANCE Overall our data bring the first insights into the possible molecular pathophysiology of CSWSS and LKS. The overrepresentation of cell adhesion genes and the strong overlap with the genetic, genomic and molecular ASD networks, provide an exciting and unifying view on the clinical links among CSWSS, LKS, and ASD.
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Affiliation(s)
- Gaetan Lesca
- Department of Constitutional Cytogenetics, Lyon Hospices Civils, Lyon, France
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Jakubowska A, Rozkrut D, Antoniou A, Hamann U, Scott RJ, McGuffog L, Healy S, Sinilnikova OM, Rennert G, Lejbkowicz F, Flugelman A, Andrulis IL, Glendon G, Ozcelik H, Thomassen M, Paligo M, Aretini P, Kantala J, Aroer B, von Wachenfeldt A, Liljegren A, Loman N, Herbst K, Kristoffersson U, Rosenquist R, Karlsson P, Stenmark-Askmalm M, Melin B, Nathanson KL, Domchek SM, Byrski T, Huzarski T, Gronwald J, Menkiszak J, Cybulski C, Serrano P, Osorio A, Cajal TR, Tsitlaidou M, Benítez J, Gilbert M, Rookus M, Aalfs CM, Kluijt I, Boessenkool-Pape JL, Meijers-Heijboer HEJ, Oosterwijk JC, van Asperen CJ, Blok MJ, Nelen MR, van den Ouweland AMW, Seynaeve C, van der Luijt RB, Devilee P, Easton DF, Peock S, Frost D, Platte R, Ellis SD, Fineberg E, Evans DG, Lalloo F, Eeles R, Jacobs C, Adlard J, Davidson R, Eccles D, Cole T, Cook J, Godwin A, Bove B, Stoppa-Lyonnet D, Caux-Moncoutier V, Belotti M, Tirapo C, Mazoyer S, Barjhoux L, Boutry-Kryza N, Pujol P, Coupier I, Peyrat JP, Vennin P, Muller D, Fricker JP, Venat-Bouvet L, Johannsson OT, Isaacs C, Schmutzler R, Wappenschmidt B, Meindl A, Arnold N, Varon-Mateeva R, Niederacher D, Sutter C, Deissler H, Preisler-Adams S, Simard J, Soucy P, Durocher F, Chenevix-Trench G, Beesley J, Chen X, Rebbeck T, Couch F, Wang X, Lindor N, Fredericksen Z, Pankratz VS, Peterlongo P, Bonanni B, Fortuzzi S, Peissel B, Szabo C, Mai PL, Loud JT, Lubinski J. Association of PHB 1630 C>T and MTHFR 677 C>T polymorphisms with breast and ovarian cancer risk in BRCA1/2 mutation carriers: results from a multicenter study. Br J Cancer 2012; 106:2016-24. [PMID: 22669161 PMCID: PMC3388557 DOI: 10.1038/bjc.2012.160] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [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: 11/14/2011] [Revised: 03/18/2012] [Accepted: 03/25/2012] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND The variable penetrance of breast cancer in BRCA1/2 mutation carriers suggests that other genetic or environmental factors modify breast cancer risk. Two genes of special interest are prohibitin (PHB) and methylene-tetrahydrofolate reductase (MTHFR), both of which are important either directly or indirectly in maintaining genomic integrity. METHODS To evaluate the potential role of genetic variants within PHB and MTHFR in breast and ovarian cancer risk, 4102 BRCA1 and 2093 BRCA2 mutation carriers, and 6211 BRCA1 and 2902 BRCA2 carriers from the Consortium of Investigators of Modifiers of BRCA1 and BRCA2 (CIMBA) were genotyped for the PHB 1630 C>T (rs6917) polymorphism and the MTHFR 677 C>T (rs1801133) polymorphism, respectively. RESULTS There was no evidence of association between the PHB 1630 C>T and MTHFR 677 C>T polymorphisms with either disease for BRCA1 or BRCA2 mutation carriers when breast and ovarian cancer associations were evaluated separately. Analysis that evaluated associations for breast and ovarian cancer simultaneously showed some evidence that BRCA1 mutation carriers who had the rare homozygote genotype (TT) of the PHB 1630 C>T polymorphism were at increased risk of both breast and ovarian cancer (HR 1.50, 95%CI 1.10-2.04 and HR 2.16, 95%CI 1.24-3.76, respectively). However, there was no evidence of association under a multiplicative model for the effect of each minor allele. CONCLUSION The PHB 1630TT genotype may modify breast and ovarian cancer risks in BRCA1 mutation carriers. This association need to be evaluated in larger series of BRCA1 mutation carriers.
