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1. The clinical value of optical genome mapping in the rapid characterization of RB1 duplication and 15q23q24.2 triplication, for more appropriate prenatal genetic counselling

Author

Malek Bouassida, Denise Molina‐Gomes, Fairouz Koraichi, Bérénice Hervé, Morgane Lhuilier, Clémence Duvillier, Jessica Le Gall, Marion Gauthier‐Villars, Valérie Serazin, Thibaud Quibel, Rodolphe Dard, and François Vialard

Subjects
15q23q24.2 triplication, optical genome mapping, prenatal diagnosis, RB1 gene, Genetics, QH426-470
Abstract

Abstract Background Despite recent advances in prenatal genetic diagnosis, medical geneticists still face considerable difficulty in interpreting the clinical outcome of copy‐number‐variant duplications and defining the mechanisms underlying the formation of certain chromosomal rearrangements. Optical genome mapping (OGM) is an emerging cytogenomic tool with proved ability to identify the full spectrum of cytogenetic aberrations. Methods Here, we report on the use of OGM in a prenatal diagnosis setting. Detailed breakpoint mapping was used to determine the relative orientations of triplicated and duplicated segments in two unrelated foetuses harbouring chromosomal aberrations: a de novo 15q23q24.2 triplication and a paternally inherited 13q14.2 duplication that overlapped partially with the RB1 gene. Results OGM enabled us to suggest a plausible mechanism for the triplication and confirmed that the RB1 duplication was direct oriented and in tandem. This enabled us to predict the pathogenic consequences, refine the prognosis and adapt the follow‐up and familial screening appropriately. Conclusion Along with an increase in diagnostic rates, OGM can rapidly highlight genotype–phenotype correlations, improve genetic counselling and significantly influence prenatal management.

Published
2024
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2. Male breast cancer: No evidence for mosaic BRCA1 promoter methylation involvement

Author

Mathias Schwartz, Sabrina Ibadioune, Sophie Vacher, Marie-Charlotte Villy, Olfa Trabelsi-Grati, Jessica Le Gall, Sandrine M. Caputo, Hélène Delhomelle, Mathilde Warcoin, Virginie Moncoutier, Christine Bourneix, Nadia Boutry-Kryza, Antoine De Pauw, Marc-Henri Stern, Bruno Buecher, Emmanuelle Mouret-Fourme, Chrystelle Colas, Dominique Stoppa-Lyonnet, Julien Masliah-Planchon, Lisa Golmard, and Ivan Bieche

Subjects
HBOC syndrome, Breast neoplasm, Genetic testing, Homologous recombination, DNA methylation, Epigenomics, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282
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.

Published
2024
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3. APCgermline pathogenic variants and epithelial ovarian cancer: causal or coincidental findings?

Author

Roseline Vibert, Jessica Le Gall, Bruno Buecher, Emmanuelle Mouret-Fourme, Guillaume Bataillon, Véronique Becette, Olfa Trabelsi-Grati, Virginie Moncoutier, Catherine Dehainault, Jennifer Carriere, Mathias Schwartz, Voreak Suybeng, Ivan Bieche, Chrystelle Colas, Anne Vincent-Salomon, Dominique Stoppa-Lyonnet, and Lisa Golmard

Subjects
Genetics, Genetics (clinical)
Abstract

APCgermline pathogenic variants result in predisposition to familial adenomatous polyposis and extraintestinal tumours such as desmoid fibromatosis, medulloblastomas and thyroid cancers. They have also been recently involved in ovarian microcystic stromal tumours.APCinactivation has been described at the tumour level in epithelial ovarian cancers (EOCs). Here, we report the identification ofAPCgermline pathogenic variants in two patients diagnosed with premenopausal EOC in early 30s, with no other pathogenic variant detected in the known ovarian cancer predisposing genes. Subsequent tumour analysis showed neither a second hit ofAPCinactivation nor β-catenin activation. Both tumours did not have a homologous recombination (HR) deficiency, pointing towards the implication of other genes than those involved in HR.APCmay contribute to the carcinogenesis of EOC in a multifactorial context. Further studies are required to clarify the role ofAPCin predisposition to EOC.

