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1. An spanish study of secondary findings in families affected with mendelian disorders: choices, prevalence and family history

Author

Marta Codina-Solà, Laura Trujillano, Anna Abulí, Eulàlia Rovira-Moreno, Patricia Muñoz-Cabello, Berta Campos, Paula Fernández-Álvarez, Dolors Palau, Estela Carrasco, Irene Valenzuela, Anna Maria. Cueto-González, Amaia Lasa-Aranzasti, Javier Limeres, Jordi Leno-Colorado, Mar Costa-Roger, Alejandro Moles-Fernández, Judith Balmaña, Orland Díez, Ivon Cuscó, Elena Garcia-Arumí, and Eduardo Fidel Tizzano

Subjects
Genetics, Genetics (clinical)
Abstract

Clinical exome sequencing has the potential to identify pathogenic variants unrelated to the purpose of the study (secondary findings, SFs). Data describing actual choices of SFs in participants in a clinical setting and factors influencing their decision are virtually non-existant in Europe. In this work, we report the acceptance rate of SFs, calculate their prevalence and study factors associated with the decision in a cohort of patients affected with a rare genetic disorder in a Spanish Hospital. Finally, we re-examine the presence of previously non reported family history in positive cases. We retrospectively reviewed informed consent choices and SF results from 824 unrelated probands affected with rare genetic disorders who underwent whole-genome or exome sequencing. Ninety percent of families (740/824) affected with rare disorders wished to be informed of SFs. Declining SFs was associated with a prenatal setting (30% vs. 8.7%, p = 0.025), consanguinity (19% vs. 8.7%, p = 0.013), male gender (10.6% vs. 1.5%, p = 0.00865) and the proband being a minor (10.6% vs. 1.5%, p = 0.014). Overall, 27 pathogenic or likely pathogenic variants were identified in 27 individuals, with an SF prevalence of 3.6%. Disclosure of SFs increased the percentage of positive family histories and resulted in early diagnosis or changes in the management of 10 individuals from five families. We show that the acceptance of SFs in Spain is high and the disclosure of SFs leads to a clinically meaningful change in the medical management of individuals.

Published
2022
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2. Discovering a new part of the phenotypic spectrum of Coffin-Siris syndrome in a fetal cohort

Author

Pleuntje J. van der Sluijs, Marieke Joosten, Caroline Alby, Tania Attié-Bitach, Kelly Gilmore, Christele Dubourg, Mélanie Fradin, Tianyun Wang, Evangeline C. Kurtz-Nelson, Kaitlyn P. Ahlers, Peer Arts, Christopher P. Barnett, Myla Ashfaq, Anwar Baban, Myrthe van den Born, Sarah Borrie, Tiffany Busa, Alicia Byrne, Miriam Carriero, Claudia Cesario, Karen Chong, Anna Maria Cueto-González, Jennifer C. Dempsey, Karin E.M. Diderich, Dan Doherty, Stense Farholt, Erica H. Gerkes, Svetlana Gorokhova, Lutgarde C.P. Govaerts, Pernille A. Gregersen, Scott E. Hickey, Mathilde Lefebvre, Francesca Mari, Jelena Martinovic, Hope Northrup, Melanie O’Leary, Kareesma Parbhoo, Sophie Patrier, Bernt Popp, Fernando Santos-Simarro, Corinna Stoltenburg, Christel Thauvin-Robinet, Elisabeth Thompson, Anneke T. Vulto-van Silfhout, Farah R. Zahir, Hamish S. Scott, Rachel K. Earl, Evan E. Eichler, Neeta L. Vora, Yael Wilnai, Jessica L. Giordano, Ronald J. Wapner, Jill A. Rosenfeld, Monique C. Haak, Gijs W.E. Santen, Leiden University Medical Center (LUMC), Universiteit Leiden, Erasmus University Medical Center [Rotterdam] (Erasmus MC), CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Imagine - Institut des maladies génétiques (IHU) (Imagine - U1163), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), University of North Carolina [Chapel Hill] (UNC), University of North Carolina System (UNC), Institut de Génétique et Développement de Rennes (IGDR), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), CHU Pontchaillou [Rennes], Hôpital de la Timone [CHU - APHM] (TIMONE), Marseille medical genetics - Centre de génétique médicale de Marseille (MMG), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Lipides - Nutrition - Cancer [Dijon - U1231] (LNC), Université de Bourgogne (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Agro Dijon, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), CHU Rouen, Normandie Université (NU), Columbia University Medical Center (CUMC), Columbia University [New York], Baylor College of Medicine (BCM), Baylor University, This work was supported, in part, by grants from the National Institutes of Health (Grant No. R01 MH101221 [to E.E.E.]). E.E.E. is an investigator of the Howard Hughes Medical Institute.Sequencing and analysis for individual 30 was provided by the Broad Institute of MIT and Harvard Center for Mendelian Genomics and was funded by the National Human Genome Research Institute, the National Eye Institute, and the National Heart, Lung, and Blood Institute (Grant Nos. UM1 HG008900 and R01 HG009141).Sequencing and analysis of cases 5 and 18 was funded by the National Institute of Child Human Development (Grant Nos. K23 HD088742 and R01 HD105868 [to N.L.V.])., Emergency Medicine, Clinical Genetics, van der Sluijs, Pleuntje J, Joosten, Marieke, Alby, Caroline, Attié-Bitach, Tania, Arts, Peer, Byrne, Alicia, Scott, Hamish S, and Santen, Gijs WE