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Affiliation(s)
- A Jakubowska
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland.
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Lefebvre S, Borson-Chazot F, Boutry-Kryza N, Wion N, Schillo F, Peix JL, Brunaud L, Finat A, Calender A, Giraud S. Screening of mutations in genes that predispose to hereditary paragangliomas and pheochromocytomas. Horm Metab Res 2012; 44:334-8. [PMID: 22517554 DOI: 10.1055/s-0032-1306308] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Thirty per cent of the paragangliomas and pheochromocytomas reported are hereditary. Mutations in SDHB, SDHC, SDHD, and more recently SDHAF2 and TMEM127 genes have been described in these hereditary tumors. We looked for mutations in these 5 genes in a series of 269 patients with paragangliomas and/or pheochromocytomas. The SDHB, SDHC, and SDHD genes were analyzed in a series of 269 unrelated index patients with paragangliomas and/or pheochromocytomas using dHPLC screening of point mutations followed by direct sequencing and Multiplex PCR Liquid Chromatography to detect large rearrangements confirmed by quantitative PCR. In a second phase, we adapted Multiplex PCR Liquid Chromatography to the SDHAF2 and TMEM127 genes. This method and direct sequencing were applied to 230 patients without the SDHB, C, D mutations. Of the 269 patients, 44 carried a mutation (16.3%). Thirty-seven different mutations were identified: 18 in SDHB (including 2 large deletions), 8 in SDHD, 6 in SDHC, 5 in TMEM127, and no mutations in SDHAF2. Thirteen mutations have not been published so far. An exhaustive study of the different genes is needed to make possible a familial genetic diagnosis in paraganglioma and pheochromocytoma hereditary syndromes. Although mutations in SDHC and TMEM127 are less frequent than mutations in SDHB and SDHD, they also have less evident clinical feature indicators. Analyzing SDHAF2 must be restricted to familial extra-adrenal paragangliomas. Multiplex PCR Liquid Chromatography is a sensitive, fast, and inexpensive method for screening large rearrangements, which are infrequent in these syndromes.
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Affiliation(s)
- S Lefebvre
- Hospices Civils de Lyon, Hôpital E. Herriot, Génétique moléculaire et clinique, 5 place d'Arsonval, Lyon, France
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Couch FJ, Gaudet MM, Antoniou AC, Ramus SJ, Kuchenbaecker KB, Soucy P, Beesley J, Chen X, Wang X, Kirchhoff T, McGuffog L, Barrowdale D, Lee A, Healey S, Sinilnikova OM, Andrulis IL, Ozcelik H, Mulligan AM, Thomassen M, Gerdes AM, Jensen UB, Skytte AB, Kruse TA, Caligo MA, von Wachenfeldt A, Barbany-Bustinza G, Loman N, Soller M, Ehrencrona H, Karlsson P, Nathanson KL, Rebbeck TR, Domchek SM, Jakubowska A, Lubinski J, Jaworska K, Durda K, Zlowocka E, Huzarski T, Byrski T, Gronwald J, Cybulski C, Górski B, Osorio A, Durán M, Tejada MI, Benitez J, Hamann U, Hogervorst FBL, van Os TA, van Leeuwen FE, Meijers-Heijboer HEJ, Wijnen J, Blok MJ, Kets M, Hooning MJ, Oldenburg RA, Ausems MGEM, Peock S, Frost D, Ellis SD, Platte R, Fineberg E, Evans DG, Jacobs C, Eeles RA, Adlard J, Davidson R, Eccles DM, Cole T, Cook J, Paterson J, Brewer C, Douglas F, Hodgson SV, Morrison PJ, Walker L, Porteous ME, Kennedy MJ, Side LE, Bove B, Godwin AK, Stoppa-Lyonnet D, Fassy-Colcombet M, Castera L, Cornelis