Published
2022

4. Hereditary cancer predispositions: Comparison of multigene panel sequencing on fresh‐frozen breast/ovarian tumor versus blood

Author

Mathias Schwartz, Virginie Moncoutier, Adrien Peytral, Jessica Le Gall, Voreak Suybeng, Mélanie Pagès, Julien Masliah‐Planchon, Olfa Trabelsi‐Grati, Samia Melaabi, Céline Callens, Ivan Bièche, Hélène Delhomelle, Antoine De Pauw, Claire Saule, Emmanuelle Mouret‐Fourme, Marion Gauthier‐Villars, Bruno Buecher, Chrystelle Colas, Dominique Stoppa‐Lyonnet, and Lisa Golmard

Subjects
Genetics, Genetics (clinical)
Published
2023

5. Classification of 101 BRCA1 and BRCA2 variants of uncertain significance by cosegregation study: A powerful approach

Author

Marie-Noëlle Bonnet-Dupeyron, Helene Dreyfus, Nadia Boutry-Kryza, Cornel Popovici, Laurent Castera, Nancy Uhrhammer, Anthony Laugé, Yves-Jean Bignon, Hélène Delhomelle, Alice Fiévet, Christophe Guy, Noémie Bronnec, Bruno Buecher, Fabienne Prieur, Sophie Demontety, Vincent Goussot, Emmanuelle Mouret-Fourme, Claire Saule, Helene Zattara, Sarah Malsa, Paul Gesta, Cindy Meira, Erell Guillerm, Isabelle Turbiez, Agathe Ricou, Mélanie Léoné, Pierre Vande Perre, Sarab Lizard, Pascaline Berthet, Norbert Lignon, Adrien Buisson, Anne-Marie Birot, Philippe Denizeau, Etienne Rouleau, Odile Cohen-Haguenauer, Veronica Goldbarg, Virginie Moncoutier, Charlotte Benigni, Emmanuelle Barouk-Simonet, Flavie Boulouard, Caroline Jacquot-Sawka, Alice Yvard, Hakima Lallaoui, Veronica Cusin, Angélina Legros, Muriel Belotti, Christine Maugard, Marine Guillaud-Bataille, Jean-Marc Limacher, Marion Gauthier-Villars, Louise Crivelli, Afane Brahimi, Odile Cabaret, Ophelie Bertrand, Michel Longy, Gabrielle Le Guyadec, Doriane Livon, Amelie Bloucard, Dominique Stoppa-Lyonnet, Capucine Delnatte, Caroline Lecerf, Jennifer Carriere, Virginie Guibert, Véronique Mari, Anne-Sophie Allary, Florence Coulet, Françoise Bonnet, Paul Vilquin, Noémie Basset, Khadija Abidallah, Pierre Macquere, Nicolas Derive, Manon Boulaire, Stephanie Chieze-Valéro, Marine Le Mentec, Mathilde Gay-Bellile, Anne-Laure Conoy, Henri Margot, Pierre Devulder, Mathias Schwartz, Isabelle Tennevet, Stéphane Bézieau, Francesca Damiola, Violaine Bourdon, Audrey Mailliez, Zoe Nevière, Nicolas Viellard, Laurence Venat, Antoine De Pauw, Brigitte Bressac-de Paillerets, Agnès Hardouin, Sofiane Lacoste, Sandra Fert-Ferrer, Maud Privat, Helene Larbre, Dominique Vaur, Etienne Muller, Françoise Revillion, Clémentine Legrand, Rosette Lidereau, Laurence Gladieff, Sabine Raad, Jean Chiesa, Diane Molière, Ahmed Bouras, Nicolas Sevenet, Patrick R. Benusiglio, Sophie Giraud, Christine Toulas, Voreak Suybeng, Florine Oca, Tetsuro Noguchi, Catherine Dehainault, Sophie Lejeune, Céline Heude, Catherine Dubois d’Enghein, Thien-vu Nguyen Minh Tuan, Olivier Caron, Mathilde Warcoin, Christine Lasset, Claude Houdayer, Jessica Moretta-Serra, Julie Tinat, Hagay Sobol, Natalie Jones, Fanny Brayotel, Anne Fajac, Virginie Bubien, Maud Blanluet, Jean-Marc Rey, Anne Durlach, Sandrine M. Caputo, Isabelle Coupier, Fatoumata Simaga, Sophie Krieger, Catherine Noguès, Fabrice Airaud, Robin Fouillet, Celine Garrec, Valérie Bonadona, Julie Menjard, Bérengère Legendre, Chrystelle Colas, Christelle Berthemin, Camille Cohen, Caroline Abadie, Olivier Ingster, Audrey Remenieras, Anaïs Dupré, Jessica Le Gall, Lisa Golmard, Marie Bidart, Henrique Tenreiro, J Bombled, Marie-Charlotte Villy, Marie-Agnès Collonge-Rame, Sophie Dussart, Alain Lortholary, Lucie Salle, Samira Fekairi, Service de Génétique Oncologique, Institut Curie [Paris], Université Paris sciences et lettres (PSL), Département de Biologie des Tumeurs, Unité de génétique et biologie des cancers (U830), Institut Curie [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Hospices Civils de Lyon (HCL), Centre Léon Bérard [Lyon], CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Institut Gustave Roussy (IGR), Génétique (Biologie pathologie), Département de biologie et pathologie médicales [Gustave Roussy], Institut Gustave Roussy (IGR)-Institut Gustave Roussy (IGR), Institut de biochimie et génétique cellulaires (IBGC), Université Bordeaux Segalen - Bordeaux 2-Centre National de la Recherche Scientifique (CNRS), Hopital Saint-Louis [AP-HP] (AP-HP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Centre hospitalier universitaire de Nantes (CHU Nantes), Centre Jean Perrin [Clermont-Ferrand] (UNICANCER/CJP), UNICANCER, Imagerie Moléculaire et Stratégies Théranostiques (IMoST), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne (UCA), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Centre de Références Cancers Rares (PREDIR), INCA, Institut national du cancer [Boulogne] (INCA), Hôpital Européen Georges Pompidou [APHP] (HEGP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO), Institut de Cancérologie de l'Ouest [Angers/Nantes] (UNICANCER/ICO), Centre Hospitalier Universitaire de Reims (CHU Reims), dormoy, valerian, Unité fonctionnelle de neurogénétique moléculaire et cellulaire, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), and Service de Génétique Cytogénétique et Embryologie [CHU Pitié-Salpêtrière]