Subjects
prenatal, genetic association, Chromosomal Proteins, Non-Histone, Micrognathism, SMARCB1, genetic vulnerability, Article, Fetal, SMARCA4, Intellectual Disability, Humans, Coffin-Siris syndrome, Abnormalities, Multiple, Genetic Association Studies, Genetics (clinical), Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7], BAF-complex, SMARCB, ARID1A, ARID1B BAFopathy, Phenotype, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, Face, abnormalities, Hand Deformities, Congenital, Neck
Abstract

Purpose: Genome-wide sequencing is increasingly being performed during pregnancy to identify the genetic cause of congenital anomalies. The interpretation of prenatally identified variants can be challenging and is hampered by our often limited knowledge of prenatal phenotypes. To better delineate the prenatal phenotype of Coffin-Siris syndrome (CSS), we collected clinical data from patients with a prenatal phenotype and a pathogenic variant in one of the CSS-associated genes. Methods: Clinical data was collected through an extensive web-based survey. Results: We included 44 patients with a variant in a CSS-associated gene and a prenatal phenotype; 9 of these patients have been reported before. Prenatal anomalies that were frequently observed in our cohort include hydrocephalus, agenesis of the corpus callosum, hypoplastic left heart syndrome, persistent left vena cava, diaphragmatic hernia, renal agenesis, and intrauterine growth restriction. Anal anomalies were frequently identified after birth in patients with ARID1A variants (6/14, 43%). Interestingly, pathogenic ARID1A variants were much more frequently identified in the current prenatal cohort (16/44, 36%) than in postnatal CSS cohorts (5%-9%). Conclusion: Our data shed new light on the prenatal phenotype of patients with pathogenic variants in CSS genes. (C) 2022 American College of Medical Genetics and Genomics. Published by Elsevier Inc. All rights reserved.

Published
2022
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3. Natural history of KBG syndrome in a large European cohort