F, Mazoyer S, Léoné M, Boutry-Kryza N, Bressac-de Paillerets B, Caron O, Pujol P, Coupier I, Delnatte C, Akloul L, Lynch HT, Snyder CL, Buys SS, Daly MB, Terry M, Chung WK, John EM, Miron A, Southey MC, Hopper JL, Goldgar DE, Singer CF, Rappaport C, Tea MKM, Fink-Retter A, Hansen TVO, Nielsen FC, Arason A, Vijai J, Shah S, Sarrel K, Robson ME, Piedmonte M, Phillips K, Basil J, Rubinstein WS, Boggess J, Wakeley K, Ewart-Toland A, Montagna M, Agata S, Imyanitov EN, Isaacs C, Janavicius R, Lazaro C, Blanco I, Feliubadalo L, Brunet J, Gayther SA, Pharoah PPD, Odunsi KO, Karlan BY, Walsh CS, Olah E, Teo SH, Ganz PA, Beattie MS, van Rensburg EJ, Dorfling CM, Diez O, Kwong A, Schmutzler RK, Wappenschmidt B, Engel C, Meindl A, Ditsch N, Arnold N, Heidemann S, Niederacher D, Preisler-Adams S, Gadzicki D, Varon-Mateeva R, Deissler H, Gehrig A, Sutter C, Kast K, Fiebig B, Heinritz W, Caldes T, de la Hoya M, Muranen TA, Nevanlinna H, Tischkowitz MD, Spurdle AB, Neuhausen SL, Ding YC, Lindor NM, Fredericksen Z, Pankratz VS, Peterlongo P, Manoukian S, Peissel B, Zaffaroni D, Barile M, Bernard L, Viel A, Giannini G, Varesco L, Radice P, Greene MH, Mai PL, Easton DF, Chenevix-Trench G, Offit K, Simard J. Common variants at the 19p13.1 and ZNF365 loci are associated with ER subtypes of breast cancer and ovarian cancer risk in BRCA1 and BRCA2 mutation carriers. Cancer Epidemiol Biomarkers Prev 2012; 21:645-57. [PMID: 22351618 PMCID: PMC3319317 DOI: 10.1158/1055-9965.epi-11-0888] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [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] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Genome-wide association studies (GWAS) identified variants at 19p13.1 and ZNF365 (10q21.2) as risk factors for breast cancer among BRCA1 and BRCA2 mutation carriers, respectively. We explored associations with ovarian cancer and with breast cancer by tumor histopathology for these variants in mutation carriers from the Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA). METHODS Genotyping data for 12,599 BRCA1 and 7,132 BRCA2 mutation carriers from 40 studies were combined. RESULTS We confirmed associations between rs8170 at 19p13.1 and breast cancer risk for BRCA1 mutation carriers [HR, 1.17; 95% confidence interval (CI), 1.07-1.27; P = 7.42 × 10(-4)] and between rs16917302 at ZNF365 (HR, 0.84; 95% CI, 0.73-0.97; P = 0.017) but not rs311499 at 20q13.3 (HR, 1.11; 95% CI, 0.94-1.31; P = 0.22) and breast cancer risk for BRCA2 mutation carriers. Analyses based on tumor histopathology showed that 19p13 variants were predominantly associated with estrogen receptor (ER)-negative breast cancer for both BRCA1 and BRCA2 mutation carriers, whereas rs16917302 at ZNF365 was mainly associated with ER-positive breast cancer for both BRCA1 and BRCA2 mutation carriers. We also found for the first time that rs67397200 at 19p13.1 was associated with an increased risk of ovarian cancer for BRCA1 (HR, 1.16; 95% CI, 1.05-1.29; P = 3.8 × 10(-4)) and BRCA2 mutation carriers (HR, 1.30; 95% CI, 1.10-1.52; P = 1.8 × 10(-3)). CONCLUSIONS 19p13.1 and ZNF365 are susceptibility loci for ovarian cancer and ER subtypes of breast cancer among BRCA1 and BRCA2 mutation carriers. IMPACT These findings can lead to an improved understanding of tumor development and may prove useful for breast and ovarian cancer risk prediction for BRCA1 and BRCA2 mutation carriers.