Subjects
Cosegregation, Genotype, [SDV]Life Sciences [q-bio], Breast Neoplasms, Biology, Article, 03 medical and health sciences, Likely benign, Genetics, medicine, Humans, Clinical significance, Genetic Predisposition to Disease, Genetic Testing, Uncertain significance, Gene, ComputingMilieux_MISCELLANEOUS, Genetics (clinical), 030304 developmental biology, BRCA2 Protein, Ovarian Neoplasms, 0303 health sciences, Cancer predisposition, BRCA1 Protein, 030305 genetics & heredity, Cancer, Genetic Variation, medicine.disease, 3. Good health, [SDV] Life Sciences [q-bio], Classification methods, Female
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.

Published
2021

6. Molecular diagnosis of retinoblastoma by circulating tumor DNA analysis

Author

Hervé Brisse, Virginie Bernard, Camille Benoist, Livia Lumbroso, Claude Houdayer, Alexandre Matet, Arnaud Gauthier, Sylvain Baulande, G Schleiermacher, Nathalie Cassoux, Lisa Golmard, Victor Renault, Mathieu Chicard, Irene Jiménez, Olivier Delattre, Dominique Stoppa-Lyonnet, François Radvanyi, Isabelle Aerts, Catherine Dehainault, Jessica Le Gall, Éléonore Frouin, Eve Lapouble, François Doz, and Marion Gauthier-Villars

Subjects
Oncology, Male, Cancer Research, medicine.medical_specialty, Somatic cell, Genetic counseling, Ubiquitin-Protein Ligases, Disease, Circulating Tumor DNA, Internal medicine, medicine, Humans, Allele, Child, Retrospective Studies, business.industry, Retinoblastoma, Computational Biology, Infant, medicine.disease, eye diseases, Retinoblastoma Binding Proteins, Cell-free fetal DNA, Circulating tumor DNA, Child, Preschool, Cohort, Mutation, Female, business
Abstract