Author

Lorenzo Loberti, Lucia Pia Bruno, Stefania Granata, Gabriella Doddato, Sara Resciniti, Francesca Fava, Michele Carullo, Elisa Rahikkala, Guillaume Jouret, Leonie A Menke, Damien Lederer, Pascal Vrielynck, Lukáš Ryba, Nicola Brunetti-Pierri, Amaia Lasa-Aranzasti, Anna Maria Cueto-González, Laura Trujillano, Irene Valenzuela, Eduardo F Tizzano, Alessandro Mauro Spinelli, Irene Bruno, Aurora Currò, Franco Stanzial, Francesco Benedicenti, Diego Lopergolo, Filippo Maria Santorelli, Constantia Aristidou, George A Tanteles, Isabelle Maystadt, Tinatin Tkemaladze, Tiia Reimand, Helen Lokke, Katrin Õunap, Maria K Haanpää, Andrea Holubová, Veronika Zoubková, Martin Schwarz, Riina Žordania, Kai Muru, Laura Roht, Annika Tihveräinen, Rita Teek, Ulvi Thomson, Isis Atallah, Andrea Superti-Furga, Sabrina Buoni, Roberto Canitano, Valeria Scandurra, Annalisa Rossetti, Salvatore Grosso, Roberta Battini, Margherita Baldassarri, Maria Antonietta Mencarelli, Caterina Lo Rizzo, Mirella Bruttini, Francesca Mari, Francesca Ariani, Alessandra Renieri, Anna Maria Pinto, Loberti, Lorenzo, Bruno, Lucia Pia, Granata, Stefania, Doddato, Gabriella, Resciniti, Sara, Fava, Francesca, Carullo, Michele, Rahikkala, Elisa, Jouret, Guillaume, Menke, Leonie A, Lederer, Damien, Vrielynck, Pascal, Ryba, Lukáš, Brunetti-Pierri, Nicola, Lasa-Aranzasti, Amaia, Cueto-González, Anna Maria, Trujillano, Laura, Valenzuela, Irene, Tizzano, Eduardo F, Spinelli, Alessandro Mauro, Bruno, Irene, Currò, Aurora, Stanzial, Franco, Benedicenti, Francesco, Lopergolo, Diego, Santorelli, Filippo Maria, Aristidou, Constantia, Tanteles, George A, Maystadt, Isabelle, Tkemaladze, Tinatin, Reimand, Tiia, Lokke, Helen, Õunap, Katrin, Haanpää, Maria K, Holubová, Andrea, Zoubková, Veronika, Schwarz, Martin, Žordania, Riina, Muru, Kai, Roht, Laura, Tihveräinen, Annika, Teek, Rita, Thomson, Ulvi, Isis, Atallah, Superti-Furga, Andrea, Buoni, Sabrina, Canitano, Roberto, Scandurra, Valeria, Rossetti, Annalisa, Grosso, Salvatore, Battini, Roberta, Baldassarri, Margherita, Mencarelli, Maria Antonietta, Rizzo, Caterina Lo, Bruttini, Mirella, Mari, Francesca, Ariani, Francesca, Renieri, Alessandra, Pinto, Anna Maria, General Paediatrics, ANS - Cellular & Molecular Mechanisms, ANS - Complex Trait Genetics, ARD - Amsterdam Reproduction and Development, and Pediatrics

Subjects
Genetics, General Medicine, Molecular Biology, Genetics (clinical)
Abstract

KBG syndrome (KBGS) is characterized by distinctive facial gestalt, short stature and variable clinical findings. With ageing, some features become more recognizable, allowing a differential diagnosis. We aimed to better characterize natural history of KBGS. In the context of a European collaborative study, we collected the largest cohort of KBGS patients (49). A combined array- based Comparative Genomic Hybridization and next generation sequencing (NGS) approach investigated both genomic Copy Number Variants and SNVs. Intellectual disability (ID) (82%) ranged from mild to moderate with severe ID identified in two patients. Epilepsy was present in 26.5%. Short stature was consistent over time, while occipitofrontal circumference (median value: −0.88 SD at birth) normalized over years. Cerebral anomalies, were identified in 56% of patients and thus represented the second most relevant clinical feature reinforcing clinical suspicion in the paediatric age when short stature and vertebral/dental anomalies are vague. Macrodontia, oligodontia and dental agenesis (53%) were almost as frequent as skeletal anomalies, such as brachydactyly, short fifth finger, fifth finger clinodactyly, pectus excavatum/carinatum, delayed bone age. In 28.5% of individuals, prenatal ultrasound anomalies were reported. Except for three splicing variants, leading to a premature termination, variants were almost all frameshift. Our results, broadening the spectrum of KBGS phenotype progression, provide useful tools to facilitate differential diagnosis and improve clinical management. We suggest to consider a wider range of dental anomalies before excluding diagnosis and to perform a careful odontoiatric/ear-nose-throat (ENT) evaluation in order to look for even submucosal palate cleft given the high percentage of palate abnormalities. NGS approaches, following evidence of antenatal ultrasound anomalies, should include ANKRD11.