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Affiliation(s)
- Fergus J Couch
- Departments of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA.
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Boutry-Kryza N, Labalme A, Till M, Schluth-Bolard C, Langue J, Turleau C, Edery P, Sanlaville D. An 800 kb deletion at 17q23.2 including the MED13 (THRAP1) gene, revealed by aCGH in a patient with a SMC 17p. Am J Med Genet A 2011; 158A:400-5. [PMID: 22162340 DOI: 10.1002/ajmg.a.34222] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2010] [Accepted: 05/22/2011] [Indexed: 01/10/2023]
Abstract
We report on clinical and cytogenetic studies in a 7-year-old child with moderate intellectual disability, short stature, mild dysmorphism, and hearing loss. R-chromosome banding showed a de novo autosomal marker originating from the 17p chromosome segment in all cells analyzed. Array comparative genome hybridization (aCGH) was used to determine the gene content and proximal and distal breakpoints of the small supernumerary marker chromosome (SMC). These breakpoints mapped to the centromere of chromosome 17 and the 17p11.2 region, respectively. Unexpectedly, aCGH analysis also revealed a de novo deletion of 800 kb encompassing six genes in the 17q23.2 region, including MED13 (also known as THRAP1). We compared our patient with other reported cases of SMC(17), to determine the respective contributions of the duplication and the deletion to the phenotype. We cannot entirely exclude a minor role for the SMC(17), but we suggest that MED13 haploinsufficiency was responsible for the phenotype of the patient particularly the cataract, hearing loss and semicircular canal dysplasia. Moreover, this report highlights the usefulness of aCGH for the specification of gene content in cases of abnormality, facilitating the establishment of accurate phenotype-genotype correlations and the detection of other, complex rearrangements.
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Affiliation(s)
- Nadia Boutry-Kryza
- Hospices Civils de Lyon, Service de Génétique Moléculaire et Clinique, Lyon, France
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Mulligan AM, Couch FJ, Barrowdale D, Domchek SM, Eccles D, Nevanlinna H, Ramus SJ, Robson M, Sherman M, Spurdle AB, Wappenschmidt B, Lee A, McGuffog L, Healey S, Sinilnikova OM, Janavicius R, Hansen TVO, Nielsen FC, Ejlertsen B, Osorio A, Muñoz-Repeto I, Durán M, Godino J, Pertesi M, Benítez J, Peterlongo P, Manoukian S, Peissel B, Zaffaroni D, Cattaneo E, Bonanni B, Viel A, Pasini B, Papi L, Ottini L, Savarese A, Bernard L, Radice P, Hamann U, Verheus M, Meijers-Heijboer HEJ, Wijnen J, Gómez García EB, Nelen MR, Kets CM, Seynaeve C, Tilanus-Linthorst MMA, van der Luijt RB, van Os T, Rookus M, Frost D, Jones JL, Evans DG, Lalloo F, Eeles R, Izatt L, Adlard J, Davidson R, Cook J, Donaldson A, Dorkins H, Gregory H, Eason J, Houghton C, Barwell J, Side LE, McCann E, Murray A, Peock S, Godwin AK, Schmutzler RK, Rhiem K, Engel C, Meindl A, Ruehl I, Arnold N, Niederacher D, Sutter C, Deissler H, Gadzicki D, Kast K, Preisler-Adams S, Varon-Mateeva R, Schoenbuchner I, Fiebig B, Heinritz W, Schäfer D, Gevensleben H, Caux-Moncoutier V, Fassy-Colcombet M, Cornelis F, Mazoyer S, Léoné M, Boutry-Kryza N, Hardouin A, Berthet P, Muller D, Fricker