Purpose The analysis of circulating tumor DNA (ctDNA), a fraction of total cell-free DNA (cfDNA), might be of special interest in retinoblastoma patients. Because the accessibility to tumor tissue is very limited in these patients, either for histopathological diagnosis of suspicious intraocular masses (biopsies are proscribed) or for somatic RB1 studies and genetic counseling (due to current successful conservative approaches), we aim to validate the detection of ctDNA in plasma of non-hereditary retinoblastoma patients by molecular analysis of RB1 gene. Experimental design In a cohort of 19 intraocular unilateral non-hereditary retinoblastoma patients for whom a plasma sample was available at diagnosis, we performed high-deep next-generation sequencing (NGS) of RB1 in cfDNA. Two different bioinformatics/statistics approaches were applied depending on whether the somatic RB1 status was available or not. Results Median plasma sample volume was 600 μL [100–1000]; median cfDNA plasma concentration was 119 [38–1980] and 27 [11–653] ng/mL at diagnosis and after complete remission, respectively. In the subgroup of patients with known somatic RB1 alterations (n = 11), seven of nine somatic mutations were detected (median allele fraction: 6.7%). In patients without identified somatic RB1 alterations (n = 8), six candidate variants were identified for seven patients. Conclusions Despite small tumor size, blood-ocular barrier, poor ctDNA blood release and limited plasma sample volumes, we confirm that it is possible to detect ctDNA with high-deep NGS in plasma from patients with intraocular non-hereditary retinoblastoma. This may aid in diagnosis of suspicious cases, family genetic counseling or follow-up of residual intraocular disease.

Published
2021

7. Sex chromosome aneuploidies and copy-number variants: a further explanation for neurodevelopmental prognosis variability?

Author

Albert David, Sylvie Jaillard, Brigitte Gilbert-Dussardier, Mélanie Fradin, Olivier Pichon, Sébastien Moutton, Tiffany Busa, Elise Schaefer, Sandra Mercier, Frédéric Bilan, Odile Boute, Sabine Baron, Sébastien Jacquemont, Caroline Rooryck, Mathilde Nizon, Bertrand Isidor, Dominique Martin-Coignard, Joris Andrieux, Valérie Cormier-Daire, Séverine Audebert-Bellanger, Jessica Le Gall, Cédric Le Caignec, Damien Sanlaville, Claire Beneteau, Claude Férec, Marie Vincent, and Aia E. Jønch

Subjects
0301 basic medicine, Male, medicine.medical_specialty, Pediatrics, DNA Copy Number Variations, Developmental Disabilities, Sex Chromosome Disorders of Sex Development, Sex Chromosome Disorders, Trisomy, Triple X syndrome, Biology, Article, 03 medical and health sciences, Neurodevelopmental disorder, Intellectual Disability, Intellectual disability, XYY Karyotype, Genetics, medicine, Humans, Copy-number variation, Genetics (clinical), Sex Chromosome Aberrations, Chromosomes, Human, X, Cytogenetics, medicine.disease, Human genetics, 030104 developmental biology, Phenotype, Medical genetics, XYY syndrome, Female
Abstract

Sex chromosome aneuploidies (SCA) is a group of conditions in which individuals have an abnormal number of sex chromosomes. SCA, such as Klinefelter’s syndrome, XYY syndrome, and Triple X syndrome are associated with a large range of neurological outcome. Another genetic event such as another cytogenetic abnormality may explain a part of this variable expressivity. In this study, we have recruited fourteen patients with intellectual disability or developmental delay carrying SCA associated with a copy-number variant (CNV). In our cohort (four patients 47,XXY, four patients 47,XXX, and six patients 47,XYY), seven patients were carrying a pathogenic CNV, two a likely pathogenic CNV and five a variant of uncertain significance. Our analysis suggests that CNV might be considered as an additional independent genetic factor for intellectual disability and developmental delay for patients with SCA and neurodevelopmental disorder.

Published
2016

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