Published
2022
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4. Missense MED12 variants in 22 males with intellectual disability: From nonspecific symptoms to complete syndromes

Author

Nuno Maia, Nekane Ibarluzea, Mala Misra‐Isrie, Daniel C. Koboldt, Isabel Marques, Gabriela Soares, Rosário Santos, Carlo L. M. Marcelis, Riikka Keski‐Filppula, Miriam Guitart, Elisabeth Gabau Vila, April Lehman, Scott Hickey, Mari Mori, Paulien Terhal, Irene Valenzuela, Amaia Lasa‐Aranzasti, Anna Maria Cueto‐González, Brian H. Chhouk, Rebecca C. Yeh, Jennifer E. Neil, Bassam Abu‐Libde, Tjitske Kleefstra, Mariet W. Elting, Andrea Császár, Judit Kárteszi, Beáta Bessenyei, Hans van Bokhoven, Paula Jorge, Johanna M. van Hagen, Arjan P. M. de Brouwer, Institut Català de la Salut, [Maia N, Marques I] Unidade de Genética Molecular, Centro de Genética Médica Doutor Jacinto de Magãlhaes (CGM), Centro Hospitalar Universitário do Porto (CHUPorto) Unit for Multidisciplinary Research In Biomedicine (UMIB), Institute of Biomedical Sciences Abel Salazar (ICBAS), and ITR - Laboratory for Integrative and Translational Research in Population Health, University of Porto, Porto, Portugal. [Ibarluzea N] Biocruces Bizkaia Health Research Institute, Barakaldo, Spain. [Misra-Isrie M] Department of Human Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands. [Koboldt DC] Steve and Cindy Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA. Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, USA. [Soares G] Unidade de Genética Médica, Centro de Genética Médica Doutor Jacinto de Magalhaes (CGM), Centro Hospitalar Universitário do Porto (CHUPorto), Porto, Portugal. [Valenzuela I] Servei de Genètica Clínica i Molecular, Vall d'Hebron Hospital Universitari, Barcelona, Spain. Grup de Recerca de Medicina Genètica, Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain, Vall d'Hebron Barcelona Hospital Campus, Human genetics, and Amsterdam Reproduction & Development (AR&D)

Subjects
Discapacitat intel·lectual - Aspectes genètics, Anomalies cromosòmiques, All institutes and research themes of the Radboud University Medical Center, Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7], Otros calificadores::Otros calificadores::/genética [Otros calificadores], Genetics, Other subheadings::Other subheadings::/genetics [Other subheadings], fenómenos genéticos::variación genética::mutación::mutación de sentido erróneo [FENÓMENOS Y PROCESOS], Genetic Phenomena::Genetic Variation::Mutation::Mutation, Missense [PHENOMENA AND PROCESSES], enfermedades del sistema nervioso::manifestaciones neurológicas::manifestaciones neuroconductuales::discapacidad intelectual [ENFERMEDADES], Genetics (clinical), Nervous System Diseases::Neurologic Manifestations::Neurobehavioral Manifestations::Intellectual Disability [DISEASES]
Abstract

Genotype; Intellectual disability; Phenotype Genotipo; Discapacidad intelectual; Fenotipo Genotip; Discapacitat intel·lectual; Fenotip We describe the phenotype of 22 male patients (20 probands) carrying a hemizygous missense variant in MED12. The phenotypic spectrum is very broad ranging from nonspecific intellectual disability (ID) to the three well-known syndromes: Opitz–Kaveggia syndrome, Lujan–Fryns syndrome, or Ohdo syndrome. The identified variants were randomly distributed throughout the gene (p = 0.993, χ2 test), but mostly outside the functional domains (p = 0.004; χ2 test). Statistical analyses did not show a correlation between the MED12-related phenotypes and the locations of the variants (p = 0.295; Pearson correlation), nor the protein domain involved (p = 0.422; Pearson correlation). In conclusion, establishing a genotype–phenotype correlation in MED12-related diseases remains challenging. Therefore, we think that patients with a causative MED12 variant are currently underdiagnosed due to the broad patients' clinical presentations. Foundation for Science and Technology (FCT), Grant/Award Number: UIDB/00215/2020 UIDP/00215/2020 LA/P/0064/2020; Broad Institute; National Eye Institute; National Heart, Lung and Blood Institute, Grant/Award Number: UM1 HG008900; National Human Genome Research Institute, Grant/Award Number: R01 HG009141.

Published
2023
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