JP, Mortemousque I, Pujol P, Coupier I, Lebrun M, Kientz C, Longy M, Sevenet N, Stoppa-Lyonnet D, Isaacs C, Caldes T, de la Hoya M, Heikkinen T, Aittomäki K, Blanco I, Lazaro C, Barkardottir RB, Soucy P, Dumont M, Simard J, Montagna M, Tognazzo S, D'Andrea E, Fox S, Yan M, Rebbeck T, Olopade O, Weitzel JN, Lynch HT, Ganz PA, Tomlinson GE, Wang X, Fredericksen Z, Pankratz VS, Lindor NM, Szabo C, Offit K, Sakr R, Gaudet M, Bhatia J, Kauff N, Singer CF, Tea MK, Gschwantler-Kaulich D, Fink-Retter A, Mai PL, Greene MH, Imyanitov E, O'Malley FP, Ozcelik H, Glendon G, Toland AE, Gerdes AM, Thomassen M, Kruse TA, Jensen UB, Skytte AB, Caligo MA, Soller M, Henriksson K, Wachenfeldt VA, Arver B, Stenmark-Askmalm M, Karlsson P, Ding YC, Neuhausen SL, Beattie M, Pharoah PDP, Moysich KB, Nathanson KL, Karlan BY, Gross J, John EM, Daly MB, Buys SM, Southey MC, Hopper JL, Terry MB, Chung W, Miron AF, Goldgar D, Chenevix-Trench G, Easton DF, Andrulis IL, Antoniou AC. Common breast cancer susceptibility alleles are associated with tumour subtypes in BRCA1 and BRCA2 mutation carriers: results from the Consortium of Investigators of Modifiers of BRCA1/2. Breast Cancer Res 2011. [PMID: 22053997 DOI: 10.1186/bcr3052.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
INTRODUCTION Previous studies have demonstrated that common breast cancer susceptibility alleles are differentially associated with breast cancer risk for BRCA1 and/or BRCA2 mutation carriers. It is currently unknown how these alleles are associated with different breast cancer subtypes in BRCA1 and BRCA2 mutation carriers defined by estrogen (ER) or progesterone receptor (PR) status of the tumour. METHODS We used genotype data on up to 11,421 BRCA1 and 7,080 BRCA2 carriers, of whom 4,310 had been affected with breast cancer and had information on either ER or PR status of the tumour, to assess the associations of 12 loci with breast cancer tumour characteristics. Associations were evaluated using a retrospective cohort approach. RESULTS The results suggested stronger associations with ER-positive breast cancer than ER-negative for 11 loci in both BRCA1 and BRCA2 carriers. Among BRCA1 carriers, single nucleotide polymorphism (SNP) rs2981582 (FGFR2) exhibited the biggest difference based on ER status (per-allele hazard ratio (HR) for ER-positive = 1.35, 95% CI: 1.17 to 1.56 vs HR = 0.91, 95% CI: 0.85 to 0.98 for ER-negative, P-heterogeneity = 6.5 × 10-6). In contrast, SNP rs2046210 at 6q25.1 near ESR1 was primarily associated with ER-negative breast cancer risk for both BRCA1 and BRCA2 carriers. In BRCA2 carriers, SNPs in FGFR2, TOX3, LSP1, SLC4A7/NEK10, 5p12, 2q35, and 1p11.2 were significantly associated with ER-positive but not ER-negative disease. Similar results were observed when differentiating breast cancer cases by PR status. CONCLUSIONS The associations of the 12 SNPs with risk for BRCA1 and BRCA2 carriers differ by ER-positive or ER-negative breast cancer status. The apparent differences in SNP associations between BRCA1 and BRCA2 carriers, and non-carriers, may be explicable by differences in the prevalence of tumour subtypes. As more risk modifying variants are identified, incorporating these associations into breast cancer subtype-specific risk models may improve clinical management for mutation carriers.
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Affiliation(s)
- Anna Marie Mulligan
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, 2 Worts Causeway, Cambridge, CB1 8RN, UK
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Mulligan AM, Couch FJ, Barrowdale D, Domchek SM, Eccles D, Nevanlinna H, Ramus SJ, Robson M, Sherman M, Spurdle AB, Wappenschmidt B, Lee A, McGuffog L, Healey S, Sinilnikova OM, Janavicius R, Hansen TVO, Nielsen FC, Ejlertsen B, Osorio A, Muñoz-Repeto I, Durán M, Godino J, Pertesi M, Benítez J, Peterlongo P, Manoukian S, Peissel B, Zaffaroni D, Cattaneo E, Bonanni B, Viel A, Pasini B, Papi L, Ottini L, Savarese A, Bernard L, Radice P, Hamann U, Verheus M, Meijers-Heijboer HEJ, Wijnen J, Gómez García EB, Nelen MR, Kets CM, Seynaeve C, Tilanus-Linthorst MMA, van der Luijt RB, van Os T, Rookus M, Frost D, Jones JL, Evans DG, Lalloo F, Eeles R, Izatt L, Adlard J, Davidson R, Cook J, Donaldson A, Dorkins H, Gregory H, Eason J, Houghton C, Barwell J, Side LE, McCann E, Murray A, Peock S, Godwin AK, Schmutzler RK, Rhiem K, Engel C, Meindl A, Ruehl I, Arnold N, Niederacher D, Sutter C, Deissler H, Gadzicki D, Kast K, Preisler-Adams S, Varon-Mateeva R, Schoenbuchner I, Fiebig B, Heinritz W, Schäfer D, Gevensleben H, Caux-Moncoutier V, Fassy-Colcombet M, Cornelis F, Mazoyer S, Léoné M, Boutry-Kryza N, Hardouin A, Berthet P, Muller D, Fricker JP, Mortemousque I, Pujol P, Coupier I, Lebrun M, Kientz C, Longy M, Sevenet N, Stoppa-Lyonnet D, Isaacs C, Caldes T, de la Hoya M, Heikkinen T, Aittomäki K, Blanco I, Lazaro C, Barkardottir RB, Soucy P, Dumont M, Simard J, Montagna M, Tognazzo S, D'Andrea E, Fox S, Yan M, Rebbeck T, Olopade O, Weitzel JN, Lynch HT, Ganz PA, Tomlinson GE, Wang X, Fredericksen Z, Pankratz VS, Lindor NM, Szabo C, Offit K, Sakr R, Gaudet M, Bhatia J, Kauff N, Singer CF, Tea MK, Gschwantler-Kaulich D, Fink-Retter A, Mai PL, Greene MH, Imyanitov E, O'Malley FP, Ozcelik H, Glendon G, Toland AE, Gerdes AM, Thomassen M, Kruse TA, Jensen UB, Skytte AB, Caligo MA, Soller M, Henriksson K, Wachenfeldt VA, Arver B, Stenmark-Askmalm M, Karlsson P, Ding YC, Neuhausen SL, Beattie M, Pharoah PDP, Moysich KB, Nathanson KL, Karlan BY, Gross J, John EM, Daly MB, Buys SM, Southey MC, Hopper JL, Terry MB, Chung W, Miron AF, Goldgar D, Chenevix-Trench G, Easton DF, Andrulis IL, Antoniou AC. Common breast cancer susceptibility alleles are associated with tumour subtypes in BRCA1 and BRCA2 mutation carriers: results from the Consortium of Investigators of Modifiers of BRCA1/2. Breast Cancer Res 2011; 13:R110. [PMID: 22053997 PMCID: PMC3326552 DOI: 10.1186/bcr3052] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [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: 04/27/2011] [Accepted: 11/02/2011] [Indexed: 12/24/2022] Open
Abstract
Introduction Previous studies have demonstrated that common breast cancer susceptibility alleles are differentially associated with breast cancer risk for BRCA1 and/or BRCA2 mutation carriers. It is currently unknown how these alleles are associated with different breast cancer subtypes in BRCA1 and BRCA2 mutation carriers defined by estrogen (ER) or progesterone receptor (PR) status of the tumour. Methods We used genotype data on up to 11,421 BRCA1 and 7,080 BRCA2 carriers, of whom 4,310 had been affected with breast cancer and had information on either ER or PR status of the tumour, to assess the associations of 12 loci with breast cancer tumour characteristics. Associations were evaluated using a retrospective cohort approach. Results The results suggested stronger associations with ER-positive breast cancer than ER-negative for 11 loci in both BRCA1 and BRCA2 carriers. Among BRCA1 carriers, single nucleotide polymorphism (SNP) rs2981582 (FGFR2) exhibited the biggest difference based on ER status (per-allele hazard ratio (HR) for ER-positive = 1.35, 95% CI: 1.17 to 1.56 vs HR = 0.91, 95% CI: 0.85 to 0.98 for ER-negative, P-heterogeneity = 6.5 × 10-6). In contrast, SNP rs2046210 at 6q25.1 near ESR1 was primarily associated with ER-negative breast cancer risk for both BRCA1 and BRCA2 carriers. In BRCA2 carriers, SNPs in FGFR2, TOX3, LSP1, SLC4A7/NEK10, 5p12, 2q35, and 1p11.2 were significantly associated with ER-positive but not ER-negative disease. Similar results were observed when differentiating breast cancer cases by PR status. Conclusions The associations of the 12 SNPs with risk for BRCA1 and BRCA2 carriers differ by ER-positive or ER-negative breast cancer status. The apparent differences in SNP associations between BRCA1 and BRCA2 carriers, and non-carriers, may be explicable by differences in the prevalence of tumour subtypes. As more risk modifying variants are identified, incorporating these associations into breast cancer subtype-specific risk models may improve clinical management for mutation carriers.
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Affiliation(s)
- Anna Marie Mulligan
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, 2 Worts Causeway, Cambridge, CB1 8RN, UK
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Boutry-Kryza N, Sanlaville D. [Genetic tools]. Rev Prat 2011; 61:526-527. [PMID: 21548236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
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Lesca G, Boutry-Kryza N, de Toffol B, Milh M, Steschenko D, Lemesle-Martin M, Maillard L, Foletti G, Rudolf G, Nielsen JE, á Rogvi-Hansen B, Erdal J, Mancini J, Thauvin-Robinet C, M'Rrabet A, Ville D, Szepetowski P, Raffo E, Hirsch E, Ryvlin P, Calender A, Genton P. Novel mutations in EPM2A and NHLRC1 widen the spectrum of Lafora disease. Epilepsia 2010; 51:1691-8. [PMID: 20738377 DOI: 10.1111/j.1528-1167.2010.02692.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
PURPOSE Lafora disease (LD) is an autosomal recessive form of progressive myoclonus epilepsy with onset in childhood or adolescence and with fatal outcome caused by mutations in two genes: EPM2A and NHLRC1. The aim of this study was to characterize the mutation spectrum in a cohort of unrelated patients with presumed LD. METHODS Sequencing of the two genes and search for large rearrangements was performed in 46 unrelated patients with suspected LD, 33 originating from France and the others from different countries. Patients were classified into two groups according to the clinical presentation. RESULTS Mutations of various types were found in EPM2A in 10 patients and in NHLRC1 in 4 patients. Mutations were found in 14 (93%) of 15 patients with classical clinical and electroencephalography (EEG) presentation of LD and in no patients with an atypical presentation. Ten mutations were novel, including the first substitution reported in a donor splice site of EPM2A, leading to the deletion of exon 2 at the RNA level. Four large deletions, including two deletions of exon 2 with different sizes and breakpoints, were found in EPM2A, corresponding to 20% of the alleles of this gene. DISCUSSION We described several novel mutations of EPM2A and NHLRC1 and brought additional data to the genetic epidemiology of LD. This study emphasized the high mutation rate in patients with classical LD as well as the high negativity rate of skin biopsy.
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Affiliation(s)
- Gaetan Lesca
- Service de génétique, hospices civils de Lyon et université Claude Bernard Lyon I, Lyon, France.
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